Search results for: contrast sensitivity
Commenced in January 2007
Frequency: Monthly
Edition: International
Paper Count: 3252

Search results for: contrast sensitivity

1122 Urea and Starch Detection on a Paper-Based Microfluidic Device Enabled on a Smartphone

Authors: Shashank Kumar, Mansi Chandra, Ujjawal Singh, Parth Gupta, Rishi Ram, Arnab Sarkar

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Milk is one of the basic and primary sources of food and energy as we start consuming milk from birth. Hence, milk quality and purity and checking the concentration of its constituents become necessary steps. Considering the importance of the purity of milk for human health, the following study has been carried out to simultaneously detect and quantify the different adulterants like urea and starch in milk with the help of a paper-based microfluidic device integrated with a smartphone. The detection of the concentration of urea and starch is based on the principle of colorimetry. In contrast, the fluid flow in the device is based on the capillary action of porous media. The microfluidic channel proposed in the study is equipped with a specialized detection zone, and it employs a colorimetric indicator undergoing a visible color change when the milk gets in touch or reacts with a set of reagents which confirms the presence of different adulterants in the milk. In our proposed work, we have used iodine to detect the percentage of starch in the milk, whereas, in the case of urea, we have used the p-DMAB. A direct correlation has been found between the color change intensity and the concentration of adulterants. A calibration curve was constructed to find color intensity and subsequent starch and urea concentration. The device has low-cost production and easy disposability, which make it highly suitable for widespread adoption, especially in resource-constrained settings. Moreover, a smartphone application has been developed to detect, capture, and analyze the change in color intensity due to the presence of adulterants in the milk. The low-cost nature of the smartphone-integrated paper-based sensor, coupled with its integration with smartphones, makes it an attractive solution for widespread use. They are affordable, simple to use, and do not require specialized training, making them ideal tools for regulatory bodies and concerned consumers.

Keywords: paper based microfluidic device, milk adulteration, urea detection, starch detection, smartphone application

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1121 Numerical Study of Nonlinear Guided Waves in Composite Laminates with Delaminations

Authors: Reza Soleimanpour, Ching Tai Ng

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Fibre-composites are widely used in various structures due to their attractive properties such as higher stiffness to mass ratio and better corrosion resistance compared to metallic materials. However, one serious weakness of this composite material is delamination, which is a subsurface separation of laminae. A low level of this barely visible damage can cause a significant reduction in residual compressive strength. In the last decade, the application of guided waves for damage detection has been a topic of significant interest for many researches. Among all guided wave techniques, nonlinear guided wave has shown outstanding sensitivity and capability for detecting different types of damages, e.g. cracks and delaminations. So far, most of researches on applications of nonlinear guided wave have been dedicated to isotropic material, such as aluminium and steel, while only a few works have been done on applications of nonlinear characteristics of guided waves in anisotropic materials. This study investigates the nonlinear interactions of the fundamental antisymmetric lamb wave (A0) with delamination in composite laminates using three-dimensional (3D) explicit finite element (FE) simulations. The nonlinearity considered in this study arises from interactions of two interfaces of sub-laminates at the delamination region, which generates contact acoustic nonlinearity (CAN). The aim of this research is to investigate the phenomena of CAN in composite laminated beams by a series of numerical case studies. In this study interaction of fundamental antisymmetric lamb wave with delamination of different sizes are studied in detail. The results show that the A0 lamb wave interacts with the delaminations generating CAN in the form of higher harmonics, which is a good indicator for determining the existence of delaminations in composite laminates.

Keywords: contact acoustic nonlinearity, delamination, fibre reinforced composite beam, finite element, nonlinear guided waves

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1120 Correlates of Work-Family Role Conflict and Well-Being: A Comparative Analysis by Gender

Authors: Liat Kulik

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The main goal of the present study was to examine gender differences in the variables that explain the experience of role conflict and well-being among Jewish working fathers and mothers in the Israel. The experience of work-family conflict arises from simultaneous pressures from the work and family domains that are mutually incompatible. In light of the expansion of women's role set following the addition of paid employment outside of the home, most of the studies dealing with the impact of multiple roles on well-being have been conducted among women. However, changes in gender roles in recent years have also affected men's role set, as reflected in the terms ‘new men’ and ‘new fathers’. Based on structural equation modeling, the study examined gender differences in variables that explain the experience of two types of role conflict – family interferes with work (FIW) and work interferes with family (WIF), as well as with the sense of well-being (positive and negative affect) among 611 employed Jewish mothers and fathers in Israel. The findings revealed that for women, both FIW and WIF conflict correlated negatively with well-being, whereas for men, a negative correlation with well-being was found only in the case of FIW conflict. For both men and women, egalitarian gender role ideology correlated with the dimension of positive effect, but the correlation was stronger for men. The findings highlight the contribution of egalitarian gender role ideology to alleviating the experience of role conflict and improving the emotional well-being of both men and women. Contrary to expectations, social support contributed more to mitigating negative effect among men than women. On the whole, the findings highlight the changes that men have experienced in the work-family system. In sum, the research findings shed new light on the masculine image in terms of the experience of FIW conflict. In contrast to the prevailing assumption that FIW role conflict is predominant among women, the findings of this study indicate that today, this type of role conflict is experienced equally by men and women whereas WIF conflict is predominant among men. Furthermore, contrary to expectations, levels of perceived social support were found to be similar for men and women, and men benefited from it even more than women did.

Keywords: FIW conflict, WIF conflict, social support, egalitarian gender role ideology, overload

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1119 Rethinking Social Work Practice with Immigrants in Child Welfare Services: The Case of Norway

Authors: Ayan Handulle, Memory J. Tembo-Pankuku

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The social work profession utilizes Western and Eurocentric perspectives on social structures, culture, history, belief systems, and education. This affects social work practice with indigenous groups as well as other minorities who have different perspectives. Some of the challenges that characterize social work with families, especially immigrants in western countries, are a result of different world views on child-rearing practices in the global north and the global south. A shift towards cultural sensitivity and the promotion of cultural competence has been a move towards addressing some of the challenges in child welfare practice with immigrants. However, emphasis on cultural differences presents other challenges of stereotyping and discrimination, which call for the examination of current practices to fit other groups of people. In this paper, we introduce the need for emancipatory social work in child welfare practice with immigrant parents. Emancipatory social work is directed at heightening awareness of external sources of oppression and/or privilege that hold the possibility of increasing self-esteem and courage to confront structural sources of marginalization, oppression, and exclusion. This paper draws on two research projects, respectively, “Immigrant parents’ perceptions and experiences of the welfare system” and “Norwegian- Somali parents’ fears of the Norwegian Child welfare service. The first data set comprises 15 in-depth interviews with 18 nonWestern immigrant parents, representing 10 families. The second data set consists of nine months of ethnography, seven months in Oslo, and two months in Somalia among returnees from Norway. Based on these data sets, we explore how immigrant parents’ child-rearing practices might be perceived through a racialized lens.

Keywords: child welfare, immigrants, racialization, social work

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1118 Thermal Image Segmentation Method for Stratification of Freezing Temperatures

Authors: Azam Fazelpour, Saeed R. Dehghani, Vlastimil Masek, Yuri S. Muzychka

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The study uses an image analysis technique employing thermal imaging to measure the percentage of areas with various temperatures on a freezing surface. An image segmentation method using threshold values is applied to a sequence of image recording the freezing process. The phenomenon is transient and temperatures vary fast to reach the freezing point and complete the freezing process. Freezing salt water is subjected to the salt rejection that makes the freezing point dynamic and dependent on the salinity at the phase interface. For a specific area of freezing, nucleation starts from one side and end to another side, which causes a dynamic and transient temperature in that area. Thermal cameras are able to reveal a difference in temperature due to their sensitivity to infrared radiance. Using Experimental setup, a video is recorded by a thermal camera to monitor radiance and temperatures during the freezing process. Image processing techniques are applied to all frames to detect and classify temperatures on the surface. Image processing segmentation method is used to find contours with same temperatures on the icing surface. Each segment is obtained using the temperature range appeared in the image and correspond pixel values in the image. Using the contours extracted from image and camera parameters, stratified areas with different temperatures are calculated. To observe temperature contours on the icing surface using the thermal camera, the salt water sample is dropped on a cold surface with the temperature of -20°C. A thermal video is recorded for 2 minutes to observe the temperature field. Examining the results obtained by the method and the experimental observations verifies the accuracy and applicability of the method.

Keywords: ice contour boundary, image processing, image segmentation, salt ice, thermal image

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1117 Improving the Genetic Diversity of Soybean Seeds and Tolerance to Drought Irradiated with Gamma Rays

Authors: Aminah Muchdar

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To increase the genetic diversity of soybean in order to adapt to agroecology in Indonesia conducted ways including introduction, cross, mutation and genetic transformation. The purpose of this research is to obtain early maturity soybean mutant lines, large seed tolerant to drought with high yield potential. This study consisted of two stages: the first is sensitivity of gamma rays carried out in the Laboratory BATAN. The genetic variety used is Anjasmoro. The method seeds irradiated with gamma rays at a rate of activity with the old ci 1046.16976 irradiation 0-71 minutes. Irradiation doses of 0, 100, 200, 300, 400, 500, 600, 700, 800, 900 and 1000gy. The results indicated all seeds irradiated with doses of 0 - 1000gy, just a dose of 200 and 300gy are able to show the percentage of germination, plant height, number of leaves, number of normal sprouts and green leaves of the best and can be continued for a second trial in order to assemble and to get mutants which is expected. The result of second stage of soybean M2 Population irradiated with diversity Gamma Irradiation performed that in the form of soybean planting, the seed planted is the first derivative of the M2 irradiated seeds. The result after the age of 30ADP has already showing growth and development of plants that vary when compared to its parent, both in terms of plant height, number of leaves, leaf shape and leaf forage level. In the generative phase, a plant that has been irradiated 200 and 300 gy seen some plants flower form packs, but not formed pods, there is also a form packs of flowers, but few pods produce soybean morphological characters such as plant height, number of branches, pods, days to flowering, harvesting, seed weight and seed number.

Keywords: gamma ray, genetic mutation, irradiation, soybean

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1116 Sounds of Power: An Ethnoorganological Approach to Understanding Colonial Music Culture in the Peruvian Andes

Authors: Natascha Reich

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In colonial Peru, the Spanish crown relied on religious orders, most notably Dominicans, Franciscans, and Jesuits, for accelerating processes of colonization. The dissemination of Christian art, architecture, and music, and most of all, the agency of indigenous people in their production played a key role in facilitating the acceptance of the new religious and political system. Current research on Peruvian colonial music culture and its role as a vehicle for colonization focus on practices in urban centers. The lack of (written) primary sources seems to turn rural areas into a less attractive research territory for musicologists. This paper advocates for a more inclusive approach. By investigating seventeenth-century pipe organs as material remains of Franciscan missionary music culture, it shows how reactions to colonial forces and Christianization in rural Andean locations could follow tendencies different from those in urban areas. Indigenous musicians in cities tried to 'fit' into the European system in order to be accepted by the ruling Spanish elite. By contrast, the indigenous-built pipe organs in the rural Peruvian Colca-Valley show distinctly native-Andean influences. This paper argues that this syncretism can be interpreted as hybridity in Homi K. Bhabha’s sense, as a means of the colonized to undermine the power of the colonizer and to advance reactionary politics. Not only will it show the necessity of considering rural Peruvian music history in modern scholarship for arriving at a more complete picture of colonial culture, but it will also evidence the advantages of a mixed-methodology approach. Historical organology, combined with concepts from ethnomusicology and post-colonial studies, proves as a useful tool in the absence or scarcity of written primary sources.

Keywords: cultural hybridity, music as reactionary politics, Latin American pipe organs, Peruvian colonial music

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1115 Supervisory Emotional Display Affects Employee’s Well-Being

Authors: Huan Zhang, Darius K. S Chan

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Despite a large number of studies linking emotional labor and its detrimental impact for laborer, research on how emotional labor would influence the receiver is still in its infancy. Especially under the call for “people management”, supervisors inside the organization are more inclined to display happy mood to support their employees, thus endorsing emotional labor. The present study focuses on the employees in the service industry as emotional labor recipients and investigates how they respond to their supervisors’ emotional display, given their sensitivity to emotional cues. Targeted at a sample of 250 survey data from a wide range of customer service professions, this ongoing study examines how perceived supervisory emotional labor would moderate the relationship between employees surface acting and their well-being. Our major hypotheses are that employees’ surface acting predicts well-being level, and that perceived supervisory emotional labor to moderate the surface acting—outcome links. Preliminary findings have provided some support to the hypothesized model. Specifically, supervisors who are perceived to be high in surface acting are also regarded as fake and pseudo, hence the enhancing the detrimental effect of employees’ surface acting is attenuated, resulting in lower job satisfaction, higher physical stress and burnout; whereas perceived high supervisor’s deep acting, as associated with genuine and authenticity, buffers the negative impact and leads to higher job satisfaction, lower physical stress and burnout. This study first confirms the negative impacts of the surface acting on well-being for service industry employees as laborer and then extends the emotional labor studies by considering them as recipients of supervisory emotional labor. The findings provide insights for leaders by pointing out the importance of authentic emotional expression in workplace.

Keywords: perceived supervisory emotional labor, surface acting, well-being

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1114 Genesis and Survival Chance of Autotriploid in Natural Diploid Population of Lilium lancifolium Thunb

Authors: Ji-Won Park, Jong-Wha Kim

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Triploid L. lancifolium have a wide geographic distribution. By contrast, diploid L. lancifolium have limited distributions in the islands and coastal regions of the South and West Korean Peninsula and northern Tsushima Island, Japan. L. lancifolium diploids and triploids are not sympatrically distributed with other lily species or ploidy lines in West Sea and South Sea Islands of the Korean Peninsula. This observation raises the following questions: 'Why have autotriploid L. lancifolium never been observed in those isolated islands?', 'What mechanism excludes the occurrence of autotriploids, if they arise?'. To determine the occurrence and survival of triploid plants in natural diploid populations of tiger lily (Lilium lancifolium), ploidy analysis was conducted on natural open-pollinated seeds produced from plants grown on isolated islands, and on hybrid seeds produced by artificial crossing between plant populations originating on different Korean islands. Normal seeds were classified into five grades depending on the ratio of embryo/endosperm lengths, including 5/5, 4/5, 3/5, 2/5, and 1/5. Triploids were not observed among seedlings produced from natural open pollinations on isolated islands. Triploids were detected only in seedlings of underdeveloped seed grades(3/5 and 2/5) from artificial crosses between populations from different isolated islands. The triploid occurrence frequency was calculated as 0.0 for natural open-pollinated seedlings and 0.000582 for artificial crosses(6 triploids from 10,303 seedlings). Triploids were produced from crosses between isolated populations located at least 70 km apart; no triploids were detected in inter-population crosses of plants originating on the same islands. Triploid seedlings have very low viability in soil. We analyzed factors affecting triploid occurrence and survival in natural diploid populations of L. lancifolium. The results suggest that triploids originate from fertilization between plants that are genetically isolated due to geographical isolation and/or genotypic differences.

Keywords: Lilium lancifolium, autotriploid, natural population, genetic distance, 2n female gamete

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1113 Poly-ε-Caprolactone Nanofibers with Synthetic Growth Factor Enriched Liposomes as Controlled Drug Delivery System

Authors: Vera Sovkova, Andrea Mickova, Matej Buzgo, Karolina Vocetkova, Eva Filova, Evzen Amler

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PCL (poly-ε-caprolactone) nanofibrous scaffolds with adhered liposomes were prepared and tested as a possible drug delivery system for various synthetic growth factors. TGFβ, bFGF, and IGF-I have been shown to increase hMSC (human mesenchymal stem cells) proliferation and to induce hMSC differentiation. Functionalized PCL nanofibers were prepared with synthetic growth factors encapsulated in liposomes adhered to them in three different concentrations. Other samples contained PCL nanofibers with adhered, free synthetic growth factors. The synthetic growth factors free medium served as a control. The interaction of liposomes with the PCL nanofibers was visualized by SEM, and the release kinetics were determined by ELISA testing. The potential of liposomes, immobilized on the biodegradable scaffolds, as a delivery system for synthetic growth factors, and as a suitable system for MSCs adhesion, proliferation and differentiation in vitro was evaluated by MTS assay, dsDNA amount determination, confocal microscopy, flow cytometry and real-time PCR. The results showed that the growth factors adhered to the PCL nanofibers stimulated cell proliferation mainly up to day 11 and that subsequently their effect was lower. By contrast, the release of the lowest concentration of growth factors from liposomes resulted in gradual proliferation of MSCs throughout the experiment. Moreover, liposomes, as well as free growth factors, stimulated type II collagen production, which was confirmed by immunohistochemical staining using monoclonal antibody against type II collagen. The results of this study indicate that growth factors enriched liposomes adhered to surface of PCL nanofibers could be useful as a drug delivery instrument for application in short timescales, be combined with nanofiber scaffolds to promote local and persistent delivery while mimicking the local microenvironment. This work was supported by project LO1508 from the Ministry of Education, Youth and Sports of the Czech Republic

Keywords: drug delivery, growth factors, hMSC, liposomes, nanofibres

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1112 CAGE Questionnaire as a Screening Tool for Hazardous Drinking in an Acute Admissions Ward: Frequency of Application and Comparison with AUDIT-C Questionnaire

Authors: Ammar Ayad Issa Al-Rifaie, Zuhreya Muazu, Maysam Ali Abdulwahid, Dermot Gleeson

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The aim of this audit was to examine the efficiency of alcohol history documentation and screening for hazardous drinkers at the Medical Admission Unit (MAU) of Northern General Hospital (NGH), Sheffield, to identify any potential for enhancing clinical practice. Data were collected from medical clerking sheets, ICE system and directly from 82 patients by three junior medical doctors using both CAGE questionnaire and AUDIT-C tool for newly admitted patients to MAU in NGH, in the period between January and March 2015. Alcohol consumption was documented in around two-third of the patient sample and this was documented fairly accurately by health care professionals. Some used subjective words such as 'social drinking' in the alcohol units’ section of the history. CAGE questionnaire was applied to only four patients and none of the patients had documented advice, education or referral to an alcohol liaison team. AUDIT-C tool had identified 30.4%, while CAGE 10.9%, of patients admitted to the NGH MAU as hazardous drinkers. The amount of alcohol the patient consumes positively correlated with the score of AUDIT-C (Pearson correlation 0.83). Re-audit is planned to be carried out after integrating AUDIT-C tool as labels in the notes and presenting a brief teaching session to junior doctors. Alcohol misuse screening is not adequately undertaken and no appropriate action is being offered to hazardous drinkers. CAGE questionnaire is poorly applied to patients and when satisfactory and adequately used has low sensitivity to detect hazardous drinkers in comparison with AUDIT-C tool. Re-audit of alcohol screening practice after introducing AUDIT-C tool in clerking sheets (as labels) is required to compare the findings and conclude the audit cycle.

Keywords: alcohol screening, AUDIT-C, CAGE, hazardous drinking

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1111 Electrochemical APEX for Genotyping MYH7 Gene: A Low Cost Strategy for Minisequencing of Disease Causing Mutations

Authors: Ahmed M. Debela, Mayreli Ortiz , Ciara K. O´Sullivan

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The completion of the human genome Project (HGP) has paved the way for mapping the diversity in the overall genome sequence which helps to understand the genetic causes of inherited diseases and susceptibility to drugs or environmental toxins. Arrayed primer extension (APEX) is a microarray based minisequencing strategy for screening disease causing mutations. It is derived from Sanger DNA sequencing and uses fluorescently dideoxynucleotides (ddNTPs) for termination of a growing DNA strand from a primer with its 3´- end designed immediately upstream of a site where single nucleotide polymorphism (SNP) occurs. The use of DNA polymerase offers a very high accuracy and specificity to APEX which in turn happens to be a method of choice for multiplex SNP detection. Coupling the high specificity of this method with the high sensitivity, low cost and compatibility for miniaturization of electrochemical techniques would offer an excellent platform for detection of mutation as well as sequencing of DNA templates. We are developing an electrochemical APEX for the analysis of SNPs found in the MYH7 gene for group of cardiomyopathy patients. ddNTPs were labeled with four different redox active compounds with four distinct potentials. Thiolated oligonucleotide probes were immobilised on gold and glassy carbon substrates which are followed by hybridisation with complementary target DNA just adjacent to the base to be extended by polymerase. Electrochemical interrogation was performed after the incorporation of the redox labelled dedioxynucleotide. The work involved the synthesis and characterisation of the redox labelled ddNTPs, optimisation and characterisation of surface functionalisation strategies and the nucleotide incorporation assays.

Keywords: array based primer extension, labelled ddNTPs, electrochemical, mutations

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1110 Hemispheric Locus and Gender Predict the Delay between the Moment of Stroke and Hospitalization

Authors: D. Anderlini, G. Wallis

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Background: The number of people experiencing stroke is steadily increasing due to changes in diet and lifestyle, to longer life expectancy resulting in older population, to higher survival rates as a consequence of improvements during the acute phase. This study considers what risk factors might contribute to delayed entry to hospital for treatment. Methods: We analyzed data from 2472 patients admitted to the Stroke Unit of the Royal Brisbane Women's Hospital, Australia, between 2002 to 2011. Results: Previous studies have reported that factors which can contribute to delay include the patient’s age, the time of day, physical location, visit the GP instead of going to the emergency, means of transport, severity of symptoms and type of stroke. Contrary to findings of other studies, we found a strong correlation between side of lesion and delay in admission: patients with right hemisphere lesions had an average delay of 3.78 days, while patients with left hemisphere lesions had an average delay of 1.49 days. Damage to the right hemisphere generally ends in motor impairment in the non-dominant hand and no speech impediment. In contrast, left hemisphere lesions can result in deficit to; dominant hand function and aphasia which will be noticed even if their impact on performance is relatively minor. A finding which goes against many previous studies, is the fact that women get to the hospital much sooner than men, showing an average delay of 0.92 days in women vs. 3.36 days in men. Conclusion: Acute surgical-pharmacological therapies are most effective if applied immediately after stroke. Hence delays to admission can be crucial to the degree of recovery. The tendency of patients to overlook symptoms of right hemisphere lesion should be the target of information campaigns both for the general public and GPs. Why do men go to hospital so late? We don't know yet! Nevertheless an awareness plan specifically direct to male population should be on the agenda of Health Departments.

Keywords: gender, admission delay, stroke location, bioinformatics, biomedicine

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1109 The Sub-Optimality of the Electricity Subsidy on Tube Wells in Balochistan (Pakistan): An Analysis Based on Socio-Cultural and Policy Distortions

Authors: Rameesha Javaid

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Agriculture is the backbone of the economy of the province of Balochistan which is known as the ‘fruit basket’ of Pakistan. Its climate zones comprising highlands and plateaus, dependent on rain water, are more suited for the production of deciduous fruit. The vagaries of weather and more so the persistent droughts prompted the government to announce flat rates of electricity bills per month irrespective of the size of the farm, quantum or water used and the category of crop group. That has, no doubt, resulted in increased cropping intensity, more production and employment but has enormously burdened the official exchequer which picks up the residual bills in certain percentages amongst the federal and provincial governments and the local electricity company. This study tests the desirability of continuing the subsidy in the present mode. Optimization of social welfare of farmers has been the focus of the study with emphasis on the contribution of positive externalities and distortions caused in terms of negative externalities. By using the optimization technique with due allowance for distortions, it has been established that the subsidy calls for limiting policy distortions as they cause sub-optimal utilization of the tube well subsidy and improved policy programming. The sensitivity analysis with changed rankings of contributing variables towards social welfare does not significantly change the result. Therefore it leads to the net findings and policy recommendations of significantly reducing the subsidy size, correcting and curtailing policy distortions and targeting the subsidy grant more towards small farmers to generate more welfare by saving a sizeable amount from the subsidy for investment in the wellbeing of the farmers in rural Balochistan.

Keywords: distortion, policy distortion, socio-cultural distortion, social welfare, subsidy

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1108 Surface-Enhanced Raman Spectroscopy-Based Detection of SARS-CoV-2 Through In Situ One-pot Electrochemical Synthesis of 3D Au-Lysate Nanocomposite Structures on Plasmonic Au Electrodes

Authors: Ansah Iris Baffour, Dong-Ho Kim, Sung-Gyu Park

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The ongoing COVID-19 pandemic, caused by the SARS-CoV-2 virus and is gradually shifting to an endemic phase which implies the outbreak is far from over and will be difficult to eradicate. Global cooperation has led to unified precautions that aim to suppress epidemiological spread (e.g., through travel restrictions) and reach herd immunity (through vaccinations); however, the primary strategy to restrain the spread of the virus in mass populations relies on screening protocols that enable rapid on-site diagnosis of infections. Herein, we employed surface enhanced Raman spectroscopy (SERS) for the rapid detection of SARS-CoV-2 lysate on an Au-modified Au nanodimple(AuND)electrode. Through in situone-pot Au electrodeposition on the AuND electrode, Au-lysate nanocomposites were synthesized, generating3D internal hotspots for large SERS signal enhancements within 30 s of the deposition. The capture of lysate into newly generated plasmonic nanogaps within the nanocomposite structures enhanced metal-spike protein contact in 3D spaces and served as hotspots for sensitive detection. The limit of detection of SARS-CoV-2 lysate was 5 x 10-2 PFU/mL. Interestingly, ultrasensitive detection of the lysates of influenza A/H1N1 and respiratory syncytial virus (RSV) was possible, but the method showed ultimate selectivity for SARS-CoV-2 in lysate solution mixtures. We investigated the practical application of the approach for rapid on-site diagnosis by detecting SARS-CoV-2 lysate spiked in normal human saliva at ultralow concentrations. The results presented demonstrate the reliability and sensitivity of the assay for rapid diagnosis of COVID-19.

Keywords: label-free detection, nanocomposites, SARS-CoV-2, surface-enhanced raman spectroscopy

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1107 Effects of Wearable Garments on Postural Regulation in Community-Dwelling Elderly Adults

Authors: Mei Teng Woo, Keith Davids, Jarmo Liukkonen, Jia Yi Chow, Timo Jaakkola

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Wearable garments such as tapes, compression garments, and braces could improve proprioception and reduced postural sway. The aim of this study was to examine the effects of wearable garments on postural regulation in a sample of community-dwelling elderly individuals, aged 65 years. It was hypothesized that wearable garments such as socks would provide stimulation to lower leg mechanoreceptors, and help participants achieve better postural regulation. Participants (N=63) performed a 30-s Romberg balance test protocol under four conditions (barefoot; wearing commercial socks; wearing clinical compression socks; wearing non-clinical compression socks), in a counterbalanced order, with four levels of performance difficulty: (1) standing on a stable surface with open eyes (SO); (2) a stable surface with closed eyes (SC); (3) a foam surface with open eyes (FO); and (4) a foam surface with closed eyes (FC). Centre of pressure (CoP) measurements included postural sway area (C90 area), trace length (TL) and sway velocity. Thirty-five participants (55.6%) showed positive effects of wearing the socks (responded group). In the responded group, it was revealed that socks showed significant differences in SO, SC and FO conditions for the two CoP measurements - TL and sway velocity (p < 0.05). In contrast, in the non-responded group, barefoot condition significantly decreased the TL and velocity in the SO condition. From the positive effects observed in the responded group, it is possible that wearable garments provide sensory cues that could interact with a biological cueing system to enhance performance in the postural regulation system. This study suggests that individuals respond to the socks treatments differently and future research should be undertaken to examine the factors that benefited the responded group of participants.

Keywords: community-dwelling, elderly adults, postural regulation, wearable garments

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1106 The Effect of Magnesium Supplement on the Athletic Performance of Field Athletes

Authors: M. Varmaziar

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Magnesium (Mg) is an essential mineral that plays a crucial role in the human body. Certain types of foods, including nuts, grains, fruits, vegetables, and whole grains, are rich sources of magnesium. Mg serves as an essential cofactor for numerous enzymatic reactions, including energy metabolism, cellular growth, glycolysis, and protein synthesis. The Mg-ATP complex serves as an energy source and is vital for many physiological functions, including nerve conduction, muscle contraction, and blood pressure regulation. Despite the vital role of magnesium in energy metabolism, maintaining adequate magnesium intake is often overlooked among the general population and athletes. The aim of this study was to investigate the effect of magnesium supplementation on the physical activities of field athletes. Field athletes were divided into two groups: those who consumed magnesium supplements and those who received a placebo. These two groups received either 500 mg of magnesium oxide or a placebo daily for 8 weeks. At the beginning and end of the study, athletes completed ISI questionnaires and physical activity assessments. Nutritional analyses were performed using N4 software, and statistical analyses were conducted using SPSS19 software. The results of this study revealed a significant difference between the two study groups. Athletes who received magnesium supplements experienced less fatigue related to field athletic activities and muscle soreness. In contrast, athletes who received the placebo reported more significant fatigue and muscle soreness. A concerning finding in these results is that the performance of athletic activities may be at risk with low magnesium levels. Therefore, magnesium is essential for maintaining health and plays a crucial role in athletic performance. Consuming a variety of magnesium-rich foods ensures that individuals receive an adequate amount of this essential nutrient in their diet. The consumption of these foods improves performance parameters in athletic exercises.

Keywords: athletic performance, effect, field athletes, magnesium supplement

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1105 Temperature Effect on Changing of Electrical Impedance and Permittivity of Ouargla (Algeria) Dunes Sand at Different Frequencies

Authors: Naamane Remita, Mohammed laïd Mechri, Nouredine Zekri, Smaïl Chihi

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The goal of this study is the estimation real and imaginary components of both electrical impedance and permittivity z', z'' and ε', ε'' respectively, in Ouargla dunes sand at different temperatures and different frequencies, with alternating current (AC) equal to 1 volt, using the impedance spectroscopy (IS). This method is simple and non-destructive. the results can frequently be correlated with a number of physical properties, dielectric properties and the impacts of the composition on the electrical conductivity of solids. The experimental results revealed that the real part of impedance is higher at higher temperature in the lower frequency region and gradually decreases with increasing frequency. As for the high frequencies, all the values of the real part of the impedance were positive. But at low frequency the values of the imaginary part were positive at all temperatures except for 1200 degrees which were negative. As for the medium frequencies, the reactance values were negative at temperatures 25, 400, 200 and 600 degrees, and then became positive at the rest of the temperatures. At high frequencies of the order of MHz, the values of the imaginary part of the electrical impedance were in contrast to what we recorded for the middle frequencies. The results showed that the electrical permittivity decreases with increasing frequency, at low frequency we recorded permittivity values of 10+ 11, and at medium frequencies it was 10+ 07, while at high frequencies it was 10+ 02. The values of the real part of the electrical permittivity were taken large values at the temperatures of 200 and 600 degrees Celsius and at the lowest frequency, while the smallest value for the permittivity was recorded at the temperature of 400 degrees Celsius at the highest frequency. The results showed that there are large values of the imaginary part of the electrical permittivity at the lowest frequency and then it starts decreasing as the latter increases (the higher the frequency the lower the values of the imaginary part of the electrical permittivity). The character of electrical impedance variation indicated an opportunity to realize the polarization of Ouargla dunes sand and acquaintance if this compound consumes or produces energy. It’s also possible to know the satisfactory of equivalent electric circuit, whether it’s miles induction or capacitance.

Keywords: electrical impedance, electrical permittivity, temperature, impedance spectroscopy, dunes sand ouargla

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1104 Provision of Different Layers of Activities for Different Iranian Intermediate English as a Foreign Language Learners for the Beneficial Use of Films within Speaking Classes

Authors: Zahra Ebrahimi, Abbas Moradan

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This study investigated the effect of applying different layers of activity for different Iranian intermediate EFL learner’s oral proficiency and two of its components (fluency and accura-cy) for the beneficial use of films within speaking classes. For this purpose, thirty Iranian EFL intermediate learners were selected based on availability sampling, they were divided into one experimental group and one control group, each consisting of 15 participants, who were proved to be homogeneous based on the results obtained from IELTS oral proficien-cy test prior to the treatment. Experimental Group received the treatment which was apply-ing different layers of speaking tasks according to learners’ level of fluency and accuracy. Control group received ordinal treatment of speaking classrooms. The materials for this study consisted of 11 English movies for each session, voice-recorder device, and IELTS oral proficiency tests as well as two interviews based on Ur’s oral scale for measuring fluen-cy and accuracy. The treatment was run for 12 sessions in six weeks. At the end of the treatment, all the students both in experimental and control group were given a post-test interview based on Ur’s scale. To compare and contrast the amount of progress of the learners in different groups the results of the pre-test and post-test of speaking were analysed by using T-tests. Moreover, Multivariate analysis of variance was also used to check the hypotheses. Results showed that application of different layers of activity with regard to students’ level, led to a significantly superior performance in experimental group. Thus, this study verified the positive effect of implementation of different layers of activity and tasks to achieve progress in speaking skill. It can also help to create a less stressful at-mosphere of learning in which all the students will be given specific time to speak and lead them to be autonomous learners.

Keywords: differentiated instruction, learners’ style, multiple intelligence, speaking skill, task-based activities

Procedia PDF Downloads 138
1103 Multivariate Data Analysis for Automatic Atrial Fibrillation Detection

Authors: Zouhair Haddi, Stephane Delliaux, Jean-Francois Pons, Ismail Kechaf, Jean-Claude De Haro, Mustapha Ouladsine

Abstract:

Atrial fibrillation (AF) has been considered as the most common cardiac arrhythmia, and a major public health burden associated with significant morbidity and mortality. Nowadays, telemedical approaches targeting cardiac outpatients situate AF among the most challenged medical issues. The automatic, early, and fast AF detection is still a major concern for the healthcare professional. Several algorithms based on univariate analysis have been developed to detect atrial fibrillation. However, the published results do not show satisfactory classification accuracy. This work was aimed at resolving this shortcoming by proposing multivariate data analysis methods for automatic AF detection. Four publicly-accessible sets of clinical data (AF Termination Challenge Database, MIT-BIH AF, Normal Sinus Rhythm RR Interval Database, and MIT-BIH Normal Sinus Rhythm Databases) were used for assessment. All time series were segmented in 1 min RR intervals window and then four specific features were calculated. Two pattern recognition methods, i.e., Principal Component Analysis (PCA) and Learning Vector Quantization (LVQ) neural network were used to develop classification models. PCA, as a feature reduction method, was employed to find important features to discriminate between AF and Normal Sinus Rhythm. Despite its very simple structure, the results show that the LVQ model performs better on the analyzed databases than do existing algorithms, with high sensitivity and specificity (99.19% and 99.39%, respectively). The proposed AF detection holds several interesting properties, and can be implemented with just a few arithmetical operations which make it a suitable choice for telecare applications.

Keywords: atrial fibrillation, multivariate data analysis, automatic detection, telemedicine

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1102 Characterization and Pcr Detection of Selected Strains of Psychrotrophic Bacteria Isolated From Raw Milk

Authors: Kidane workelul, Li xu, Xiaoyang Pang, Jiaping Lv

Abstract:

Dairy products are exceptionally ideal media for the growth of microorganisms because of their high nutritional content. There are several ways that milk might get contaminated throughout the milking process, including how the raw milk is transported and stored, as well as how long it is kept before being processed. Psychrotrophic bacteria are among the one which can deteriorate the quality of milk mainly their heat resistance proteas and lipase enzyme. For this research purpose 8 selected strains of Psychrotrophic bacteria (Entrococcus hirae, Pseudomonas fluorescens, Pseudomonas azotoformans, Pseudomonas putida, Exiguobacterium indicum, Pseudomonas paralactice, Acinetobacter indicum, Serratia liquefacients)are chosen and try to determine their characteristics based on the research methodology protocol. Thus, the 8 selected strains are cultured, plated incubate, extracted their genomic DNA and genome DNA was amplified, the purpose of the study was to identify their Psychrotrophic properties, lipase hydrolysis positive test, their optimal incubation temperature, designed primer using the noble strain P,flourescens conserved region area in target with lipA gene, optimized primer specificity as well as sensitivity and PCR detection for lipase positive strains using the design primers. Based on the findings both the selected 8 strains isolated from stored raw milk are Psychrotrophic bacteria, 6 of the selected strains except the 2 strains are positive for lipase hydrolysis, their optimal temperature is 20 to 30 OC, the designed primer specificity is very accurate and amplifies for those strains only with lipase positive but could not amplify for the others. Thus, the result is promising and could help in detecting the Psychrotrophic bacteria producing heat resistance enzymes (lipase) at early stage before the milk is processed and this will safe production loss for the dairy industry.

Keywords: dairy industry, heat-resistant, lipA, milk, primer and psychrotrophic

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1101 Mordechai Vanunu: “The Atomic Spy” as a Nuclear Threat to Discourse in Israeli Society

Authors: Ada Yurman

Abstract:

Using the case of Israeli Atomic Spy Mordechai Vanunu as an example, this study sought to examine social response to political deviance whereby social response can be mobilized in order to achieve social control. Mordechai Vanunu, a junior technician in the Dimona Atomic Research Center, played a normative role in the militaristic discourse while working in the “holy shrine” of the Israeli defense system for many years. At a certain stage, however, Vanunu decided to detach himself from this collective and launched an assault on this top-secret circle. Israeli society in general and the security establishment in particular found this attack intolerable and unforgivable. They presented Vanunu as a ticking time bomb, delegitimized him and portrayed him as “other”. In addition, Israeli enforcement authorities imposed myriad prohibitions and sanctions on Vanunu even after his release from prison – “as will be done to he who desecrates holiness.” Social response to Vanunu at the time of his capture and trial was studied by conducting a content analysis of six contemporary daily newspapers. The analysis focused on use of language and forms of expression. In contrast with traditional content analysis methodology, this study did not just look at frequency of expressions of ideas and terms in the text and covert content; rather, the text was analyzed as a structural whole, and included examination of style, tone and unusual use of imagery, and more, in order to uncover hidden messages within the text. The social response to this case was extraordinarily intense, not only because in this case of political deviance, involving espionage and treason, Vanunu’s actions comprised a real potential threat to the country, but also because of the threat his behavior posed to the symbolic universe of society. Therefore, the response to this instance of political deviance can be seen as being part of a mechanism of social control aiming to protect world view of society as a whole, as well as to punish the criminal.

Keywords: militarism, political deviance, social construction, social control

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1100 Probabilistic Analysis of Bearing Capacity of Isolated Footing using Monte Carlo Simulation

Authors: Sameer Jung Karki, Gokhan Saygili

Abstract:

The allowable bearing capacity of foundation systems is determined by applying a factor of safety to the ultimate bearing capacity. Conventional ultimate bearing capacity calculations routines are based on deterministic input parameters where the nonuniformity and inhomogeneity of soil and site properties are not accounted for. Hence, the laws of mathematics like probability calculus and statistical analysis cannot be directly applied to foundation engineering. It’s assumed that the Factor of Safety, typically as high as 3.0, incorporates the uncertainty of the input parameters. This factor of safety is estimated based on subjective judgement rather than objective facts. It is an ambiguous term. Hence, a probabilistic analysis of the bearing capacity of an isolated footing on a clayey soil is carried out by using the Monte Carlo Simulation method. This simulated model was compared with the traditional discrete model. It was found out that the bearing capacity of soil was found higher for the simulated model compared with the discrete model. This was verified by doing the sensitivity analysis. As the number of simulations was increased, there was a significant % increase of the bearing capacity compared with discrete bearing capacity. The bearing capacity values obtained by simulation was found to follow a normal distribution. While using the traditional value of Factor of safety 3, the allowable bearing capacity had lower probability (0.03717) of occurring in the field compared to a higher probability (0.15866), while using the simulation derived factor of safety of 1.5. This means the traditional factor of safety is giving us bearing capacity that is less likely occurring/available in the field. This shows the subjective nature of factor of safety, and hence probability method is suggested to address the variability of the input parameters in bearing capacity equations.

Keywords: bearing capacity, factor of safety, isolated footing, montecarlo simulation

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1099 Parameters Identification and Sensitivity Study for Abrasive WaterJet Milling Model

Authors: Didier Auroux, Vladimir Groza

Abstract:

This work is part of STEEP Marie-Curie ITN project, and it focuses on the identification of unknown parameters of the proposed generic Abrasive WaterJet Milling (AWJM) PDE model, that appears as an ill-posed inverse problem. The necessity of studying this problem comes from the industrial milling applications where the possibility to predict and model the final surface with high accuracy is one of the primary tasks in the absence of any knowledge of the model parameters that should be used. In this framework, we propose the identification of model parameters by minimizing a cost function, measuring the difference between experimental and numerical solutions. The adjoint approach based on corresponding Lagrangian gives the opportunity to find out the unknowns of the AWJM model and their optimal values that could be used to reproduce the required trench profile. Due to the complexity of the nonlinear problem and a large number of model parameters, we use an automatic differentiation software tool (TAPENADE) for the adjoint computations. By adding noise to the artificial data, we show that in fact the parameter identification problem is highly unstable and strictly depends on input measurements. Regularization terms could be effectively used to deal with the presence of data noise and to improve the identification correctness. Based on this approach we present results in 2D and 3D of the identification of the model parameters and of the surface prediction both with self-generated data and measurements obtained from the real production. Considering different types of model and measurement errors allows us to obtain acceptable results for manufacturing and to expect the proper identification of unknowns. This approach also gives us the ability to distribute the research on more complex cases and consider different types of model and measurement errors as well as 3D time-dependent model with variations of the jet feed speed.

Keywords: Abrasive Waterjet Milling, inverse problem, model parameters identification, regularization

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1098 Resting-State Functional Connectivity Analysis Using an Independent Component Approach

Authors: Eric Jacob Bacon, Chaoyang Jin, Dianning He, Shuaishuai Hu, Lanbo Wang, Han Li, Shouliang Qi

Abstract:

Objective: Refractory epilepsy is a complicated type of epilepsy that can be difficult to diagnose. Recent technological advancements have made resting-state functional magnetic resonance (rsfMRI) a vital technique for studying brain activity. However, there is still much to learn about rsfMRI. Investigating rsfMRI connectivity may aid in the detection of abnormal activities. In this paper, we propose studying the functional connectivity of rsfMRI candidates to diagnose epilepsy. Methods: 45 rsfMRI candidates, comprising 26 with refractory epilepsy and 19 healthy controls, were enrolled in this study. A data-driven approach known as independent component analysis (ICA) was used to achieve our goal. First, rsfMRI data from both patients and healthy controls were analyzed using group ICA. The components that were obtained were then spatially sorted to find and select meaningful ones. A two-sample t-test was also used to identify abnormal networks in patients and healthy controls. Finally, based on the fractional amplitude of low-frequency fluctuations (fALFF), a chi-square statistic test was used to distinguish the network properties of the patient and healthy control groups. Results: The two-sample t-test analysis yielded abnormal in the default mode network, including the left superior temporal lobe and the left supramarginal. The right precuneus was found to be abnormal in the dorsal attention network. In addition, the frontal cortex showed an abnormal cluster in the medial temporal gyrus. In contrast, the temporal cortex showed an abnormal cluster in the right middle temporal gyrus and the right fronto-operculum gyrus. Finally, the chi-square statistic test was significant, producing a p-value of 0.001 for the analysis. Conclusion: This study offers evidence that investigating rsfMRI connectivity provides an excellent diagnosis option for refractory epilepsy.

Keywords: ICA, RSN, refractory epilepsy, rsfMRI

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1097 Geometrical Analysis of an Atheroma Plaque in Left Anterior Descending Coronary Artery

Authors: Sohrab Jafarpour, Hamed Farokhi, Mohammad Rahmati, Alireza Gholipour

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In the current study, a nonlinear fluid-structure interaction (FSI) biomechanical model of atherosclerosis in the left anterior descending (LAD) coronary artery is developed to perform a detailed sensitivity analysis of the geometrical features of an atheroma plaque. In the development of the numerical model, first, a 3D geometry of the diseased artery is developed based on patient-specific dimensions obtained from the experimental studies. The geometry includes four influential geometric characteristics: stenosis ratio, plaque shoulder-length, fibrous cap thickness, and eccentricity intensity. Then, a suitable strain energy density function (SEDF) is proposed based on the detailed material stability analysis to accurately model the hyperelasticity of the arterial walls. The time-varying inlet velocity and outlet pressure profiles are adopted from experimental measurements to incorporate the pulsatile nature of the blood flow. In addition, a computationally efficient type of structural boundary condition is imposed on the arterial walls. Finally, a non-Newtonian viscosity model is implemented to model the shear-thinning behaviour of the blood flow. According to the results, the structural responses in terms of the maximum principal stress (MPS) are affected more compared to the fluid responses in terms of wall shear stress (WSS) as the geometrical characteristics are varying. The extent of these changes is critical in the vulnerability assessment of an atheroma plaque.

Keywords: atherosclerosis, fluid-Structure interaction modeling, material stability analysis, and nonlinear biomechanics

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1096 Uncertainty and Multifunctionality as Bridging Concepts from Socio-Ecological Resilience to Infrastructure Finance in Water Resource Decision Making

Authors: Anita Lazurko, Laszlo Pinter, Jeremy Richardson

Abstract:

Uncertain climate projections, multiple possible development futures, and a financing gap create challenges for water infrastructure decision making. In contrast to conventional predict-plan-act methods, an emerging decision paradigm that enables social-ecological resilience supports decisions that are appropriate for uncertainty and leverage social, ecological, and economic multifunctionality. Concurrently, water infrastructure project finance plays a powerful role in sustainable infrastructure development but remains disconnected from discourse in socio-ecological resilience. At the time of research, a project to transfer water from Lesotho to Botswana through South Africa in the Orange-Senqu River Basin was at the pre-feasibility stage. This case was analysed through documents and interviews to investigate how uncertainty and multifunctionality are conceptualised and considered in decisions for the resilience of water infrastructure and to explore bridging concepts that might allow project finance to better enable socio-ecological resilience. Interviewees conceptualised uncertainty as risk, ambiguity and ignorance, and multifunctionality as politically-motivated shared benefits. Numerous efforts to adopt emerging decision methods that consider these terms were in use but required compromises to accommodate the persistent, conventional decision paradigm, though a range of future opportunities was identified. Bridging these findings to finance revealed opportunities to consider a more comprehensive scope of risk, to leverage risk mitigation measures, to diffuse risks and benefits over space, time and to diverse actor groups, and to clarify roles to achieve multiple objectives for resilience. In addition to insights into how multiple decision paradigms interact in real-world decision contexts, the research highlights untapped potential at the juncture between socio-ecological resilience and project finance.

Keywords: socio-ecological resilience, finance, multifunctionality, uncertainty

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1095 Topology Optimization of Heat and Mass Transfer for Two Fluids under Steady State Laminar Regime: Application on Heat Exchangers

Authors: Rony Tawk, Boutros Ghannam, Maroun Nemer

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Topology optimization technique presents a potential tool for the design and optimization of structures involved in mass and heat transfer. The method starts with an initial intermediate domain and should be able to progressively distribute the solid and the two fluids exchanging heat. The multi-objective function of the problem takes into account minimization of total pressure loss and maximization of heat transfer between solid and fluid subdomains. Existing methods account for the presence of only one fluid, while the actual work extends optimization distribution of solid and two different fluids. This requires to separate the channels of both fluids and to ensure a minimum solid thickness between them. This is done by adding a third objective function to the multi-objective optimization problem. This article uses density approach where each cell holds two local design parameters ranging from 0 to 1, where the combination of their extremums defines the presence of solid, cold fluid or hot fluid in this cell. Finite volume method is used for direct solver coupled with a discrete adjoint approach for sensitivity analysis and method of moving asymptotes for numerical optimization. Several examples are presented to show the ability of the method to find a trade-off between minimization of power dissipation and maximization of heat transfer while ensuring the separation and continuity of the channel of each fluid without crossing or mixing the fluids. The main conclusion is the possibility to find an optimal bi-fluid domain using topology optimization, defining a fluid to fluid heat exchanger device.

Keywords: topology optimization, density approach, bi-fluid domain, laminar steady state regime, fluid-to-fluid heat exchanger

Procedia PDF Downloads 388
1094 A Structure-Switching Electrochemical Aptasensor for Rapid, Reagentless and Single-Step, Nanomolar Detection of C-Reactive Protein

Authors: William L. Whitehouse, Louisa H. Y. Lo, Andrew B. Kinghorn, Simon C. C. Shiu, Julian. A. Tanner

Abstract:

C-reactive protein (CRP) is an acute-phase reactant and sensitive indicator for sepsis and other life-threatening pathologies, including systemic inflammatory response syndrome (SIRS). Currently, clinical turn-around times for established CRP detection methods take between 30 minutes to hours or even days from centralized laboratories. Here, we report the development of an electrochemical biosensor using redox probe-tagged DNA aptamers functionalized onto cheap, commercially available screen-printed electrodes. Binding-induced conformational switching of the CRP-targeting aptamer induces a specific and selective signal-ON event, which enables single-step and reagentless detection of CRP in as little as 1 minute. The aptasensor dynamic range spans 5-1000nM (R=0.97) or 5-500nM (R=0.99) in 50% diluted human serum, with a LOD of 3nM, corresponding to 2-orders of magnitude sensitivity under the clinically relevant cut-off for CRP. The sensor is stable for up to one week and can be reused numerous times, as judged from repeated real-time dosing and dose-response assays. By decoupling binding events from the signal induction mechanism, structure-switching electrochemical aptamer-based sensors (SS-EABs) provide considerable advantages over their adsorption-based counterparts. Our work expands on the retinue of such sensors reported in the literature and is the first instance of an SS-EAB for reagentless CRP detection. We hope this study can inspire further investigations into the suitability of SS-EABs for diagnostics, which will aid translational R&D toward fully realized devices aimed at point-of-care applications or for use more broadly by the public.

Keywords: structure-switching, C-reactive protein, electrochemical, biosensor, aptasensor.

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1093 Scalable and Accurate Detection of Pathogens from Whole-Genome Shotgun Sequencing

Authors: Janos Juhasz, Sandor Pongor, Balazs Ligeti

Abstract:

Next-generation sequencing, especially whole genome shotgun sequencing, is becoming a common approach to gain insight into the microbiomes in a culture-independent way, even in clinical practice. It does not only give us information about the species composition of an environmental sample but opens the possibility to detect antimicrobial resistance and novel, or currently unknown, pathogens. Accurately and reliably detecting the microbial strains is a challenging task. Here we present a sensitive approach for detecting pathogens in metagenomics samples with special regard to detecting novel variants of known pathogens. We have developed a pipeline that uses fast, short read aligner programs (i.e., Bowtie2/BWA) and comprehensive nucleotide databases. Taxonomic binning is based on the lowest common ancestor (LCA) principle; each read is assigned to a taxon, covering the most significantly hit taxa. This approach helps in balancing between sensitivity and running time. The program was tested both on experimental and synthetic data. The results implicate that our method performs as good as the state-of-the-art BLAST-based ones, furthermore, in some cases, it even proves to be better, while running two orders magnitude faster. It is sensitive and capable of identifying taxa being present only in small abundance. Moreover, it needs two orders of magnitude less reads to complete the identification than MetaPhLan2 does. We analyzed an experimental anthrax dataset (B. anthracis strain BA104). The majority of the reads (96.50%) was classified as Bacillus anthracis, a small portion, 1.2%, was classified as other species from the Bacillus genus. We demonstrate that the evaluation of high-throughput sequencing data is feasible in a reasonable time with good classification accuracy.

Keywords: metagenomics, taxonomy binning, pathogens, microbiome, B. anthracis

Procedia PDF Downloads 123