Search results for: variation sets

Authors: Amesh P, Suneesh A S, Venkatesan K A

Abstract:

The magnetic solid-phase extraction is a relatively new method among the other solid-phase extraction techniques for the separating of metal ions from aqueous solutions, such as mine water and groundwater, contaminated wastes, etc. However, the bare magnetic particles (Fe3O4) exhibit poor selectivity due to the absence of target-specific functional groups for sequestering the metal ions. The selectivity of these magnetic particles can be remarkably improved by covalently tethering the task-specific ligands on magnetic surfaces. The magnetic particles offer a number of advantages such as quick phase separation aided by the external magnetic field. As a result, the solid adsorbent can be prepared with the particle size ranging from a few micrometers to the nanometer, which again offers the advantages such as enhanced kinetics of extraction, higher extraction capacity, etc. Conventionally, the magnetite (Fe3O4) particles were prepared by the hydrolysis and co-precipitation of ferrous and ferric salts in aqueous ammonia solution. Since the covalent linking of task-specific functionalities on Fe3O4 was difficult, and it is also susceptible to redox reaction in the presence of acid or alkali, it is necessary to modify the surface of Fe3O4 by silica coating. This silica coating is usually carried out by hydrolysis and condensation of tetraethyl orthosilicate over the surface of magnetite to yield a thin layer of silica-coated magnetite particles. Since the silica-coated magnetite particles amenable for further surface modification, it can be reacted with task-specific functional groups to obtain the functionalized magnetic particles. The surface area exhibited by such magnetic particles usually falls in the range of 50 to 150 m2.g-1, which offer advantage such as quick phase separation, as compared to the other solid-phase extraction systems. In addition, the magnetic (Fe3O4) particles covalently linked on mesoporous silica matrix (MCM-41) and task-specific ligands offer further advantages in terms of extraction kinetics, high stability, longer reusable cycles, and metal extraction capacity, due to the large surface area, ample porosity and enhanced number of functional groups per unit area on these adsorbents. In view of this, the present paper deals with the synthesis of uranium specific diethylenetriamine ligand (DETA) ligand anchored on silica-coated magnetite (Fe-DETA) as well as on magnetic mesoporous silica (MCM-Fe-DETA) and studies on the extraction of uranium from aqueous solution spiked with uranium to mimic the mine water or groundwater contaminated with uranium. The synthesized solid-phase adsorbents were characterized by FT-IR, Raman, TG-DTA, XRD, and SEM. The extraction behavior of uranium on the solid-phase was studied under several conditions like the effect of pH, initial concentration of uranium, rate of extraction and its variation with pH and initial concentration of uranium, effect of interference ions like CO32-, Na+, Fe+2, Ni+2, and Cr+3, etc. The maximum extraction capacity of 233 mg.g-1 was obtained for Fe-DETA, and a huge capacity of 1047 mg.g-1 was obtained for MCM-Fe-DETA. The mechanism of extraction, speciation of uranium, extraction studies, reusability, and the other results obtained in the present study suggests Fe-DETA and MCM-Fe-DETA are the potential candidates for the extraction of uranium from mine water, and groundwater.

Keywords: diethylenetriamine, magnetic mesoporous silica, magnetic solid-phase extraction, uranium extraction, wastewater treatment

Procedia PDF Downloads 135

Authors: T. P. Sathishkumar, P. Navaneethakrishnan

Abstract:

The research work investigates the variation of tensile properties for the sansevieria ehrenbergii fiber (SEF) and SEF reinforced polyester composites respect to various water absorption time. The experiments were conducted according to ATSM D3379-75 and ASTM D570 standards. The percentage of water absorption for composite specimens was measured according to ASTM D570 standard. The fiber of SE was cut in to 30 mm length for preparation of the composites. The simple hand lay-up method followed by compression moulding process adopted to prepare the randomly oriented SEF reinforced polyester composites at constant fiber weight fraction of 40%. The surface treatment was done on the SEFs with various chemicals such as NaOH, KMnO4, Benzoyl Peroxide, Benzoyl Chloride and Stearic Acid before preparing the composites. NaOH was used for pre-treatment of all other chemical treatments. The morphology of the tensile fractured specimens studied using the Scanning Electron Microscopic. The tensile strength of the SEF and SEF reinforced polymer composites were carried out with various water absorption time such as 4, 8, 12, 16, 20 and 24 hours respectively. The result shows that the tensile strength was drop off with increase in water absorption time for all composites. The highest tensile property of raw fiber was found due to lowest moistures content. Also the chemical bond between the cellulose and cementic materials such as lignin and wax was highest due to lowest moisture content. Tensile load was lowest and elongation was highest for the water absorbed fibers at various water absorption time ranges. During this process, the fiber cellulose inhales the water and expands the primary and secondary fibers walls. This increases the moisture content in the fibers. Ultimately this increases the hydrogen cation and the hydroxide anion from the water. In tensile testing, the water absorbed fibers shows highest elongation by stretching of expanded cellulose walls and the bonding strength between the fiber cellulose is low. The load carrying capability was stable at 20 hours of water absorption time. This could be directly affecting the interfacial bonding between the fiber/matrix and composite strength. The chemically treated fibers carry higher load and lower elongation which is due to removal of lignin, hemicellulose and wax content. The water time absorption decreases the tensile strength of the composites. The chemically SEF reinforced composites shows highest tensile strength compared to untreated SEF reinforced composites. This was due to highest bonding area between the fiber/matrix. This was proven in the morphology at the fracture zone of the composites. The intra-fiber debonding was occurred by water capsulation in the fiber cellulose. Among all, the tensile strength was found to be highest for KMnO4 treated SEF reinforced composite compared to other composites. This was due to better interfacial bonding between the fiber-matrix compared to other treated fiber composites. The percentage of water absorption of composites increased with time of water absorption. The percentage weight gain of chemically treated SEF composites at 4 hours to zero water absorption are 9, 9, 10, 10.8 and 9.5 for NaOH, BP, BC, KMnO4 and SA respectively. The percentage weight gain of chemically treated SEF composites at 24 hours to zero water absorption 5.2, 7.3, 12.5, 16.7 and 13.5 for NaOH, BP, BC, KMnO4 and SA respectively. Hence the lowest weight gain was found for KMnO4 treated SEF composites by highest percentage with lowest water uptake. However the chemically treated SEF reinforced composites is possible materials for automotive application like body panels, bumpers and interior parts, and household application like tables and racks etc.

Keywords: fibres, polymer-matrix composites (PMCs), mechanical properties, scanning electron microscopy (SEM)

Procedia PDF Downloads 388

Authors: Abiodun Amusan, Olugbenga Akinola, Kazeem Akano, María Hernández-Castañeda, Jenna Dick, Akintunde Sowunmi, Geoffrey Hart, Grace Gbotosho

Abstract:

Introduction: Artemisinin-based Combination Therapy (ACTs) is the cornerstone malaria treatment option in most malaria-endemic countries. Unfortunately, the malaria control effort is constantly being threatened by resistance of Plasmodium falciparum to ACTs. The recent evidence of artemisinin resistance in East Africa and its possibility of spreading to other African regions portends an imminent health catastrophe. This study aimed at evaluating the occurrence, prevalence, and influence of artemisinin-resistance markers on treatment outcomes in Ibadan before and after post-adoption of artemisinin combination therapy (ACTs) in Nigeria in 2005. Method: The study involved day zero dry blood spot (DBS) obtained from malaria patients during retrospective (2000-2005) and prospective (2021) studies. A cohort in the prospective study received oral dihydroartemisinin-piperaquine and underwent a 42-day follow-up to observe treatment outcomes. Genomic DNA was extracted from the DBS samples using a QIAamp blood extraction kit. Fragments of P. falciparum kelch13 (Pfkelch13), P. falciparum coronin (Pfcoronin), P. falciparum multidrug resistance 2 (PfMDR2), and P. falciparum chloroquine resistance transporter (PfCRT) genes were amplified and sequenced on a sanger sequencing platform to identify artemisinin resistance-associated mutations. Mutations were identified by aligning sequenced data with reference sequences obtained from the National Center for Biotechnology Information. Data were analyzed using descriptive statistics and student t-tests. Results: Mean parasite clearance time (PCT) and fever clearance time (FCT) were 2.1 ± 0.6 days (95% CI: 1.97-2.24) and 1.3 ± 0.7 days (95% CI: 1.1-1.6) respectively. Four mutations, K189T [34/53(64.2%)], R255K [2/53(3.8%)], K189N [1/53(1.9%)] and N217H [1/53(1.9%)] were identified within the N-terminal (Coiled-coil containing) domain of Pfkelch13. No artemisinin resistance-associated mutation usually found within the β-propeller domain of the Pfkelch13 gene was found in these analyzed samples. However, K189T and R255K mutations showed a significant correlation with longer parasite clearance time in the patients (P<0.002). The observed Pfkelch13 gene changes did not influence the baseline mean parasitemia (P = 0.44). P76S [17/100 (17%)] and V62M [1/100 (1%)] changes were identified in the Pfcoronin gene fragment without any influence on the parasitological parameters. No change was observed in the PfMDR2 gene, while no artemisinin resistance-associated mutation was found in the PfCRT gene. Furthermore, a sample each in the retrospective study contained the Pfkelch13 K189T and Pfcoronin P76S mutations. Conclusion: The study revealed absence of genetic-based evidence of artemisinin resistance in the study population at the time of study. The high frequency of K189T Pfkelch13 mutation and its correlation with increased parasite clearance time in this study may depict geographical variation of resistance mediators and imminent artemisinin resistance, respectively. The study also revealed an inherent potential of parasites to harbour drug-resistant genotypes before the introduction of ACTs in Nigeria.

Keywords: artemisinin resistance, plasmodium falciparum, Pfkelch13 mutations, Pfcoronin

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Authors: Roshanak Afrakhteh, Abdolrasoul Salman Mahini, Mahdi Motagh, Hamidreza Kamyab

Abstract:

Urban Heat Islands (UHIs) are distinctive urban areas characterized by densely populated central cores surrounded by less densely populated peripheral lands. These areas experience elevated temperatures, primarily due to impermeable surfaces and specific land use patterns. The consequences of these temperature variations are far-reaching, impacting the environment and society negatively, leading to increased energy consumption, air pollution, and public health concerns. This paper emphasizes the need for simplified approaches to comprehend UHI temperature dynamics and explains how urban development patterns contribute to land surface temperature variation. To illustrate this relationship, the study focuses on the Guilan Plain, utilizing techniques like principal component analysis and generalized additive models. The research centered on mapping land use and land surface temperature in the low-lying area of Guilan province. Satellite data from Landsat sensors for three different time periods (2002, 2012, and 2021) were employed. Using eCognition software, a spatial unit known as a "city block" was utilized through object-based analysis. The study also applied the normalized difference vegetation index (NDVI) method to estimate land surface radiance. Predictive variables for urban land surface temperature within residential city blocks were identified categorized as intrinsic (related to the block's structure) and neighboring (related to adjacent blocks) variables. Principal Component Analysis (PCA) was used to select significant variables, and a Generalized Additive Model (GAM) approach, implemented using R's mgcv package, modeled the relationship between urban land surface temperature and predictor variables.Notable findings included variations in urban temperature across different years attributed to environmental and climatic factors. Block size, shared boundary, mother polygon area, and perimeter-to-area ratio were identified as main variables for the generalized additive regression model. This model showed non-linear relationships, with block size, shared boundary, and mother polygon area positively correlated with temperature, while the perimeter-to-area ratio displayed a negative trend. The discussion highlights the challenges of predicting urban surface temperature and the significance of block size in determining urban temperature patterns. It also underscores the importance of spatial configuration and unit structure in shaping urban temperature patterns. In conclusion, this study contributes to the growing body of research on the connection between land use patterns and urban surface temperature. Block size, along with block dispersion and aggregation, emerged as key factors influencing urban surface temperature in residential areas. The proposed methodology enhances our understanding of parameter significance in shaping urban temperature patterns across various regions, particularly in Iran.

Keywords: urban heat island, land surface temperature, LST modeling, GAM, Gilan province

Procedia PDF Downloads 45

Authors: Babak Forouraghi

Abstract:

A genetic circuit is a collection of interacting genes and proteins that enable individual cells to implement and perform vital biological functions such as cell division, growth, death, and signaling. In cell engineering, synthetic gene circuits are engineered networks of genes specifically designed to implement functionalities that are not evolved by nature. These engineered networks enable scientists to tackle complex problems such as engineering cells to produce therapeutics within the patient's body, altering T cells to target cancer-related antigens for treatment, improving antibody production using engineered cells, tissue engineering, and production of genetically modified plants and livestock. Construction of computational models to realize genetic circuits is an especially challenging task since it requires the discovery of flow of genetic information in complex biological systems. Building synthetic biological models is also a time-consuming process with relatively low prediction accuracy for highly complex genetic circuits. The primary goal of this study was to investigate the utility of a pre-trained bidirectional encoder transformer that can accurately predict gene expressions in genetic circuit designs. The main reason behind using transformers is their innate ability (attention mechanism) to take account of the semantic context present in long DNA chains that are heavily dependent on spatial representation of their constituent genes. Previous approaches to gene circuit design, such as CNN and RNN architectures, are unable to capture semantic dependencies in long contexts as required in most real-world applications of synthetic biology. For instance, RNN models (LSTM, GRU), although able to learn long-term dependencies, greatly suffer from vanishing gradient and low-efficiency problem when they sequentially process past states and compresses contextual information into a bottleneck with long input sequences. In other words, these architectures are not equipped with the necessary attention mechanisms to follow a long chain of genes with thousands of tokens. To address the above-mentioned limitations of previous approaches, a transformer model was built in this work as a variation to the existing DNA Bidirectional Encoder Representations from Transformers (DNABERT) model. It is shown that the proposed transformer is capable of capturing contextual information from long input sequences with attention mechanism. In a previous work on genetic circuit design, the traditional approaches to classification and regression, such as Random Forrest, Support Vector Machine, and Artificial Neural Networks, were able to achieve reasonably high R2 accuracy levels of 0.95 to 0.97. However, the transformer model utilized in this work with its attention-based mechanism, was able to achieve a perfect accuracy level of 100%. Further, it is demonstrated that the efficiency of the transformer-based gene expression classifier is not dependent on presence of large amounts of training examples, which may be difficult to compile in many real-world gene circuit designs.

Keywords: transformers, generative ai, gene expression design, classification

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Authors: Mandeep Singh Azad.Dibyendu Chakraborty, Vikas Vohra

Abstract:

Introduction: Poonch is one of the remotest districts of the Jammu and Kashmir (UT) and situated on international borders. This native poultry population in these areas is quite hardy and thrives well in adverse climatic conditions. Till date, no local breed from this area (Jammu Province) has been characterized thus present study was undertaken with the main objectives of molecular characterization of ChB6 gene in local native chicken of Poonch region located at international borders between India and Pakistan. The chicken B-cell marker (ChB6) gene has been proposed as a candidate gene in regulating B-cell development. Material and Method: RNA was isolated by Blood RNA Purification Kit (HiPura) and Trizol method from whole blood samples. Positive PCR products with size 1110 bp were selected for further purification, sequencing and analysis. The amplified PCR product was sequenced by Sangers dideoxy chain termination method. The obtained sequence of ChB6 gene of Poonchi chicken were compared by MEGAX software. BioEdit software was used to construct phylogenic tree, and Neighbor Joining method was used to infer evolutionary history. In order to compute evolutionary distance Maximum Composite Likelihood method was used. Results: The positively amplified samples of ChB6 genes were then subjected to Sanger sequencing with “Primer Walking. The sequences were then analyzed using MEGA X and BioEdit software. The sequence results were compared with other reported sequence from different breed of chicken and with other species obtained from the NCBI (National Center for Biotechnology Information). ClustalW method using MEGA X software was used for multiple sequence alignment. The sequence results of ChB6 gene of Poonchi chicken was compared with Centrocercus urophasianus, G. gallus mRNA for B6.1 protein, G. gallus mRNA for B6.2, G. gallus mRNA for B6.3, Gallus gallus B6.1, Halichoeres bivittatus, Miniopterus fuliginosus Ferringtonia patagonica, Tympanuchus phasianellus. The genetic distances were 0.2720, 0.0000, 0.0245, 0.0212, 0.0147, 1.6461, 2.2394, 2.0070 and 0.2363 for ChB6 gene of Poonchi chicken sequence with other sequences in the present study respectively. Sequencing results showed variations between different species. It was observed that AT content were higher then GC content for ChB6 gene. The lower AT content suggests less thermostable. It was observed that there was no sequence difference within the Poonchi population for ChB6 gene. The high homology within chicken population indicates the conservation of ChB6 gene. The maximum difference was observed with Miniopterus fuliginosus (Eastern bent-wing bat) followed by Ferringtonia patagonica and Halichoeres bivittatus. Conclusion: Genetic variation is the essential component for genetic improvement. The results of immune related gene Chb6 shows between population genetic variability. Therefore, further association studies of this gene with some prevalent diseases in large population would be helpful to identify disease resistant/ susceptible genotypes in the indigenous chicken population.

Keywords: ChB6, sequencing, ClustalW, genetic distance, poonchi chicken, SNP

Procedia PDF Downloads 36

Authors: Hiroshi Kinoshita, Yasuto Nakanishi, Ryuhei Okuno, Toshio Higashi

Abstract:

Various kinds of pegboards have been developed and used widely in research and clinics of rehabilitation for evaluation and training of patient’s hand function. A common measure in these peg boards is a total time of performance execution assessed by a tester’s stopwatch. Introduction of electrical and automatic measurement technology to the apparatus, on the other hand, has been delayed. The present work introduces the development of a pegboard with an electric sensor to detect moments of individual peg’s insertion and removal. The work also gives fundamental data obtained from a group of healthy young individuals who performed peg transfer tasks using the pegboard developed. Through trails and errors in pilot tests, two 10-hole peg-board boxes installed with a small photo-reflector and a DC amplifier at the bottom of each hole were designed and built by the present authors. The amplified electric analogue signals from the 20 reflectors were automatically digitized at 500 Hz per channel, and stored in a PC. The boxes were set on a test table at different distances (25, 50, 75, and 125 mm) in parallel to examine the effect of hole-to-hole distance. Fifty healthy young volunteers (25 in each gender) as subjects of the study performed successive fast 80 time peg transfers at each distance using their dominant and non-dominant hands. The data gathered showed a clear-cut light interruption/continuation moment by the pegs, allowing accurately (no tester’s error involved) and precisely (an order of milliseconds) to determine the pull out and insertion times of each peg. This further permitted computation of individual peg movement duration (PMD: from peg-lift-off to insertion) apart from hand reaching duration (HRD: from peg insertion to lift-off). An accidental drop of a peg led to an exceptionally long ( < mean + 3 SD) PMD, which was readily detected from an examination of data distribution. The PMD data were commonly right-skewed, suggesting that the median can be a better estimate of individual PMD than the mean. Repeated measures ANOVA using the median values revealed significant hole-to-hole distance, and hand dominance effects, suggesting that these need to be fixed in the accurate evaluation of PMD. The gender effect was non-significant. Performance consistency was also evaluated by the use of quartile variation coefficient values, which revealed no gender, hole-to-hole, and hand dominance effects. The measurement reliability was further examined using interclass correlation obtained from 14 subjects who performed the 25 and 125 mm hole distance tasks at two 7-10 days separate test sessions. Inter-class correlation values between the two tests showed fair reliability for PMD (0.65-0.75), and for HRD (0.77-0.94). We concluded that a sensor peg board developed in the present study could provide accurate (excluding tester’s errors), and precise (at a millisecond rate) time information of peg movement separated from that used for hand movement. It could also easily detect and automatically exclude erroneous execution data from his/her standard data. These would lead to a better evaluation of hand dexterity function compared to the widely used conventional used peg boards.

Keywords: hand, dexterity test, peg movement time, performance consistency

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Authors: Mohamed Sameer Mughal, Andrew D. Ross, Damian J. Fearon

Abstract:

Background: The fast-paced changing landscape of UK Higher Education Institution (HEIs) is poised by changes and challenges affecting Middle Managers (MM) in their job roles. MM contribute to the success of HEIs by balancing the equilibrium and pass organization strategies from senior staff towards operationalization directives to junior staff. However, this study showcased from the data analyzed during the semi structured interviews; MM job role is becoming more complex due to changes and challenges creating colossal pressures and workloads in day-to-day working. Current development programmes provisions by Human Resources (HR) departments in such HEIs are not feasible, applicable, and matching the true essence and requirements of MM who suggest that programmes offered by HR are too generic to suit their precise needs and require tailor made espousal to work effectively in their pertinent job roles. Methodologies: This study aims to capture demands of MM Development Needs (DN) by means of a conceptual model as conclusive part of the research that is divided into 2 phases. Phase 1 initiated by carrying out 2 pilot interviews with a retired Emeritus status professor and HR programmes development coordinator. Key themes from the pilot and literature review subsidized into formulation of 22 set of questions (Kvale and Brinkmann) in form of interviewing questionnaire during qualitative data collection. Data strategy and collection consisted of purposeful sampling of 12 semi structured interviews (n=12) lasting approximately an hour for all participants. The MM interviewed were at faculty and departmental levels which included; deans (n=2), head of departments (n=4), subject leaders (n=2), and lastly programme leaders (n=4). Participants recruitment was carried out via emails and snowballing technique. The interviews data was transcribed (verbatim) and managed using Computer Assisted Qualitative Data Analysis using Nvivo ver.11 software. Data was meticulously analyzed using Miles and Huberman inductive approach of positivistic style grounded theory, whereby key themes and categories emerged from the rich data collected. The data was precisely coded and classified into case studies (Robert Yin); with a main case study, sub cases (4 classes of MM) and embedded cases (12 individual MMs). Major Findings: An interim conceptual model emerged from analyzing the data with main concepts that included; key performance indicators (KPI’s), HEI effectiveness and outlook, practices, processes and procedures, support mechanisms, student events, rules, regulations and policies, career progression, reporting/accountability, changes and challenges, and lastly skills and attributes. Conclusion: Dynamic elements affecting MM includes; increase in government pressures, student numbers, irrelevant development programmes, bureaucratic structures, transparency and accountability, organization policies, skills sets… can only be confronted by employing structured development programmes originated by HR that are not provided generically. Future Work: Stage 2 (Quantitative method) of the study plans to validate the interim conceptual model externally through fully completed online survey questionnaire (Bram Oppenheim) from external HEIs (n=150). The total sample targeted is 1500 MM. Author contribution focuses on enhancing management theory and narrow the gap between by HR and MM development programme provision.

Keywords: development needs (DN), higher education institutions (HEIs), human resources (HR), middle managers (MM)

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Authors: Kuo Chieh Chao, Thishani Amarathunga, Sangam Shrestha

Abstract:

Rainfall induced slope failures are one of the most damaging and disastrous natural hazards which occur frequently in the world. This type of sliding mainly occurs in the zone above the groundwater level in silty/sandy soils. When the rainwater begins to infiltrate into the vadose zone of the soil, the negative pore-water pressure tends to decrease and reduce the shear strength of soil material. Climate change has resulted in excessive and unpredictable rainfall in all around the world, resulting in landslides with dire consequences to human lives and infrastructure. Such problems could be overcome by examining in detail the causes for such slope failures and recommending effective repair plans for vulnerable locations by considering future climatic change. The selected area for this study is located in the road rehabilitation section from Maubara to Mota Ain road in Timor-Leste. Slope failures and cracks have occurred in 2013 and after repairs reoccurred again in 2017 subsequent to heavy rains. Both observed and future predicted climate data analyses were conducted to understand the severe precipitation conditions in past and future. Observed climate data were collected from NOAA global climate data portal. CORDEX data portal was used to collect Regional Climate Model (RCM) future predicted climate data. Both observed and RCM data were extracted to location-based data using ArcGIS Software. Linear scaling method was used for the bias correction of future data and bias corrected climate data were assigned to GeoStudio Software. Precipitations of wet seasons (December to March ) in 2007 to 2013 is higher than 2001-2006 period and it is more than nearly 40% higher precipitation than usual monthly average precipitation of 160mm.The results of seepage analyses which were carried out using SEEP/W model with observed climate, clearly demonstrated that the pore water pressure within the fill slope was significantly increased due to the increase of the infiltration during the wet season of 2013.One main Regional Climate Models (RCM) was analyzed in order to predict future climate variation under two Representative Concentration Pathways (RCPs).In the projected period of 76 years ahead from 2014, shows that the amount of precipitation is considerably getting higher in the future in both RCP 4.5 and RCP 8.5 emission scenarios. Critical pore water pressure conditions during 2014-2090 were used in order to recommend appropriate remediation methods. Results of slope stability analyses indicated that the factor of safety of the fill slopes was reduced from 1.226 to 0.793 during the dry season to wet season in 2013.Results of future slope stability which were obtained using SLOPE/W model for the RCP emissions scenarios depict that, the use of tieback anchors and geogrids in slope protection could be effective in increasing the stability of slopes to an acceptable level during the wet seasons. Moreover, methods and procedures like monitoring of slopes showing signs or susceptible for movement and installing surface protections could be used to increase the stability of slopes.

Keywords: climate change, precipitation, SEEP/W, SLOPE/W, unsaturated soil

Procedia PDF Downloads 102

Authors: Irina Mizeva, Elena Potapova, Viktor Dremin, Mikhail Mezentsev, Valeri Shupletsov

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The local tissue perfusion is regulated by the microvascular tone which is under the control of a number of physiological mechanisms. Laser Doppler flowmetry (LDF) together with wavelet analyses is the most commonly used technique to study the regulatory mechanisms of cutaneous microcirculation. External factors such as temperature, local pressure of the probe on the skin, etc. influence on the blood flow characteristics and are used as physiological tests to evaluate microvascular regulatory mechanisms. Local probe pressure influences on the microcirculation parameters measured by optical methods: diffuse reflectance spectroscopy, fluorescence spectroscopy, and LDF. Therefore, further study of probe pressure effects can be useful to improve the reliability of optical measurement. During pressure tests variation of the mean perfusion measured by means of LDF usually is estimated. An additional information concerning the physiological mechanisms of the vascular tone regulation system in response to local pressure can be obtained using spectral analyses of LDF samples. The aim of the present work was to develop protocol and algorithm of data processing appropriate for study physiological response to the local pressure test. Involving 6 subjects (20±2 years) and providing 5 measurements for every subject we estimated intersubject and-inter group variability of response of both averaged and oscillating parts of the LDF sample on external surface pressure. The final purpose of the work was to find special features which further can be used in wider clinic studies. The cutaneous perfusion measurements were carried out by LAKK-02 (SPE LAZMA Ltd., Russia), the skin loading was provided by the originally designed device which allows one to distribute the pressure around the LDF probe. The probe was installed on the dorsal part of the distal finger of the index figure. We collected measurements continuously for one hour and varied loading from 0 to 180mmHg stepwise with a step duration of 10 minutes. Further, we post-processed the samples using the wavelet transform and traced the energy of oscillations in five frequency bands over time. Weak loading leads to pressure-induced vasodilation, so one should take into account that the perfusion measured under pressure conditions will be overestimated. On the other hand, we revealed a decrease in endothelial associated fluctuations. Further loading (88 mmHg) induces amplification of pulsations in all frequency bands. We assume that such loading leads to a higher number of closed capillaries, higher input of arterioles in the LDF signal and as a consequence more vivid oscillations which mainly are formed in arterioles. External pressure higher than 144 mmHg leads to the decrease of oscillating components, after removing the loading very rapid restore of the tissue perfusion takes place. In this work, we have demonstrated that local skin loading influence on the microcirculation parameters measured by optic technique; this should be taken into account while developing portable electronic devices. The proposed protocol of local loading allows one to evaluate PIV as far as to trace dynamic of blood flow oscillations. This study was supported by the Russian Science Foundation under project N 18-15-00201.

Keywords: blood microcirculation, laser Doppler flowmetry, pressure-induced vasodilation, wavelet analyses blood

Procedia PDF Downloads 120

Authors: Babak Forouraghi

Abstract:

A genetic circuit is a collection of interacting genes and proteins that enable individual cells to implement and perform vital biological functions such as cell division, growth, death, and signaling. In cell engineering, synthetic gene circuits are engineered networks of genes specifically designed to implement functionalities that are not evolved by nature. These engineered networks enable scientists to tackle complex problems such as engineering cells to produce therapeutics within the patient's body, altering T cells to target cancer-related antigens for treatment, improving antibody production using engineered cells, tissue engineering, and production of genetically modified plants and livestock. Construction of computational models to realize genetic circuits is an especially challenging task since it requires the discovery of the flow of genetic information in complex biological systems. Building synthetic biological models is also a time-consuming process with relatively low prediction accuracy for highly complex genetic circuits. The primary goal of this study was to investigate the utility of a pre-trained bidirectional encoder transformer that can accurately predict gene expressions in genetic circuit designs. The main reason behind using transformers is their innate ability (attention mechanism) to take account of the semantic context present in long DNA chains that are heavily dependent on the spatial representation of their constituent genes. Previous approaches to gene circuit design, such as CNN and RNN architectures, are unable to capture semantic dependencies in long contexts, as required in most real-world applications of synthetic biology. For instance, RNN models (LSTM, GRU), although able to learn long-term dependencies, greatly suffer from vanishing gradient and low-efficiency problem when they sequentially process past states and compresses contextual information into a bottleneck with long input sequences. In other words, these architectures are not equipped with the necessary attention mechanisms to follow a long chain of genes with thousands of tokens. To address the above-mentioned limitations, a transformer model was built in this work as a variation to the existing DNA Bidirectional Encoder Representations from Transformers (DNABERT) model. It is shown that the proposed transformer is capable of capturing contextual information from long input sequences with an attention mechanism. In previous works on genetic circuit design, the traditional approaches to classification and regression, such as Random Forrest, Support Vector Machine, and Artificial Neural Networks, were able to achieve reasonably high R2 accuracy levels of 0.95 to 0.97. However, the transformer model utilized in this work, with its attention-based mechanism, was able to achieve a perfect accuracy level of 100%. Further, it is demonstrated that the efficiency of the transformer-based gene expression classifier is not dependent on the presence of large amounts of training examples, which may be difficult to compile in many real-world gene circuit designs.

Keywords: machine learning, classification and regression, gene circuit design, bidirectional transformers

Procedia PDF Downloads 33

Authors: Devin Doos, Ashley Hughes, Trang Pham, Paul Barach, Rami Ahmed

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Over 115,000 Health Care Workers (HCWs) have died from COVID-19, and millions have been infected while caring for patients. HCWs have filed thousands of safety complaints surrounding safety concerns due to Personal Protective Equipment (PPE) shortages, which included concerns around inadequate and PPE reuse. Protocols for donning and doffing PPE remain ambiguous, lacking an evidence-base, and often result in wide deviations in practice. PPE donning and doffing protocol deviations commonly result in self-contamination but have not been thoroughly addressed. No evidence-driven protocols provide guidance on protecting HCW during periods of PPE reuse. Objective: The aim of this study was to examine safety-related threats and risks to Health Care Workers (HCWs) due to the reuse of PPE among Emergency Department personnel. Method: We conducted a prospective observational study to examine the risks of reusing PPE. First, ED personnel were asked to don and doff PPE in a simulation lab. Each participant was asked to don and doff PPE five times, according to the maximum reuse recommendation set by the Centers for Disease Control and Prevention (CDC). Each participant was videorecorded; video recordings were reviewed and coded independently by at least 2 of the 3trained coders for safety behaviors and riskiness of actions. A third coder was brought in when the agreement between the 2 coders could not be reached. Agreement between coders was high (81.9%), and all disagreements (100%) were resolved via consensus. A bowtie risk assessment chart was constructed analyzing the factors that contribute to increased risks HCW are faced with due to PPE use and reuse. Agreement amongst content experts in the field of Emergency Medicine, Human Factors, and Anesthesiology was used to select aspects of health care that both contribute and mitigate risks associated with PPE reuse. Findings: Twenty-eight clinician participants completed five rounds of donning/doffing PPE, yielding 140 PPE donning/doffing sequences. Two emerging threats were associated with behaviors in donning, doffing, and re-using PPE: (i) direct exposure to contaminant, and (ii) transmission/spread of contaminant. Protective behaviors included: hand hygiene, not touching the patient-facing surface of PPE, and ensuring a proper fit and closure of all PPE materials. 100% of participants (n= 28) deviated from the CDC recommended order, and most participants (92.85%, n=26) self-contaminated at least once during reuse. Other frequent errors included failure to tie all ties on the PPE (92.85%, n=26) and failure to wash hands after a contamination event occurred (39.28%, n=11). Conclusions: There is wide variation and regular errors in how HCW don and doffPPE while including in reusing PPE that led to self-contamination. Some errors were deemed “recoverable”, such as hand washing after touching a patient-facing surface to remove the contaminant. Other errors, such as using a contaminated mask and accidentally spreading to the neck and face, can lead to compound risks that are unique to repeated PPE use. A more comprehensive understanding of the contributing threats to HCW safety and complete approach to mitigating underlying risks, including visualizing with risk management toolsmay, aid future PPE designand workflow and space solutions.

Keywords: bowtie analysis, health care, PPE reuse, risk management

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Authors: Alison C. Essary, Victor Trastek

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Introduction: The current state of the health care system in the U.S. is characterized by an unprecedented number of people living with multiple chronic conditions, unsustainable rise in health care costs, inadequate access to care, and wide variation in health outcomes throughout the country. An estimated two-thirds of Americans are living with two or more chronic conditions, contributing to 75% of all health care spending. In 2013, the School for the Science of Health Care Delivery (SHCD) was charged with redesigning the health care system through education and research. Faculty in business, law, and public policy, and thought leaders in health care delivery, administration, public health and health IT created undergraduate, graduate, and executive academic programs to address this pressing need. Faculty and students work across disciplines, and with community partners and employers to improve care delivery and increase value for patients. Methods: Curricula apply content in health care administration and operations within the clinical context. Graduate modules are team-taught by faculty across academic units to model team-based practice. Seminars, team-based assignments, faculty mentoring, and applied projects are integral to student success. Cohort-driven models enhance networking and collaboration. This observational study evaluated two years of admissions data, and one year of graduate data to assess program outcomes and inform the current graduate-level curricula. Descriptive statistics includes means, percentages. Results: Fall 2013, the program received 51 applications. The mean GPA of the entering class of 37 students was 3.38. Ninety-seven percent of the fall 2013 cohort successfully completed the program (n=35). Sixty-six percent are currently employed in the health care industry (n=23). Of the remaining 12 graduates, two successfully matriculated to medical school; one works in the original field of study; four await results on the MCAT or DAT, and five were lost to follow up. Attrition of one student was attributed to non-academic reasons. Fall 2014, the program expanded to include both on-ground and online cohorts. Applications were evenly distributed between on-ground (n=70) and online (n=68). Thirty-eight students enrolled in the on-ground program. The mean GPA was 3.95. Ninety-five percent of students successfully completed the program (n=36). Thirty-six students enrolled in the online program. The mean GPA was 3.85. Graduate outcomes are pending. Discussion: Challenges include demographic variability between online and on-ground students; yet, both profiles are similar in that students intend to become change agents in the health care system. In the past two years, on-ground applications increased by 31%, persistence to graduation is > 95%, mean GPA is 3.67, graduates report admission to six U.S. medical schools, the Mayo Medical School integrates SHCD content within their curricula, and there is national interest in collaborating on industry and academic partnerships. This places SHCD at the forefront of developing innovative curricula in order to improve high-value, patient-centered care.

Keywords: delivery science, education, health care delivery, high-value care, innovation in education, patient-centered

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Authors: Mukul Sharma, Madhusmita Das, Sundeep Chaitanya Vedithi

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Leprosy is a chronic human disease caused by Mycobacterium leprae, that cannot be cultured in vitro. Though treatable with multidrug therapy (MDT), recently, bacteria reported resistance to multiple antibiotics. Targeting DNA replication and repair pathways can serve as the foundation of developing new anti-leprosy drugs. Due to the absence of an axenic culture medium for the propagation of M. leprae, studying cellular processes, especially those belonging to DNA repair pathways, is challenging. Genomic understanding of M. Leprae harbors several protein-coding genes with no previously assigned function known as 'hypothetical proteins'. Here, we report identification and expression of known and hypothetical DNA repair genes from a human skin biopsy and mouse footpads that are involved in base excision repair, direct reversal repair, and SOS response. Initially, a bioinformatics approach was employed based on sequence similarity, identification of known protein domains to screen the hypothetical proteins in the genome of M. leprae, that are potentially related to DNA repair mechanisms. Before testing on clinical samples, pure stocks of bacterial reference DNA of M. leprae (NHDP63 strain) was used to construct standard graphs to validate and identify lower detection limit in the qPCR experiments. Primers were designed to amplify the respective transcripts, and PCR products of the predicted size were obtained. Later, excisional skin biopsies of newly diagnosed untreated, treated, and drug resistance leprosy cases from SIHR & LC hospital, Vellore, India were taken for the extraction of RNA. To determine the presence of the predicted transcripts, cDNA was generated from M. leprae mRNA isolated from clinically confirmed leprosy skin biopsy specimen across all the study groups. Melting curve analysis was performed to determine the integrity of the amplification and to rule out primer‑dimer formation. The Ct values obtained from qPCR were fitted to standard curve to determine transcript copy number. Same procedure was applied for M. leprae extracted after processing a footpad of nude mice of drug sensitive and drug resistant strains. 16S rRNA was used as positive control. Of all the 16 genes involved in BER, DR, and SOS, differential expression pattern of the genes was observed in terms of Ct values when compared to human samples; this was because of the different host and its immune response. However, no drastic variation in gene expression levels was observed in human samples except the nth gene. The higher expression of nth gene could be because of the mutations that may be associated with sequence diversity and drug resistance which suggests an important role in the repair mechanism and remains to be explored. In both human and mouse samples, SOS system – lexA and RecA, and BER genes AlkB and Ogt were expressing efficiently to deal with possible DNA damage. Together, the results of the present study suggest that DNA repair genes are constitutively expressed and may provide a reference for molecular diagnosis, therapeutic target selection, determination of treatment and prognostic judgment in M. leprae pathogenesis.

Keywords: DNA repair, human biopsy, hypothetical proteins, mouse footpads, Mycobacterium leprae, qPCR

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Authors: Pedro Llanos, Diego García

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Spaceflight is considered the last frontier in terms of science, technology, and engineering. But it is also the next frontier in terms of human physiology and performance. After more than 200,000 years humans have evolved under earth’s gravity and atmospheric conditions, spaceflight poses environmental stresses for which human physiology is not adapted. Hypoxia, accelerations, and radiation are among such stressors, our research involves suborbital flights aiming to develop effective countermeasures in order to assure sustainable human space presence. The physiologic baseline of spaceflight participants is subject to great variability driven by age, gender, fitness, and metabolic reserve. The objective of the present study is to characterize different physiologic variables in a population of STEM practitioners during an aerobatic flight. Cardiovascular and pulmonary responses were determined in Science Astronaut Candidates (SACs) during unusual attitude aerobatic flight indoctrination. Physiologic data recordings from 20 subjects participating in high-G flight training were analyzed. These recordings were registered by wearable sensor-vest that monitored electrocardiographic tracings (ECGs), signs of dysrhythmias or other electric disturbances during all the flight. The same cardiovascular parameters were also collected approximately 10 min pre-flight, during each high-G/unusual attitude maneuver and 10 min after the flights. The ratio (pre-flight/in-flight/post-flight) of the cardiovascular responses was calculated for comparison of inter-individual differences. The resulting tracings depicting the cardiovascular responses of the subjects were compared against the G-loads (Gs) during the aerobatic flights to analyze cardiovascular variability aspects and fluid/pressure shifts due to the high Gs. In-flight ECG revealed cardiac variability patterns associated with rapid Gs onset in terms of reduced heart rate (HR) and some scattered dysrhythmic patterns (15% premature ventricular contractions-type) that were considered as triggered physiological responses to high-G/unusual attitude training and some were considered as instrument artifact. Variation events were observed in subjects during the +Gz and –Gz maneuvers and these may be due to preload and afterload, sudden shift. Our data reveal that aerobatic flight influenced the breathing rate of the subject, due in part by the various levels of energy expenditure due to the increased use of muscle work during these aerobatic maneuvers. Noteworthy was the high heterogeneity in the different physiological responses among a relatively small group of SACs exposed to similar aerobatic flights with similar Gs exposures. The cardiovascular responses clearly demonstrated that SACs were subjected to significant flight stress. Routine ECG monitoring during high-G/unusual attitude flight training is recommended to capture pathology underlying dangerous dysrhythmias in suborbital flight safety. More research is currently being conducted to further facilitate the development of robust medical screening, medical risk assessment approaches, and suborbital flight training in the context of the evolving commercial human suborbital spaceflight industry. A more mature and integrative medical assessment method is required to understand the physiology state and response variability among highly diverse populations of prospective suborbital flight participants.

Keywords: g force, aerobatic maneuvers, suborbital flight, hypoxia, commercial astronauts

Procedia PDF Downloads 100

Authors: L. Abubakar, B. M. Sokoto, I. U. Mohammed, M. S. Na’allah, A. Mohammad, A. N. Garba, T. S. Bubuche

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Onion (Allium cepa var. cepa L.), is the most important species of the Allium group belonging to family Alliaceae and genus Allium. It can be regarded as the single important vegetable species in the world after tomatoes. Despite the similarities, which bring the species together, the genus is a strikingly diverse one, with more than five hundred species, which are perennial and mostly bulbous plants. Out of these, only seven species are in cultivation, and five are the most important species of the cultivated Allium. However, Allium cepa (onion) and Allium sativum (Garlic) are the two major cultivated species grown all over the world of which the onion crop is the most important. Heritability defined as the proportion of the observed total variability that is genetic, and its estimates from variance components give more useful information of genotypic variation from the total phenotypic differences and environmental effects on the individuals or families. It therefore guide the breeder with respect to the ease with which selection of traits can be carried out. Heritability estimates guide the breeder with respect to ease of selection of traits while correlations suggest how selection among characters can be practiced. Correlations explain relationship between characters and suggest how selection among characters can be practiced in breeding programmes. Highly significant correlations have been reported, between yield, maturity, rings/bulb and storage loss in onions. Similarly significant positive correlation exists between total bulb yield and plant height, leaf number/plant, bulb diameter and bulb yield/plant. Moderate positive correlations have been observed between maturity date and yield, dry matter content was highly correlated with soluble solids, and higher correlations were also observed between storage loss and soluble solids. The objective of the study is to determine heritability estimates and correlations for characters among onion cultivars of North Western Nigeria. This is envisaged will assist in the breeding of superior onion cultivars within the zone. Thirteen onion cultivars were collected during an expedition covering north western Nigeria and Southern part of Niger Republic during 2013, which are areas noted for onion production. The cultivars were evaluated at two locations; Sokoto, in Sokoto State and Jega in Kebbi State all in Nigeria during the 2013/14 onion season (dry season) under irrigation. Combined analysis of the results revealed fresh bulb yield is highly significantly positively correlated with bulb height and cured bulb yield, and significant positive correlation with plant height and bulb diameter. It also recorded significant negative correlation with mean No. of leaves/plant and non significant negative correlation with bolting %. Cured bulb yield (marketable yield) had highly significant positive correlation with mean bulb weight and fresh bulb yield/ha, with significant positive correlation with bulb height. It also recorded highly significant negative correlation with No. of leaves/plant and significant negative correlation with bolting % and non significant positive correlation with plant height and non significant negative correlation with bulb diameter. High broad sense heritability estimates were recorded for plant height, fresh bulb yield, number of leaves/plant, bolting % and cured bulb yield. Medium to low broad sense heritabilities were also observed for mean bulb weight, plant height and bulb diameter.

Keywords: correlation, heritability, onions, North Western Nigeria

Procedia PDF Downloads 362

Authors: Gail Schofield, Antoine M. Dujon, Nicole Esteban, Rebecca M. Lester, Graeme C. Hays

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Variation in diel movement patterns during migration provides information on the strategies used by animals to maximize energy efficiency and ensure the successful completion of migration. For instance, many flying and land-based terrestrial species stop to rest and refuel at regular intervals along the migratory route, or at transitory ‘stopover’ sites, depending on resource availability. However, in cases where stopping is not possible (such as over–or through deep–open oceans, or over deserts and mountains), non-stop travel is required, with animals needing to develop strategies to rest while actively traveling. Recent advances in biologging technologies have identified mid-flight micro sleeps by swifts in Africa during the 10-month non-breeding period, and the use of lateralized sleep behavior in orca and bottlenose dolphins during migration. Here, highly accurate locations obtained by Argos-linked Fastloc-GPS transmitters of adult green (n=8 turtles, 9487 locations) and loggerhead (n=46 turtles, 47,588 locations) sea turtles migrating around thousand kilometers (over several weeks) from breeding to foraging grounds across the Indian and Mediterranean oceans were used to identify potential resting strategies. Stopovers were only documented for seven turtles, lasting up to 6 days; thus, this strategy was not commonly used, possibly due to the lack of potential ‘shallow’ ( < 100 m seabed depth) sites along routes. However, observations of the day versus night speed of travel indicated that turtles might use other mechanisms to rest. For instance, turtles traveled an average 31% slower at night compared to day during oceanic crossings. Slower travel speeds at night might be explained by turtles swimming in a less direct line at night and/or deeper dives reducing their forward motion, as indicated through studies using Argos-linked transmitters and accelerometers. Furthermore, within the first 24 h of entering waters shallower than 100 m towards the end of migration (the depth at which sea turtles can swim and rest on the seabed), some individuals travelled 72% slower at night, repeating this behavior intermittently (each time for a one-night duration at 3–6-day intervals) until reaching the foraging grounds. If the turtles were, in fact, resting on the seabed at this point, they could be inactive for up to 8-hours, facilitating protracted periods of rest after several weeks of constant swimming. Turtles might not rest every night once within these shallower depths, due to the time constraints of reaching foraging grounds and restoring depleted energetic reserves (as sea turtles are capital breeders, they tend not to feed for several months during migration to and from the breeding grounds and while breeding). In conclusion, access to data-rich, highly accurate Argos-linked Fastloc-GPS provided information about differences in the day versus night activity at different stages of migration, allowing us, for the first time, to compare the strategies used by a marine vertebrate with terrestrial land-based and flying species. However, the question of what resting strategies are used by individuals that remain in oceanic waters to forage, with combinations of highly accurate Argos-linked Fastloc-GPS transmitters and accelerometry or time-depth recorders being required for sufficient numbers of individuals.

Keywords: argos-linked fastloc GPS, data loggers, migration, resting strategy, telemetry

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Authors: Shuo Li, Yannick Coffinier, Chann Lagadec, Fabrizio Cleri, Katsuhiko Nishiguchi, Akira Fujiwara, Soo Hyeon Kim, Nicolas Clément

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The need for single cell detection and analysis techniques has increased in the past decades because of the heterogeneity of individual living cells, which increases the complexity of the pathogenesis of malignant tumors. In the search for early cancer detection, high-precision medicine and therapy, the technologies most used today for sensitive detection of target analytes and monitoring the variation of these species are mainly including two types. One is based on the identification of molecular differences at the single-cell level, such as flow cytometry, fluorescence-activated cell sorting, next generation proteomics, lipidomic studies, another is based on capturing or detecting single tumor cells from fresh or fixed primary tumors and metastatic tissues, and rare circulating tumors cells (CTCs) from blood or bone marrow, for example, dielectrophoresis technique, microfluidic based microposts chip, electrochemical (EC) approach. Compared to other methods, EC sensors have the merits of easy operation, high sensitivity, and portability. However, despite various demonstrations of low limits of detection (LOD), including aptamer sensors, arrayed EC sensors for detecting single-cell have not been demonstrated. In this work, a new technique based on 20-nm-thick nanopillars array to support cells and keep them at ideal recognition distance for redox-labeled aptamers grafted on the surface. The key advantages of this technology are not only to suppress the false positive signal arising from the pressure exerted by all (including non-target) cells pushing on the aptamers by downward force but also to stabilize the aptamer at the ideal hairpin configuration thanks to a confinement effect. With the first implementation of this technique, a LOD of 13 cells (with5.4 μL of cell suspension) was estimated. In further, the nanosupported cell technology using redox-labeled aptasensors has been pushed forward and fully integrated into a single-cell electrochemical aptasensor array. To reach this goal, the LOD has been reduced by more than one order of magnitude by suppressing parasitic capacitive electrochemical signals by minimizing the sensor area and localizing the cells. Statistical analysis at the single-cell level is demonstrated for the recognition of cancer cells. The future of this technology is discussed, and the potential for scaling over millions of electrodes, thus pushing further integration at sub-cellular level, is highlighted. Despite several demonstrations of electrochemical devices with LOD of 1 cell/mL, the implementation of single-cell bioelectrochemical sensor arrays has remained elusive due to their challenging implementation at a large scale. Here, the introduced nanopillar array technology combined with redox-labeled aptamers targeting epithelial cell adhesion molecule (EpCAM) is perfectly suited for such implementation. Combining nanopillar arrays with microwells determined for single cell trapping directly on the sensor surface, single target cells are successfully detected and analyzed. This first implementation of a single-cell electrochemical aptasensor array based on Brownian-fluctuating redox species opens new opportunities for large-scale implementation and statistical analysis of early cancer diagnosis and cancer therapy in clinical settings.

Keywords: bioelectrochemistry, aptasensors, single-cell, nanopillars

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Authors: Avdhesh K. Sharma

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Key, in the development of energy-efficient micro-scale heat exchanger devices, is to select large heat transfer surface to volume ratio without much expanse on re-circulated pumps. The increased interest in short heat exchanger (SHE) is due to accessibility of advanced technologies for manufacturing of micro-tubes in range of 1 micron m - 1 mm. Such SHE using micro-tubes are highly effective for high flux heat transfer technologies. Nanofluids, are used to enhance the thermal conductivity of re-circulated coolant and thus enhances heat transfer rate further. Higher viscosity associated with nanofluid expands more pumping power. Thus, there is a trade-off between heat transfer rate and pressure drop with geometry of micro-tubes. Herein, a novel design of short counter flow heat exchanger (SCFHE) using non-circular micro-tubes flooded with CuO-water nanofluid is conceptualized by varying the ratio of surface area to cross-sectional area of micro-tubes. A framework for comparative analysis of SCFHE using micro-tubes non-circular shape flooded by CuO-water nanofluid is presented. In SCFHE concept, micro-tubes having various geometrical shapes (viz., triangular, rectangular and trapezoidal) has been arranged row-wise to facilitate two aspects: (1) allowing easy flow distribution for cold and hot stream, and (2) maximizing the thermal interactions with neighboring channels. Adequate distribution of rows for cold and hot flow streams enables above two aspects. For comparative analysis, a specific volume or cross-section area is assigned to each elemental cell (which includes flow area and area corresponds to half wall thickness). A specific volume or cross-section area is assumed to be constant for each elemental cell (which includes flow area and half wall thickness area) and variation in surface area is allowed by selecting different geometry of micro-tubes in SCFHE. Effective thermal conductivity model for CuO-water nanofluid has been adopted, while the viscosity values for water based nanofluids are obtained empirically. Correlations for Nusselt number (Nu) and Poiseuille number (Po) for micro-tubes have been derived or adopted. Entrance effect is accounted for. Thermal and hydrodynamic performances of SCFHE are defined in terms of effectiveness and pressure drop or pumping power, respectively. For defining the overall performance index of SCFHE, two links are employed. First one relates heat transfer between the fluid streams q and pumping power PP as (=qj/PPj); while another link relates effectiveness eff and pressure drop dP as (=effj/dPj). For analysis, the inlet temperatures of hot and cold streams are varied in usual range of 20dC-65dC. Fully turbulent regime is seldom encountered in micro-tubes and transition of flow regime occurs much early (i.e., ~Re=1000). Thus, Re is fixed at 900, however, the uncertainty in Re due to addition of nanoparticles in base fluid is quantified by averaging of Re. Moreover, for minimizing error, volumetric concentration is limited to range 0% to ≤4% only. Such framework may be helpful in utilizing maximum peripheral surface area of SCFHE without any serious severity on pumping power and towards developing advanced short heat exchangers.

Keywords: CuO-water nanofluid, non-circular micro-tubes, performance index, short counter flow heat exchanger

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Authors: Rawan Hakawati, Beatrice Smyth, David Rooney, Geoffrey McCullough

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Targets have been set in the EU to increase the share of renewable energy consumption to 20% by 2020, but developments have not occurred evenly across the member states. Northern Ireland is almost 90% dependent on imported fossil fuels. With such high energy dependency, Northern Ireland is particularly susceptible to the security of supply issues. Linked to fossil fuels are greenhouse gas emissions, and the EU plans to reduce emissions by 20% by 2020. The use of indigenously produced biomass could reduce both greenhouse gas emissions and external energy dependence. With a wide range of both crop and waste feedstock potentially available in Northern Ireland, anaerobic digestion has been put forward as a possible solution for renewable energy production, waste management, and greenhouse gas reduction. Not all feedstock, however, is the same, and an understanding of feedstock suitability is important for both plant operators and policy makers. The aim of this paper is to investigate biomass suitability for anaerobic digestion in Northern Ireland. It is also important that decisions are based on solid scientific evidence. For this reason, the methodology used is multi-criteria decision matrix analysis which takes multiple criteria into account simultaneously and ranks alternatives accordingly. The model uses the weighted sum method (which follows the Entropy Method to measure uncertainty using probability theory) to decide on weights. The Topsis method is utilized to carry out the mathematical analysis to provide the final scores. Feedstock that is currently available in Northern Ireland was classified into two categories: wastes (manure, sewage sludge and food waste) and energy crops, specifically grass silage. To select the most suitable feedstock, methane yield, feedstock availability, feedstock production cost, biogas production, calorific value, produced kilowatt-hours, dry matter content, and carbon to nitrogen ratio were assessed. The highest weight (0.249) corresponded to production cost reflecting a variation of £41 gate fee to 22£/tonne cost. The weights calculated found that grass silage was the most suitable feedstock. A sensitivity analysis was then conducted to investigate the impact of weights. The analysis used the Pugh Matrix Method which relies upon The Analytical Hierarchy Process and pairwise comparisons to determine a weighting for each criterion. The results showed that the highest weight (0.193) corresponded to biogas production indicating that grass silage and manure are the most suitable feedstock. Introducing co-digestion of two or more substrates can boost the biogas yield due to a synergistic effect induced by the feedstock to favor positive biological interactions. A further benefit of co-digesting manure is that the anaerobic digestion process also acts as a waste management strategy. From the research, it was concluded that energy from agricultural biomass is highly advantageous in Northern Ireland because it would increase the country's production of renewable energy, manage waste production, and would limit the production of greenhouse gases (current contribution from agriculture sector is 26%). Decision-making methods based on scientific evidence aid policy makers in classifying multiple criteria in a logical mathematical manner in order to reach a resolution.

Keywords: anaerobic digestion, biomass as feedstock, decision matrix, renewable energy

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Authors: Utkarsh Tripathi, Bikalp C. Mandal, Ravi Kumar Umrao, Sirsha Das, M. K. Bhowmic, Joyesh Bagchi, Hemant Kumar

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The Central India Diamond Province (CIDP) is known for the occurrences of primary and secondary sources for diamonds from the Vindhyan platformal sediments, which host several kimberlites, with one operating mine. The known kimberlites are Neo-Proterozoic in age and intrude into the Kaimur Group of rocks. Based on the interpretation of areo-geomagnetic data, three potential zones were demarcated in parts of Chitrakoot and Banda districts, Uttar Pradesh, and Satna district, Madhya Pradesh, India. To validate the aero-geomagnetic interpretation, ground magnetic coupled with a gravity survey was conducted to validate the anomaly and explore the possibility of some pipes concealed beneath the Vindhyan sedimentary cover. Geologically the area exposes the milky white to buff-colored arkosic and arenitic sandstone belonging to the Dhandraul Formation of the Kaimur Group, which are undeformed and unmetamorphosed providing almost transparent media for geophysical exploration. There is neither surface nor any geophysical indication of intersections of linear structures, but the joint patterns depict three principal joints along NNE-SSW, ENE-WSW, and NW-SE directions with vertical to sub-vertical dips. Aeromagnetic data interpretation brings out three promising zones with the bi-polar magnetic anomaly (69-602nT) that represent potential kimberlite intrusive concealed below at an approximate depth of 150-170m. The ground magnetic survey has brought out the above-mentioned anomalies in zone-I, which is congruent with the available aero-geophysical data. The magnetic anomaly map shows a total variation of 741 nT over the area. Two very high magnetic zones (H1 and H2) have been observed with around 500 nT and 400 nT magnitudes, respectively. Anomaly zone H1 is located in the west-central part of the area, south of Madulihai village, while anomaly zone H2 is located 2km apart in the north-eastern direction. The Euler 3D solution map indicates the possible existence of the ultramafic body in both the magnetic highs (H1 and H2). The H2 high shows the shallow depth, and H1 shows a deeper depth solution. In the reduced-to-pole (RTP) method, the bipolar anomaly disappears and indicates the existence of one causative source for both anomalies, which is, in all probabilities, an ultramafic suite of rock. The H1 magnetic high represents the main body, which persists up to depths of ~500m, as depicted through the upward continuation derivative map. Radially Averaged Power Spectrum (RAPS) shows the thickness of loose sediments up to 25m with a cumulative depth of 154m for sandstone overlying the ultramafic body. The average depth range of the shallower body (H2) is 60.5-86 meters, as estimated through the Peters half slope method. Magnetic (TF) anomaly with BA contour also shows high BA value around the high zones of magnetic anomaly (H1 and H2), which suggests that the causative body is with higher density and susceptibility for the surrounding host rock. The ground magnetic survey coupled with the gravity confirms a potential target for further exploration as the findings are co-relatable with the presence of the known diamondiferous kimberlites in this region, which post-date the rocks of the Kaimur Group.

Keywords: Kaimur, kimberlite, Euler 3D solution, magnetic

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Authors: Khiem M. Nguyen, Ming C. Yang

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Chloroplast pigments are extremely important during photosynthesis since they play essential roles in light absorption and energy transfer. Therefore, understanding the efficiency of chlorophyll (Chl) biosynthesis could facilitate enhancement in photo-assimilates accumulation, and ultimately, in crop yield. The Chl-deficient mutants have been used extensively to study the Chl biosynthetic pathways and the biogenesis of the photosynthetic apparatus. Rice (Oryza sativa L.) is one of the most leading food crops, serving as staple food for many parts of the world. To author’s best knowledge, Chl b–lacking rice has been found; however the molecular mechanism of Chl biosynthesis still remains unclear compared to wild-type rice. In this study, the ultrastructure analysis, photosynthetic properties, and transcriptome profile of wild-type rice (Norin No.8, N8) and its Chl b-lacking mutant (Chlorina 1, C1) were examined. The finding concluded that total Chl content and Chl b content in the C1 leaves were strongly reduced compared to N8 leaves, suggesting that reduction in the total Chl content contributes to leaf color variation at the physiological level. Plastid ultrastructure of C1 possessed abnormal thylakoid membranes with loss of starch granule, large number of vesicles, and numerous plastoglobuli. The C1 rice also exhibited thinner stacked grana, which was caused by a reduction in the number of thylakoid membranes per granum. Thus, the different Chl a/b ratio of C1 may reflect the abnormal plastid development and function. Transcriptional analysis identified 23 differentially expressed genes (DEGs) and 671 transcription factors (TFs) that were involved in Chl metabolism, chloroplast development, cell division, and photosynthesis. The transcriptome profile and DEGs revealed that the gene encoding PsbR (PSII core protein) was down-regulated, therefore suggesting that the lower in light-harvesting complex proteins are responsible for the lower photosynthetic capacity in C1. In addition, expression level of cell division protein (FtsZ) genes were significantly reduced in C1, causing chloroplast division defect. A total of 19 DEGs were identified based on KEGG pathway assignment involving Chl biosynthesis pathway. Among these DEGs, the GluTR gene was down-regulated, whereas the UROD, CPOX, and MgCH genes were up-regulated. Observation through qPCR suggested that later stages of Chl biosynthesis were enhanced in C1, whereas the early stages were inhibited. Plastid structure analysis together with transcriptomic analysis suggested that the Chl a/b ratio was amplified both by the reduction in Chl contents accumulation, owning to abnormal chloroplast development, and by the enhanced conversion of Chl b to Chl a. Moreover, the results indicated the same Chl-cycle pattern in the wild-type and C1 rice, indicating another Chl b degradation pathway. Furthermore, the results demonstrated that normal grana stacking, along with the absence of Chl b and greatly reduced levels of Chl a in C1, provide evidence to support the conclusion that other factors along with LHCII proteins are involved in grana stacking. The findings of this study provide insight into the molecular mechanisms that underlie different Chl a/b ratios in rice.

Keywords: Chl-deficient mutant, grana stacked, photosynthesis, RNA-Seq, transcriptomic analysis

Procedia PDF Downloads 91

Authors: Chuyuan Wang, Nayan Khare, Lily Villa, Patricia Solis, Elizabeth A. Wentz

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Maricopa County, Arizona, has a semi-arid hot desert climate that is one of the hottest regions in the United States. The exacerbated urban heat island (UHI) effect caused by rapid urbanization has made the urban area even hotter than the rural surroundings. The Phoenix metropolitan area experiences extremely high temperatures in the summer from June to September that can reach the daily highest of 120 °F (48.9 °C). Morbidity and mortality due to the environmental heat is, therefore, a significant public health issue in Maricopa County, especially because it is largely preventable. Public records from the Maricopa County Department of Public Health (MCDPH) revealed that between 2012 and 2016, there were 10,825 incidents of heat-related morbidity incidents, 267 outdoor environmental heat deaths, and 173 indoor heat-related deaths. A lot of research has examined heat-related death and its contributing factors around the world, but little has been done regarding heat-related morbidity issues, especially for regions that are naturally hot in the summer. The objective of this study is to examine the demographic, socio-economic, housing, and environmental factors that contribute to heat-related morbidity in Maricopa County. We obtained heat-related morbidity data between 2012 and 2016 at census tract level from MCDPH. Demographic, socio-economic, and housing variables were derived using 2012-2016 American Community Survey 5-year estimate from the U.S. Census. Remotely sensed Landsat 7 ETM+ and Landsat 8 OLI satellite images and Level-1 products were acquired for all the summer months (June to September) from 2012 and 2016. The National Land Cover Database (NLCD) 2016 percent tree canopy and percent developed imperviousness data were obtained from the U.S. Geological Survey (USGS). We used ordinary least squares (OLS) regression analysis to examine the empirical relationship between all the independent variables and heat-related morbidity rate. Results showed that higher morbidity rates are found in census tracts with higher values in population aged 65 and older, population under poverty, disability, no vehicle ownership, white non-Hispanic, population with less than high school degree, land surface temperature, and surface reflectance, but lower values in normalized difference vegetation index (NDVI) and housing occupancy. The regression model can be used to explain up to 59.4% of total variation of heat-related morbidity in Maricopa County. The multiscale geographically weighted regression (MGWR) technique was then used to examine the spatially varying relationships between heat-related morbidity rate and all the significant independent variables. The R-squared value of the MGWR model increased to 0.691, that shows a significant improvement in goodness-of-fit than the global OLS model, which means that spatial heterogeneity of some independent variables is another important factor that influences the relationship with heat-related morbidity in Maricopa County. Among these variables, population aged 65 and older, the Hispanic population, disability, vehicle ownership, and housing occupancy have much stronger local effects than other variables.

Keywords: census, empirical modeling, heat-related morbidity, spatial analysis

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Authors: Galit Shiff, Yael Gilad

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The need to retrofit old buildings lies in the fact that buildings are responsible for the main energy use and CO₂ emission. Existing old structures are more dominant in their effect than new energy-efficient buildings. Nevertheless not every case of urban renewal that aims to replace old buildings with new neighbourhoods necessarily has a financial or sustainable justification. Façade design plays a vital role in the building's energy performance and the unit's comfort conditions. A retrofit façade residential methodology and feasibility applicative study has been carried out for the past four years, with two projects already fully renovated. The intention of this study is to serve as a case study for limited budget façade retrofit in Mediterranean climate urban areas. The two case study buildings are set in Israel. However, they are set in different local climatic conditions. One is in 'Sderot' in the south of the country, and one is in' Migdal Hahemek' in the north of the country. The building typology is similar. The budget of the projects is around $14,000 per unit and includes interventions at the buildings' envelope while tenants are living in. Extensive research and analysis of the existing conditions have been done. The building's components, materials and envelope sections were mapped, examined and compared to relevant updated standards. Solar radiation simulations for the buildings in their surroundings during winter and summer days were done. The energy rate of each unit, as well as the building as a whole, was calculated according to the Israeli Energy Code. The buildings’ facades were documented with the use of a thermal camera during different hours of the day. This information was superimposed with data about the electricity use and the thermal comfort that was collected from the residential units. Later in the process, similar tools were further used in order to compare the effectiveness of different design options and to evaluate the chosen solutions. Both projects showed that the most problematic units were the ones below the roof and the ones on top of the elevated entrance floor (pilotis). Old buildings tend to have poor insulation on those two horizontal surfaces which require treatment. Different radiation levels and wall sections in the two projects influenced the design strategies: In the southern project, there was an extreme difference in solar radiations levels between the main façade and the back elevation. Eventually, it was decided to invest in insulating the main south-west façade and the side façades, leaving the back north-east façade almost untouched. Lower levels of radiation in the northern project led to a different tactic: a combination of basic insulation on all façades, together with intense treatment on areas with problematic thermal behavior. While poor execution of construction details and bad installation of windows in the northern project required replacing them all, in the southern project it was found that it is more essential to shade the windows than replace them. Although the buildings and the construction typology was chosen for this study are similar, the research shows that there are large differences due to the location in different climatic zones and variation in local conditions. Therefore, in order to reach a systematic and cost-effective method of work, a more extensive catalogue database is needed. Such a catalogue will enable public housing companies in the Mediterranean climate to promote massive projects of renovating existing old buildings, drawing on minimal analysis and planning processes.

Keywords: facade, low budget, residential, retrofit

Procedia PDF Downloads 174

Authors: L. Salomon, P. Sklenar

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The Andes hold the highest plant species diversity in the world. How this occurred is one of the most intriguing questions in studies addressing the origin and patterning of plant diversity worldwide. Recently, the explosive adaptive radiations found in high Andean groups have been pointed as triggers to this spectacular diversity. The Andes is the species-richest area for the biggest genus from the Asteraceae family: Senecio. There, the genus presents an incredible diversity of species, striking growth form variation, and large niche span. Even when some studies tried to disentangle the evolutionary story for some Andean species in Senecio, they obtained partially resolved and low supported phylogenies, as expected for recently radiated groups. The high-throughput sequencing (HTS) approaches have proved to be a powerful tool answering phylogenetic questions in those groups whose evolutionary stories are recent and traditional techniques like Sanger sequencing are not informative enough. Although these tools have been used to understand the evolution of an increasing number of Andean groups, nowadays, their scope has not been applied for Senecio. This project aims to contribute to a better knowledge of the mechanisms shaping the hyper diversity of Senecio in the Andean region, using HTS focusing on Senecio ser. Culcitium (Asteraceae), recently recircumscribed. Firstly, reconstructing a highly resolved and supported phylogeny, and after assessing the role of allopatric differentiation, hybridization, and genome duplication in the diversification of the group. Using the Hyb-Seq approach, combining target enrichment using Asteraceae COS loci baits and genome skimming, more than 100 new accessions were generated. HybPhyloMaker and HybPiper pipelines were used for the phylogenetic analyses, and another pipeline in development (Paralogue Wizard) was used to deal with paralogues. RAxML was used to generate gene trees and Astral for species tree reconstruction. Phyparts were used to explore as first step of gene tree discordance along the clades. Fully resolved with moderated supported trees were obtained, showing Senecio ser. Culcitium as monophyletic. Within the group, some species formed well-supported clades with morphologically related species, while some species would not have exclusive ancestry, in concordance with previous studies using amplified fragment length polymorphism (AFLP) showing geographical differentiation. Discordance between gene trees was detected. Paralogues were detected for many loci, indicating possible genome duplications; ploidy level estimation using flow cytometry will be carried out during the next months in order to identify the role of this process in the diversification of the group. Likewise, TreeSetViz package for Mesquite, hierarchical likelihood ratio congruence test using Concaterpillar, and Procrustean Approach to Cophylogeny (PACo), will be used to evaluate the congruence among different inheritance patterns. In order to evaluate the influence of hybridization and Incomplete Lineage Sorting (ILS) in each resultant clade from the phylogeny, Joly et al.'s 2009 method in a coalescent scenario and Paterson’s D-statistic will be performed. Even when the main discordance sources between gene trees were not explored in detail yet, the data show that at least to some degree, processes such as genome duplication, hybridization, and/or ILS could be involved in the evolution of the group.

Keywords: adaptive radiations, Andes, genome duplication, hybridization, Senecio

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Authors: Arifur Rahman, Ardeshir Amirkhani, Honghua Hu, Mark Molloy, Karen Vickery

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Introduction and Objectives: Staphylococcus aureus and coagulase-negative staphylococci comprises approximately 65% of infections associated with medical devices and are well known for their biofilm formatting ability. Biofilm-related infections are extremely difficult to eradicate owing to their high tolerance to antibiotics and host immune defences. Currently, there is no efficient method for early biofilm detection. A better understanding to enable detection of biofilm specific proteins in vitro and in vivo can be achieved by studying planktonic and different growth phases of biofilms using a proteome analysis approach. Our goal was to construct a reference map of planktonic and biofilm associated proteins of S. aureus. Methods: S. aureus reference strain (ATCC 25923) was used to grow 24 hours planktonic, 3-day wet biofilm (3DWB), and 12-day wet biofilm (12DWB). Bacteria were grown in tryptic soy broth (TSB) liquid medium. Planktonic growth was used late logarithmic bacteria, and the Centres for Disease Control (CDC) biofilm reactor was used to grow 3 days, and 12-day hydrated biofilms, respectively. Samples were subjected to reduction, alkylation and digestion steps prior to Multiplex labelling using Tandem Mass Tag (TMT) 10-plex reagent (Thermo Fisher Scientific). The labelled samples were pooled and fractionated by high pH RP-HPLC which followed by loading of the fractions on a nanoflow UPLC system (Eksigent UPLC system, AB SCIEX). Mass spectrometry (MS) data were collected on an Orbitrap Elite (Thermo Fisher Scientific) Mass Spectrometer. Protein identification and relative quantitation of protein levels were performed using Proteome Discoverer (version 1.3, Thermo Fisher Scientific). After the extraction of protein ratios with Proteome Discoverer, additional processing, and statistical analysis was done using the TMTPrePro R package. Results and Discussion: The present study showed that a considerable proteomic difference exists among planktonic and biofilms from S. aureus. We identified 1636 total extracellular secreted proteins, of which 350 and 137 proteins of 3DWB and 12DWB showed significant abundance variation from planktonic preparation, respectively. Of these, simultaneous up-regulation in between 3DWB and 12DWB proteins such as extracellular matrix-binding protein ebh, enolase, transketolase, triosephosphate isomerase, chaperonin, peptidase, pyruvate kinase, hydrolase, aminotransferase, ribosomal protein, acetyl-CoA acetyltransferase, DNA gyrase subunit A, glycine glycyltransferase and others we found in this biofilm producer. On the contrary, simultaneous down-regulation in between 3DWB and 12DWB proteins such as alpha and delta-hemolysin, lipoteichoic acid synthase, enterotoxin I, serine protease, lipase, clumping factor B, regulatory protein Spx, phosphoglucomutase, and others also we found in this biofilm producer. In addition, we also identified a big percentage of hypothetical proteins including unique proteins. Therefore, a comprehensive knowledge of planktonic and biofilm associated proteins identified by S. aureus will provide a basis for future studies on the development of vaccines and diagnostic biomarkers. Conclusions: In this study, we constructed an initial reference map of planktonic and various growth phase of biofilm associated proteins which might be helpful to diagnose biofilm associated infections.

Keywords: bacterial biofilms, CDC bioreactor, S. aureus, mass spectrometry, TMT

Procedia PDF Downloads 141

Authors: Shagufta Jabeen, Faez J. Firdaus Abdullah, Zunita Zakaria, Nurulfiza M. Isa, Yung C. Tan, Wai Y. Yee, Abdul R. Omar

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Pasteurella multocida (PM) is an important veterinary opportunistic pathogen particularly associated with septicemic pasteurellosis, pneumonic pasteurellosis and hemorrhagic septicemia in cattle and buffaloes. P. multocida serotype A has been reported to cause fatal pneumonia and septicemia. Pasteurella multocida subspecies multocida of serotype A Malaysian isolate PMTB2.1 was first isolated from buffaloes died of septicemia. In this study, the genome of P. multocida strain PMTB2.1 was sequenced using third-generation sequencing technology, PacBio RS2 system and analyzed bioinformatically via de novo analysis followed by in-depth analysis based on comparative genomics. Bioinformatics analysis based on de novo assembly of PacBio raw reads generated 3 contigs followed by gap filling of aligned contigs with PCR sequencing, generated a single contiguous circular chromosome with a genomic size of 2,315,138 bp and a GC content of approximately 40.32% (Accession number CP007205). The PMTB2.1 genome comprised of 2,176 protein-coding sequences, 6 rRNA operons and 56 tRNA and 4 ncRNAs sequences. The comparative genome sequence analysis of PMTB2.1 with nine complete genomes which include Actinobacillus pleuropneumoniae, Haemophilus parasuis, Escherichia coli and five P. multocida complete genome sequences including, PM70, PM36950, PMHN06, PM3480, PMHB01 and PMTB2.1 was carried out based on OrthoMCL analysis and Venn diagram. The analysis showed that 282 CDs (13%) are unique to PMTB2.1and 1,125 CDs with orthologs in all. This reflects overall close relationship of these bacteria and supports the classification in the Gamma subdivision of the Proteobacteria. In addition, genomic distance analysis among all nine genomes indicated that PMTB2.1 is closely related with other five Pasteurella species with genomic distance less than 0.13. Synteny analysis shows subtle differences in genetic structures among different P.multocida indicating the dynamics of frequent gene transfer events among different P. multocida strains. However, PM3480 and PM70 exhibited exceptionally large structural variation since they were swine and chicken isolates. Furthermore, genomic structure of PMTB2.1 is more resembling that of PM36950 with a genomic size difference of approximately 34,380 kb (smaller than PM36950) and strain-specific Integrative and Conjugative Elements (ICE) which was found only in PM36950 is absent in PMTB2.1. Meanwhile, two intact prophages sequences of approximately 62 kb were found to be present only in PMTB2.1. One of phage is similar to transposable phage SfMu. The phylogenomic tree was constructed and rooted with E. coli, A. pleuropneumoniae and H. parasuis based on OrthoMCL analysis. The genomes of P. multocida strain PMTB2.1 were clustered with bovine isolates of P. multocida strain PM36950 and PMHB01 and were separated from avian isolate PM70 and swine isolates PM3480 and PMHN06 and are distant from Actinobacillus and Haemophilus. Previous studies based on Single Nucleotide Polymorphism (SNPs) and Multilocus Sequence Typing (MLST) unable to show a clear phylogenetic relatedness between Pasteurella multocida and the different host. In conclusion, this study has provided insight on the genomic structure of PMTB2.1 in terms of potential genes that can function as virulence factors for future study in elucidating the mechanisms behind the ability of the bacteria in causing diseases in susceptible animals.

Keywords: comparative genomics, DNA sequencing, phage, phylogenomics

Procedia PDF Downloads 154

Authors: Anushka Naidoo, Veron Ramsuran, Maxwell Chirehwa, Paolo Denti, Kogieleum Naidoo, Helen McIlleron, Nonhlanhla Yende-Zuma, Ravesh Singh, Sinaye Ngcapu, Nesri Padayatachi

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Background: Despite efforts to introduce new drugs and shorter drug regimens for drug-susceptible tuberculosis (TB), the standard first-line treatment has not changed in over 50 years. Rifampicin, isoniazid, and pyrazinamide are critical components of the current standard treatment regimens. Some studies suggest that microbiologic failure and acquired drug resistance are primarily driven by low drug concentrations that result from pharmacokinetic (PK) variability independent of adherence to treatment. Wide between-patient pharmacokinetic variability for rifampin, isoniazid, and pyrazinamide has been reported in prior studies. There may be several reasons for this variability. However, genetic variability in genes coding for drug metabolizing and transporter enzymes have been shown to be a contributing factor for variable tuberculosis drug exposures. Objective: We describe the pharmacokinetics of first-line TB drugs rifampicin, isoniazid, and pyrazinamide and assess the effect of genetic variability in relevant selected drug metabolizing and transporter enzymes on pharmacokinetic parameters of isoniazid and rifampicin. Methods: We conducted the randomized-controlled Improving retreatment success TB trial in Durban, South Africa. The drug regimen included rifampicin, isoniazid, and pyrazinamide. Drug concentrations were measured in plasma, and concentration-time data were analysed using nonlinear-mixed-effects models to quantify the effects of relevant covariates and single nucleotide polymorphisms (SNP’s) of drug metabolizing and transporter genes on rifampicin, isoniazid and pyrazinamide exposure. A total of 25 SNP’s: four NAT2 (used to determine acetylator status), four SLCO1B1, three Pregnane X receptor (NR1), six ABCB1 and eight UGT1A, were selected for analysis in this study. Genotypes were determined for each of the SNP’s using a TaqMan® Genotyping OpenArray™. Results: Among fifty-eight patients studied; 41 (70.7%) were male, 97% black African, 42 (72.4%) HIV co-infected and 40 (95%) on efavirenz-based ART. Median weight, fat-free mass (FFM), and age at baseline were 56.9 kg (interquartile range, IQR: 51.1-65.2), 46.8 kg (IQR: 42.5-50.3) and 37 years (IQR: 31-42), respectively. The pharmacokinetics of rifampicin and pyrazinamide was best described using one-compartment models with first-order absorption and elimination, while for isoniazid two-compartment disposition was used. The median (interquartile range: IQR) AUC (h·mg/L) and Cmax (mg/L) for rifampicin, isoniazid, and pyrazinamide were; 25.62 (23.01-28.53) and 4.85 (4.36-5.40), 10.62 (9.20-12.25) and 2.79 (2.61-2.97), 345.74 (312.03-383.10) and 28.06 (25.01-31.52), respectively. Eighteen percent of patients were classified as rapid acetylators, and 34% and 43% as slow and intermediate acetylators, respectively. Rapid and intermediate acetylator status based on NAT 2 genotype resulted in 2.3 and 1.6 times higher isoniazid clearance than slow acetylators. We found no effects of the SLCO1B1 genotypes on rifampicin pharmacokinetics. Conclusion: Plasma concentrations of rifampicin, isoniazid, and pyrazinamide were low overall in our patients. Isoniazid clearance was high overall and as expected higher in rapid and intermediate acetylators resulting in lower drug exposures. In contrast to reports from previous South African or Ugandan studies, we did not find any effects of the SLCO1B1 or other genotypes tested on rifampicin PK. However, our findings are in keeping with more recent studies from Malawi and India emphasizing the need for geographically diverse and adequately powered studies. The clinical relevance of the low tuberculosis drug concentrations warrants further investigation.

Keywords: rifampicin, isoniazid pharmacokinetics, genetics, NAT2, SLCO1B1, tuberculosis

Procedia PDF Downloads 154

Authors: Nisha Govender, Siju Senan, Zeti-Azura Hussein, Wickneswari Ratnam

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Jatropha curcas, a well-described bioenergy crop has been extensively accepted as future fuel need especially in tropical regions. Ideal planting material required for large-scale plantation is still lacking. Breeding programmes for improved J. curcas varieties are rendered difficult due to limitations in genetic diversity. Using a combined transcriptome and physiological data, we investigated the molecular and physiological differences in high and low yielding Jatropha curcas to address plausible heritable variations underpinning these differences, in regard to photosynthesis, a key metabolism affecting yield potentials. A total of 6 individual Jatropha plant from 4 accessions described as high and low yielding planting materials were selected from the Experimental Plot A, Universiti Kebangsaan Malaysia (UKM), Bangi. The inflorescence and shoots were collected for transcriptome study. For the physiological study, each individual plant (n=10) from the high and low yielding populations were screened for agronomic traits, chlorophyll content and stomatal patterning. The J. curcas transcriptomes are available under BioProject PRJNA338924 and BioSample SAMN05827448-65, respectively Each transcriptome was subjected to functional annotation analysis of sequence datasets using the BLAST2Go suite; BLASTing, mapping, annotation, statistical analysis and visualization Large-scale phenotyping of the number of fruits per plant (NFPP) and fruits per inflorescence (FPI) classified the high yielding Jatropha accessions with average NFPP =60 and FPI > 10, whereas the low yielding accessions yielded an average NFPP=10 and FPI < 5. Next generation sequencing revealed genes with differential expressions in the high yielding Jatropha relative to the low yielding plants. Distinct differences were observed in transcript level associated to photosynthesis metabolism. DEGs collection in the low yielding population showed comparable CAM photosynthetic metabolism and photorespiration, evident as followings: phosphoenolpyruvate phosphate translocator chloroplastic like isoform with 2.5 fold change (FC) and malate dehydrogenase (2.03 FC). Green leaves have the most pronounced photosynthetic activity in a plant body due to significant accumulation of chloroplast. In most plants, the leaf is always the dominant photosynthesizing heart of the plant body. Large number of the DEGS in the high-yielding population were found attributable to chloroplast and chloroplast associated events; STAY-GREEN chloroplastic, Chlorophyllase-1-like (5.08 FC), beta-amylase (3.66 FC), chlorophyllase-chloroplastic-like (3.1 FC), thiamine thiazole chloroplastic like (2.8 FC), 1-4, alpha glucan branching enzyme chloroplastic amyliplastic (2.6FC), photosynthetic NDH subunit (2.1 FC) and protochlorophyllide chloroplastic (2 FC). The results were parallel to a significant increase in chlorophyll a content in the high yielding population. In addition to the chloroplast associated transcript abundance, the TOO MANY MOUTHS (TMM) at 2.9 FC, which code for distant stomatal distribution and patterning in the high-yielding population may explain high concentration of CO2. The results were in agreement with the role of TMM. Clustered stomata causes back diffusion in the presence of gaps localized closely to one another. We conclude that high yielding Jatropha population corresponds to a collective function of C3 metabolism with a low degree of CAM photosynthetic fixation. From the physiological descriptions, high chlorophyll a content and even distribution of stomata in the leaf contribute to better photosynthetic efficiency in the high yielding Jatropha compared to the low yielding population.

Keywords: chlorophyll, gene expression, genetic variation, stomata

Procedia PDF Downloads 210

Authors: Mariana Stuparu-Cretu, Doina-Carina Voinescu, Rodica-Mihaela Dinica, Daniela Borda, Camelia Vizireanu, Gabriela Iordachescu, Camelia Busila

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Obesity is involved in the etiology or acceleration of progression of important non-communicable diseases, such as: metabolic, cardiovascular, rheumatological, oncological and depression. It is a need to prevent the obesity occurrence, like a key link in disease management. From this point of view, the best approach is to early educate youngsters upon the need for a healthy nutrition lifestyle associated with constant physical activities. The objective of the study was to assess correlations between weight condition, physical activities and food preferences of students from South East Romania. Questionnaires were applied on high school students in Galati: 1006 girls and 880 boys, aged between 14 and 19 years (being approved by Local School Inspectorate and the Ethics Committee of the 'Dunarea de Jos' University of Galati). The collected answers have been statistically processed by using the multivariate regression method (PLS2) by Unscramble X program (Camo, Norway). Multiple variables such as age group, body mass index, nutritional habits and physical activities were separately analysed, depending on gender and general mathematical models were proposed to explain the obesity trend at an early age. The study results show that overweight and obesity are present in less than a fifth of the adolescents who were surveyed. With a very small variation and a strong correlation of over 86% for 99% of the cases, a general preference for sweet foods, nocturnal eating associated with computer work and a reduced period of physical activity is noticed for girls. In addition, the overweight girls consume sweet juices and alcohol, although a percentage of them also practice the gym. There is also a percentage of the normoponderal girls that consume high caloric foods which predispose this group to turn into overweight cases in time. Within the studied group, statistics for the boys show a positive correlation of almost 87% for over 96% of cases. They prefer high calories foods, fast food, and sweet juices, and perform medium physical activities. Both overweight and underweight boys are more sedentary. Over 15% of girls and over a quarter of boys consume alcohol. All these bad eating habits seem to increase with age, for both sexes. To conclude, obesity and overweight assessed in adolescents in S-E Romania reveal nonsignificant percentage differences between boys and girls. However, young people in this area of the country are sedentary in general; a significant percentage prefers sweets / sweet juices / fast-food and practice computer nourishing. The authors consider that at this age, it is very useful to adapt nutritional education by new methods of food processing and market supply. This would require an early understanding of the difference among foods and nutrients and the benefits of physical activities integrated into the healthy current lifestyle, as a measure for preventing and managing non-communicable chronic diseases related to nutritional errors and sedentarism. Acknowledgment— This study has been partial founded by the Francophone University Agency, Project Réseau régional dans le domaine de la santé, la nutrition et la sécurité alimentaire (SaIN), no.21899/ 06.09.2017.

Keywords: adolescents, body mass index, nutritional habits, obesity, physical activity

Procedia PDF Downloads 238