Estimating flood characteristics using geomorphologic flood index with regards to rainfall intensity-duration-frequency-area curves and CADDIES-2D model in three Iranian basins

This is the final version. Available on open access from MDPI via the DOI in this recordThere is not enough data and computational power for conventional flood mapping methods in many parts of the world, thus fast and low-data-demanding methods are very useful in facing the disaster. This paper presents an innovative procedure for estimating flood extent and depth using only DEM SRTM 30 m and the Geomorphic Flood Index (GFI). The Geomorphologic Flood Assessment (GFA) tool which is the corresponding application of the GFI in QGIS is implemented to achieved the results in three basins in Iran. Moreover, the novel concept of Intensity-Duration-Frequency-Area (IDFA) curves is introduced to modify the GFI model by imposing a constraint on the maximum hydrologically contributing area of a basin. The GFA model implements the linear binary classification algorithm to classify a watershed into flooded and non-flooded areas using an optimized GFI threshold that minimizes the errors with a standard flood map of a small region in the study area. The standard hydraulic model envisaged for this study is the Cellular Automata Dual-DraInagE Simulation (CADDIES) 2D model which employs simple transition rules and a weight-based system rather than complex shallow water equations allowing fast flood modelling for large-scale problems. The results revealed that the floodplains generated by the GFI has a good agreement with the standard maps, especially in the fluvial rivers. However, the performance of the GFI decreases in the less steep and alluvial rivers. With some overestimation, the GFI model is also able to capture the general trend of water depth variations in comparison with the CADDIES-2D flood depth map. The modifications made in the GFI model, to confine the maximum precipitable area through implementing the IDFAs, improved the classification of flooded area and estimation of water depth in all study areas. Finally, the calibrated GFI thresholds were used to achieve the complete 100-year floodplain maps of the study areas.University of BasilicataCNR-IMAAOpenet TechnologiesRoyal Academy of Engineering (RAE

Primary antibody deficiency in a tertiary referral hospital: A 30-year experiment

Background: Primary antibody deficiency (PAD) is the most common group of primary immunodeficiency disorders (PID), with a broad spectrum of clinical features ranging from severe and recurrent infections to asymptomatic disease. Objectives: The current study was performed to evaluate and compare demographic and clinical data in the most common types of PAD. Materials and Methods: We performed a retrospective review of the medical records of all PAD patients with a confirmed diagnosis of common variable immunodeficiency (CVID), hyper IgM syndrome (HIgM), selective IgA deficiency (SIgAD), and X-linked agammaglobulinemia (XLA) who were diagnosed during the last 30 years at the Children�s Medical Center, Tehran, Iran. Results: A total number of 280 cases of PAD (125 CVID, 32 HIgM, 63 SIgAD, and 60 XLA) were enrolled in the study. The median (range) age at the onset of disease in CVID, HIgM, SIgAD, and XLA was 2 (0-46), 0.91 (0-9), 1 (0-26), and 1 (0-10) years, respectively. Gastrointestinal infections were more prevalent in CVID patients, as were central nervous system infections in XLA patients. Autoimmune complications were more prevalent in HIgM patients, malignancies in CVID patients, and allergies in SIgAD patients. The mortality rate for CVID, HIgM, and XLA was 27.2, 28.1, and 25, respectively. No deaths were reported in SIgAD patients. Conclusions: SIgAD patients had the best prognosis. While all PAD patients should be monitored for infectious complications, special attention should be paid to the finding of malignancy and autoimmune disorders in CVID and HIgM patients, respectively. © 2015 Esmon Publicidad

Consensus Middle East and North Africa Registry on Inborn Errors of Immunity

Background: Inborn errors of immunity (IEIs) are a heterogeneous group of genetic defects of immunity, which cause high rates of morbidity and mortality mainly among children due to infectious and non-infectious complications. The IEI burden has been critically underestimated in countries from middle- and low-income regions and the majority of patients with IEI in these regions lack a molecular diagnosis. Methods: We analyzed the clinical, immunologic, and genetic data of IEI patients from 22 countries in the Middle East and North Africa (MENA) region. The data was collected from national registries and diverse databases such as the Asian Pacific Society for Immunodeficiencies (APSID) registry, African Society for Immunodeficiencies (ASID) registry, Jeffrey Modell Foundation (JMF) registry, J Project centers, and International Consortium on Immune Deficiency (ICID) centers. Results: We identified 17,120 patients with IEI, among which females represented 39.4%. Parental consanguinity was present in 60.5% of cases and 27.3% of the patients were from families with a confirmed previous family history of IEI. The median age of patients at the onset of disease was 36 months and the median delay in diagnosis was 41 months. The rate of registered IEI patients ranges between 0.02 and 7.58 per 100,000 population, and the lowest rates were in countries with the highest rates of disability-adjusted life years (DALY) and death rates for children. Predominantly antibody deficiencies were the most frequent IEI entities diagnosed in 41.2% of the cohort. Among 5871 patients genetically evaluated, the diagnostic yield was 83% with the majority (65.2%) having autosomal recessive defects. The mortality rate was the highest in patients with non-syndromic combined immunodeficiency (51.7%, median age: 3.5 years) and particularly in patients with mutations in specific genes associated with this phenotype (RFXANK, RAG1, and IL2RG). Conclusions: This comprehensive registry highlights the importance of a detailed investigation of IEI patients in the MENA region. The high yield of genetic diagnosis of IEI in this region has important implications for prevention, prognosis, treatment, and resource allocation

Transient anhedonia phenotype and altered circadian timing of behaviour during night-time dim light exposure in Per3(-/-) mice, but not wildtype mice.

Industrialisation greatly increased human night-time exposure to artificial light, which in animal models is a known cause of depressive phenotypes. Whilst many of these phenotypes are 'direct' effects of light on affect, an 'indirect' pathway via altered sleep-wake timing has been suggested. We have previously shown that the Period3 gene, which forms part of the biological clock, is associated with altered sleep-wake patterns in response to light. Here, we show that both wild-type and Per3(-/-) mice showed elevated levels of circulating corticosterone and increased hippocampal Bdnf expression after 3 weeks of exposure to dim light at night, but only mice deficient for the PERIOD3 protein (Per3(-/-)) exhibited a transient anhedonia-like phenotype, observed as reduced sucrose preference, in weeks 2-3 of dim light at night, whereas WT mice did not. Per3(-/-) mice also exhibited a significantly smaller delay in behavioural timing than WT mice during weeks 1, 2 and 4 of dim light at night exposure. When treated with imipramine, neither Per3(-/-) nor WT mice exhibited an anhedonia-like phenotype, and neither genotypes exhibited a delay in behavioural timing in responses to dLAN. While the association between both Per3(-/-) phenotypes remains unclear, both are alleviated by imipramine treatment during dim night-time light

Calibration and Validation Parameter of Hydrologic Model HEC-HMS using Particle Swarm Optimization Algorithms – Single Objective

Introduction: Planning and management of water resource and river basins needs use of conceptual hydrologic models which play a significant role in predicting basins response to different climatic and meteorological processes. Evaluating watershed response through mathematical hydrologic models requires finding a set of parameter values of the model which provides thebest fit between observed and estimated hydrographs in a procedure called calibration. Asmanual calibration is tedious, time consuming and requires personal experience, automaticcalibration methods make application of more significant CRR models which are based onusing a systematic search procedure to find good parameter sets in terms of at least oneobjective function. Materials and Methods: Conceptual hydrologic models play a significant role inpredicting a basin’s response to different climatic and meteorological processes within natural systems. However, these models require a number of estimated parameters. Model calibration is the procedure of adjusting the parametervalues until the model predictions match the observed data. Manual calibration of high-fidelity hydrologic (simulation) models is tedious, time consuming and sometimesimpractical, especially when the number of parameters islarge. Moreover, the high degrees of nonlinearity involved in different hydrologic processes and non-uniqueness ofinverse-type calibration problems make it difficult to find asingle set of parameter values. In this research, the conceptual HEC-HMS model is integrated with the Particle Swarm Optimization (PSO) algorithm.The HEC-HMS model was developed as areplacement for HEC-1, which has long been considered as astandard model for hydrologic simulation. Most of thehydrologic models employed in HEC-HMS are event-basedmodels simulating a single storm requiring the specificationof all conditions at the beginning of the simulation. The soil moistureaccounting model in the HEC-HMS is the onlycontinuous model that simulates both wet and dry weatherbehavior.Programming of HEC –HMS has been done by MATLAB and techniques such as elite mutation and creating confusion have been used in order to strengthen the algorithm and improve the results. The event-based HEC-HMS model simulatesthe precipitation-runoff process for each set of parameter values generated by PSO. Turbulentand elitism with mutation are also employed to deal with PSO premature convergence. The integrated PSO-HMS model is tested on the Kardeh dam basin located in the Khorasan Razavi province. Results and Discussion: Input parameters of hydrologic models are seldomknown with certainty. Therefore, they are not capable ofdescribing the exact hydrologic processes. Input data andstructural uncertainties related to scale and approximationsin system processes are different sources of uncertainty thatmake it difficult to model exact hydrologic phenomena.In automatic calibration, the parameter values dependon the objective function of the search or optimization algorithm.In characterizing a runoff hydrograph, threecharacteristics of time-to-peak, peak of discharge and totalrunoff volume are of the most importance. It is thereforeimportant that we simulate and observe hydrographs matchas much as possible in terms of those characteristics. Calibration was carried out in single objective cases. Model calibration in single-objective approach with regard to the objective function in the event of NASH and RMSE were conducted separately.The results indicated that the capability of the model was calibrated to an acceptable level of events. Continuing calibration results were evaluated by four different criteria.Finally, to validate the model parameters with those obtained from the calibration, tests perfomed indicated poor results. Although, based on the calibration and verification of individual events one event remains, suggesting set is a possible parameter. Conclusion: All events were evaluated by validations and the results show that the performance model is not desirable. The results emphasized the impossibility of obtaining unique parameters for a basin. This method of solution, because of non-single solutions of calibration, could be helpful as an inverse problem that could limit the number of candidates. The above analysis revealed the existence of differentparameter sets that can altogether simulate verificationevents quite well, which shows the non-uniqueness featureof the calibration problem under study. However, the methodologyhas benefited from that feature by finding newparameter intervals that should be fine-tuned further inorder to decrease input and model prediction uncertainties.The proposed methodology performed well in the automatedcalibration of an event-based hydrologic model;however, the authors are aware of a drawback of the presentedanalysis – this undertakingwas not a completely fair validationprocedure. It is because validation events represent possiblefuture scenarios and thus are not available at the time ofmodel calibration. Hence, an event being selected as a validationevent should not be used to receive any morefeedback for adjusting parameter values and ranges.However,this remark was not fully taken into consideration, mostlybecause of being seriously short of enough observed eventsin this calibration study. Therefore, the proposed methodology,although sound and useful, should be validated inother case studies with more observed flood events

Long-term evaluation of a historical cohort of Iranian common variable immunodeficiency patients

Objectives: Common variable immune deficiency (CVID) is the most frequent form of symptomatic primary immunodeficiency disease, characterized by hypogammaglobulinemia, recurrent infections and increased predisposition to autoimmunity and malignancies. The aim of this study was to reconsider important points of previously performed studies on Iranian CVID patients diagnosed and followed from 1984 to 2013. Methods: Diagnosis was made using approved criteria including reductions of serum levels of immunoglobulins and exclusion of well-known single gene defects in individuals with an age >4 years and evidence of specific antibody deficiency. Results: Detailed information on demographic data, survival rates, clinical phenotypes, immunologic and genetic data and treatment of 173 patients are provided. The early onset presentation (74.5) and rate of consanguineous marriage (61.2) were considerably higher in our cohort. Our study revealed clinically related correlations regarding consanguinity, the population of naïve CD4+T cells and switched-memory B cells, cytokine levels and special genetic factors (including HLA and AID genes). Conclusion: Despite current efforts, more comprehensive studies are needed, especially for classification and investigation of the genetic background and prognostic factors for patients with CVID in order to better managment and followup of patinets. © 2014 Informa UK, Ltd

Clinical, immunologic, and genetic spectrum of 696 patients with combined immunodeficiency

Background: Combined immunodeficiencies (CIDs) are diseases of defective adaptive immunity with diverse clinical phenotypes. Although CIDs are more prevalent in the Middle East than Western countries, the resources for genetic diagnosis are limited. Objectives: This study aims to characterize the categories of patients with CIDs in Iran clinically and genetically. Methods: Clinical and laboratory data were obtained from 696 patients with CIDs. Patients were subdivided into those with syndromic (344 patients) and nonsyndromic (352 patients) CIDs. Targeted DNA sequencing was performed on 243 (34.9%) patients. Results: The overall diagnostic yield of the 243 sequenced patients was 77.8% (189 patients). The clinical diagnosis of hyper-IgE syndrome (P <.001), onset of disease at greater than 5 years (P =.02), and absence of multiple affected family members (P =.04) were significantly more frequent in the patients without a genetic diagnosis. An autosomal recessive disease was found in 62.9% of patients, reflecting the high rate of consanguinity in this cohort. Mutations impairing VDJ recombination and DNA repair were the most common underlying causes of CIDs. However, in patients with syndromic CIDs, autosomal recessive mutations in ataxia-telangiectasia mutated (ATM), autosomal dominant mutations in signal transducer and activator of transcription 3 (STAT3), and microdeletions in 22q11.21 were the most commonly affected genomic loci. Patients with syndromic CIDs had a significantly lower 5-year survival rate rather than those with nonsyndromic CIDs. Conclusions: This study provides proof of principle for the application of targeted next-generation sequencing panels in countries with limited diagnostic resources. The effect of genetic diagnosis on clinical care requires continued improvements in therapeutic resources for these patients

Clinical, immunologic, and genetic spectrum of 696 patients with combined immunodeficiency

Background: Combined immunodeficiencies (CIDs) are diseases of defective adaptive immunity with diverse clinical phenotypes. Although CIDs are more prevalent in the Middle East than Western countries, the resources for genetic diagnosis are limited. Objectives: This study aims to characterize the categories of patients with CIDs in Iran clinically and genetically. Methods: Clinical and laboratory data were obtained from 696 patients with CIDs. Patients were subdivided into those with syndromic (344 patients) and nonsyndromic (352 patients) CIDs. Targeted DNA sequencing was performed on 243 (34.9) patients. Results: The overall diagnostic yield of the 243 sequenced patients was 77.8 (189 patients). The clinical diagnosis of hyper-IgE syndrome (P <.001), onset of disease at greater than 5 years (P =.02), and absence of multiple affected family members (P =.04) were significantly more frequent in the patients without a genetic diagnosis. An autosomal recessive disease was found in 62.9 of patients, reflecting the high rate of consanguinity in this cohort. Mutations impairing VDJ recombination and DNA repair were the most common underlying causes of CIDs. However, in patients with syndromic CIDs, autosomal recessive mutations in ataxia-telangiectasia mutated (ATM), autosomal dominant mutations in signal transducer and activator of transcription 3 (STAT3), and microdeletions in 22q11.21 were the most commonly affected genomic loci. Patients with syndromic CIDs had a significantly lower 5-year survival rate rather than those with nonsyndromic CIDs. Conclusions: This study provides proof of principle for the application of targeted next-generation sequencing panels in countries with limited diagnostic resources. The effect of genetic diagnosis on clinical care requires continued improvements in therapeutic resources for these patients. © 2017 American Academy of Allergy, Asthma & Immunolog

Fourth Update on the Iranian National Registry of Primary Immunodeficiencies: Integration of Molecular Diagnosis

Abstract Background The number of inherited diseases and the spectrum of clinical manifestations of primary immunodeficiency disorders (PIDs) are ever-expanding. Molecular diagnosis using genomic approaches should be performed for all PID patients since it provides a resource to improve the management and to estimate the prognosis of patients with these rare immune disorders. Method The current update of Iranian PID registry (IPIDR) contains the clinical phenotype of newly registered patients during last 5 years (2013–2018) and the result of molecular diagnosis in patients enrolled for targeted and next-generation sequencing. Results Considering the newly diagnosed patients (n = 1395), the total number of registered PID patients reached 3056 (1852 male and 1204 female) from 31 medical centers. The predominantly antibody deficiency was the most common subcategory of PID (29.5%). The putative causative genetic defect was identified in 1014 patients (33.1%) and an autosomal recessive pattern was found in 79.3% of these patients. Among the genetically different categories of PID patients, the diagnostic rate was highest in defects in immune dysregulation and lowest in predominantly antibody deficiencies and mutations in the MEFV gene were the most frequent genetic disorder in our cohort. Conclusions During a 20-year registration of Iranian PID patients, significant changes have been observed by increasing the awareness of the medical community, national PID network establishment, improving therapeutic facilities, and recently by inclusion of the molecular diagnosis. The current collective study of PID phenotypes and genotypes provides a major source for ethnic surveillance, newborn screening, and genetic consultation for prenatal and preimplantation genetic diagnosis. Keywords Epidemiology Iran primary immunodeficiency molecular diagnosi