Search results for: site specificity

Authors: Wiyanti Fransisca Simanullang, Shinya Yamanaka

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Grinding method was used to control the active site and to improve the specific surface area (SSA) of calcium oxide (CaO) derived from scallop shell as a sustainable resource. The dry grinding of CaO with acetone and tertiary butanol as a liquid additive was carried out using a planetary ball mill with a laboratory scale. The experiments were operated by stepwise addition with time variations to determine the grinding limit. The active site of CaO was measured by X-Ray Diffraction and FT-IR. The SSA variations of products with grinding time were measured by BET method. The morphology structure of CaO was observed by SEM. The use of liquid additive was effective for increasing the SSA and controlling the active site of CaO. SSA of CaO was increased in proportion to the amount of the liquid additive and the grinding time. The performance of CaO as a solid base catalyst for biodiesel production was tested in the transesterification reaction of used cooking oil to produce fatty acid methyl ester (FAME).

Keywords: active site, calcium oxide, grinding, specific surface area

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Authors: Mi-Ju Kim, Hae-Yeong Kim

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Product mislabeling and adulteration have been increasing the concerns in processed meat products. Relatively inexpensive pork meat compared to meat such as beef was adulterated for economic benefit. These food fraud incidents related to pork were concerned due to economic, religious and health reasons. In this study, a rapid on-site detection method using loop-mediated isothermal amplification (LAMP) was developed for the simultaneous identification of beef and pork. Each specific LAMP primer for beef and pork was designed targeting on mitochondrial D-loop region. The LAMP assay reaction was performed at 65 ℃ for 40 min. The specificity of each primer for beef and pork was evaluated using DNAs extracted from 13 animal species including beef and pork. The sensitivity of duplex LAMP assay was examined by serial dilution of beef and pork DNAs, and reference binary mixtures. This assay was applied to processed meat products including beef and pork meat for monitoring. Each set of primers amplified only the targeted species with no cross-reactivity with animal species. The limit of detection of duplex real-time LAMP was 1 pg for each DNA of beef and pork and 1% pork in a beef-meat mixture. Commercial meat products that declared the presence of beef and/or pork meat on the label showed positive results for those species. This method was successfully applied to detect simultaneous beef and pork meats in processed meat products. The optimized duplex LAMP assay can identify simultaneously beef and pork meat within less than 40 min. A portable real-time fluorescence device used in this study is applicable for on-site detection of beef and pork in processed meat products. Thus, this developed assay was considered to be an efficient tool for monitoring meat products.

Keywords: beef, duplex real-time LAMP, meat identification, pork

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Authors: Kyung Jin Kim, Jiwon Kwak, Jae-Hoon Lee, Soo Suk Lee

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We describe an innovative method for highly specific detection of miRNAs using a specially modified method of poly(A) adaptor RT-qPCR. We use uniquely designed specific extension sequence, which plays important role in providing an opportunity to affect high specificity of miRNA detection. This method involves two steps of reactions as like previously reported and which are poly(A) tailing and reverse-transcription followed by real-time PCR. Firstly, miRNAs are extended by a poly(A) tailing reaction and then converted into cDNA. Here, we remarkably reduced the reaction time by the application of short length of poly(T) adaptor. Next, cDNA is hybridized to the 3’-end of a specific extension sequence which contains miRNA sequence and results in producing a novel PCR template. Thereafter, the SYBR Green-based RT-qPCR progresses with a universal poly(T) adaptor forward primer and a universal reverse primer. The target miRNA, miR-106b in human brain total RNA, could be detected quantitatively in the range of seven orders of magnitude, which demonstrate that the assay displays a dynamic range of at least 7 logs. In addition, the better specificity of this novel extension-based assay against well known poly(A) tailing method for miRNA detection was confirmed by melt curve analysis of real-time PCR product, clear gel electrophoresis and sequence chromatogram images of amplified DNAs.

Keywords: microRNA(miRNA), specific extension sequence, RT-qPCR, poly(A) tailing assay, reverse transcription

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Authors: Osama Moustafa Zayed

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Aim of the work: To evaluate the effectiveness of venous glucose, levels of serum lactate and base deficit in polytraumatized patients as simple parameters to predict the mortality in these patients. Compared to the predictive value of Trauma and injury severity (TRISS) and Acute Physiology And Chronic Health Evaluation IV (APACHE IV). Introduction: Trauma is a serious global health problem, accounting for approximately one in 10 deaths worldwide. Trauma accounts for 5 million deaths per year. Prediction of mortality in trauma patients is an important part of trauma care. Several trauma scores have been devised to predict injury severity and risk of mortality. The trauma and injury severity score (TRISS) was most common used. Regardless of the accuracy of trauma scores, is based on an anatomical description of every injury and cannot be assigned to the patients until a full diagnostic procedure has been performed. So we hypothesized that alterations in admission glucose, lactate levels and base deficit would be an early and easy rapid predictor of mortality. Patient and Method: a comparative cross-sectional study. 282 Polytraumatized patients attended to the Emergency Department(ED) of the Suez Canal university Hospital constituted. The period from 1/1/2012 to 1/4/2013 was included. Results: We found that the best cut off value of TRISS probability of survival score for prediction of mortality among poly-traumatized patients is = 90, with 77% sensitivity and 89% specificity using area under the ROC curve (0.89) at (95%CI). APACHE IV demonstrated 67% sensitivity and 95% specificity at 95% CI at cut off point 99. The best cutoff value of Random Blood Sugar (RBS) for prediction of mortality was>140 mg/dl, with 89%, sensitivity, 49% specificity. The best cut off value of base deficit for prediction of mortality was less than -5.6 with 64% sensitivity, 93% specificity. The best cutoff point of lactate for prediction of mortality was > 2.6 mmol/L with 92%, sensitivity, 42% specificity. Conclusion: According to our results from all evaluated predictors of mortality (laboratory and scores) and mortality based on the estimated cutoff values using ROC curves analysis, the highest risk of mortality was found using a cutoff value of 90 in TRISS score while with laboratory parameters the highest risk of mortality was with serum lactate > 2.6 . Although that all of the three parameter are accurate in predicting mortality in poly-traumatized patients and near with each other, as in serum lactate the area under the curve 0.82, in BD 0.79 and 0.77 in RBS.

Keywords: APACHE IV, emergency department, polytraumatized patients, serum lactate

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Authors: Mohammad Raihan Mukhlis, M. Abdur Rahman Bhuiyan

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Bangladesh is a developing country in which a lot of multi-span simply/continuous supported flyovers are being constructed in its major cities. Being situated in a seismically active region, seismic safety evaluation of flyovers is essential for seismic risk reduction. Effects of site amplification on seismic safety evaluation of flyover piers are the main concern of this study. In this regard, failure mode, lateral strength and displacement ductility of piers of a typical multi-span simply supported flyover have been evaluated by Japan Road Association (JRA) recommended guidelines, with and without considering site amplification. Ultimate flexural strengths of piers have been computed using the pushover analysis results. Shear capacity of piers has been calculated using the guidelines of JRA. Lateral strengths have been determined depending on the failure modes of the piers. Displacement ductility of piers has been computed using yield and ultimate displacements of the piers obtained from the pushover analysis results. Selected earthquake time history is used in seismic safety evaluation of the flyover piers. Finally, the ductility design method is used to conduct the seismic safety evaluation of the piers with and without considering site amplification. From the numerical results, it has been revealed that the effects of site amplification on seismic safety evaluation of bridge structures should be carefully taken into account.

Keywords: displacement ductility, flyover pier, lateral strength, safety evaluation, site amplification

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Authors: Weng Jiantao, Wu Yiqun

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The efficiency of natural ventilation, wind pressure distribution on building surface, wind comfort for pedestrians and buildings’ wind tolerance in traditional settlements are closely related to the pattern of terrain. On the basis of field research on the typical island terrain in China, the physical and mathematical models are established by using CFD software, and then the simulation results of the wind field are exported. We discuss the relationship between wind direction and wind field results. Furthermore simulation results are imported into ArcGIS platform. The evaluation model of island site selection is established with considering slope factor. We realize the visual model of site selection on complex island terrain. The multi-plans of certain residential are discussed based on wind simulation; at last the optimal project is selected. Results can provide the theory guidance for settlement planning and construction in China's traditional island.

Keywords: CFD, island terrain, site selection, construction mechanism

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Authors: Adewoyin O. Olusegun, Akinwumi I. Isaac

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In some part of the world where legislations related to site investigations before constructions are not strictly enforced, the expenses and time required for carrying out a comprehensive geotechnical investigation to characterize a site can discourage prospective private residential building developers. Another factor that can discourage a developer is the fact that most of the geotechnical tests procedures utilized during site investigations, to a certain extent, alter the existing environment of the site. This study suggests a quick, non-destructive and non-intrusive method of obtaining key subsoil geotechnical properties necessary for foundation design for proposed engineering facilities. Seismic wave velocities generated from near surface refraction method was used to determine the bulk density of soil, Young’s modulus, bulk modulus, shear modulus and allowable bearing capacity of a competent layer that can bear structural load at the particular study site. Also, regression equations were developed in order to directly obtain the bulk density of soil, Young’s modulus, bulk modulus, shear modulus and allowable bearing capacity from the compressional wave velocities. The results obtained correlated with the results of standard geotechnical investigations carried out.

Keywords: characterize, environment, geophysical, geotechnical, regression

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Authors: Orsolya Kegyes-Brassai, Zsolt Szilvágyi, Ákos Wolf, Richard P. Ray

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Local ground conditions have a substantial influence on the seismic response of structures. Their inclusion in seismic hazard assessment and structural design can be realized at different levels of sophistication. However, response results based on more advanced calculation methods e.g. nonlinear or equivalent linear site analysis tend to show significant discrepancies when compared to simpler approaches. This project's main objective was to compare results from several 1-D response programs to Eurocode 8 design spectra. Data from in-situ site investigations were used for assessing local ground conditions at several locations in Hungary. After discussion of the in-situ measurements and calculation methods used, a comprehensive evaluation of all major contributing factors for site response is given. While the Eurocode spectra should account for local ground conditions based on soil classification, there is a wide variation in peak ground acceleration determined from 1-D analyses versus Eurocode. Results show that current Eurocode 8 design spectra may not be conservative enough to account for local ground conditions typical for Hungary.

Keywords: 1-D site response analysis, multichannel analysis of surface waves (MASW), seismic CPT, seismic hazard assessment

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Authors: Sean Taylor, Sayantani Neogi, Julia Budka

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The important Egyptian New Kingdom settlement at Sai Island Sudan presents a complex stratigraphic archaeological record. This study takes the theoretic stance that it, not just the archaeological material being retrieved from the deposits but the sediments themselves that reflect human agency. These anthropogenic sediments reflect the use life of the buildings and spaces between and the post-depositional processes which operate to complicate the archaeological record. The application of soil micromorphology is a technique that takes intact block samples of sediment and analyses them in thin section under a petrological microscope. A detailed understanding of site formation processes and a contextualized knowledge of the material culture can be understood through careful and systematic observation of the changing facies. The major findings of the study are that soil and sedimentary information can provide valuable insights to the use of space during the New Kingdom and elucidate the complexities of site formation processes.

Keywords: anthropogenic sediment, New Kingdom, site formation processes, soil micromorphology

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Authors: Ting Wang, Pierre Marle, Vera I. Slaveykova, Kristin Schirmer, Wei Liu

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Metal-based nanoparticles (NPs) are considered detrimental to aquatic organisms due to their potential accumulation. However, little is known about the mechanisms underlying these effects and their species-specificity. Here, we used stable silver (Ag) NPs (20 nm, from 10 to 500 μg/L) with a low dissolution rate (≤2.4%) to study the bioaccumulation and biological impacts in two freshwater gastropods: Lymnaea stagnalis and Planorbarius corneus. No mortality was detected during the experiments. Ag bioaccumulation showed a dose-related increase with an enhanced concentration in both species after 7d exposure. L. stagnalis displayed a higher accumulation for AgNPs than P. corneus (e.g., up to 18- and 15-fold in hepatopancreas and hemolymph, respectively), which could be due to the more active L. stagnalis having greater contact with suspended AgNPs. Furthermore, the hepatopancreas and stomach were preferred organs for bioaccumulation compared to the kidney, mantle and foot. Regarding biological responses, the hemolymph rather than hepatopancreas appeared more susceptible to oxidative stress elicited by AgNPs, as shown by significantly increasing lipid peroxidation (i.e., formation of malondialdehyde). Neurotoxicity was detected in L. stagnalis when exposed to high concentrations (500 μg/L). Comparison with impacts elicited by dissolved Ag revealed that the effects observed on AgNPs exposure were mainly attributable to NPs. These results highlighted the relationship between the physiological traits, bioaccumulation, and toxicity responses of these two species to AgNPs and demonstrated the necessity of species-specificity considerations when assessing the toxicity of NPs.

Keywords: nanotoxicity, freshwater gastropods, species-specificity, metals, physiological traits

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Authors: Nouira Mariem, Ben Rayana Hazem, Ennigrou Samir

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Background and aim: During the past decade, the frequency of extrapulmonary forms of tuberculosis has increased. These forms are under-diagnosed using conventional tests. The aim of this study was to evaluate the performance of the Tuberculin Skin Test (TST) for the diagnosis of tuberculosis, using the ROC curve and Fagan’s Nomogram methodology. Methods: This was a case-control, multicenter study in 11 anti-tuberculosis centers in Tunisia, during the period from June to November2014. The cases were adults aged between 18 and 55 years with confirmed tuberculosis. Controls were free from tuberculosis. A data collection sheet was filled out and a TST was performed for each participant. Diagnostic accuracy measures of TST were estimated using ROC curve and Area Under Curve to estimate sensitivity and specificity of a determined cut-off point. Fagan’s nomogram was used to estimate its predictive values. Results: Overall, 1053 patients were enrolled, composed of 339 cases (sex-ratio (M/F)=0.87) and 714 controls (sex-ratio (M/F)=0.99). The mean age was 38.3±11.8 years for cases and 33.6±11 years for controls. The mean diameter of the TST induration was significantly higher among cases than controls (13.7mm vs.6.2mm;p=10-6). Area Under Curve was 0.789 [95% CI: 0.758-0.819; p=0.01], corresponding to a moderate discriminating power for this test. The most discriminative cut-off value of the TST, which were associated with the best sensitivity (73.7%) and specificity (76.6%) couple was about 11 mm with a Youden index of 0.503. Positive and Negative predictive values were 3.11% and 99.52%, respectively. Conclusion: In view of these results, we can conclude that the TST can be used for tuberculosis diagnosis with a good sensitivity and specificity. However, the skin induration measurement and its interpretation is operator dependent and remains difficult and subjective. The combination of the TST with another test such as the Quantiferon test would be a good alternative.

Keywords: tuberculosis, tuberculin skin test, ROC curve, cut-off

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Authors: Dechen Tshering Vogel, Johannes T. Heverhagen, Bernard Kiss, Spyridon Arampatzis

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In addition to computed tomography (CT), contrast enhanced ultrasound (CEUS), and magnetic resonance imaging (MRI) are being increasingly used for imaging of renal lesions. The aim of this prospective study was to compare the classification of complex cystic renal lesions using the Bosniak classification with CEUS and MRI to CT. Forty-eight patients with 65 cystic renal lesions were included in this study. All participants signed written informed consent. The agreement between the Bosniak classifications of complex renal lesions ( ≥ BII-F) on CEUS and MRI were compared to that of CT and were tested using Cohen’s Kappa. Sensitivity, specificity, positive and negative predictive values (PPV/NPV) and the accuracy of CEUS and MRI compared to CT in the detection of complex renal lesions were calculated. Twenty-nine (45%) out of 65 cystic renal lesions were classified as complex using CT. The agreement between CEUS and CT in the classification of complex cysts was fair (agreement 50.8%, Kappa 0.31), and was excellent between MRI and CT (agreement 93.9%, Kappa 0.88). Compared to CT, MRI had a sensitivity of 96.6%, specificity of 91.7%, a PPV of 54.7%, and an NPV of 54.7% with an accuracy of 63.1%. The corresponding values for CEUS were sensitivity 100.0%, specificity 33.3%, PPV 90.3%, and NPV 97.1% with an accuracy 93.8%. The classification of complex renal cysts based on MRI and CT scans correlated well, and MRI can be used instead of CT for this purpose. CEUS can exclude complex lesions, but due to higher sensitivity, cystic lesions tend to be upgraded. However, it is useful for initial imaging, for follow up of lesions and in those patients with contraindications to CT and MRI.

Keywords: Bosniak classification, computed tomography, contrast enhanced ultrasound, cystic renal lesions, magnetic resonance imaging

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Authors: Rasha Al-Saedi, Anthony Meijer

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The progress of new porous materials has increased rapidly over the past decade for use in applications such as catalysis, gas storage and removal of environmentally unfriendly species due to their high surface area and high thermal stability. In this work, a theoretical study of the zirconium-based metal organic framework (MOFs) were examined in order to determine their potential for gas adsorption of various guest molecules: CO2, N2, CH4 and H2. The zirconium cluster consists of an inner Zr6O4(OH)4 core in which the triangular faces of the Zr6- octahedron are alternatively capped by O and OH groups which bound to nine formate groups and three benzoate groups linkers. General formula is [Zr(μ-O)4(μ-OH)4(HCOO)9((phyO2C)3X))] where X= CH2OH, CH2NH2, CH2CONH2, n(NH2); (n = 1-3). Three types of adsorption sites on the Zr metal center have been studied, named according to capped chemical groups as the ‘−O site’; the H of (μ-OH) site removed and added to (μ-O) site, ‘–OH site’; (μ-OH) site removed, the ‘void site’ where H2O molecule removed; (μ-OH) from one site and H from other (μ-OH) site, in addition to no defect versions. A series of investigations have been performed aiming to address this important issue. First, density functional theory DFT-B3LYP method with 6-311G(d,p) basis set was employed using Gaussian 09 package in order to evaluate the gas adsorption performance of missing-linker defects in zirconium cluster. Next, study the gas adsorption behaviour on different functionalised zirconium clusters. Those functional groups as mentioned above include: amines, alcohol, amide, in comparison with non-substitution clusters. Then, dispersion-corrected density functional theory (DFT-D) calculations were performed to further understand the enhanced gas binding on zirconium clusters. Finally, study the water effect on CO2 and N2 adsorption. The small functionalized Zr clusters were found to result in good CO2 adsorption over N2, CH4, and H2 due to the quadrupole moment of CO2 while N2, CH4 and H2 weakly polar or non-polar. The adsorption efficiency was determined using the dispersion method where the adsorption binding improved as most of the interactions, for example, van der Waals interactions are missing with the conventional DFT method. The calculated gas binding strengths on the no defect site are higher than those on the −O site, −OH site and the void site, this difference is especially notable for CO2. It has been stated that the enhanced affinity of CO2 of no defect versions is most likely due to the electrostatic interactions between the negatively charged O of CO2 and the positively charged H of (μ-OH) metal site. The uptake of the gas molecule does not enhance in presence of water as the latter binds to Zr clusters more strongly than gas species which attributed to the competition on adsorption sites.

Keywords: density functional theory, gas adsorption, metal- organic frameworks, molecular simulation, porous materials, theoretical chemistry

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Authors: Anna Trusek-Holownia, Andrzej Noworyta

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Using an enzyme of known specificity the hydrolysis of protein was carried out in a controlled manner. The aim was to obtain oligopeptides being the so-called active peptides or their direct precursors. An original way of expression of the protein hydrolysis kinetics was introduced. Peptide bonds contained in the protein were recognized as a diverse-quality substrate for hydrolysis by the applied protease. This assumption was positively verified taking as an example the hydrolysis of albumin by thermolysin. Peptide linkages for this system should be divided into at least four groups. One of them is a group of bonds non-hydrolyzable by this enzyme. These that are broken are hydrolyzed at a rate that differs even by tens of thousands of times. Designated kinetic constants were k'F = 10991.4 L/g.h, k'M = 14.83L/g.h, k'S about 10-1 L/g.h for fast, medium and slow bonds, respectively. Moreover, a procedure for unfolding of the protein, conducive to the improved susceptibility to enzymatic hydrolysis (approximately three-fold increase in the rate) was proposed.

Keywords: peptide bond hydrolysis, kinetics, enzyme specificity, biologically active peptides

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Authors: Gong Zhang

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The villages surrounding protected areas of the Sites are a unique vernacular heritage due to their geographical location, long history, and the combination of nature and humanity. With the construction of more and more heritage sites, the villages around them are faced with the conflict between conservation and development. How to carry out sustainable micro-renewal while preserving the authenticity of the vernacular heritage is of great importance for the co-growth of the village residents and the site. This paper focuses on the process of revitalization of the villages nearby the Erlitou Site Park in China, aiming to study how sustainable village regeneration and conservation can be carried out through the activation of public culture. Firstly, through field research and literature review, this paper studies the vernacular morphology and architecture types of more than ten historical villages around the Erlitou site and investigates the traditional vernacular culture and the daily public activities of the local villagers. Secondly, taking the nearest village to the site area, Ranzhuang Village, as an example, the paper studies the role of public cultural activity interventions on the three different stages of vernacular heritage renewal: master planning, architecture group, and acupuncture-style micro-renewal of individual buildings, aiming to summarise its impact on villagers' lives and vernacular heritage. This paper concludes that a living regeneration with a moderate public cultural activity intervention can promote the symbiosis between the heritage site and the life of the villagers and increase the vitality of the village. This study aims to use the example of village regeneration in Henan, China, as a sustainable reference for the co-development of heritage sites and villages in other parts of the world.

Keywords: Erlitou site, public culture intervention, sustainable, vernacular heritage

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Authors: Moon Jung Kim, Guil Rhim

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The clinical sensitivity of the “VEUPLEXTM TBI assay”, a clinical trial medical device, in mild traumatic brain injury was 28.6% (95% CI, 19.7%-37.5%), and the clinical specificity was 94.0% (95% CI, 89.3%). -98.7%). In addition, when the results analyzed by marker were put together, the sensitivity was higher when interpreting the two tests together than the two tests, UCHL1 and GFAP alone. Additionally, when sensitivity and specificity were analyzed based on CT results for the mild traumatic brain injury patient group, the clinical sensitivity for 2 CT-positive cases was 50.0% (95% CI: 1.3%-98.7%), and 19 CT-negative cases. The clinical specificity for cases was 68.4% (95% CI: 43.5% - 87.4%). Since the low clinical sensitivity for the two CT-positive cases was not statistically significant due to the small number of samples analyzed, it was judged necessary to secure and analyze more samples in the future. Regarding the clinical specificity analysis results for 19 CT-negative cases, there were a large number of patients who were actually clinically diagnosed with mild traumatic brain injury but actually received a CT-negative result, and about 31.6% of them showed abnormal results on VEUPLEXTM TBI assay. Although traumatic brain injury could not be detected in 31.6% of the CT scans, the possibility of actually suffering a mild brain injury could not be ruled out, so it was judged that this could be confirmed through follow-up observation of the patient. In addition, among patients with mild traumatic brain injury, CT examinations were not performed in many cases because the symptoms were very mild, but among these patients, about 25% or more showed abnormal results in the VEUPLEXTM TBI assay. In fact, no damage is observed with the naked eye immediately after traumatic brain injury, and traumatic brain injury is not observed even on CT. But in some cases, brain hemorrhage may occur (delayed cerebral hemorrhage) after a certain period of time, so the patients who did show abnormal results on VEUPLEXTM TBI assay should be followed up for the delayed cerebral hemorrhage. In conclusion, it was judged that it was difficult to judge mild traumatic brain injury with the VEUPLEXTM TBI assay only through clinical findings without CT results, that is, based on the GCS value. Even in the case of CT, it does not detect all mild traumatic brain injury, so it is difficult to necessarily judge that there is no traumatic brain injury, even if there is no evidence of traumatic brain injury in CT. And in the long term, more patients should be included to evaluate the usefulness of the VEUPLEXTM TBI assay in the detection of microscopic traumatic brain injuries without using CT.

Keywords: brain injury, traumatic brain injury, GFAP, UCHL1

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Authors: Connor Dunlop, Bassim Abbassi, Richard G. Zytner

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Life cycle assessment (LCA) is a powerful tool established by the International Organization for Standardization (ISO) that can be used to assess the environmental impacts of a product or process from cradle to grave. Many studies utilize the LCA methodology within the site remediation field to compare various decontamination methods, including bioremediation, soil vapor extraction or excavation, and off-site disposal. However, with the authors' best knowledge, limited information is available in the literature on a sustainability tool that could be used to help with the selection of the optimal remediation technology. This tool, based on the LCA methodology, would consider site conditions like environmental, economic, and social impacts. Accordingly, this project was undertaken to develop a tool to assist with the selection of optimal sustainable technology. Developing a proper tool requires a large amount of data. As such, data was collected from previous LCA studies looking at site remediation technologies. This step identified knowledge gaps or limitations within project data. Next, utilizing the data obtained from the literature review and other organizations, an extensive LCA study is being completed following the ISO 14040 requirements. Initial technologies being compared include bioremediation, excavation with off-site disposal, and a no-remediation option for a generic gasoline-contaminated site. To complete the LCA study, the modelling software SimaPro is being utilized. A sensitivity analysis of the LCA results will also be incorporated to evaluate the impact on the overall results. Finally, the economic and social impacts associated with each option will then be reviewed to understand how they fluctuate at different sites. All the results will then be summarized, and an interactive tool using Excel will be developed to help select the best sustainable site remediation technology. Preliminary LCA results show improved sustainability for the decontamination of a gasoline-contaminated site for each technology compared to the no-remediation option. Sensitivity analyses are now being completed on on-site parameters to determine how the environmental impacts fluctuate at other contaminated gasoline locations as the parameters vary, including soil type and transportation distances. Additionally, the social improvements and overall economic costs associated with each technology are being reviewed. Utilizing these results, the sustainability tool created to assist in the selection of the overall best option will be refined.

Keywords: life cycle assessment, site remediation, sustainability tool, contaminated sites

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Authors: D. Bąk-Grabowska, K. Grzesik, A. Iwanicka, A. Jagoda

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The process of human resources management in the structures of corporate groups demonstrates certain specificity, resulting from the division of decision-making and executive competencies, which occurs within these structures between a parent company and its subsidiaries. The subprocess of employee assessment is considered crucial, since it provides information for the implementation of personnel function. The empirical studies conducted in corporate groups, within which at least one company is located in Poland, confirmed the critical significance of employee assessment systems in the process of human resources management in corporate groups. Parent companies, most often, retain their decision-making authority within the framework of the discussed process and introduce uniform employee assessment and personnel controlling systems to subsidiary companies. However, the instruments for employee assessment applied in corporate groups do not present such specificity.

Keywords: corporate groups, employee periodical assessment system, holding, human resources management

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Authors: Siobhan O’Shea, Sangeetha Vijaysri Nair, Hee Cheol Kim, Charles Thomas Nugent, Cheuk Yan William Tong, Sam Douthwaite, Andrew Worlock

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The Aptima® HIV-1 Quant Dx Assay is a fully automated assay on the Panther system. It is based on Transcription-Mediated Amplification and real time detection technologies. This assay is intended for monitoring HIV-1 viral load in plasma specimens and for the detection of HIV-1 in plasma and serum specimens. Nine-hundred and seventy nine specimens selected at random from routine testing at St Thomas’ Hospital, London were anonymised and used to compare the performance of the Aptima HIV-1 Quant Dx assay and Roche COBAS® AmpliPrep/COBAS® TaqMan® HIV-1 Test, v2.0. Two-hundred and thirty four specimens gave quantitative HIV-1 viral load results in both assays. The quantitative results reported by the Aptima Assay were comparable those reported by the Roche COBAS AmpliPrep/COBAS TaqMan HIV-1 Test, v2.0 with a linear regression slope of 1.04 and an intercept on -0.097. The Aptima assay detected HIV-1 in more samples than the Roche assay. This was not due to lack of specificity of the Aptima assay because this assay gave 99.83% specificity on testing plasma specimens from 600 HIV-1 negative individuals. To understand the reason for this higher detection rate a side-by-side comparison of low level panels made from the HIV-1 3rd international standard (NIBSC10/152) and clinical samples of various subtypes were tested in both assays. The Aptima assay was more sensitive than the Roche assay. The good sensitivity, specificity and agreement with other commercial assays make the HIV-1 Quant Dx Assay appropriate for both viral load monitoring and detection of HIV-1 infections.

Keywords: HIV viral load, Aptima, Roche, Panther system

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Authors: Lesley Northrop, Justin DeGrazia, Jessica Greenwood

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ASPIRA Labs now offers an en-suit and ready-to-implement technology transfer solution to enable labs and hospitals that lack the resources to build it themselves to offer in-house genetic testing. This unique platform employs a patented Molecular Inversion Probe (MIP) technology that combines the specificity of a hybrid capture protocol with the ease of an amplicon-based protocol and utilizes an advanced bioinformatics analysis pipeline based on machine learning. To demonstrate its efficacy, two independent genetic tests were validated on this technology transfer platform: expanded carrier screening (ECS) and hereditary cancer testing (HC). The analytical performance of ECS and HC was validated separately in a blinded manner for calling three different types of variants: SNVs, short indels (typically, <50 bp), and large indels/CNVs defined as multi-exonic del/dup events. The reference set was constructed using samples from Coriell Institute, an external clinical genetic testing laboratory, Maine Molecular Quality Controls Inc. (MMQCI), SeraCare and GIAB Consortium. Overall, the analytical performance showed a sensitivity and specificity of >99.4% for both ECS and HC in detecting SNVs. For indels, both tests reported specificity of 100%, and ECS demonstrated a sensitivity of 100%, whereas HC exhibited a sensitivity of 96.5%. The bioinformatics pipeline also correctly called all reference CNV events resulting in a sensitivity of 100% for both tests. No additional calls were made in the HC panel, leading to a perfect performance (specificity and F-measure of 100%). In the carrier panel, however, three additional positive calls were made outside the reference set. Two of these calls were confirmed using an orthogonal method and were re-classified as true positives leaving only one false positive. The pipeline also correctly identified all challenging carrier statuses, such as positive cases for spinal muscular atrophy and alpha-thalassemia, resulting in 100% sensitivity. After confirmation of additional positive calls via long-range PCR and MLPA, specificity for such cases was estimated at 99%. These performance metrics demonstrate that this tech-transfer solution can be confidently internalized by clinical labs and hospitals to offer mainstream ECS and HC as part of their test catalog, substantially increasing access to quality germline genetic testing for labs of all sizes and resources levels.

Keywords: clinical genetics, genetic testing, molecular genetics, technology transfer

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Authors: Giovanni Forte, Melania De Falco, Antonio Santo

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On 24th August 2016, central Italy was affected by a Mw 6.0 earthquake, representing the main shock of a long seismic sequence, which had a second shock Mw 6.6 on 26th October and lasts still nowadays. After the event, several field survey were carried out in the affected areas, which is made of historical masonry buildings. The post event reconnaissance missions were aimed at collecting information on the damage states of the buildings, the triggering of the landslides and the relationships with site effects. In this paper, the data collected after the event are analyzed considering the role of the geological and geomorphological setting and the ground motion scenario. The buildings displayed an uneven damage distribution, which was affected by both topographic and stratigraphic amplification. As pertains the landslides, which were the most recurrent among the ground failures, consisted mainly of rock falls and subordinately of translational slides. Finally, the collected knowledge showed a strong contribution of the local geological and geomorphological site condition on the resulting damage.

Keywords: Amatrice earthquake, damage states, landslides, site effects

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Authors: Suzan Salem, Heba Moustafa, Abd El-Aziz Abd El-Aal

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Seismic micro hazard zonation for urban areas is the first step towards a seismic risk analysis and mitigation strategy. Essential here is to obtain a proper understanding of the local subsurface conditions and to evaluate ground-shaking effects. In the present study, an attempt has been made to evaluate the seismic hazard considering local site effects by carrying out detailed geotechnical and geophysical site characterization in El-Fayoum New City. Seismic hazard analysis and microzonation of El-Fayoum New City are addressed in three parts: in the first part, estimation of seismic hazard is done using seismotectonic and geological information. The second part deals with site characterization using geotechnical and shallow geophysical techniques. In the last part, local site effects are assessed by carrying out one-dimensional (1-D) ground response analysis using the equivalent linear method by program SHAKE 2000. Finally, microzonation maps have been prepared. The detailed methodology, along with experimental details, collected data, results and maps are presented in this paper.

Keywords: El-Fayoum, microzonation, seismotectonic, Egypt

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Authors: Arzu Baloglu, Ugur Kaplancali

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This paper focuses on Background Check Systems and Pre-Employment Screening. In our study, we attempted to make an online background checking site that will help employers when hiring employees. Our site has two types of users which are free and powered user. Free users are the employees and powered users are the employers which will hire employers. The database of the site will contain all the information about the employees and employers which are registered in the system so the employers can make a search based on their searching criteria to find the suitable employee for the job. The web site also has a comments and points system. The current employer can make comments to his/her employees and can also give them points. The comments will be shown on employee’s profile, so; when an employer searches for an employee he/she can check the points and comments of the employee to see whether he or she is capable of the job or not. The employers can also follow some employees if they desire. This paper has been designed and implemented with using ASP.NET, C# and JavaScript. The outputs have a user friendly interface. The interface also aimed to provide the useful information for Turkish Technology Companies.

Keywords: background, checking, verification, human resources, online

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Authors: Priyanka Tamta, Sukanya Sharma

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The Kamakhya Temple in Assam plays a very important role in the development of Assam as not only a historical place but also as an archaeologically important site. Temple building activity on the site began in 5th century AD when a cave temple dedicated to Lord Balabhadraswami was constructed here by King Maharajadhiraja Sri Surendra Varman. In the history of Assam, the name of this king is not found and neither the name of this form of Vishnu is known in this region. But this inscription sanctified the place as it recorded the first ever temple building activity in this region. The fifteen hundred years habitation history of the Kamakhya temple sites shows a gradual progression of the site from a religious site to an archaeological site and finally as a historical landmark. Here, in this paper, our main objective is to understand the evolution of Kamakhya temple site as a historical landscape and as an important landmark in the history of Assam. The central theme of the paper is the gradual development of the religious site to a historical landmark. From epigraphical records, it is known that the site received patronage from all ruling dynasties of Assam and its adjoining regions. Royal households of Kashmir, Nepal, Bengal, Orissa, Bihar, etc. have left their footprints on the site. According to records they donated wealth, constructed or renovated temples and participated in the overall maintenance of the deity. This made Kamakhya temple a ground of interaction of faiths, communities, and royalties of the region. Since the 5th century AD, there was a continuous struggle between different beliefs, faiths, and power on the site to become the dominant authority of the site. In the process, powerful beliefs system subsumed minor ones into a larger doctrine of beliefs. This can be seen in the case of the evolution of the Kamakhya temple site as one of the important Shakta temples in India. Today, it is cultural identity marker of the state of Assam within which it is located. Its diverse faiths and beliefs have been appropriated by powerful legends to the dominant faith of the land. The temple has evolved from a cave temple to a complex of seventeen temples. The faith has evolved from the worship of water, an element of nature to the worship of the ten different forms of the goddess with their five male consorts or Bhairavas. Today, it represents and symbolizes the relationship of power and control out of which it has emerged. During different periods of occupation certain architectural and iconographical characters developed which indicated diffusion and cultural adaptation. Using this as sources and the epigraphical records this paper will analyze the interactive and dynamic processes which operated in the building of this cultural marker, the archaeological site of Kamakhya.

Keywords: cultural adaptation and diffusion, cultural and historical landscape, Kamakhya, Saktism, temple art and architecture, historiography

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Authors: Dan W. Rhodes, Juliane Hey, Magali Karagueuzian, Florianne Martinez, Yael Sandowski, Vanessa Roulet, Mahmoud Badawi, Mohammed-Amine Chakir, Valérie Simon, Jérémie Gautier, Françoise Le Boulaire, Catherine Coignard, Claire Vincent, Sandrine Greaume, Isabelle Voisin

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Background: Beckman Coulter, Inc. (BEC) has recently developed a fully automated second-generation anti-HCV test on a new immunoassay platform. The objective of this multicenter study conducted in Europe was to evaluate the performance of the ACCESS anti-HCV assay on the recently CE-marked DxI 9000 ACCESS Immunoassay Analyzer as an aid in the diagnosis of HCV (Hepatitis C Virus) infection and as a screening test for blood and plasma donors. Methods: The clinical specificity of the ACCESS anti-HCV assay was determined using HCV antibody-negative samples from blood donors and hospitalized patients. Sample antibody status was determined by a CE-marked anti-HCV assay (Abbott ARCHITECTTM anti-HCV assay or Abbott PRISM HCV assay) with an additional confirmation method (Immunoblot testing with INNO-LIATM HCV Score - Fujirebio), if necessary, according to pre-determined testing algorithms. The clinical sensitivity was determined using known HCV antibody-positive samples, identified positive by Immunoblot testing with INNO-LIATM HCV Score - Fujirebio. HCV RNA PCR or genotyping was available on all Immunoblot positive samples for further characterization. The false initial reactive rate was determined on fresh samples from blood donors and hospitalized patients. Thirty (30) commercially available seroconversion panels were tested to assess the sensitivity for early detection of HCV infection. The study was conducted from November 2019 to March 2022. Three (3) external sites and one (1) internal site participated. Results: Clinical specificity (95% CI) was 99.7% (99.6 – 99.8%) on 5852 blood donors and 99.0% (98.4 – 99.4%) on 1527 hospitalized patient samples. There were 15 discrepant samples (positive on ACCESS anti-HCV assay and negative on both ARCHITECT and Immunoblot) observed with hospitalized patient samples, and of note, additional HCV RNA PCR results showed five (5) samples had positive HCV RNA PCR results despite the absence of HCV antibody detection by ARCHITECT and Immunoblot, suggesting a better sensitivity of the ACCESS anti-HCV assay with these five samples compared to the ARCHITECT and Immunoblot anti-HCV assays. Clinical sensitivity (95% CI) on 510 well-characterized, known HCV antibody-positive samples was 100.0% (99.3 – 100.0%), including 353 samples with known HCV genotypes (1 to 6). The overall false initial reactive rate (95% CI) on 6630 patient samples was 0.02% (0.00 – 0.09%). Results obtained on 30 seroconversion panels demonstrated that the ACCESS anti-HCV assay had equivalent sensitivity performances, with an average bleed difference since the first reactive bleed below one (1), compared to the ARCHITECTTM anti-HCV assay. Conclusion: The newly developed ACCESS anti-HCV assay from BEC for use on the DxI 9000 ACCESS Immunoassay Analyzer demonstrated high clinical sensitivity and specificity, equivalent to currently marketed anti-HCV assays, as well as a low false initial reactive rate.

Keywords: DxI 9000 ACCESS Immunoassay Analyzer, HCV, HCV antibody, Hepatitis C virus, immunoassay

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Authors: Kai-Cheng Hsu, Tzu-Ying Sung, Jinn-Moon Yang

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Colorectal cancer (CRC) is one of the main causes of cancer death in the world. Although several drugs have been developed to treat colorectal cancer, such as Regorafenib and 5-FU, their efficacy is often limited by the development of drug resistance. Therefore, development of new drugs with new scaffolds is necessary to treat CRC. Here, we used site-moiety maps to identify inhibitors against PIM1, LIMK1, SRC, and mTOR, which are often overexpressed in CRC. A site-moiety map represents physicochemical properties and moiety preferences of a binding site through anchors. An anchor contains three elements: (1) conserved interacting residues of a binding pocket; (2) moiety preference of the binding pocket; and (3) the type (e.g., hydrogen-bonding or van der Waals interactions) of interaction between the moieties and the binding pocket. Then, we performed a structure-based virtual screening of ~260,000 compounds and selected compound candidates with high site-moiety map scores for bioassays. Among these candidates, compound 1 and compound 2 inhibited the growth of CRC cells with IC50 values of <10 μM. The experimental result of enzyme-based assays indicated that compound 1 is a dual inhibitor against PIM1 (IC50 6 μM) and LIMK1(IC50 11 μM). Compound 2 was predicted as a SRC inhibitor and will be further validated. The compounds inhibited different protein targets compared to the current drugs. We believe that the compounds provide a starting point to design new drugs for CRC treatment.

Keywords: colorectal cancer, drug discovery, site-moiety map, virtual screening, PIM1, LIMK1

Procedia PDF Downloads 218

Authors: Sherif A. Abu El-Magd, Ahmed M. Sefelnasr, Ahmed M. Masoud

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Groundwater modeling is the way and tool for assessing and managing groundwater resources efficiently. The present work was carried out in the ancient Egyptian archeological site (Abydos) fromDynastyIandII.Theareaislocated about 13km west of the River Nilecourse, Upper Egypt. The main problem in this context is that the ground water level rise threatens and damages fragile carvings and paintings of the ancient buildings. The main objective of the present work is to identify the sources of the groundwater recharge in the site, further more, equally important there is to control the ground water level rise. Numerical modeling combined with field water level measurements was implemented to understand the ground water recharge sources. However, building a conceptual model was an important step in the groundwater modeling to phase to satisfy the modeling objectives. Therefore, boreholes, crosssections, and a high-resolution digital elevation model were used to construct the conceptual model. To understand the hydrological system in the site, the model was run under both steady state and transient conditions. Then, the model was calibrated agains the observation of the water level measurements. Finally, the results based on the modeling indicated that the groundwater recharge is originating from an indirect flow path mainly from the southeast. Besides, there is a hydraulic connection between the surface water and groundwater in the study site. The decision-makers and archeologyists could consider the present work to understand the behavior of groundwater recharge and water table level rise.

Keywords: numerical modeling, archeological site, groundwater recharge, egypt

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Authors: M. Shemis, O. Maher, G. Casterou, F. Gauffre

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Hepatitis C virus (HCV) is a major cause of chronic liver disease with a global 170 million chronic carriers at risk of developing liver cirrhosis and/or liver cancer. Egypt reports the highest prevalence of HCV worldwide. Currently, two classes of assays are used in the diagnosis and management of HCV infection. Despite the high sensitivity and specificity of the available diagnostic assays, they are time-consuming, labor-intensive, expensive, and require specialized equipment and highly qualified personal. It is therefore important for clinical and economic terms to develop a low-tech assay for the direct detection of HCV RNA with acceptable sensitivity and specificity, short turnaround time, and cost-effectiveness. Such an assay would be critical to control HCV in developing countries with limited resources and high infection rates, such as Egypt. The unique optical and physical properties of gold nanoparticles (AuNPs) have allowed the use of these nanoparticles in developing simple and rapid colorimetric assays for clinical diagnosis offering higher sensitivity and specificity than current detection techniques. The current research aims to develop a detection assay for HCV RNA using gold nanoparticles (AuNPs). Methods: 200 anti-HCV positive samples and 50 anti-HCV negative plasma samples were collected from Egyptian patients. HCV viral load was quantified using m2000rt (Abbott Molecular Inc., Des Plaines, IL). HCV genotypes were determined using multiplex nested RT- PCR. The assay is based on the aggregation of AuNPs in presence of the target RNA. Aggregation of AuNPs causes a color shift from red to blue. AuNPs were synthesized using citrate reduction method. Different sets of probes within the 5’ UTR conserved region of the HCV genome were designed, grafted on AuNPs and optimized for the efficient detection of HCV RNA. Results: The nano-gold assay could colorimetrically detect HCV RNA down to 125 IU/ml with sensitivity and specificity of 91.1% and 93.8% respectively. The turnaround time of the assay is < 30 min. Conclusions: The assay allows sensitive and rapid detection of HCV RNA and represents an inexpensive and simple point-of-care assay for resource-limited settings.

Keywords: HCV, gold nanoparticles, point of care, viral load

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Authors: Hamidrza Joodaki

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The most complex issue in urban land use planning is site selection that needs to assess the verity of elements and factors. Multi Criteria Decision Making (MCDM) methods are the best approach to deal with complex problems. In this paper, combination of the analytical hierarchy process (AHP) model and FUZZY logic was used as MCDM methods to select the best site for gas station in the 4th gas zone of Tehran. The first and the most important step in FUZZY-AHP model is selection of criteria and sub-criteria. Population, accessibility, proximity and natural disasters were considered as the main criteria in this study. After choosing the criteria, they were weighted based on AHP by EXPERT CHOICE software, and FUZZY logic was used to enhance accuracy and to approach the reality. After these steps, criteria layers were produced and weighted based on FUZZY-AHP model in GIS. Finally, through ARC GIS software, the layers were integrated and the 4th gas zone in TEHRAN was selected as the best site to locate gas station.

Keywords: multiple criteria decision making (MCDM), analytic hierarchy process (AHP), FUZZY logic, geographic information system (GIS)

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Authors: Fatima Chaudhary, Rehan Ul Haq

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Spatial and anthropogenic factors influencing nest-site selection in birds need to be identified for effective conservative practices. Environmental attributes such as food availability, predator density, previous reproductive success, etc., provide information regarding the site's quality. An artificial nest box experiment was carried out to evaluate the effect of various factors on nest-site selection, as it is hard to assess the natural cavities. The experiment was conducted whereby half of the boxes were filled with old nest material. Artificial nest boxes created with different materials and different sizes and colors were installed at different heights. A total of 14 out of 60 nest boxes were occupied and four of them faced predation. The birds explored a total of 32 out of 60 nests, whereas anthropogenic factors destroyed 25 out of 60 nests. Birds chose empty nest boxes at higher rates however, there was no obvious avoidance of sites having high ectoparasites load due to old nest material. It is also possible that the preference towards the artificial nest boxes may differ from year to year because of several climatic factors and the age of old nest material affecting the parasite's survival. These variables may fluctuate from one season to another. Considering these factors, nest-site selection experiments concerning the effectiveness of artificial nest boxes should be carried out over several successive seasons. This topic may stimulate further studies, which could lead to a fully understanding the birds' evolutionary ecology. Precise information on these factors influencing nest-site selection can be essential from an economic point of view as well.

Keywords: artificial nesting, nest box, old nest material, birds

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