Search results for: electron-hole pairs

Authors: Qi Liu, Jiqin Yao, Xiaohu Zhou, Bo Zheng

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The first artificial cell was produced by Thomas Chang in the 1950s when he was trying to make a mimic of red blood cells. Since then, many different types of artificial cells have been constructed from one of the two approaches: a so-called bottom-up approach, which aims to create a cell from scratch, and a top-down approach, in which genes are sequentially knocked out from organisms until only the minimal genome required for sustaining life remains. In this project, bottom-up approach was used to build a new cell-free expression system which mimics artificial cell that capable of protein expression and communicate with each other. The artificial cells constructed from the bottom-up approach are usually lipid vesicles, polymersomes, hydrogels or aqueous droplets containing the nucleic acids and transcription-translation machinery. However, lipid vesicles based artificial cells capable of communication present several issues in the cell communication research: (1) The lipid vesicles normally lose the important functions such as protein expression within a few hours. (2) The lipid membrane allows the permeation of only small molecules and limits the types of molecules that can be sensed and released to the surrounding environment for chemical communication; (3) The lipid vesicles are prone to rupture due to the imbalance of the osmotic pressure. To address these issues, the hydrogel-based artificial cells were constructed in this work. To construct the artificial cell, polyacrylamide hydrogel was functionalized with Acrylate PEG Succinimidyl Carboxymethyl Ester (ACLT-PEG2000-SCM) moiety on the polymer backbone. The proteinaceous factors can then be immobilized on the polymer backbone by the reaction between primary amines of proteins and N-hydroxysuccinimide esters (NHS esters) of ACLT-PEG2000-SCM, the plasmid template and ribosome were encapsulated inside the hydrogel particles. Because the artificial cell could continuously express protein with the supply of nutrients and energy, the artificial cell-artificial cell communication and artificial cell-natural cell communication could be achieved by combining the artificial cell vector with designed plasmids. The plasmids were designed referring to the quorum sensing (QS) system of bacteria, which largely relied on cognate acyl-homoserine lactone (AHL) / transcription pairs. In one communication pair, “sender” is the artificial cell or natural cell that can produce AHL signal molecule by synthesizing the corresponding signal synthase that catalyzed the conversion of S-adenosyl-L-methionine (SAM) into AHL, while the “receiver” is the artificial cell or natural cell that can sense the quorum sensing signaling molecule form “sender” and in turn express the gene of interest. In the experiment, GFP was first immobilized inside the hydrogel particle to prove that the functionalized hydrogel particles could be used for protein binding. After that, the successful communication between artificial cell-artificial cell and artificial cell-natural cell was demonstrated, the successful signal between artificial cell-artificial cell or artificial cell-natural cell could be observed by recording the fluorescence signal increase. The hydrogel-based artificial cell designed in this work can help to study the complex communication system in bacteria, it can also be further developed for therapeutic applications.

Keywords: artificial cell, cell-free system, gene circuit, synthetic biology

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Authors: Lucia Liu, Matthew Koziol

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Obsessive-compulsive disorder (OCD), a long-lasting anxiety disorder involving recurrent, intrusive thoughts, affects over 2 million adults in the United States. Transcranial magnetic stimulation (TMS) stands out as a noninvasive, cutting-edge therapy that has been shown to reduce symptoms in patients with treatment-resistant OCD. The Food and Drug Administration (FDA) approved protocol pairs TMS sessions with individualized symptom provocation, aiming to improve the susceptibility of brain circuits to stimulation. However, limited standardization or guidance exists on how to conduct symptom provocation and which methods are most effective. This study aims to compare the effect of internal versus external techniques to induce obsessional stress in a clinical setting during TMS therapy. Two symptom provocation methods, (i) Asking patients thought-provoking questions about their obsessions (internal) and (ii) Requesting patients to perform obsession-related tasks (external), were employed in a crossover design with repeated measurement. Thirty-six treatments of NeuroStar TMS were administered to each of two patients over 8 weeks in an outpatient clinic. Patient One received 18 sessions of internal provocation followed by 18 sessions of external provocation, while Patient Two received 18 sessions of external provocation followed by 18 sessions of internal provocation. The primary outcome was the level of self-reported obsessional stress on a visual analog scale from 1 to 10. The secondary outcome was self-reported OCD severity, collected biweekly in a four-level Likert-scale (1 to 4) of bad, fair, good and excellent. Outcomes were compared and tested between provocation arms through repeated measures ANOVA, accounting for intra-patient correlations. Ages were 42 for Patient One (male, White) and 57 for Patient Two (male, White). Both patients had similar moderate symptoms at baseline, as determined through the Yale-Brown Obsessive Compulsive Scale (YBOCS). When comparing obsessional stress induced across the two arms of internal and external provocation methods, the mean (SD) was 6.03 (1.18) for internal and 4.01 (1.28) for external strategies (P=0.0019); ranges were 3 to 8 for internal and 2 to 8 for external strategies. Internal provocation yielded 5 (31.25%) bad, 6 (33.33%) fair, 3 (18.75%) good, and 2 (12.5%) excellent responses for OCD status, while external provocation yielded 5 (31.25%) bad, 9 (56.25%) fair, 1 (6.25%) good, and 1 (6.25%) excellent responses (P=0.58). Internal symptom provocation tactics had a significantly stronger impact on inducing obsessional stress and led to better OCD status (non-significant). This could be attributed to the fact that answering questions may prompt patients to reflect more on their lived experiences and struggles with OCD. In the future, clinical trials with larger sample sizes are warranted to validate this finding. Results support the increased integration of internal methods into structured provocation protocols, potentially reducing the time required for provocation and achieving greater treatment response to TMS.

Keywords: obsessive-compulsive disorder, transcranial magnetic stimulation, mental health, symptom provocation

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Authors: Sukhvinder Kaur, Ashok Agarwal

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Background: For the first time in 2009, India was able to generate estimates of HIV incidence (the number of new HIV infections per year). Analysis of epidemic projections helped in revealing that the number of new annual HIV infections in India had declined by more than 50% during the last decade (GOI Ministry of Health and Family Welfare, 2010). Then, National AIDS Control Organisation (NACO) planned to scale up its efforts in generating projections through epidemiological analysis and modelling by taking recent available sources of evidence such as HIV Sentinel Surveillance (HSS), India Census data and other critical data sets. Recently, NACO generated current round of HIV estimates-2012 through globally recommended tool “Spectrum Software” and came out with the estimates for adult HIV prevalence, annual new infections, number of people living with HIV, AIDS-related deaths and treatment needs. State level prevalence and incidence projections produced were used to project consequences of the epidemic in spectrum. In presence of HIV estimates generated at state level in India by NACO, USIAD funded PIPPSE project under the leadership of NACO undertook the estimations and projections to district level using same Spectrum software. In 2011, adult HIV prevalence in one of the high prevalent States, Maharashtra was 0.42% ahead of the national average of 0.27%. Considering the heterogeneity of HIV epidemic between districts, two districts of Maharashtra – Thane and Mumbai were selected to estimate and project the number of People-Living-with-HIV/AIDS (PLHIV), HIV-prevalence among adults and annual new HIV infections till 2017. Methodology: Inputs in spectrum included demographic data from Census of India since 1980 and sample registration system, programmatic data on ‘Alive and on ART (adult and children)’,‘Mother-Baby pairs under PPTCT’ and ‘High Risk Group (HRG)-size mapping estimates’, surveillance data from various rounds of HSS, National Family Health Survey–III, Integrated Biological and Behavioural Assessment and Behavioural Sentinel Surveillance. Major Findings: Assuming current programmatic interventions in these districts, an estimated decrease of 12% points in Thane and 31% points in Mumbai among new infections in HRGs and migrants is observed from 2011 by 2017. Conclusions: Project also validated decrease in HIV new infection among one of the high risk groups-FSWs using program cohort data since 2012 to 2016. Though there is a decrease in HIV prevalence and new infections in Thane and Mumbai, further decrease is possible if appropriate programme response, strategies and interventions are envisaged for specific target groups based on this evidence. Moreover, evidence need to be validated by other estimation/modelling techniques; and evidence can be generated for other districts of the state, where HIV prevalence is high and reliable data sources are available, to understand the epidemic within the local context.

Keywords: HIV sentinel surveillance, high risk groups, projections, new infections

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Authors: Jessie Rapoza, Petr Moroshkin, Jimmy Xu

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Chirality is omnipresent, in nature, in life, and in the field of physics. One intriguing example is the homochirality that has remained a great secret of life. Another is the pairs of mirror-image molecules – enantiomers. They are identical in atomic composition and therefore indistinguishable in the scalar physical properties. Yet, they can be either therapeutic or toxic, depending on their chirality. Recent studies suggest a potential link between abnormal levels of certain D-amino acids and some serious health impairments, including schizophrenia, amyotrophic lateral sclerosis, and potentially cancer. Although indistinguishable in their scalar properties, the chirality of a molecule reveals itself in interaction with the surrounding of a certain chirality, or more generally, a broken mirror-symmetry. In this work, we report on a system for chiral molecule detection, in which the mirror-symmetry is doubly broken, first by asymmetric structuring a nanopatterned plasmonic surface than by the incidence of circularly polarized light (CPL). In this system, the incident circularly-polarized light induces a surface plasmon polariton (SPP) wave, propagating along the asymmetric plasmonic surface. This SPP field itself is chiral, evanescently bound to a near-field zone on the surface (~10nm thick), but with an amplitude greatly intensified (by up to 104) over that of the incident light. It hence probes just the molecules on the surface instead of those in the volume. In coupling to molecules along its path on the surface, the chiral SPP wave favors one chirality over the other, allowing for chirality detection via the change in an optical rectification current measured at the edges of the sample. The asymmetrically structured surface converts the high-frequency electron plasmonic-oscillations in the SPP wave into a net DC drift current that can be measured at the edge of the sample via the mechanism of optical rectification. The measured results validate these design concepts and principles. The observed optical rectification current exhibits a clear differentiation between a pair of enantiomers. Experiments were performed by focusing a 1064nm CW laser light at the sample - a gold grating microchip submerged in an approximately 1.82M solution of either L-arabinose or D-arabinose and water. A measurement of the current output was then recorded under both rights and left circularly polarized lights. Measurements were recorded at various angles of incidence to optimize the coupling between the spin-momentums of the incident light and that of the SPP, that is, spin-momentum locking. In order to suppress the background, the values of the photocurrent for the right CPL are subtracted from those for the left CPL. Comparison between the two arabinose enantiomers reveals a preferential signal response of one enantiomer to left CPL and the other enantiomer to right CPL. In sum, this work reports on the first experimental evidence of the feasibility of chiral molecule detection via optical rectification in a metal meta-grating. This nanoscale interfaced electrical detection technology is advantageous over other detection methods due to its size, cost, ease of use, and integration ability with read-out electronic circuits for data processing and interpretation.

Keywords: Chirality, detection, molecule, spin

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Authors: Adriana Salgado, Sandra Castaneda, Ivan Perez

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Learning to read and write is a complex process involving several cognitive skills, contextual, and cultural environments. The basis of this development is linguistic skills, such as the ability to name and understand vocabulary, retell a story, phonological awareness, letter knowledge, among others. In children with autism spectrum disorder (ASD), one of the main concerns is related to language disorders. Nevertheless, most of the children with ASD are able to decode written information but have difficulties in reading comprehension. The research of these processes in the Spanish-speaking population is limited. However, the increasing prevalence of this diagnosis (1 in 115 children) in Mexico has implications at different levels. Educational research is an important area of interest in ASD children, such as emergent literacy. Reading and writing expand the possibilities of academic, cultural, and social information access. Taking this information into account, the objective of this research was to identify the relationship between language skills, alphabet knowledge, phonological awareness, and early reading and writing in ASD Spanish-speaking children. The method used for this research was based on tasks that were selected, adapted and in some cases designed to measure initial reading and writing, as well as language skills (naming, receptive vocabulary, and narrative skills), phonological awareness (similar phonological word pairs, beginning sound awareness and spelling) and letter knowledge, in a sample of 45 children (38 boys and 7 girls) with prior diagnosis of ASD. Descriptive analyses, as well as bivariate correlations, cluster analysis, and canonical correspondence, were obtained for the data results. Results showed that variability was large; however, it was possible to characterize the sample in low, medium, and high score groups regarding children performance. The low score group (46.7% of the sample), had a null or deficient performance in language skills and phonological awareness, some could identify up to five letters of the alphabet, showed no early reading skills but they could scribble. The middle score group was characterized by a highly variable performance in different tasks, with better language skills in receptive and naming vocabulary, some narrative, letter knowledge, and phonological awareness (beginning sound awareness) skills. The high score group, (24.4% of the sample) had the best performance in language skills in relation to the sample data, as well as in the rest of the measured skills. Finally, scores were canonically correlated between naming, receptive vocabulary, narrative, phonological awareness, letter knowledge and initial learning of reading and writing skills for the high score group and letter knowledge, naming and receptive vocabulary for the lower score group, which is consistent with previous research in typical and ASD children. In conclusion, the obtained data is consistent with previous studies. Despite large variability, it was possible to identify performance profiles and relations based on linguistic, phonological awareness, and letter knowledge skills. These skills were predictor variables of the initial development of reading and writing. The above has implications for a future program and strategies development that may benefit the acquisition of reading and writing in ASD children.

Keywords: autism, autism spectrum disorders, early literacy, emergent literacy

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Authors: Kaomud Tyagi, Rajasree Chakraborty, Shantanu Kundu, Devkant Singha, Kailash Chandra, Vikas Kumar

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The melon thrips, Thrips palmi is a serious pest of a wide range of agriculture crops and also act as vectors for plant viruses (genus Tospovirus, family Bunyaviridae). More molecular data on this species is required to understand the cryptic speciation and evolutionary affiliations. Mitochondrial genomes have been widely used in phylogenetic and evolutionary studies in insect. So far, mitogenomes of five thrips species (Anaphothrips obscurus, Frankliniella intonsa, Frankliniella occidentalis, Scirtothrips dorsalis and Thrips imaginis) is available in the GenBank database. In this study, we sequenced the first complete mitogenome T. palmi and compared it with available thrips mitogenomes. We assembled the mitogenome from the whole genome sequencing data generated using Illumina Hiseq2500. Annotation was performed using MITOS web-server to estimate the location of protein coding genes (PCGs), transfer RNA (tRNAs), ribosomal RNAs (rRNAs) and their secondary structures. The boundaries of PCGs and rRNAs was confirmed manually in NCBI. Phylogenetic analyses were performed using the 13 PCGs data using maximum likelihood (ML) in PAUP, and Bayesian inference (BI) in MrBayes 3.2. The complete mitogenome of T. palmi was 15,333 base pairs (bp), which was greater than the genomes of A. obscurus (14,890bp), F. intonsa (15,215 bp), F. occidentalis (14,889 bp) and S. dorsalis South Asia strain (SA1) (14,283 bp), but smaller than the genomes of T. imaginis (15,407 bp) and S. dorsalis East Asia strain (EA1) (15,343bp). Like in other thrips species, the mitochondrial genome of T. palmi was represented by 37 genes, including 13 PCGs, large and small ribosomal RNA (rrnL and rrnS) genes, 22 transfer RNA (tRNAs) genes (with one extra gene for trn-Serine) and two A+T-rich control regions (CR1 and CR2). Thirty one genes were observed on heavy (H) strand and six genes on the light (L) strand. The six tRNA genes (trnG,trnK, trnY, trnW, trnF, and trnH) were found to be conserved in all thrips species mitogenomes in their locations relative to a protein-coding or rRNA gene upstream or downstream. The gene arrangements of T. palmi is very close to T. imaginis except the rearrangements in tRNAs genes: trnR (arginine), and trnE (glutamic acid) were found to be located between cox3 and CR2 in T. imaginis which were translocated between atp6 and CR1 in T. palmi; trnL1 (Leucine) and trnS1(Serine) were located between atp6 and CR1 in T. imaginis which were translocated between cox3 and CR2 in T. palmi. The location of CR1 upstream of nad5 gene was suggested to be ancestral condition of the thrips species in subfamily Thripinae, was also observed in T. palmi. Both the Maximum likelihood (ML) and Bayesian Inference (BI) phylogenetic trees generated resulted in similar topologies. The T. palmi was clustered with T. imaginis. We concluded that more molecular data on the diverse thrips species from different hierarchical level is needed, to understand the phylogenetic and evolutionary relationships among them.

Keywords: thrips, comparative mitogenomics, gene rearrangements, phylogenetic analysis

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Authors: Salima Bijapuri, Shweta Bhatbolan, Sejalben Patel

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Ergonomics concerns the fitting of the environment and the equipment to the worker. Ergonomic principles can be employed in different dimensions of the industrial sector. Participation of all the stakeholders is the key to the formulation of a multifaceted and comprehensive approach to lessen the burden of occupational hazards. Taking responsibility for one’s own work activities by acquiring sufficient knowledge and potential to influence the practices and outcomes is the basis of participatory ergonomics and even hastens the process to identify workplace hazards. The study was aimed to check how participatory ergonomics can be effective in the management of work-related musculoskeletal disorders. Method: A mega kitchen was identified in a twin city of Karnataka, India. Consent was taken, and the screening of workers was done using observation methods. Kitchen work was structured to include different tasks, which included preparation, cooking, distributing, and serving food, packing food to be delivered to schools, dishwashing, cleaning and maintenance of kitchen and equipment, and receiving and storing raw material. Total 100 workers attended the education session on participatory ergonomics and its role in implementing the correct ergonomic practices, thus preventing WRMSDs. Demographic details and baseline data on related musculoskeletal pain and discomfort were collected using the Nordic pain questionnaire and VAS score pre- and post-study. Monthly visits were made, and the education sessions were reiterated on each visit, thus reminding, correcting, and problem-solving of each worker. After 9 months with a total of 4 such education session, the post education data was collected. The software SPSS 20 was used to analyse the collected data. Results: The majority of them (78%), depending on the availability and feasibility, participated in the intervention workshops were arranged four times. The average age of the participants was 39 years. The percentage of female participants was 79.49%, and 20.51% of participants comprised of males. The Nordic Musculoskeletal Questionnaire (NMQ) showed that knee pain was the most commonly reported complaint (62%) from the last 12 months with a mean VAS of 6.27, followed by low back pain. Post intervention, the mean VAS Score was reduced significantly to 2.38. The comparison of pre-post scores was made using Wilcoxon matched pairs test. Upon enquiring, it was found that, the participants learned the importance of applying ergonomics at their workplace which inturn was beneficial for them to handle any problems arising at their workplace on their own with self confidence. Conclusion: The participatory ergonomics proved effective with workers of mega kitchen, and it is a feasible and practical approach. The advantage of the given study area was that it had a sophisticated and ergonomically designed workstation; thus it was the lack of education and practical knowledge to use these stations was of utmost need. There was a significant reduction in VAS scores with the implementation of changes in the working style, and the knowledge of ergonomics helped to decrease physical load and improve musculoskeletal health.

Keywords: ergonomic awareness session, mega kitchen, participatory ergonomics, work related musculoskeletal disorders

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Authors: Claudia Mertens, Amanda Shufflebarger

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Step one: What we know about effective learning for pupils with SEN: results of 2 systematic reviews: Before establishing principles and practices for teaching and learning of pupils with SEN, we need a good overview of the results of empirical studies conducted in the respective field. Therefore, two systematic reviews on the use of digital tools in inclusive and non-inclusive school settings were conducted - taking into consideration studies published in German: One systematic review included studies having undergone a peer review process, and the second included studies without peer review). The results (collaboration of two German universities) will be presented during the conference. Step two: Students’ results of a research lab on “inclusive media education”: On this basis, German students worked on “inclusive media education” in small research projects (duration: 1 year). They were “education majors” enrolled in a course on inclusive media education. They conducted research projects on topics ranging from smartboards in inclusive settings, digital media in gifted math education, Tik Tok in German as a Foreign Language education and many more. As part of their course, the German students created an academic conference poster. In the conference, the results of these research projects/papers are put into the context of the results of the systematic reviews. Step three: Global Classroom: The German students’ posters were critically discussed in a global classroom in cooperation with Indiana University East (USA) and Hamburg University (Germany) in the winter/spring term of 2022/2023. 15 students in Germany collaborated with 15 students at Indiana University East. The IU East student participants were enrolled in “Writing in the Arts and Sciences,” which is specifically designed for pre-service teachers. The joint work began at the beginning of the Spring 2023 semester in January 2023 and continued until the end of the Uni Hamburg semester in February 2023. Before January, Uni Hamburg students had been working on a research project individually or in pairs. Didactic Approach: Both groups of students posted a brief video or audio introduction to a shared Canvas discussion page. In the joint long synchronous session, the students discussed key content terms such as inclusion, inclusive, diversity, etc., with the help of prompt cards, and they compared how they understood or applied these terms differently. Uni Hamburg students presented drafts of academic posters. IU East students gave them specific feedback. After that, IU East students wrote brief reflections summarizing what they learned from the poster. After the class, small groups were expected to create a voice recording reflecting on their experiences. In their recordings, they examined critical incidents, highlighting what they learned from these incidents. Major results of the student research and of the global classroom collaboration can be highlighted during the conference. Results: The aggregated results of the two systematic reviews AND of the research lab/global classroom can now be a sound basis for 1) improving accessibility for students with SEN and 2) for adjusting teaching materials and concepts to the needs of the students with SEN - in order to create successful learning.

Keywords: digitalization, inclusion, inclusive media education, global classroom, systematic review

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Authors: Eric Bang

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Interactions between receptors and ligands are crucial for many essential biological processes, including neurotransmission and metabolism. Ligand-receptor analyses that examine cell behavior and interactions often utilize cell type-specific RNA expressions from single-cell RNA sequencing (scRNA-seq) data. Using CellPhoneDB, a public repository consisting of ligands, receptors, and ligand-receptor interactions, the cell-cell interactions were explored in a specific scRNA-seq dataset from kidney tissue and portrayed the results with dot plots and heat maps. Depending on the type of cell, each ligand-receptor pair was aligned with the interacting cell type and calculated the positori probabilities of these associations, with corresponding P values reflecting average expression values between the triads and their significance. Using single-cell data (sample kidney cell references), genes in the dataset were cross-referenced with ones in the existing CellPhoneDB dataset. For example, a gene such as Pleiotrophin (PTN) present in the single-cell data also needed to be present in the CellPhoneDB dataset. Using the single-cell transcriptomics data via slide-seq and reference data, the CellPhoneDB program defines cell types and plots them in different formats, with the two main ones being dot plots and heat map plots. The dot plot displays derived measures of the cell to cell interaction scores and p values. For the dot plot, each row shows a ligand-receptor pair, and each column shows the two interacting cell types. CellPhoneDB defines interactions and interaction levels from the gene expression level, so since the p-value is on a -log10 scale, the larger dots represent more significant interactions. By performing an interaction analysis, a significant interaction was discovered for myeloid and T-cell ligand-receptor pairs, including those between Secreted Phosphoprotein 1 (SPP1) and Fibronectin 1 (FN1), which is consistent with previous findings. It was proposed that an effective protocol would involve a filtration step where cell types would be filtered out, depending on which ligand-receptor pair is activated in that part of the tissue, as well as the incorporation of the CellPhoneDB data in a streamlined workflow pipeline. The filtration step would be in the form of a Python script that expedites the manual process necessary for dataset filtration. Being in Python allows it to be integrated with the CellPhoneDB dataset for future workflow analysis. The manual process involves filtering cell types based on what ligand/receptor pair is activated in kidney cells. One limitation of this would be the fact that some pairings are activated in multiple cells at a time, so the manual manipulation of the data is reflected prior to analysis. Using the filtration script, accurate sorting is incorporated into the CellPhoneDB database rather than waiting until the output is produced and then subsequently applying spatial data. It was envisioned that this would reveal wherein the cell various ligands and receptors are interacting with different cell types, allowing for easier identification of which cells are being impacted and why, for the purpose of disease treatment. The hope is this new computational method utilizing spatially explicit ligand-receptor association data can be used to uncover previously unknown specific interactions within kidney tissue.

Keywords: bioinformatics, Ligands, kidney tissue, receptors, spatial transcriptome

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Authors: Ahmed Elaksher, Islam Omar

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Accurate geometric relation algorithms are imperative in Earth and planetary satellite and aerial image processing, particularly for high-resolution images that are used for topographic mapping. Most of these satellites carry push-broom sensors. These sensors are optical scanners equipped with linear arrays of CCDs. These sensors have been deployed on most EOSs. In addition, the LROC is equipped with two push NACs that provide 0.5 meter-scale panchromatic images over a 5 km swath of the Moon. The HiRISE carried by the MRO and the HRSC carried by MEX are examples of push-broom sensor that produces images of the surface of Mars. Sensor models developed in photogrammetry relate image space coordinates in two or more images with the 3D coordinates of ground features. Rigorous sensor models use the actual interior orientation parameters and exterior orientation parameters of the camera, unlike approximate models. In this research, we generate a generic push-broom sensor model to process imageries acquired through linear array cameras and investigate its performance, advantages, and disadvantages in generating topographic models for the Earth, Mars, and the Moon. We also compare and contrast the utilization, effectiveness, and applicability of available photogrammetric techniques and softcopies with the developed model. We start by defining an image reference coordinate system to unify image coordinates from all three arrays. The transformation from an image coordinate system to a reference coordinate system involves a translation and three rotations. For any image point within the linear array, its image reference coordinates, the coordinates of the exposure center of the array in the ground coordinate system at the imaging epoch (t), and the corresponding ground point coordinates are related through the collinearity condition that states that all these three points must be on the same line. The rotation angles for each CCD array at the epoch t are defined and included in the transformation model. The exterior orientation parameters of an image line, i.e., coordinates of exposure station and rotation angles, are computed by a polynomial interpolation function in time (t). The parameter (t) is the time at a certain epoch from a certain orbit position. Depending on the types of observations, coordinates, and parameters may be treated as knowns or unknowns differently in various situations. The unknown coefficients are determined in a bundle adjustment. The orientation process starts by extracting the sensor position and, orientation and raw images from the PDS. The parameters of each image line are then estimated and imported into the push-broom sensor model. We also define tie points between image pairs to aid the bundle adjustment model, determine the refined camera parameters, and generate highly accurate topographic maps. The model was tested on different satellite images such as IKONOS, QuickBird, and WorldView-2, HiRISE. It was found that the accuracy of our model is comparable to those of commercial and open-source software, the computational efficiency of the developed model is high, the model could be used in different environments with various sensors, and the implementation process is much more cost-and effort-consuming.

Keywords: photogrammetry, push-broom sensors, IKONOS, HiRISE, collinearity condition

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Authors: Yi H. Wong, Li L. Chan, Chee O. Leong, Stephen Ambu, Joon W. Mak, Priyadashi S. Sahu

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Background: Acanthamoeba is a free-living opportunistic protist which is ubiquitously distributed in the environment. Virulent Acanthamoeba can cause fatal encephalitis in immunocompromised patients and potential blinding keratitis in immunocompetent contact lens wearers. Approximately 24 species have been identified but only the A. castellanii, A. polyphaga and A. culbertsoni are commonly associated with human infections. Until to date, the precise molecular basis for Acanthamoeba pathogenesis remains unclear. Previous studies reported that Acanthamoeba virulence can be diminished through prolonged axenic culture but revived through serial mouse passages. As no clear explanation on this reversible pathogenesis is established, hereby, we postulate that the epigenetic regulators, DNA-methyltransferases (DNMT) and histone-deacetylases (HDAC), could possibly be involved in granting the virulence plasticity of Acanthamoeba spp. Methods: Four rounds of mouse passages were conducted to revive the virulence potential of the virulence-attenuated Acanthamoeba castellanii strain (ATCC 50492). Briefly, each mouse (n=6/group) was inoculated intraperitoneally with Acanthamoebae cells (2x 105 trophozoites/mouse) and incubated for 2 months. Acanthamoebae cells were isolated from infected mouse organs by culture method and subjected to subsequent mouse passage. In vitro cytopathic, encystment and gelatinolytic assays were conducted to evaluate the virulence characteristics of Acanthamoebae isolates for each passage. PCR primers which targeted on the 2 members (DNMT1 and DNMT2) and 5 members (HDAC1 to 5) of the DNMT and HDAC gene families respectively were custom designed. Quantitative real-time PCR (qPCR) was performed to detect and quantify the relative expression of the two gene families in each Acanthamoeba isolates. Beta-tubulin of A. castellanii (Genbank accession no: XP_004353728) was included as housekeeping gene for data normalisation. PCR mixtures were also analyzed by electrophoresis for amplicons detection. All statistical analyses were performed using the paired one-tailed Student’s t test. Results: Our pathogenicity tests showed that the virulence-reactivated Acanthamoeba had a higher degree of cytopathic effect on vero cells, a better resistance to encystment challenge and a higher gelatinolytic activity which was catalysed by serine protease. qPCR assay showed that DNMT1 expression was significantly higher in the virulence-reactivated compared to the virulence-attenuated Acanthamoeba strain (p ≤ 0.01). The specificity of primers which targeted on DNMT1 was confirmed by sequence analysis of PCR amplicons, which showed a 97% similarity to the published DNA-methyltransferase gene of A. castellanii (GenBank accession no: XM_004332804.1). Out of the five primer pairs which targeted on the HDAC family genes, only HDAC4 expression was significantly difference between the two variant strains. In contrast to DNMT1, HDAC4 expression was much higher in the virulence-attenuated Acanthamoeba strain. Conclusion: Our mouse passages had successfully restored the virulence of the attenuated strain. Our findings suggested that DNA-methyltransferase (DNMT1) and histone deacetylase (HDAC4) expressions are associated with virulence potential of Acanthamoeba spp.

Keywords: acanthamoeba, DNA-methyltransferase, histone deacetylase, virulence-associated proteins

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Authors: Osman Adiguzel

Abstract:

Shape-memory alloys are a new class of functional materials with a peculiar property known as shape memory effect. These alloys return to a previously defined shape on heating after deformation in low temperature product phase region and take place in a class of functional materials due to this property. The origin of this phenomenon lies in the fact that the material changes its internal crystalline structure with changing temperature. Shape memory effect is based on martensitic transitions, which govern the remarkable changes in internal crystalline structure of materials. Martensitic transformation, which is a solid state phase transformation, occurs in thermal manner in material on cooling from high temperature parent phase region. This transformation is governed by changes in the crystalline structure of the material. Shape memory alloys cycle between original and deformed shapes in bulk level on heating and cooling, and can be used as a thermal actuator or temperature-sensitive elements due to this property. Martensitic transformations usually occur with the cooperative movement of atoms by means of lattice invariant shears. The ordered parent phase structures turn into twinned structures with this movement in crystallographic manner in thermal induced case. The twinned martensites turn into the twinned or oriented martensite by stressing the material at low temperature martensitic phase condition. The detwinned martensite turns into the parent phase structure on first heating, first cycle, and parent phase structures turn into the twinned and detwinned structures respectively in irreversible and reversible memory cases. On the other hand, shape memory materials are very important and useful in many interdisciplinary fields such as medicine, pharmacy, bioengineering, metallurgy and many engineering fields. The choice of material as well as actuator and sensor to combine it with the host structure is very essential to develop main materials and structures. Copper based alloys exhibit this property in metastable beta-phase region, which has bcc-based structures at high temperature parent phase field, and these structures martensitically turn into layered complex structures with lattice twinning following two ordered reactions on cooling. Martensitic transition occurs as self-accommodated martensite with inhomogeneous shears, lattice invariant shears which occur in two opposite directions, <110 > -type directions on the {110}-type plane of austenite matrix which is basal plane of martensite. This kind of shear can be called as {110}<110> -type mode and gives rise to the formation of layered structures, like 3R, 9R or 18R depending on the stacking sequences on the close-packed planes of the ordered lattice. In the present contribution, x-ray diffraction and transmission electron microscopy (TEM) studies were carried out on two copper based alloys which have the chemical compositions in weight; Cu-26.1%Zn 4%Al and Cu-11%Al-6%Mn. X-ray diffraction profiles and electron diffraction patterns reveal that both alloys exhibit super lattice reflections inherited from parent phase due to the displacive character of martensitic transformation. X-ray diffractograms taken in a long time interval show that locations and intensities of diffraction peaks change with the aging time at room temperature. In particular, some of the successive peak pairs providing a special relation between Miller indices come close each other.

Keywords: Shape memory effect, martensite, twinning, detwinning, self-accommodation, layered structures

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Authors: Olga Smilevska Spasova, Katerina Boshkovska, Gorica Popova, Mirjana Popovska

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Introduction: Pneumonia is an infection of the pulmonary parenchyma. HPIV 3 is one of four viruses that is a member of the Paramyxoviridae family designated types 1-4 that have a nonsegmented, single-stranded RNA genome with a lipid-containing envelope. They are spread from the respiratory tract by aerosolized secretions or by direct contact with secretions. Type 3 is endemic and can cause serious illness in immunocompromised patients. Illness caused by parainfluenza occurs shortly after inoculation with the virus. The level of immunoglobulin A antibody in serum is the best predictor of susceptibility to infection. Streptococcus pneumonia or pneumococcus is a Gram-positive, spherical bacteria, usually found in pairs and it is a member of the genus Streptococcus. Streptococcus pneumonia resides asymptomatically in healthy carriers typically colonizing the respiratory tract, sinuses, and nasal cavity. In individuals with weaker immune systems like young infants, pneumococcal bacterium is the most common cause of community-acquired pneumonia in the world. Case Report: The aim is to present a case of lower respiratory tract infection in an infant caused by parainfluenza virus 3, S. pneumonia and undifferentiated gram-negative bacteria that was successfully treated. The infant is with a history of recurrent episodes of wheezing in the past 3mounts.Infant of 10months presents 2weeks before admittance with high fever, runny nose, and cough. The primary pediatrician prescribed oral cefpodoxime for 10days and inhaled salbutamol. Two days before admittance in hospital the infant with high fever, cough, and difficulty breathing. At admittance, infant is pale, anxious with rapid respirations, cough, wheezing and tachycardia. On auscultation: vesicular breathing sounds with high pitched wheezing and on the right coarse crackles. Investigations: Blood analysis: RBC: 4, 7 x1012L, WBC: 8,3x109L: Neut: 42.73% Lym: 41.57%, Hgb: 9.38 g/dl MCV: 62.7fl, MCH: 20.0pg MCHC: 31.8 g/dl RDW: 18.7% Plt-307.9 x109LCRP: 2,5mg/l, serum iron-7.92umol/l, O2sat-97% on blood gas analysis, puls-125/min.X-ray of chest with hyperinflationand right pericardial consolidation. Microbiological analysis of sputum sample is positive for undifferentiated gram-negative bacteria (colonizer)–resistant to cefotaxime, ampicillin, cefoxitin, sulfamet.+trimetoprim and sensitive to amikacin, gentamicin, and ciprofloxacin. Molecular multiplex RT-PCR for 19 viruses and multiplex PCR for 7 bacteria test for respiratory pathogens positive for Parainfluenza virus 3(Ct=22.73), Streptococcus pneumonia (Ct=26.75).IED: IgG-9.31g/l, IgA-0.351g/l, IgM-0.86g/l. Therapy: Treatment was started with inhaled salbutamol, intravenous antibiotic cefotaxime as well as systemic corticosteroids. On day 7 because of slow clinical resolution of chest auscultation findings and an etiologic clue with a positive sputum sample for resistant undifferentiated gram negative bacteria, a second intravenous antibiotic was administered amikacin. The infant is discharged on day 14 with resolution of clinical findings. Conclusion: Mixed co-infections with respiratory viruses and bacteria in immunocompromised infants are likely to lead to a more severe form of community acquired pneumonia that will need hospitalization.

Keywords: HPIV- 3, infant, pneumonia, S. pneumonia, x-ray chest

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Authors: Rachana Tank, Donald. M. Lyall, Kristin Flegal, Joey Ward, Jonathan Cavanagh

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Alzheimer’s research UK estimates by 2050, 2 million individuals will be living with Late Onset Alzheimer’s disease (LOAD). However, individuals experience considerable cognitive deficits and brain pathology over decades before reaching clinically diagnosable LOAD and studies have utilised gene candidate studies such as genome wide association studies (GWAS) and polygenic risk (PGR) scores to identify high risk individuals and potential pathways. This investigation aims to determine whether high genetic risk of LOAD is associated with worse brain MRI and cognitive performance in healthy older adults within the UK Biobank cohort. Previous studies investigating associations of PGR for LOAD and measures of MRI or cognitive functioning have focused on specific aspects of hippocampal structure, in relatively small sample sizes and with poor ‘controlling’ for confounders such as smoking. Both the sample size of this study and the discovery GWAS sample are bigger than previous studies to our knowledge. Genetic interaction between loci showing largest effects in GWAS have not been extensively studied and it is known that APOE e4 poses the largest genetic risk of LOAD with potential gene-gene and gene-environment interactions of e4, for this reason we  also analyse genetic interactions of PGR with the APOE e4 genotype. High genetic loading based on a polygenic risk score of 21 SNPs for LOAD is associated with worse brain MRI and cognitive outcomes in healthy individuals within the UK Biobank cohort. Summary statistics from Kunkle et al., GWAS meta-analyses (case: n=30,344, control: n=52,427) will be used to create polygenic risk scores based on 21 SNPs and analyses will be carried out in N=37,000 participants in the UK Biobank. This will be the largest study to date investigating PGR of LOAD in relation to MRI. MRI outcome measures include WM tracts, structural volumes. Cognitive function measures include reaction time, pairs matching, trail making, digit symbol substitution and prospective memory. Interaction of the APOE e4 alleles and PGR will be analysed by including APOE status as an interaction term coded as either 0, 1 or 2 e4 alleles. Models will be adjusted partially for adjusted for age, BMI, sex, genotyping chip, smoking, depression and social deprivation. Preliminary results suggest PGR score for LOAD is associated with decreased hippocampal volumes including hippocampal body (standardised beta = -0.04, P = 0.022) and tail (standardised beta = -0.037, P = 0.030), but not with hippocampal head. There were also associations of genetic risk with decreased cognitive performance including fluid intelligence (standardised beta = -0.08, P<0.01) and reaction time (standardised beta = 2.04, P<0.01). No genetic interactions were found between APOE e4 dose and PGR score for MRI or cognitive measures. The generalisability of these results is limited by selection bias within the UK Biobank as participants are less likely to be obese, smoke, be socioeconomically deprived and have fewer self-reported health conditions when compared to the general population. Lack of a unified approach or standardised method for calculating genetic risk scores may also be a limitation of these analyses. Further discussion and results are pending.

Keywords: Alzheimer's dementia, cognition, polygenic risk, MRI

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Authors: Alessandra Swiny, Michalis Georgiou, Yiorgos Hadjichristou

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This paper focuses on the questions raised through the work of Unit 5: ‘In/Out of crisis, emergent and adaptive’; an architectural research-based studio at the University of Nicosia. It focusses on sustainable architectural and urban explorations tackling with the ever growing crises in its various types, phases and locations. ‘Great crisis situations’ are seen as ‘great chances’ that trigger investigations for further development and evolution of the built environment in an ultimate sustainable approach. The crisis is taken as an opportunity to rethink the urban and architectural directions as new forces for inventions leading to emergent and adaptive built environments. The Unit 5’s identity and environment facilitates the students to respond optimistically, alternatively and creatively towards the global current crisis. Mark Wigley’s notion that “crises are ultimately productive” and “They force invention” intrigued and defined the premises of the Unit. ‘Weather and nature are coauthors of the built environment’ Jonathan Hill states in his ‘weather architecture’ discourse. The weather is constantly changing and new environments, the subnatures are created which derived from the human activities David Gissen explains. The above set of premises triggered innovative responses by the Unit’s students. They thoroughly investigated the various kinds of crisis and their causes in relation to their various types of Terrains. The tools used for the research and investigation were chosen in contradictive pairs to generate further crisis situations: The re-used/salvaged competed with the new, the handmade rivalling with the fabrication, the analogue juxtaposed with digital. Students were asked to delve into state of art technologies in order to propose sustainable emergent and adaptive architectures and Urbanities, having though always in mind that the human and the social aspects of the community should be the core of the investigation. The resulting unprecedented spatial conditions and atmospheres of the emergent new ways of living are deemed to be the ultimate aim of the investigation. Students explored a variety of sites and crisis conditions such as: The vague terrain of the Green Line in Nicosia, the lost footprints of the sinking Venice, the endangered Australian coral reefs, the earthquake torn town of Crevalcore, and the decaying concrete urbanscape of Athens. Among other projects, ‘the plume project’ proposes a cloud-like, floating and almost dream-like living environment with unprecedented spatial conditions to the inhabitants of the coal mine of Centralia, USA, not just to enable them to survive but even to prosper in this unbearable environment due to the process of the captured plumes of smoke and heat. Existing water wells inspire inversed vertical structures creating a new living underground network, protecting the nomads from catastrophic sand storms in the Araoune of Mali. “Inverted utopia: Lost things in the sand”, weaves a series of tea-houses and a library holding lost artifacts and transcripts into a complex underground labyrinth by the utilization of the sand solidification technology. Within this methodology, crisis is seen as a mechanism for allowing an emergence of new and fascinating ultimate sustainable future cultures and cities.

Keywords: adaptive built environments, crisis as opportunity, emergent urbanities, forces for inventions

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Authors: Osman Adiguzel

Abstract:

Shape memory alloys take place in a class of smart materials by exhibiting a peculiar property called the shape memory effect. This property is characterized by the recoverability of two certain shapes of material at different temperatures. These materials are often called smart materials due to their functionality and their capacity of responding to changes in the environment. Shape memory materials are used as shape memory devices in many interdisciplinary fields such as medicine, bioengineering, metallurgy, building industry and many engineering fields. The shape memory effect is performed thermally by heating and cooling after first cooling and stressing treatments, and this behavior is called thermoelasticity. This effect is based on martensitic transformations characterized by changes in the crystal structure of the material. The shape memory effect is the result of successive thermally and stress-induced martensitic transformations. Shape memory alloys exhibit thermoelasticity and superelasticity by means of deformation in the low-temperature product phase and high-temperature parent phase region, respectively. Superelasticity is performed by stressing and releasing the material in the parent phase region. Loading and unloading paths are different in the stress-strain diagram, and the cycling loop reveals energy dissipation. The strain energy is stored after releasing, and these alloys are mainly used as deformation absorbent materials in control of civil structures subjected to seismic events, due to the absorbance of strain energy during any disaster or earthquake. Thermal-induced martensitic transformation occurs thermally on cooling, along with lattice twinning with cooperative movements of atoms by means of lattice invariant shears, and ordered parent phase structures turn into twinned martensite structures, and twinned structures turn into the detwinned structures by means of stress-induced martensitic transformation by stressing the material in the martensitic condition. Thermal induced transformation occurs with the cooperative movements of atoms in two opposite directions, <110 > -type directions on the {110} - type planes of austenite matrix which is the basal plane of martensite. Copper-based alloys exhibit this property in the metastable β-phase region, which has bcc-based structures at high-temperature parent phase field. Lattice invariant shear and twinning is not uniform in copper-based ternary alloys and gives rise to the formation of complex layered structures, depending on the stacking sequences on the close-packed planes of the ordered parent phase lattice. In the present contribution, x-ray diffraction and transmission electron microscopy (TEM) studies were carried out on two copper-based CuAlMn and CuZnAl alloys. X-ray diffraction profiles and electron diffraction patterns reveal that both alloys exhibit superlattice reflections inherited from the parent phase due to the displacive character of martensitic transformation. X-ray diffractograms taken in a long time interval show that diffraction angles and intensities of diffraction peaks change with the aging duration at room temperature. In particular, some of the successive peak pairs providing a special relation between Miller indices come close to each other. This result refers to the rearrangement of atoms in a diffusive manner.

Keywords: shape memory effect, martensitic transformation, reversibility, superelasticity, twinning, detwinning

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Authors: Piotr Wadolowski, Grzegorz Krzesinski, Piotr Gutowski

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The aim of the presented work is to recognize the impact of mini-plate application approach on the stress and displacement within the stabilization devices and surrounding bones. The mini-plate osteosynthesis technique is widely used by craniofacial surgeons as an improved replacement of wire connection approach. Many different types of metal plates and screws are used to the physical connection of fractured bones. Below investigation is based on a clinical observation of patient hospitalized with mini-plate stabilization system. Analysis was conducted on a solid mandible geometry, which was modeled basis on the computed tomography scan of the hospitalized patient. In order to achieve most realistic connected system behavior, the cortical and cancellous bone layers were assumed. The temporomandibular joint was simplified to the elastic element to allow physiological movement of loaded bone. The muscles of mastication system were reduced to three pairs, modeled as shell structures. Finite element grid was created by the ANSYS software, where hexahedral and tetrahedral variants of SOLID185 element were used. A set of nonlinear contact conditions were applied on connecting devices and bone common surfaces. Properties of particular contact pair depend on screw - mini-plate connection type and possible gaps between fractured bone around osteosynthesis region. Some of the investigated cases contain prestress introduced to the mini-plate during the application, what responds the initial bending of the connecting device to fit the retromolar fossa region. Assumed bone fracture occurs within the mandible angle zone. Due to the significant deformation of the connecting plate in some of the assembly cases the elastic-plastic model of titanium alloy was assumed. The bone tissues were covered by the orthotropic material. As a loading were used the gauge force of magnitude of 100N applied in three different locations. Conducted analysis shows significant impact of mini-plate application methodology on the stress distribution within the miniplate. Prestress effect introduces additional loading, which leads to locally exceed the titanium alloy yield limit. Stress in surrounding bone increases rapidly around the screws application region, exceeding assumed bone yield limit, what indicate the local bone destruction. Approach with the doubled mini-plate shows increased stress within the connector due to the too rigid connection, where the main path of loading leads through the mini-plates instead of plates and connected bones. Clinical observations confirm more frequent plate destruction of stiffer connections. Some of them could be an effect of decreased low cyclic fatigue capability caused by the overloading. The executed analysis prove that the mini-plate system provides sufficient support to mandible fracture treatment, however, many applicable solutions shifts the entire system to the allowable material limits. The results show that connector application with the initial loading needs to be carefully established due to the small material capability tolerances. Comparison to the clinical observations allows optimizing entire connection to prevent future incidents.

Keywords: mandible fracture, mini-plate connection, numerical analysis, osteosynthesis

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Authors: Alejandra Martin-Dominguez, Javier Canto-Rios, Velitchko Tzatchkov

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Electrocoagulation is a water treatment technology that consists of generating coagulant species in situ by electrolytic oxidation of sacrificial anode materials triggered by electric current. It removes suspended solids, heavy metals, emulsified oils, bacteria, colloidal solids and particles, soluble inorganic pollutants and other contaminants from water, offering an alternative to the use of metal salts or polymers and polyelectrolyte addition for breaking stable emulsions and suspensions. The method essentially consists of passing the water being treated through pairs of consumable conductive metal plates in parallel, which act as monopolar electrodes, commonly known as ‘sacrificial electrodes’. Physicochemical, electrochemical and hydraulic processes are involved in the efficiency of this type of treatment. While the physicochemical and electrochemical aspects of the technology have been extensively studied, little is known about the influence of the hydraulics. However, the hydraulic process is fundamental for the reactions that take place at the electrode boundary layers and for the coagulant mixing. Electrocoagulation reactors can be open (with free water surface) and closed (pressurized). Independently of the type of rector, hydraulic head loss is an important factor for its design. The present work focuses on the study of the total hydraulic head loss and flow velocity and pressure distribution in electrocoagulation reactors with single or multiple concentric annular cross sections. An analysis of the head loss produced by hydraulic wall shear friction and accessories (minor head losses) is presented, and compared to the head loss measured on a semi-pilot scale laboratory model for different flow rates through the reactor. The tests included laminar, transitional and turbulent flow. The observed head loss was compared also to the head loss predicted by several known conceptual theoretical and empirical equations, specific for flow in concentric annular pipes. Four single concentric annular cross section and one multiple concentric annular cross section reactor configuration were studied. The theoretical head loss resulted higher than the observed in the laboratory model in some of the tests, and lower in others of them, depending also on the assumed value for the wall roughness. Most of the theoretical models assume that the fluid elements in all annular sections have the same velocity, and that flow is steady, uniform and one-dimensional, with the same pressure and velocity profiles in all reactor sections. To check the validity of such assumptions, a computational fluid dynamics (CFD) model of the concentric annular pipe reactor was implemented using the ANSYS Fluent software, demonstrating that pressure and flow velocity distribution inside the reactor actually is not uniform. Based on the analysis, the equations that predict better the head loss in single and multiple annular sections were obtained. Other factors that may impact the head loss, such as the generation of coagulants and gases during the electrochemical reaction, the accumulation of hydroxides inside the reactor, and the change of the electrode material with time, are also discussed. The results can be used as tools for design and scale-up of electrocoagulation reactors, to be integrated into new or existing water treatment plants.

Keywords: electrocoagulation reactors, hydraulic head loss, concentric annular pipes, computational fluid dynamics model

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Authors: Katarzyna Lubecka, Kirsty Flower, Megan Beetch, Lucinda Kurzava, Hannah Buvala, Samer Gawrieh, Suthat Liangpunsakul, Tracy Gonzalez, George McCabe, Naga Chalasani, James M. Flanagan, Barbara Stefanska

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Hepatocellular carcinoma (HCC), the most prevalent type of primary liver cancer, is the second leading cause of cancer death worldwide. Late onset of clinical symptoms in HCC results in late diagnosis and poor disease outcome. Approximately 85% of individuals with HCC have underlying liver cirrhosis. However, not all cirrhotic patients develop cancer. Reliable early detection biomarkers that can distinguish cirrhotic patients who will develop cancer from those who will not are urgently needed and could increase the cure rate from 5% to 80%. We used Illumina-450K microarray to test whether blood DNA, an easily accessible source of DNA, bear site-specific changes in DNA methylation in response to HCC before diagnosis with conventional tools (pre-diagnostic). Top 11 differentially methylated sites were selected for validation by pyrosequencing. The diagnostic potential of the 11 pyrosequenced probes was tested in blood samples from a prospective cohort of cirrhotic patients. We identified 971 differentially methylated CpG sites in pre-diagnostic HCC cases as compared with healthy controls (P < 0.05, paired Wilcoxon test, ICC ≥ 0.5). Nearly 76% of differentially methylated CpG sites showed lower levels of methylation in cases vs. controls (P = 2.973E-11, Wilcoxon test). Classification of the CpG sites according to their location relative to CpG islands and transcription start site revealed that those hypomethylated loci are located in regulatory regions important for gene transcription such as CpG island shores, promoters, and 5’UTR at higher frequency than hypermethylated sites. Among 735 CpG sites hypomethylated in cases vs. controls, 482 sites were assigned to gene coding regions whereas 236 hypermethylated sites corresponded to 160 genes. Bioinformatics analysis using GO, KEGG and DAVID knowledgebase indicate that differentially methylated CpG sites are located in genes associated with functions that are essential for gene transcription, cell adhesion, cell migration, and regulation of signal transduction pathways. Taking into account the magnitude of the difference, statistical significance, location, and consistency across the majority of matched pairs case-control, we selected 11 CpG loci corresponding to 10 genes for further validation by pyrosequencing. We established that methylation of CpG sites within 5 out of those 10 genes distinguish cirrhotic patients who subsequently developed HCC from those who stayed cancer free (cirrhotic controls), demonstrating potential as biomarkers of early detection in populations at risk. The best predictive value was detected for CpGs located within BARD1 (AUC=0.70, asymptotic significance ˂0.01). Using an additive logistic regression model, we further showed that 9 CpG loci within those 5 genes, that were covered in pyrosequenced probes, constitute a panel with high diagnostic accuracy (AUC=0.887; 95% CI:0.80-0.98). The panel was able to distinguish pre-diagnostic cases from cirrhotic controls free of cancer with 88% sensitivity at 70% specificity. Using blood as a minimally invasive material and pyrosequencing as a straightforward quantitative method, the established biomarker panel has high potential to be developed into a routine clinical test after validation in larger cohorts. This study was supported by Showalter Trust, American Cancer Society (IRG#14-190-56), and Purdue Center for Cancer Research (P30 CA023168) granted to BS.

Keywords: biomarker, DNA methylation, early detection, hepatocellular carcinoma

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Authors: Xue Bai, Ranran He, Chang Liu

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Care planning before the onset of intensive care needs can benefit older adults’ psychological well-being and increases families’ ability to manage caregiving crises and cope with care transitions. Effective care planning requires collaborative ‘team-work’ in families. However, future care planning has not been substantially examined in intergenerational or family contexts, let alone among immigrant families who have to face particular challenges in parental caregiving. From a family systems perspective, this study intends to explore the extent, processes, and contents of intergenerational care planning of Mainland immigrant ageing families in Hong Kong and to examine the intergenerational congruence and discrepancies in the care planning process. Adopting a qualitative research design, semi-structured in-depth interviews were conducted with 17 adult child-older parent pairs and another 33 adult children. In total, 50 adult children who migrated to Hong Kong after the age of 18 with more than three years’ work experience in Hong Kong had at least one parent aged over 55 years old who was not a Hong Kong resident and considered his/herself as the primary caregiver of the parent were recruited. Seventeen ageing parents of the recruited adult children were invited for dyadic interviews. Scarcity of caregiving resources in the context of cross-border migration, intergenerational discrepancies in care planning stages, both generations’ struggle and ambivalence toward filial care, intergenerational transmission of care values, and facilitating role of accumulated family capital in care preparation were primary themes concluded from participants’ narratives. Compared with ageing parents, immigrant adult children generally displayed lower levels of care planning. Although with a strong awareness of parents’ future care needs, few adult children were found engaged in concrete planning activities. This is largely due to their uncertainties toward future life and career, huge work and living pressure, the relatively good health status of their parents, and restrictions of public welfare policies in the receiving society. By contrast, children’s cross-border migration encouraged ageing parents to have early and clear preparation for future care. Ageing parents mostly expressed low filial care expectations when realizing the scarcity of family caregiving resources in the cross-border context. Even though they prefer in-person support from children, most of them prepare themselves for independent ageing to prioritize the next generation’s needs or choose to utilize paid services, welfare systems, friend networks, or extended family networks in their sending society. Adult children were frequently found caught in the dilemma of desiring to provide high quality and in-person support for their parents but lacking sufficient resources. Notably, a salient pattern of intergenerational transmission in terms of family and care values and ideal care arrangement emerged from intergenerational care preparation. Moreover, the positive role of accumulated family capital generated by a reunion in care preparation and joint decision-making were also identified. The findings of the current study will enhance professionals’ and service providers’ awareness of intergenerational care planning in cross-border migration contexts, inform services to alleviate unpreparedness for elderly care and intergenerational discrepancies concerning care arrangements and broaden family services to encompass intergenerational care planning interventions. Acknowledgment: This study is supported by a General Research Grant from the Research Grants Council of the HKSAR, China (Project Number: 15603818).

Keywords: intergenerational care planning, mainland immigrants in Hong Kong, migrant family, older adults

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Authors: Reham K. Sebaih, Afaf I. Shehata , Awatif A. Hindi, Tarek Gheith, Amal A. Hazzani Anas Al-Orjan

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Staphylococci spp are ubiquitous gram-positive bacteria is often associated with infections, especially nosocomial infections, and antibiotic resistanceStudy pathogenic bacteria and its use as a tool in the technology of Nano biology and molecular genetics research of the latest research trends of modern characterization and definition of different multiresistant of bacteria including Staphylococci. The Staphylococci are widespread all over the world and particularly in Saudi Arabia The present work study was conducted to evaluate the effect of five different types of nanoparticles (biosynthesized zinc oxide, Spherical and rod of each silver and gold nanoparticles) and their antibacterial impact on the Staphylococcus species. Ninety-six isolates of Staphylococcus species. Staphylococcus aureus, Staphylococcus epidermidis, MRSA were collected from different sources during the period between March 2011G to June 2011G. All isolates were isolated from inpatients and outpatients departments at Royal Commission Hospital in Yanbu Industrial, Saudi Arabia. High percentage isolation from males(55%) than females (45%). Staphylococcus epidermidis from males was (47%), (28%), and(25%). For Staphylococcus aureus and Methicillin-resistant Staphylococcus aureus (MRSA. Isolates from females were Staphylococcus aureus with higher percent of (47%), (30%), and (23%) for MRSA, Staphylococcus epidermidis. Staphylococcus aureus from wound swab were the highest percent (51.42%) followed by vaginal swab (25.71%). Staphylococcus epidermidis were founded with higher percentage in blood (37.14%) and wound swab (34.21%) respectively related to other. The highest percentage of methicillin-resistant Staphylococcus aureus (MRSA)(80.77%) were isolated from wound swab, while those from nostrils were (19.23%). Staphylococcus species were isolates in highest percentage from hospital Emergency department with Staphylococcus aureus (59.37%), Methicillin-resistant Staphylococcus aureus (MRSA) (28.13%)and Staphylococcus epidermidis (12.5%) respectively. Evaluate the antibacterial property of Zinc oxide, Silver, and Gold nanoparticles as an alternative to conventional antibacterial agents Staphylococci isolates from hospital sources we screened them. Gold and Silver rods Nanoparticles to be sensitive to all isolates of Staphylococcus species. Zinc oxide Nanoparticles gave sensitivity impact range(52%) and (48%). The Gold and Silver spherical nanoparticles did not showed any effect on Staphylococci species. Zinc Oxide Nanoparticles gave bactericidal impact (25%) and bacteriostatic impact (75%) for of Staphylococci species. Detecting the association of nanoparticles with Staphylococci isolates imaging by scanning electron microscope (SEM) of some bacteriostatic isolates for Zinc Oxide nanoparticles on Staphylococcus aureus, Staphylococcus epidermidis and Methicillin resistant Staphylococcus aureus(MRSA), showed some Overlapping Bacterial cells with lower their number and appearing some appendages with deformities in external shape. Molecular analysis was applied by Multiplex polymerase chain reaction (PCR) used for the identification of genes within Staphylococcal pathogens. A multiplex polymerase chain reaction (PCR) method has been developed using six primer pairs to detect different genes using 50bp and 100bp DNA ladder marker. The range of Molecular gene typing ranging between 93 bp to 326 bp for Staphylococcus aureus and Methicillin resistant Staphylococcus aureus by TSST-1,mecA,femA and eta, while the bands border were from 546 bp to 682 bp for Staphylococcus epidermidis using icaAB and atlE. Sixteen isolation of Staphylococcus aureus and Methicillin resistant Staphylococcus aureus were positive for the femA gene at 132bp,this allowed the using of this gene as an internal positive control, fifteen isolates of Staphylococcus aureus and Methicillin resistant Staphylococcus aureus were positive for mecA gene at163bp.This gene was responsible for antibiotic resistant Methicillin, Two isolates of Staphylococcus aureus and Methicillin resistant Staphylococcus aureus were positive for the TSST-1 gene at326bp which is responsible for toxic shock syndrome in some Staphylococcus species, None were positive for eta gene at 102bpto that was responsible for Exfoliative toxins. Six isolates of Staphylococcus epidermidis were positive for atlE gene at 682 bp which is responsible for the initial adherence, three isolates of Staphylococcus epidermidis were positive for icaAB gene at 546bp that are responsible for mediates the formation of the biofilm. In conclusion, this study demonstrates the ability of the detection of the genes to discriminate between infecting Staphylococcus strains and considered biological tests, they may potentiate the clinical criteria used for the diagnosis of septicemia or catheter-related infections.

Keywords: multiplex polymerase chain reaction, toxic shock syndrome, Staphylococcus aureus, nosocomial infections

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Authors: Savvas Rogotis, Nikolaos Kalatzis, Stergios Dimou-Sakellariou, Nikolaos Marianos

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As precision holds the key for the introduction of distinct benefits in agriculture (e.g., energy savings, reduced labor costs, optimal application of inputs, improved products, and yields), it steadily becomes evident that new initiatives should focus on rendering Precision Agriculture (PA) more accessible to the average farmer. PA leverages on technologies such as the Internet of Things (IoT), earth observation, robotics and positioning systems (e.g., the Global Navigation Satellite System – GNSS - as well as individual positioning systems like GPS, Glonass, Galileo) that allow: from simple data georeferencing to optimal navigation of agricultural machinery to even more complex tasks like Variable Rate Applications. An identified customer pain point is that, from one hand, typical triangulation-based positioning systems are not accurate enough (with errors up to several meters), while on the other hand, high precision positioning systems reaching centimeter-level accuracy, are very costly (up to thousands of euros). Within this paper, a Ground-Based Augmentation System (GBAS) is introduced, that can be adapted to any existing IoT field-sensing station infrastructure. The latter should cover a minimum set of requirements, and in particular, each station should operate as a fixed, obstruction-free towards the sky, energy supplying unit. Station augmentation will allow them to function in pairs with GNSS rovers following the differential GNSS base-rover paradigm. This constitutes a key innovation element for the proposed solution that encompasses differential GNSS capabilities into an IoT field-sensing infrastructure. Integrating this kind of information supports the provision of several additional PA beneficial services such as spatial mapping, route planning, and automatic field navigation of unmanned vehicles (UVs). Right at the heart of the designed system, there is a high-end GNSS toolkit with base-rover variants and Real-Time Kinematic (RTK) capabilities. The GNSS toolkit had to tackle all availability, performance, interfacing, and energy-related challenges that are faced for a real-time, low-power, and reliable in the field operation. Specifically, in terms of performance, preliminary findings exhibit a high rover positioning precision that can even reach less than 10-centimeters. As this precision is propagated to the full dataset collection, it enables tractors, UVs, Android-powered devices, and measuring units to deal with challenging real-world scenarios. The system is validated with the help of Gaiatrons, a mature network of agro-climatic telemetry stations with presence all over Greece and beyond ( > 60.000ha of agricultural land covered) that constitutes part of “gaiasense” (www.gaiasense.gr) smart farming (SF) solution. Gaiatrons constantly monitor atmospheric and soil parameters, thus, providing exact fit to operational requirements asked from modern SF infrastructures. Gaiatrons are ultra-low-cost, compact, and energy-autonomous stations with a modular design that enables the integration of advanced GNSS base station capabilities on top of them. A set of demanding pilot demonstrations has been initiated in Stimagka, Greece, an area with a diverse geomorphological landscape where grape cultivation is particularly popular. Pilot demonstrations are in the course of validating the preliminary system findings in its intended environment, tackle all technical challenges, and effectively highlight the added-value offered by the system in action.

Keywords: GNSS, GBAS, precision agriculture, RTK, smart farming

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Authors: F. Varga, Z. Liber, J. Jakše, A. Turudić, Z. Šatović, I. Radosavljević, N. Jeran, M. Grdiša

Abstract:

Dalmatian pyrethrum (Tanacetum cinerariifolium (Trevir.) Sch. Bip.; Asteraceae), a source of the commercially dominant plant insecticide pyrethrin, is a species endemic to the eastern Adriatic. Genetic diversity of T. cinerariifolium was previously studied using amplified fragment length polymorphism (AFLP) markers. However, microsatellite markers (single sequence repeats - SSRs) are more informative because they are codominant, highly polymorphic, locus-specific, and more reproducible, and thus are most often used to assess the genetic diversity of plant species. Dalmatian pyrethrum is an outcrossing diploid (2n = 18) whose large genome size and high repeatability have prevented the success of the traditional approach to SSR markers development. The advent of next-generation sequencing combined with the specifically developed method recently enabled the development of, to the author's best knowledge, the first set of SSRs for genomic characterization of Dalmatian pyrethrum, which is essential from the perspective of plant genetic resources conservation. To evaluate the effectiveness of the developed SSR markers in genetic differentiation of Dalmatian pyrethrum populations, a preliminary genetic diversity study was conducted on 30 individuals from three geographically distinct natural populations in Croatia (northern Adriatic island of Mali Lošinj, southern Adriatic island of Čiovo, and Mount Biokovo) based on 12 SSR loci. Analysis of molecular variance (AMOVA) by randomization test with 10,000 permutations was performed in Arlequin 3.5. The average number of alleles per locus, observed and expected heterozygosity, probability of deviations from Hardy-Weinberg equilibrium, and inbreeding coefficient was calculated using GENEPOP 4.4. Genetic distance based on the proportion of common alleles (DPSA) was calculated using MICROSAT. Cluster analysis using the neighbor-joining method with 1,000 bootstraps was performed with PHYLIP to generate a dendrogram. The results of the AMOVA analysis showed that the total SSR diversity was 23% within and 77% between the three populations. A slight deviation from Hardy-Weinberg equilibrium was observed in the Mali Lošinj population. Allele richness ranged from 2.92 to 3.92, with the highest number of private alleles observed in the Mali Lošinj population (17). The average observed DPSA between 30 individuals was 0.557. The highest DPSA (0.875) was observed between several pairs of Dalmatian pyrethrum individuals from the Mali Lošinj and Mt. Biokovo populations, and the lowest between two individuals from the Čiovo population. Neighbor-joining trees, based on DPSA, grouped individuals into clusters according to their population affiliation. The separation of Mt. Biokovo clade was supported (bootstrap value 58%), which is consistent with the previous study on AFLP markers, where isolated populations from Mt. Biokovo differed from the rest of the populations. The developed SSR markers are an effective tool for assessing the genetic diversity and structure of natural Dalmatian pyrethrum populations. These preliminary results are encouraging for a future comprehensive study with a larger sample size across the species' range. Combined with the biochemical data, these highly informative markers could help identify potential genotypes of interest for future development of breeding lines and cultivars that are both resistant to environmental stress and high in pyrethrins. Acknowledgment: This work has been supported by the Croatian Science Foundation under the project ‘Genetic background of Dalmatian pyrethrum (Tanacetum cinerariifolium /Trevir./ Sch. Bip.) insecticidal potential’- (PyrDiv) (IP-06-2016-9034) and by project KK.01.1.1.01.0005, Biodiversity and Molecular Plant Breeding, at the Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Zagreb, Croatia.

Keywords: Asteraceae, genetic diversity, genomic SSRs, NGS, pyrethrum, Tanacetum cinerariifolium

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Authors: Nanine Fouche

Abstract:

The Cape Flats is a low-lying sand-covered expanse of approximately 460 square kilometres, situated to the southeast of the central business district of Cape Town in the Western Cape of South Africa. The aeolian sands masking this area are often loose and compressible in the upper 1m to 1.5m of the surface, and there is a general exceedance of the maximum allowable settlement in these sands. The settlement of shallow foundations on Cape Flats sands is commonly predicted using the results of in-situ tests such as the SPT or DPSH due to the difficulty of retrieving undisturbed samples for laboratory testing. Varying degrees of accuracy and reliability are associated with these methods. More recently, shear wave velocity (Vs) profiles obtained from seismic testing, such as continuous surface wave tests (CSW), are being used for settlement prediction. Such predictions have the advantage of considering non-linear stress-strain behaviour of soil and the degradation of stiffness with increasing strain. CSW tests are rarely executed in the Cape Flats, whereas SPT’s are commonly performed. For this reason, and to facilitate better settlement predictions in Cape Flats sand, equations representing shear wave velocity (Vs) as a function of SPT blow count (N60) and vertical effective stress (v’) were generated by statistical regression of site investigation data. To reveal the most appropriate method of overburden correction, analyses were performed with a separate overburden term (Pa/σ’v) as well as using stress corrected shear wave velocity and SPT blow counts (correcting Vs. and N60 to Vs1and (N1)60respectively). Shear wave velocity profiles and SPT blow count data from three sites masked by Cape Flats sands were utilised to generate 80 Vs-SPT N data pairs for analysis. Investigated terrains included sites in the suburbs of Athlone, Muizenburg, and Atlantis, all underlain by windblown deposits comprising fine and medium sand with varying fines contents. Elastic settlement analysis was also undertaken for the Cape Flats sands, using a non-linear stepwise method based on small-strain stiffness estimates, which was obtained from the best Vs-N60 model and compared to settlement estimates using the general elastic solution with stiffness profiles determined using Stroud’s (1989) and Webb’s (1969) SPT N60-E transformation models. Stroud’s method considers strain level indirectly whereasWebb’smethod does not take account of the variation in elastic modulus with strain. The expression of Vs. in terms of N60 and Pa/σv’ derived from the Atlantis data set revealed the best fit with R2 = 0.83 and a standard error of 83.5m/s. Less accurate Vs-SPT N relations associated with the combined data set is presumably the result of inversion routines used in the analysis of the CSW results showcasing significant variation in relative density and stiffness with depth. The regression analyses revealed that the inclusion of a separate overburden term in the regression of Vs and N60, produces improved fits, as opposed to the stress corrected equations in which the R2 of the regression is notably lower. It is the correction of Vs and N60 to Vs1 and (N1)60 with empirical constants ‘n’ and ‘m’ prior to regression, that introduces bias with respect to overburden pressure. When comparing settlement prediction methods, both Stroud’s method (considering strain level indirectly) and the small strain stiffness method predict higher stiffnesses for medium dense and dense profiles than Webb’s method, which takes no account of strain level in the determination of soil stiffness. Webb’s method appears to be suitable for loose sands only. The Versak software appears to underestimate differences in settlement between square and strip footings of similar width. In conclusion, settlement analysis using small-strain stiffness data from the proposed Vs-N60 model for Cape Flats sands provides a way to take account of the non-linear stress-strain behaviour of the sands when calculating settlement.

Keywords: sands, settlement prediction, continuous surface wave test, small-strain stiffness, shear wave velocity, penetration resistance

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