Search results for: small cells
Commenced in January 2007
Frequency: Monthly
Edition: International
Paper Count: 7768

Search results for: small cells

5278 Clay Hydrogel Nanocomposite for Controlled Small Molecule Release

Authors: Xiaolin Li, Terence Turney, John Forsythe, Bryce Feltis, Paul Wright, Vinh Truong, Will Gates

Abstract:

Clay-hydrogel nanocomposites have attracted great attention recently, mainly because of their enhanced mechanical properties and ease of fabrication. Moreover, the unique platelet structure of clay nanoparticles enables the incorporation of bioactive molecules, such as proteins or drugs, through ion exchange, adsorption or intercalation. This study seeks to improve the mechanical and rheological properties of a novel hydrogel system, copolymerized from a tetrapodal polyethylene glycol (PEG) thiol and a linear, triblock PEG-PPG-PEG (PPG: polypropylene glycol) α,ω-bispropynoate polymer, with the simultaneous incorporation of various amounts of Na-saturated, montmorillonite clay (MMT) platelets (av. lateral dimension = 200 nm), to form a bioactive three-dimensional network. Although the parent hydrogel has controlled swelling ability and its PEG groups have good affinity for the clay platelets, it suffers from poor mechanical stability and is currently unsuitable for potential applications. Nanocomposite hydrogels containing 4wt% MMT showed a twelve-fold enhancement in compressive strength, reaching 0.75MPa, and also a three-fold acceleration in gelation time, when compared with the parent hydrogel. Interestingly, clay nanoplatelet incorporation into the hydrogel slowed down the rate of its dehydration in air. Preliminary results showed that protein binding by the MMT varied with the nature of the protein, as horseradish peroxidase (HRP) was more strongly bound than bovine serum albumin. The HRP was no longer active when bound, presumably as a result of extensive structural refolding. Further work is being undertaken to assess protein binding behaviour within the nanocomposite hydrogel for potential diabetic wound healing applications.

Keywords: hydrogel, nanocomposite, small molecule, wound healing

Procedia PDF Downloads 271
5277 Estimation of Soil Nutrient Content Using Google Earth and Pleiades Satellite Imagery for Small Farms

Authors: Lucas Barbosa Da Silva, Jun Okamoto Jr.

Abstract:

Precision Agriculture has long being benefited from crop fields’ aerial imagery. This important tool has allowed identifying patterns in crop fields, generating useful information to the production management. Reflectance intensity data in different ranges from the electromagnetic spectrum may indicate presence or absence of nutrients in the soil of an area. Different relations between the different light bands may generate even more detailed information. The knowledge of the nutrients content in the soil or in the crop during its growth is a valuable asset to the farmer that seeks to optimize its yield. However, small farmers in Brazil often lack the resources to access this kind information, and, even when they do, it is not presented in a comprehensive and/or objective way. So, the challenges of implementing this technology ranges from the sampling of the imagery, using aerial platforms, building of a mosaic with the images to cover the entire crop field, extracting the reflectance information from it and analyzing its relationship with the parameters of interest, to the display of the results in a manner that the farmer may take the necessary decisions more objectively. In this work, it’s proposed an analysis of soil nutrient contents based on image processing of satellite imagery and comparing its outtakes with commercial laboratory’s chemical analysis. Also, sources of satellite imagery are compared, to assess the feasibility of using Google Earth data in this application, and the impacts of doing so, versus the application of imagery from satellites like Landsat-8 and Pleiades. Furthermore, an algorithm for building mosaics is implemented using Google Earth imagery and finally, the possibility of using unmanned aerial vehicles is analyzed. From the data obtained, some soil parameters are estimated, namely, the content of Potassium, Phosphorus, Boron, Manganese, among others. The suitability of Google Earth Imagery for this application is verified within a reasonable margin, when compared to Pleiades Satellite imagery and to the current commercial model. It is also verified that the mosaic construction method has little or no influence on the estimation results. Variability maps are created over the covered area and the impacts of the image resolution and sample time frame are discussed, allowing easy assessments of the results. The final results show that easy and cheaper remote sensing and analysis methods are possible and feasible alternatives for the small farmer, with little access to technological and/or financial resources, to make more accurate decisions about soil nutrient management.

Keywords: remote sensing, precision agriculture, mosaic, soil, nutrient content, satellite imagery, aerial imagery

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5276 Immunocytochemical Stability of Antigens in Cytological Samples Stored in In-house Liquid-Based Medium

Authors: Anamarija Kuhar, Veronika Kloboves Prevodnik, Nataša Nolde, Ulrika Klopčič

Abstract:

The decision for immunocytochemistry (ICC) is usually made in the basis of the findings in Giemsa- and/or Papanicolaou- smears. More demanding diagnostic cases require preparation of additional cytological preparations. Therefore, it is convenient to suspend cytological samples in a liquid based medium (LBM) that preserve antigen and morphological properties. However, the duration of these properties being preserved in the medium is usually unknown. Eventually, cell morphology becomes impaired and altered, as well as antigen properties may be lost or become diffused. In this study, the influence of cytological sample storage length in in-house liquid based medium on antigen properties and cell morphology is evaluated. The question is how long the cytological samples in this medium can be stored so that the results of immunocytochemical reactions are still reliable and can be safely used in routine cytopathological diagnostics. The stability of 6 ICC markers that are most frequently used in everyday routine work were tested; Cytokeratin AE1/AE3, Calretinin, Epithelial specific antigen Ep-CAM (MOC-31), CD 45, Oestrogen receptor (ER), and Melanoma triple cocktail were tested on methanol fixed cytospins prepared from fresh fine needle aspiration biopsies, effusion samples, and disintegrated lymph nodes suspended in in-house cell medium. Cytospins were prepared on the day of the sampling as well as on the second, fourth, fifth, and eight day after sample collection. Next, they were fixed in methanol and immunocytochemically stained. Finally, the percentage of positive stained cells, reaction intensity, counterstaining, and cell morphology were assessed using two assessment methods: the internal assessment and the UK NEQAS ICC scheme assessment. Results show that the antigen properties for Cytokeratin AE1/AE3, MOC-31, CD 45, ER, and Melanoma triple cocktail were preserved even after 8 days of storage in in-house LBM, while the antigen properties for Calretinin remained unchanged only for 4 days. The key parameters for assessing detection of antigen are the proportion of cells with a positive reaction and intensity of staining. Well preserved cell morphology is highly important for reliable interpretation of ICC reaction. Therefore, it would be valuable to perform a similar analysis for other ICC markers to determine the duration in which the antigen and morphological properties are preserved in LBM.

Keywords: cytology samples, cytospins, immunocytochemistry, liquid-based cytology

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5275 On the Monitoring of Structures and Soils by Tromograph

Authors: Magarò Floriana, Zinno Raffaele

Abstract:

Since 2009, with the coming into force of the January 14, 2008 Ministerial Decree "New technical standards for construction", and the explanatory ministerial circular N°.617 of February 2, 2009, the question of seismic hazard and the design of seismic-resistant structures in Italy has acquired increasing importance. One of the most discussed aspects in recent Italian and international scientific literature concerns the dynamic interaction between land and structure, and the effects which dynamic coupling may have on individual buildings. In effect, from systems dynamics, it is well known that resonance can have catastrophic effects on a stimulated system, leading to a response that is not compatible with the previsions in the design phase. The method used in this study to estimate the frequency of oscillation of the structure is as follows: the analysis of HVSR (Horizontal to Vertical Spectral Ratio) relations. This allows for evaluation of very simple oscillation frequencies for land and structures. The tool used for data acquisition is an experimental digital tromograph. This is an engineered development of the experimental Languamply RE 4500 tromograph, equipped with an engineered amplification circuit and improved electronically using extremely small electronic components (size of each individual amplifier 16 x 26 mm). This tromograph is a modular system, completely "free" and "open", designed to interface Windows, Linux, OSX and Android with the outside world. It an amplifier designed to carry out microtremor measurements, yet which will also be useful for seismological and seismic measurements in general. The development of single amplifiers of small dimension allows for a very clean signal since being able to position it a few centimetres from the geophone eliminates cable “antenna” phenomena, which is a necessary characteristic in seeking to have signals which are clean at the very low voltages to be measured.

Keywords: microtremor, HVSR, tromograph, structural engineering

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5274 Influence of Bacterial Motility on Biofilm Formation

Authors: Li Cheng, Zhang Yilei, Cohen Yehuda

Abstract:

Two motility mechanisms were introduced into iDynoMiCs software, which adopts an individual-based modeling method. Based on the new capabilities, along with the pressure motility developed before, influence of bacterial motility on biofilm formation was studied. Simulation results were evaluated both qualitatively through 3D structure inspections and quantitatively by parameter characterizations. It was showed that twitching motility increased the biofilm surface irregularity probably due to movement of cells towards higher nutrient concentration location whereas free motility, on the other hand, could make biofilms flatter and smoother relatively. Pressure motility showed no significant influence in this study.

Keywords: iDynoMics, biofilm structure, bacterial motility, motility mechanisms

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5273 Faster Pedestrian Recognition Using Deformable Part Models

Authors: Alessandro Preziosi, Antonio Prioletti, Luca Castangia

Abstract:

Deformable part models achieve high precision in pedestrian recognition, but all publicly available implementations are too slow for real-time applications. We implemented a deformable part model algorithm fast enough for real-time use by exploiting information about the camera position and orientation. This implementation is both faster and more precise than alternative DPM implementations. These results are obtained by computing convolutions in the frequency domain and using lookup tables to speed up feature computation. This approach is almost an order of magnitude faster than the reference DPM implementation, with no loss in precision. Knowing the position of the camera with respect to horizon it is also possible prune many hypotheses based on their size and location. The range of acceptable sizes and positions is set by looking at the statistical distribution of bounding boxes in labelled images. With this approach it is not needed to compute the entire feature pyramid: for example higher resolution features are only needed near the horizon. This results in an increase in mean average precision of 5% and an increase in speed by a factor of two. Furthermore, to reduce misdetections involving small pedestrians near the horizon, input images are supersampled near the horizon. Supersampling the image at 1.5 times the original scale, results in an increase in precision of about 4%. The implementation was tested against the public KITTI dataset, obtaining an 8% improvement in mean average precision over the best performing DPM-based method. By allowing for a small loss in precision computational time can be easily brought down to our target of 100ms per image, reaching a solution that is faster and still more precise than all publicly available DPM implementations.

Keywords: autonomous vehicles, deformable part model, dpm, pedestrian detection, real time

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5272 Synthesis and Biological Activity Evaluation of U Complexes

Authors: Mohammad Kazem Mohammadi

Abstract:

The use of anticancer agents forms an important part of the treatment of cancer of various types. Uranyl Complexes with DPHMP ligand have been used for the prevention and treatment of cancers. U(IV) metal complexes prepared by reaction of uranyl salt UO2 (NO3)2.6H2O with DPHMP in dry acetonitrile. Characterization of the ligand and its complexes was made by microanalyses, FT-IR, 1H NMR, 13C NMR and UV–Visible spectroscopy. These new complex showed excellent antitumor activity against two kinds of cancer cells that that are HT29:Haman colon adenocarcinoma cell line and T47D:human breast adenocarcinoma cell line.

Keywords: uranyl complexes, DPHMP ligand, antitumor activity, HT29, T47D

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5271 Mitigation of Wind Loads on a Building Using Small Wind Turbines

Authors: Arindam Chowdhury, Andres Tremante, Mohammadtaghi Moravej, Bodhisatta Hajra, Ioannis Zisis, Peter Irwin

Abstract:

Extreme wind events, such as hurricanes, have caused significant damage to buildings, resulting in losses worth millions of dollars. The roof of a building is most vulnerable to wind-induced damage due to the high suctions experienced by the roof in extreme wind conditions. Wind turbines fitted to buildings can help generate energy, but to our knowledge, their application to wind load mitigation is not well known. This paper presents results from an experimental study to assess the effect of small wind turbines (developed and patented by the first and second authors) on the wind loads on a low rise building roof. The tests were carried out for an open terrain at the Wall of Wind (WOW) experimental facility at Florida International University (FIU), Miami, Florida, USA, for three cases – bare roof, roof fitted with wind turbines placed closer to the roof edges, and roof with wind turbines placed away from the roof edges. Results clearly indicate that the presence of the wind turbines reduced the mean and peak pressure coefficients (less suction) on the roof when compared to the bare deck case. Furthermore, the peak pressure coefficients were found to be lower (less suction) when the wind turbines were placed closer to the roof, than away from the roof. Flow visualization studies using smoke and gravel clearly showed that the presence of the turbines disrupted the formation of vortices formed by cornering winds, thereby reducing roof suctions and preventing lift off of roof coverings. This study shows that the wind turbines besides generating wind energy, can be used for mitigating wind induced damage to the building roof. Future research must be directed towards understanding the effect of these wind turbines on other roof geometries (e.g. hip/gable) in different terrain conditions.

Keywords: wall of wind, wind loads, wind turbine, building

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5270 Self-Stigma Regarding Mental Illness: An Empirical Study

Authors: Linta Koka

Abstract:

Aim: The way people with severe mental disorders deal with self-stigma and how it affects their self-esteem is a problem that has gained much attention in recent years. The primary aim of this study was to empirically explore the link between self-stigma and self-esteem of individuals with the presence of a mental illness, offering a novel perspective by exploring the same variables amongst a sample without a mental illness. Methods: This study utilized a cross-sectional study. Participants with (N=85) and without (N=75) a mental health issue were included from Darlingdon's Mind organization. Participants completed two scales, one of Self-Stigma of Mental Illness Scale and one of Self-Esteem, following some demographics questions. Results: According to the primary hypothesis, self-stigma significantly correlates with self-esteem in the clinical population. Furthermore, gender and ethnicity, above all the demographics, positively correlates to the relationship of self-stigma with self-esteem in people who endure a mental health issue. Limitations: A significant limitation is that of the size of the sample of participants conducted in this study. The clinical population was limited to 85 participants, and the control group consisted of 76 participants. Since the sample was not representative. The small size used did not allow any comparisons between the group with mental illness and the control group. There was a restricted time to approach the participants since the online survey was released by the end of May. Conclusions: Individuals suffering from mental illnesses may internalize stigmatizing stereotypes on an explicit level. Efforts should be made to lessen the harmful impact stigma may have on mentally ill people, such as worsening symptoms or delays in receiving care. Further study is needed within this small research topic to improve awareness and regulate mental health among the general population. Undoubtedly, people with mental disorders are stigmatized; therefore, more research is required to explore all factors contributing to mentally ill patients' devaluation.

Keywords: self-stigma, mental illness, self-esteem, clinical population, non-clinical population

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5269 The Influence of Emotion on Numerical Estimation: A Drone Operators’ Context

Authors: Ludovic Fabre, Paola Melani, Patrick Lemaire

Abstract:

The goal of this study was to test whether and how emotions influence drone operators in estimation skills. The empirical study was run in the context of numerical estimation. Participants saw a two-digit number together with a collection of cars. They had to indicate whether the stimuli collection was larger or smaller than the number. The two-digit numbers ranged from 12 to 27, and collections included 3-36 cars. The presentation of the collections was dynamic (each car moved 30 deg. per second on the right). Half the collections were smaller collections (including fewer than 20 cars), and the other collections were larger collections (i.e., more than 20 cars). Splits between the number of cars in a collection and the two-digit number were either small (± 1 or 2 units; e.g., the collection included 17 cars and the two-digit number was 19) or larger (± 8 or 9 units; e.g., 17 cars and '9'). Half the collections included more items (and half fewer items) than the number indicated by the two-digit number. Before and after each trial, participants saw an image inducing negative emotions (e.g., mutilations) or neutral emotions (e.g., candle) selected from International Affective Picture System (IAPS). At the end of each trial, participants had to say if the second picture was the same as or different from the first. Results showed different effects of emotions on RTs and percent errors. Participants’ performance was modulated by emotions. They were slower on negative trials compared to the neutral trials, especially on the most difficult items. They errored more on small-split than on large-split problems. Moreover, participants highly overestimated the number of cars when in a negative emotional state. These findings suggest that emotions influence numerical estimation, that effects of emotion in estimation interact with stimuli characteristics. They have important implications for understanding the role of emotions on estimation skills, and more generally, on how emotions influence cognition.

Keywords: drone operators, emotion, numerical estimation, arithmetic

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5268 In vitro Study on Characterization and Viability of Vero Cell Lines after Supplementation with Porcine Follicular Fluid Proteins in Culture Medium

Authors: Mayuva Youngsabanant, Suphaphorn Rabiab, Hatairuk Tungkasen, Nongnuch Gumlungpat, Mayuree Pumipaiboon

Abstract:

The porcine follicular fluid proteins (pFF) of healthy small size ovarian follicles (1-3 mm in diameters) of Large White pig ovaries were collected by sterile technique. They were used for testing the effect on cell viability and characterization of Vero cell lines using MTT assay. Two hundred microliter of round shape Vero cell lines were culture in 96 well plates with DMEM for 24 h. After that, they were attachment to substrate and some changed into fibroblast shape and spread over the surface after culture for 48 h. Then, Vero cell lines were treated with pFF at concentration of 2, 4, 20, 40, 200, 400, 500, and 600 µg proteins/mL for 24 h. Yields of the best results were analyzed by using one-way ANOVA. MTT assay reviewed an increasing in percentage of viability of Vero cell lines indicated that at concentration of 400-600 µg proteins/mL showed higher percentage of viability (115.64 ± 6.95, 106.91 ± 5.27 and 116.73 ± 20.15) than control group. They were significantly different from the control group (p < 0.05) but lower than the positive control group (DMEM with 10% heat treated fetal bovine serum). Cell lines showed normal character in fibroblast elongate shape after treated with pFF except in high concentration of pFF. This result implies that pFF of small size ovarian follicle at concentration of 400-600 µg proteins/mL could be optimized concentration for using as a supplement in Vero cell line culture medium to promote cell viability instead of growth hormone from fetal bovine serum. This merit could be applied in other cell biotechnology researches. Acknowledgements: This work was funded by a grant from Silpakorn University and Faculty of Science, Silpakorn University, Thailand.

Keywords: cell viability, porcine follicular fluid, MTT assay, Vero cell line

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5267 Public Policy as a Component of Entrepreneurship Ecosystems: Challenges of Implementation

Authors: José Batista de Souza Neto

Abstract:

This research project has as its theme the implementation of public policies to support micro and small businesses (MSEs). The research problem defined was how public policies for access to markets that drive the entrepreneurial ecosystem of MSEs are implemented. The general objective of this research is to understand the process of implementing a public policy to support the entrepreneurial ecosystem of MSEs by the Support Service for Micro and Small Enterprises of the State of São Paulo (SEBRAESP). Public policies are constituent elements of entrepreneurship ecosystems that influence the creation and development of ventures from the action of the entrepreneur. At the end of the research, it is expected to achieve the results for the following specific objectives: (a) understand how the entrepreneurial ecosystem of MSEs is constituted; (b) understand how market access public policies for MSEs are designed and implemented; (c) understand SEBRAE's role in the entrepreneurship ecosystem; and (d) offer an action plan and monitor its execution up to march, 2023. The field research will be conducted based on Action Research, with a qualitative and longitudinal approach to the data. Data collection will be based on narratives produced since 2019 when the decision to implement Comércio Brasil program, a public policy focused on generating market access for 4280 MSEs yearly, was made. The narratives will be analyzed by the method of document analysis and narrative analysis. It is expected that the research will consolidate the relevance of public policies to market access for MSEs and the role of SEBRAE as a protagonist in the implementation of these public policies in the entrepreneurship ecosystem will be demonstrated. Action research is recognized as an intervention method, it is expected that this research will corroborate its role in supporting management processes.

Keywords: entrepreneurship, entrepreneurship ecosystem, public policies, SEBRAE, action research

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5266 Global Analysis of HIV Virus Models with Cell-to-Cell

Authors: Hossein Pourbashash

Abstract:

Recent experimental studies have shown that HIV can be transmitted directly from cell to cell when structures called virological synapses form during interactions between T cells. In this article, we describe a new within-host model of HIV infection that incorporates two mechanisms: infection by free virions and the direct cell-to-cell transmission. We conduct the local and global stability analysis of the model. We show that if the basic reproduction number R0 1, the virus is cleared and the disease dies out; if R0 > 1, the virus persists in the host. We also prove that the unique positive equilibrium attracts all positive solutions under additional assumptions on the parameters.

Keywords: HIV virus model, cell-to-cell transmission, global stability, Lyapunov function, second compound matrices

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5265 In2S3 Buffer Layer Properties for Thin Film Solar Cells Based on CIGS Absorber

Authors: A. Bouloufa, K. Djessas

Abstract:

In this paper, we reported the effect of substrate temperature on the structural, electrical and optical properties of In2S3 thin films deposited on soda-lime glass substrates by physical vapor deposition technique at various substrate temperatures. The In2Se3 material used for deposition was synthesized from its constituent elements. It was found that all samples exhibit one phase which corresponds to β-In2S3 phase. Values of band gap energy of the films obtained at different substrate temperatures vary in the range of 2.38-2.80 eV and decrease with increasing substrate temperature.

Keywords: buffer layer, In2S3, optical properties, PVD, structural properties

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5264 The Effect of SIAH1 on PINK1 Homeostasis in Parkinson Disease

Authors: Fatimah Abd Elghani, Raymonde Szargel, Vered Shani, Hazem Safory, Haya Hamza, Mor Savyon, Ruth Rott, Rina Bandopadhyay, Simone Engelender

Abstract:

Background: PINK1 is a mitochondrial kinase mutated in some familial cases of Parkinson’s disease. Down regulation of PINK1 results in abnormal mitochondrial morphology and altered membrane potential. Although PINK1 has a predicted mitochondrial import sequence, it’s cellular, and submitochondrial localization remains unclear, in part because it is rapidly degraded. In this work, we investigated the mechanisms involved in PINK1 degradation and how this may affect PINK1 stability and function, with implications for mitochondrial function in PD. In addition, pharmacological inhibition of proteasome activity was shown to lead to PINK1 accumulation, indicating that PINK1 degradation depends on the ubiquitin-proteasome system (UPS). Methods: Using co-immunoprecipitation assays, we identified E3 ubiquitin ligase SIAH1 as a PINK1-interacting protein in HEK293 cells as well as on rat brain tissues. In addition, we determined the effect of SIAH 1, SIAH2 and Parkin on PINK1 steady-state levels by Western blot analysis, and checked their possibility to ubiquitinate and mediate PINK1 degradation through the proteasome carried out in vivo ubiquitination experiments. Results: We have obtained results showing that SIAH-1 interacts with and ubiquitinates PINK1. The ubiquitination promoted by SIAH-1 leads to the proteasomal degradation of PINK1. We confirmed these findings by knocking down SIAH-1 and observing important accumulation of PINK1 in cells. Besides, we found that SIAH-1 decreases PINK1 steady-state levels but not the E3 ligase Parkin. We also investigated the interaction of SIAH-1 with PINK1 disease mutants and its ability to promote their ubiquitination and degradation. Although, no clear difference in the ability of SIAH-1 to promote the degradation of PINK1 disease mutants was observed. It is possible that dysfunction of proteasomal activity in the disease may lead to the accumulation and aggregation of ubiquitinated PINK1 in patients with PINK1 mutations, with possible implications to the pathogenesis of PD. Conclusions: Here, we demonstrated that SIAH-1 ubiquitinates and promotes the degradation of PINK1. In addition, SIAH-1 represents now a target that may help the improvement of mitophagy in PD. Further investigations needed to understand how mitophagy is regulated by PINK1-SIAH-1 axis to provide targets for future therapeutics.

Keywords: PD, Parkinson's disease, PINK1, PTEN-induced kinase1, SIAH, seven in absentia homolog, SN, substantia nigra

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5263 Full-Scale 3D Simulation of the Electroslag Rapid Remelting Process

Authors: E. Karimi-Sibaki, A. Kharicha, M. Wu, A. Ludwig

Abstract:

The standard electroslag remelting (ESR) process can ideally control the solidification of an ingot and produce homogeneous structure with minimum defects. However, the melt rate of electrode is rather low that makes the whole process uneconomical especially to produce small ingot sizes. In contrast, continuous casting is an economical process to produce small ingots such as billets at high casting speed. Unfortunately, deep liquid melt pool forms in the billet ingot of continuous casting that leads to center porosity and segregation. As such, continuous casting is not suitable to produce segregation prone alloys like tool steel or several super alloys. On the other hand, the electro slag rapid remelting (ESRR) process has advantages of both traditional ESR and continuous casting processes to produce billets. In the ESRR process, a T-shaped mold is used including a graphite ring that takes major amount of current through the mold. There are only a few reports available in the literature discussing about this topic. The research on the ESRR process is currently ongoing aiming to improve the design of the T-shaped mold, to decrease overall heat loss in the process, and to obtain a higher temperature at metal meniscus. In the present study, a 3D model is proposed to investigate the electromagnetic, thermal, and flow fields in the whole process as well as solidification of the billet ingot. We performed a fully coupled numerical simulation to explore the influence of the electromagnetically driven flow (MHD) on the thermal field in the slag and ingot. The main goal is to obtain some fundamental understanding of the formation of melt pool of the solidifying billet ingot in the ESRR process.

Keywords: billet ingot, magnetohydrodynamics (mhd), numerical simulation, remelting, solidification, t-shaped mold.

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5262 Physiochemical and Histological Study on the Effect of the Hibernation on the Liver of Uromastyx acanthinura (Bell, 1825)

Authors: Youssef. K. A. Abdalhafid, Ezaldin A. M. Mohammed, Masoud M. M. Zatout

Abstract:

This study described the changes in the liver of Uromastyx acanthinura (Bell, 1825) males and females during hibernation and activity seasons. The results revealed that, hibernation causes increase fatty liver and pigment cells with abundant damage, comparing with nearly normal structure and less fatty liver after the hibernation with almost normal pattern. Genomic DNA showed apparent separation during hibernation. Also, caspase 3 and caspase 7 activity reached a high level in the liver tissue during hibernation comparing with activity season.

Keywords: histological liver, DNA fragmentation, hibernation, caspase 3 and caspase 7

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5261 Study of Information Technology Support to Knowledge Sharing in Social Enterprises

Authors: Maria Granados

Abstract:

Information technology (IT) facilitates the management of knowledge in organisations through the effective leverage of collective experience and knowledge of employees. This supports information processing needs, as well as enables and facilitates sense-making activities of knowledge workers. The study of IT support for knowledge management (KM) has been carried out mainly in larger organisations where resources and competitive conditions can trigger the use of KM. However, there is still a lack of understanding on how IT can support the management of knowledge under different organisational settings influenced by: constant tensions between social and economic objectives, more focus on sustainability than competiveness, limited resources, and high levels of democratic participation and intrinsic motivations among employees. All these conditions are presented in Social Enterprises (SEs), which are normally micro and small businesses that trade to tackle social problems, improve communities, people’s life chances, and the environment. Thus, their importance to society and economies is increasing. However, there is still a need for more understanding of how these organisations operate, perform, innovate and scale-up. This knowledge is crucial to design and provide accurate strategies to enhance the sector and increase its impact and coverage. To obtain a conceptual and empirical understanding of how IT can facilitate KM in the particular organisational conditions of SEs, a quantitative study was conducted with 432 owners and senior members of SEs in UK, underpinned by 21 interviews. The findings demonstrated how IT was supporting more the recovery and storage of necessary information in SEs, and less the collaborative work and communication among enterprise members. However, it was established that SEs were using cloud solutions, web 2.0 tools, Skype and centralised shared servers to manage informally their knowledge. The possible impediments for SEs to support themselves more on IT solutions can be linked mainly to economic and human constraints. These findings elucidate new perspectives that can contribute not only to SEs and SE supporters, but also to other businesses.

Keywords: social enterprises, knowledge management, information technology, collaboration, small firms

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5260 Barriers and Facilitators for Telehealth Use during Cervical Cancer Screening and Care: A Literature Review

Authors: Reuben Mugisha, Stella Bakibinga

Abstract:

The cervical cancer burden is a global threat, but more so in low income settings where more than 85% of mortality cases occur due to lack of sufficient screening programs. There is consequently a lack of early detection of cancer and precancerous cells among women. Studies show that 3% to 35% of deaths could have been avoided through early screening depending on prognosis, disease progression, environmental and lifestyle factors. In this study, a systematic literature review is undertaken to understand potential barriers and facilitators as documented in previous studies that focus on the application of telehealth in cervical cancer screening programs for early detection of cancer and precancerous cells. The study informs future studies especially those from low income settings about lessons learned from previous studies and how to be best prepared while planning to implement telehealth for cervical cancer screening. It further identifies the knowledge gaps in the research area and makes recommendations. Using a specified selection criterion, 15 different articles are analyzed based on the study’s aim, theory or conceptual framework used, method applied, study findings and conclusion. Results are then tabulated and presented thematically to better inform readers about emerging facts on barriers and facilitators to telehealth implementation as documented in the reviewed articles, and how they consequently lead to evidence informed conclusions that are relevant to telehealth implementation for cervical cancer screening. Preliminary findings of this study underscore that use of low cost mobile colposcope is an appealing option in cervical cancer screening, particularly when coupled with onsite treatment of suspicious lesions. These tools relay cervical images to the online databases for storage and retrieval, they permit integration of connected devices at the point of care to rapidly collect clinical data for further analysis of the prevalence of cervical dysplasia and cervical cancer. Results however reveal the need for population sensitization prior to use of mobile colposcopies among patients, standardization of mobile colposcopy programs across screening partners, sufficient logistics and good connectivity, experienced experts to review image cases at the point-of-care as important facilitators to the implementation of mobile colposcope as a telehealth cervical cancer screening mechanism.

Keywords: cervical cancer screening, digital technology, hand-held colposcopy, knowledge-sharing

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5259 Heritage of the Ancient Greco-Roman Cities and Harbors in the North West Coast of Egypt

Authors: Wessam Fekry Ibrahim Moussa

Abstract:

The northwest coast of Egypt embraces about 500 km of the Mediterranean coastline. The area covered extends from Alexandria on the East to the village of Sallum at Egypt's border with Libya in the west with an average depth of 20-70 km. When one looks at this long strip of land, one is struck by the fact that, from the archaeological point of view, one knows relatively little about this region during ancient times, its history, villages, inhabitants, and heritage. According to classical writers, in antiquity, the area seemed to be more populated and characterized by its rich buildings and inhabitants. They mentioned several Greco-Roman towns and harbors scattered along the coast nearly 2 thousand years ago. Strabo, for instance, in his book 17, confirmed the existence of about 12 several clusters along the coast, which varied between cities, villages, harbors, and small islands. Claudius Ptolemaeus also enumerated many marina sites as well as some small cities and villages. Unfortunately, nowadays, most of them have been lost either due to the extensive development of the north coast, Natural Disasters, or Erosion Factors. However, recent excavations carried out within the area revealed just a little of these settlements. The aim of this study is to reveal the secrets of the hidden heritage of those ancient sites and shed light on the role they played in the past, as some of them used to be stops on the trade route between Libya and Egypt (Strabo 17) or major centers for some of the international imports. The study will explore the archeological evidence using the analytical methodology to analyze each site and identify its features and significances in order to conclude the importance and role it once played during the past. Findings could be used by authorities and policymakers to utilize these heritage resources to improve cultural tourism within the area and enhance the tourist's experience.

Keywords: Greco Roman, heritage, ancient cities, north west coast

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5258 Electrotechnology for Silicon Refining: Plasma Generator and Arc Furnace Installations and Theoretical Base

Authors: Ashot Navasardian, Mariam Vardanian, Vladik Vardanian

Abstract:

The photovoltaic and the semiconductor industries are in growth and it is necessary to supply a large amount of silicon to maintain this growth. Since silicon is still the best material for the manufacturing of solar cells and semiconductor components so the pure silicon like solar grade and semiconductor grade materials are demanded. There are two main routes for silicon production: metallurgical and chemical. In this article, we reviewed the electrotecnological installations and systems for semiconductor manufacturing. The main task is to design the installation which can produce SOG Silicon from river sand by one work unit.

Keywords: metallurgical grade silicon, solar grade silicon, impurity, refining, plasma

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5257 Tailorability of Poly(Aspartic Acid)/BSA Complex by Self-Assembling in Aqueous Solutions

Authors: Loredana E. Nita, Aurica P. Chiriac, Elena Stoleru, Alina Diaconu, Tudorachi Nita

Abstract:

Self-assembly processes are an attractive method to form new and complex structures between macromolecular compounds to be used for specific applications. In this context, intramolecular and intermolecular bonds play a key role during self-assembling processes in preparation of carrier systems of bioactive substances. Polyelectrolyte complexes (PECs) are formed through electrostatic interactions, and though they are significantly below of the covalent linkages in their strength, these complexes are sufficiently stable owing to the association processes. The relative ease way of PECs formation makes from them a versatile tool for preparation of various materials, with properties that can be tuned by adjusting several parameters, such as the chemical composition and structure of polyelectrolytes, pH and ionic strength of solutions, temperature and post-treatment procedures. For example, protein-polyelectrolyte complexes (PPCs) are playing an important role in various chemical and biological processes, such as protein separation, enzyme stabilization and polymer drug delivery systems. The present investigation is focused on evaluation of the PPC formation between a synthetic polypeptide (poly(aspartic acid) – PAS) and a natural protein (bovine serum albumin - BSA). The PPC obtained from PAS and BSA in different ratio was investigated by corroboration of various techniques of characterization as: spectroscopy, microscopy, thermo-gravimetric analysis, DLS and zeta potential determination, measurements which were performed in static and/or dynamic conditions. The static contact angle of the sample films was also determined in order to evaluate the changes brought upon surface free energy of the prepared PPCs in interdependence with the complexes composition. The evolution of hydrodynamic diameter and zeta potential of the PPC, recorded in situ, confirm changes of both co-partners conformation, a 1/1 ratio between protein and polyelectrolyte being benefit for the preparation of a stable PPC. Also, the study evidenced the dependence of PPC formation on the temperature of preparation. Thus, at low temperatures the PPC is formed with compact structure, small dimension and hydrodynamic diameter, close to those of BSA. The behavior at thermal treatment of the prepared PPCs is in agreement with the composition of the complexes. From the contact angle determination results the increase of the PPC films cohesion, which is higher than that of BSA films. Also, a higher hydrophobicity corresponds to the new PPC films denoting a good adhesion of the red blood cells onto the surface of PSA/BSA interpenetrated systems. The SEM investigation evidenced as well the specific internal structure of PPC concretized in phases with different size and shape in interdependence with the interpolymer mixture composition.

Keywords: polyelectrolyte – protein complex, bovine serum albumin, poly(aspartic acid), self-assembly

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5256 A Study Problem and Needs Compare the Held of the Garment Industries in Nonthaburi and Bangkok Area

Authors: Thepnarintra Praphanphat

Abstract:

The purposes of this study were to investigate garment industry’s condition, problems, and need for assistance. The population of the study was 504 managers or managing directors of garment establishments finished apparel industrial manager and permission of the Department of Industrial Works 28, Ministry of Industry until January 1, 2012. In determining the sample size with the opening of the Taro Yamane finished at 95% confidence level is ± 5% deviation was 224 managers. Questionnaires were used to collect the data. Percentage, frequency, arithmetic mean, standard deviation, t-test, ANOVA, and LSD were used to analyze the data. It was found that most establishments were of a large size, operated in a form of limited company for more than 15 years most of which produced garments for working women. All investment was made by Thai people. The products were made to order and distributed domestically and internationally. The total sale of the year 2010, 2011, and 2012 was almost the same. With respect to the problems of operating the business, the study indicated, as a whole, by- aspects, and by-items, that they were at a high level. The comparison of the level of problems of operating garment business as classified by general condition showed that problems occurring in business of different sizes were, as a whole, not different. In taking aspects into consideration, it was found that the level of problem in relation to production was different; medium establishments had more problems in production than those of small and large sizes. According to the by-items analysis, five problems were found different; namely, problems concerning employees, machine maintenance, number of designers, and price competition. Such problems in the medium establishments were at a higher level than those in the small and large establishments. Regarding business age, the examination yielded no differences as a whole, by-aspects, and by-items. The statistical significance level of this study was set at .05.

Keywords: garment industry, garment, fashion, competitive enhancement project

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5255 Defect Modes in Multilayered Piezoelectric Structures

Authors: D. G. Piliposyan

Abstract:

Propagation of electro-elastic waves in a piezoelectric waveguide with finite stacks and a defect layer is studied using a modified transfer matrix method. The dispersion equation for a periodic structure consisting of unit cells made up from two piezoelectric materials with metallized interfaces is obtained. An analytical expression, for the transmission coefficient for a waveguide with finite stacks and a defect layer, that is found can be used to accurately detect and control the position of the passband within a stopband. The result can be instrumental in constructing a tunable waveguide made of layers of different or identical piezoelectric crystals and separated by metallized interfaces.

Keywords: piezoelectric layered structure, periodic phononic crystal, bandgap, bloch waves

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5254 Modification of Magneto-Transport Properties of Ferrimagnetic Mn₄N Thin Films by Ni Substitution and Their Magnetic Compensation

Authors: Taro Komori, Toshiki Gushi, Akihito Anzai, Taku Hirose, Kaoru Toko, Shinji Isogami, Takashi Suemasu

Abstract:

Ferrimagnetic antiperovskite Mn₄₋ₓNiₓN thin film exhibits both small saturation magnetization and rather large perpendicular magnetic anisotropy (PMA) when x is small. Both of them are suitable features for application to current induced domain wall motion devices using spin transfer torque (STT). In this work, we successfully grew antiperovskite 30-nm-thick Mn₄₋ₓNiₓN epitaxial thin films on MgO(001) and STO(001) substrates by MBE in order to investigate their crystalline qualities and magnetic and magneto-transport properties. Crystalline qualities were investigated by X-ray diffraction (XRD). The magnetic properties were measured by vibrating sample magnetometer (VSM) at room temperature. Anomalous Hall effect was measured by physical properties measurement system. Both measurements were performed at room temperature. Temperature dependence of magnetization was measured by VSM-Superconducting quantum interference device. XRD patterns indicate epitaxial growth of Mn₄₋ₓNiₓN thin films on both substrates, ones on STO(001) especially have higher c-axis orientation thanks to greater lattice matching. According to VSM measurement, PMA was observed in Mn₄₋ₓNiₓN on MgO(001) when x ≤ 0.25 and on STO(001) when x ≤ 0.5, and MS decreased drastically with x. For example, MS of Mn₃.₉Ni₀.₁N on STO(001) was 47.4 emu/cm³. From the anomalous Hall resistivity (ρAH) of Mn₄₋ₓNiₓN thin films on STO(001) with the magnetic field perpendicular to the plane, we found out Mr/MS was about 1 when x ≤ 0.25, which suggests large magnetic domains in samples and suitable features for DW motion device application. In contrast, such square curves were not observed for Mn₄₋ₓNiₓN on MgO(001), which we attribute to difference in lattice matching. Furthermore, it’s notable that although the sign of ρAH was negative when x = 0 and 0.1, it reversed positive when x = 0.25 and 0.5. The similar reversal occurred for temperature dependence of magnetization. The magnetization of Mn₄₋ₓNiₓN on STO(001) increases with decreasing temperature when x = 0 and 0.1, while it decreases when x = 0.25. We considered that these reversals were caused by magnetic compensation which occurred in Mn₄₋ₓNiₓN between x = 0.1 and 0.25. We expect Mn atoms of Mn₄₋ₓNiₓN crystal have larger magnetic moments than Ni atoms do. The temperature dependence stated above can be explained if we assume that Ni atoms preferentially occupy the corner sites, and their magnetic moments have different temperature dependence from Mn atoms at the face-centered sites. At the compensation point, Mn₄₋ₓNiₓN is expected to show very efficient STT and ultrafast DW motion with small current density. What’s more, if angular momentum compensation is found, the efficiency will be best optimized. In order to prove the magnetic compensation, X-ray magnetic circular dichroism will be performed. Energy dispersive X-ray spectrometry is a candidate method to analyze the accurate composition ratio of samples.

Keywords: compensation, ferrimagnetism, Mn₄N, PMA

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5253 Computationally Efficient Electrochemical-Thermal Li-Ion Cell Model for Battery Management System

Authors: Sangwoo Han, Saeed Khaleghi Rahimian, Ying Liu

Abstract:

Vehicle electrification is gaining momentum, and many car manufacturers promise to deliver more electric vehicle (EV) models to consumers in the coming years. In controlling the battery pack, the battery management system (BMS) must maintain optimal battery performance while ensuring the safety of a battery pack. Tasks related to battery performance include determining state-of-charge (SOC), state-of-power (SOP), state-of-health (SOH), cell balancing, and battery charging. Safety related functions include making sure cells operate within specified, static and dynamic voltage window and temperature range, derating power, detecting faulty cells, and warning the user if necessary. The BMS often utilizes an RC circuit model to model a Li-ion cell because of its robustness and low computation cost among other benefits. Because an equivalent circuit model such as the RC model is not a physics-based model, it can never be a prognostic model to predict battery state-of-health and avoid any safety risk even before it occurs. A physics-based Li-ion cell model, on the other hand, is more capable at the expense of computation cost. To avoid the high computation cost associated with a full-order model, many researchers have demonstrated the use of a single particle model (SPM) for BMS applications. One drawback associated with the single particle modeling approach is that it forces to use the average current density in the calculation. The SPM would be appropriate for simulating drive cycles where there is insufficient time to develop a significant current distribution within an electrode. However, under a continuous or high-pulse electrical load, the model may fail to predict cell voltage or Li⁺ plating potential. To overcome this issue, a multi-particle reduced-order model is proposed here. The use of multiple particles combined with either linear or nonlinear charge-transfer reaction kinetics enables to capture current density distribution within an electrode under any type of electrical load. To maintain computational complexity like that of an SPM, governing equations are solved sequentially to minimize iterative solving processes. Furthermore, the model is validated against a full-order model implemented in COMSOL Multiphysics.

Keywords: battery management system, physics-based li-ion cell model, reduced-order model, single-particle and multi-particle model

Procedia PDF Downloads 113
5252 Government Payments to Minority American Producers

Authors: Anil K. Giri, Dipak Subedi, Kathleen Kassel, Ashok Mishra

Abstract:

The United States Department of Agriculture’s programs has been accused of being discriminatory in the past based on the race of the farmer, especially African-American producers. This study examines if there was racial discrimination in payments from the most recent new USDA programs, including those made in response to the pandemic. This study uses the Analysis of Variance (ANOVA) to examine the payments after normalizing them relative to cash receipts to test if discrimination in the number of payments received exists. Three programs investigated in this study are: i) the Coronavirus Food Assistance Program (CFAP), ii) the Market Facilitation Program (MFP), and (iii) the Paycheck Protection Program (PPP). The PPP program was administered by the Small Business Administration, whereas the other two were designed and implemented by the USDA. The PPP made forgivable loans to small businesses and, initially, was heavily criticized for not reaching minority businesses (in general). The Small Business Administration then initiated a second draw of PPP loans, prioritizing minority-owned businesses. This study compares attributes of PPP loans made to African-American farming businesses and other farming businesses in the two draws of the PPP. We find that the number of African-American farming businesses participating in the second draw of PPP loans decreased significantly from the first draw. However, the average amount of PPP loans to African-American farming businesses increased in the second draw. In the first draw, the average cost of jobs reported per loan was higher for African-American farming businesses than for other producers. In the second draw, the average cost of jobs reported per loan was significantly higher for other farming businesses than for African-American businesses. The share of PPP loans forgiven for African-American farming businesses is significantly below the national rate of 89 percent. The rate of forgiveness for PPP loans made to African-American producers is unlikely to increase significantly without policy changes. This can increase financial burdens in the future to farm operations operated by African- Americans. Finally, we conclude that the initial goal of increasing minority participation in PPP loans in the second draw, at least among African-Americans in the agricultural sector, did not meet. CFAP made almost $600 million in direct payments to minority producers, including Black producers. Black or African American producers received more than $52 million in CFAP payments. CFAP payments were proportional to the value of agricultural commodities sold for most minority producers. The 2017 Census of Agriculture showed that the majority of minority producers, including African American producers but excluding Asian producers, raised livestock. CFAP made the highest payments to livestock minority producers.

Keywords: United States department of agriculture (USDA), coronavirus food assistance program (CFAP), paycheck protection program (PPP), African-American producers, minority American producers

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5251 Anti-Acanthamoeba Activities of Fatty Acid Salts and Fatty Acids

Authors: Manami Masuda, Mariko Era, Takayoshi Kawahara, Takahide Kanyama, Hiroshi Morita

Abstract:

Objectives: Fatty acid salts are a type of anionic surfactant and are produced from fatty acids and alkali. Moreover, fatty acid salts are known to have potent antibacterial activities. Acanthamoeba is ubiquitously distributed in the environment including sea water, fresh water, soil and even from the air. Although generally free-living, Acanthamoeba can be an opportunistic pathogen, which could cause a potentially blinding corneal infection known as Acanthamoeba keratitis. So, in this study, we evaluated the anti-amoeba activity of fatty acid salts and fatty acids to Acanthamoeba castellanii ATCC 30010. Materials and Methods: The antibacterial activity of 9 fatty acid salts (potassium butyrate (C4K), caproate (C6K), caprylate (C8K), caprate (C10K), laurate (C12K), myristate (C14K), oleate (C18:1K), linoleate (C18:2K), linolenate (C18:3K)) tested on cells of Acanthamoeba castellanii ATCC 30010. Fatty acid salts (concentration of 175 mM and pH 10.5) were prepared by mixing the fatty acid with the appropriate amount of KOH. The amoeba suspension mixed with KOH with a pH adjusted solution was used as the control. Fatty acids (concentration of 175 mM) were prepared by mixing the fatty acid with Tween 80 (20 %). The amoeba suspension mixed with Tween 80 (20 %) was used as the control. The anti-amoeba method, the amoeba suspension (3.0 × 104 cells/ml trophozoites) was mixed with the sample of fatty acid potassium (final concentration of 175 mM). Samples were incubated at 30°C, for 10 min, 60 min, and 180 min and then the viability of A. castellanii was evaluated using plankton counting chamber and trypan blue stainings. The minimum inhibitory concentration (MIC) against Acanthamoeba was determined using the two-fold dilution method. The MIC was defined as the minimal anti-amoeba concentration that inhibited visible amoeba growth following incubation (180 min). Results: C8K, C10K, and C12K were the anti-amoeba effect of 4 log-unit (99.99 % growth suppression of A. castellanii) incubated time for 180 min against A. castellanii at 175mM. After the amoeba, the suspension was mixed with C10K or C12K, destroying the cell membrane had been observed. Whereas, the pH adjusted control solution did not exhibit any effect even after 180 min of incubation with A. castellanii. Moreover, C6, C8, and C18:3 were the anti-amoeba effect of 4 log-unit incubated time for 60 min. C4 and C18:2 exhibited a 4-log reduction after 180 min incubation. Furthermore, the minimum inhibitory concentration (MIC) was determined. The MIC of C10K, C12K and C4 were 2.7 mM. These results indicate that C10K, C12K and C4 have high anti-amoeba activity against A. castellanii and suggest C10K, C12K and C4 have great potential for antimi-amoeba agents.

Keywords: Fatty acid salts, anti-amoeba activities, Acanthamoeba, fatty acids

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5250 Photoluminescence in Cerium Doped Fluorides Prepared by Slow Precipitation Method

Authors: Aarti Muley, S. J. Dhoblae

Abstract:

CaF₂ and BaF₂ doped with cerium were prepared by slow precipitation method with different molar concentration and different cerium concentration. Both the samples were also prepared by direct method for comparison. The XRD of BaF₂:Ce shows that it crystallizes to BCC structure. The peak matches with JCPDS file no. 4-0452. Also, The XRD pattern of CaF₂:Ce matches well with the JCPDS file number 75- 0363 and crystallized to BCC phase. In CaF₂, the double-humped photoluminescence spectra were observed at 320nm and 340nm when the sample was prepared by the direct precipitation method, and the ratio between these peaks is unity. However when the sample prepared by slow precipitation method the double-humped emission spectra of CaF₂:Ce was observed at 323nm and 340nm. The ratio between these peaks is 0.58, and the optimum concentration is obtained for 0.1 molar CaF₂ with Ce concentration 1.5%. When the cerium concentration is increased by 2% the peak at 323nm vanishes, and the emission was observed at 342nm with the shoulder at 360nm. In this case, the intensity reduces drastically. The excitation is observed at 305nm with a small peak at 254nm. One molar BaF₂ doped with 0.1% of cerium was synthesized by direct precipitation method gives double humped spectra at 308nm and 320nm, when it is prepared with slow precipitation method with the cerium concentration 0.05m%, 0.1m%, 0.15m%, 0.2m% the broad emission is observed around 325nm with the shoulder at 350nm. The excitation spectra are narrow and observed at 290nm. As the percentage of cerium is increased further again shift is observed. The emission spectra were observed at 360nm with a small peak at 330nm. The phenomenon of shifting of emission spectra at low concentration of cerium can directly relate with the particle size and reported for nanomaterials also.

Keywords: calcium fluoride, barium fluoride, photoluminescence, slow precipitation method

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5249 Scalable and Accurate Detection of Pathogens from Whole-Genome Shotgun Sequencing

Authors: Janos Juhasz, Sandor Pongor, Balazs Ligeti

Abstract:

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

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

Procedia PDF Downloads 138