Search results for: vascular biology

Authors: Maik Kschischo, Dominik Kahl, Philipp Wendland, Andreas Weber

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Understanding and modelling of real-world complex dynamic systems in biology, engineering and other fields is often made difficult by incomplete knowledge about the interactions between systems states and by unknown disturbances to the system. In fact, most real-world dynamic networks are open systems receiving unknown inputs from their environment. To understand a system and to estimate the state dynamics, these inputs need to be reconstructed from output measurements. Reconstructing the input of a dynamic system from its measured outputs is an ill-posed problem if only a limited number of states is directly measurable. A first requirement for solving this problem is the invertibility of the input-output map. In our work, we exploit the fact that invertibility of a dynamic system is a structural property, which depends only on the network topology. Therefore, it is possible to check for invertibility using a structural invertibility algorithm which counts the number of node disjoint paths linking inputs and outputs. The algorithm is efficient enough, even for large networks up to a million nodes. To understand structural features influencing the invertibility of a complex dynamic network, we analyze synthetic and real networks using the structural invertibility algorithm. We find that invertibility largely depends on the degree distribution and that dense random networks are easier to invert than sparse inhomogeneous networks. We show that real networks are often very difficult to invert unless the sensor nodes are carefully chosen. To overcome this problem, we present a sensor node placement algorithm to achieve invertibility with a minimum set of measured states. This greedy algorithm is very fast and also guaranteed to find an optimal sensor node-set if it exists. Our results provide a practical approach to experimental design for open, dynamic systems. Since invertibility is a necessary condition for unknown input observers and data assimilation filters to work, it can be used as a preprocessing step to check, whether these input reconstruction algorithms can be successful. If not, we can suggest additional measurements providing sufficient information for input reconstruction. Invertibility is also important for systems design and model building. Dynamic models are always incomplete, and synthetic systems act in an environment, where they receive inputs or even attack signals from their exterior. Being able to monitor these inputs is an important design requirement, which can be achieved by our algorithms for invertibility analysis and sensor node placement.

Keywords: data-driven dynamic systems, inversion of dynamic systems, observability, experimental design, sensor node placement

Procedia PDF Downloads 127

Authors: Angela U. Makolo

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Protein-coding and Non-coding regions determine the biology of a sequenced transcriptome. Research advances have shown that Non-coding regions are important in disease progression and clinical diagnosis. Existing bioinformatics tools have been targeted towards Protein-coding regions alone. Therefore, there are challenges associated with gaining biological insights from transcriptome sequence data. These tools are also limited to computationally intensive sequence alignment, which is inadequate and less accurate to identify both Protein-coding and Non-coding regions. Alignment-free techniques can overcome the limitation of identifying both regions. Therefore, this study was designed to develop an efficient sequence alignment-free model for identifying both Protein-coding and Non-coding regions in sequenced transcriptomes. Feature grouping and randomization procedures were applied to the input transcriptomes (37,503 data points). Successive iterations were carried out to compute the gradient vector that converged the developed Protein-coding and Non-coding Region Identifier (PNRI) model to the approximate coefficient vector. The logistic regression algorithm was used with a sigmoid activation function. A parameter vector was estimated for every sample in 37,503 data points in a bid to reduce the generalization error and cost. Maximum Likelihood Estimation (MLE) was used for parameter estimation by taking the log-likelihood of six features and combining them into a summation function. Dynamic thresholding was used to classify the Protein-coding and Non-coding regions, and the Receiver Operating Characteristic (ROC) curve was determined. The generalization performance of PNRI was determined in terms of F1 score, accuracy, sensitivity, and specificity. The average generalization performance of PNRI was determined using a benchmark of multi-species organisms. The generalization error for identifying Protein-coding and Non-coding regions decreased from 0.514 to 0.508 and to 0.378, respectively, after three iterations. The cost (difference between the predicted and the actual outcome) also decreased from 1.446 to 0.842 and to 0.718, respectively, for the first, second and third iterations. The iterations terminated at the 390th epoch, having an error of 0.036 and a cost of 0.316. The computed elements of the parameter vector that maximized the objective function were 0.043, 0.519, 0.715, 0.878, 1.157, and 2.575. The PNRI gave an ROC of 0.97, indicating an improved predictive ability. The PNRI identified both Protein-coding and Non-coding regions with an F1 score of 0.970, accuracy (0.969), sensitivity (0.966), and specificity of 0.973. Using 13 non-human multi-species model organisms, the average generalization performance of the traditional method was 74.4%, while that of the developed model was 85.2%, thereby making the developed model better in the identification of Protein-coding and Non-coding regions in transcriptomes. The developed Protein-coding and Non-coding region identifier model efficiently identified the Protein-coding and Non-coding transcriptomic regions. It could be used in genome annotation and in the analysis of transcriptomes.

Keywords: sequence alignment-free model, dynamic thresholding classification, input randomization, genome annotation

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Authors: Mahmoud Farrag, Alaa Elhaweet, El-Sayed Akel, Mohsen Moustafa

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The present work aimed to study the reproductive strategy of the common lesspsian puffer fish Lagocephalus sceleratus (Gmeln, 1879) from the Egyptian Mediterranean Waters. It is a famous migratory species plays an important role in the field of fisheries and ecology of aquatic ecosystem. The obtained results illustrated seven maturity stages of gonads as; I- Thread like stage: II- Immature stage (Virgin stage), III- Maturing stage (Developing Virgin and recovering spent), IV - Nearly ripe stage, V- Fully ripe; VI-Spawning stage, VII- Spent stage. Sex ratio, exhibited males had higher number than females representing 52.44 % of the total fishes with sex ratio 1: 0.91. Fish length corresponding to 50% maturation was 38.5 cm for males and 41 cm for females. The corresponding ages (age at first maturity) are equal to 2.14 and 2.27 years for male and female respectively. The gonado somatic index (GSI) increased from April for both sexes with peak in June (8.567±4.729) for males and May (6.769±4.662) for females, then the sharp decrease was observed in October showing prolong spawning season from April to September for both sexes. The hepato somatic indices (HSI) for males were lower values than those of females, it were high from December to early spawning (April & May), with the peak in April (5.217 ± 2.167) for males, and in March (5.453± 1.792) for females, then these values started to decrease towards the end of spawning period. The ova diameter ranged from 0.02 to 0.85mm, the mature ova ranged from 0.16 to 0.85mm and showed progressive increase from April towards September during spawning period introducing one peak of mature and ripe eggs. The absolute fecundity increased as the fish grew in weight and length; it was ranged from 260288 to 2372931 for fish weight and ranged from 698 to 3285 cm for length with an average of 1449522±720975. The relative fecundity ranged from 373 to 722 for fish weight with an average of 776±231, while it range from 5784 to 32957 for fish length groups ranged from 43-45 to 70-72 cm with an average of 24478 ±10011 eggs. Histological characters of gonads during the year of study indicating this fish species has prolonged spawning season from April to September where ripe oocytes were observed during this period. This species is considered totally or uni spawner with synchronous group as it contained one to two developmental stages at the same gonad and releases its ripe ova in one batch during the spawning season. These results illustrated more adaptation of this species in new habitat.

Keywords: reproductive biology, histology, Lagocephalus sceleratus, Mediterranean Sea, Egypt

Procedia PDF Downloads 402

Authors: Sophie Baudel, Aline Duplaa, Jean Muller, Stephan Lauriol, Yann Bernard

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Argos is the main satellite telemetry system used by the wildlife research community, since its creation in 1978, for animal tracking and scientific data collection all around the world, to analyze and understand animal migrations and behavior. The marine mammals' biology is one of the major disciplines which had benefited from Argos telemetry, and conversely, marine mammals biologists’ community has contributed a lot to the growth and development of Argos use cases. The Argos constellation with 6 satellites in orbit in 2017 (Argos 2 payload on NOAA 15, NOAA 18, Argos 3 payload on NOAA 19, SARAL, METOP A and METOP B) is being extended in the following years with Argos 3 payload on METOP C (launch in October 2018), and Argos 4 payloads on Oceansat 3 (launch in 2019), CDARS in December 2021 (to be confirmed), METOP SG B1 in December 2022, and METOP-SG-B2 in 2029. Argos 4 will allow more frequency bands (600 kHz for Argos4NG, instead of 110 kHz for Argos 3), new modulation dedicated to animal (sea turtle) tracking allowing very low transmission power transmitters (50 to 100mW), with very low data rates (124 bps), enhancement of high data rates (1200-4800 bps), and downlink performance, at the whole contribution to enhance the system capacity (50,000 active beacons per month instead of 20,000 today). In parallel of this ‘institutional Argos’ constellation, in the context of a miniaturization trend in the spatial industry in order to reduce the costs and multiply the satellites to serve more and more societal needs, the French Space Agency CNES, which designs the Argos payloads, is innovating and launching the Argos ANGELS project (Argos NEO Generic Economic Light Satellites). ANGELS will lead to a nanosatellite prototype with an Argos NEO instrument (30 cm x 30 cm x 20cm) that will be launched in 2019. In the meantime, the design of the renewal of the Argos constellation, called Argos For Next Generations (Argos4NG), is on track and will be operational in 2022. Based on Argos 4 and benefitting of the feedback from ANGELS project, this constellation will allow revisiting time of fewer than 20 minutes in average between two satellite passes, and will also bring more frequency bands to improve the overall capacity of the system. The presentation will then be an overview of the Argos system, present and future and new capacities coming with it. On top of that, use cases of two Argos hardware modules will be presented: the goniometer pathfinder allowing recovering Argos beacons at sea or on the ground in a 100 km radius horizon-free circle around the beacon location and the new Argos 4 chipset called ‘Artic’, already available and tested by several manufacturers.

Keywords: Argos satellite telemetry, marine protected areas, oceanography, maritime services

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Authors: Michela Quadrini

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Chord diagrams occur in mathematics, from the study of RNA to knot theory. They are widely used in theory of knots and links for studying the finite type invariants, whereas in molecular biology one important motivation to study chord diagrams is to deal with the problem of RNA structure prediction. An RNA molecule is a linear polymer, referred to as the backbone, that consists of four types of nucleotides. Each nucleotide is represented by a point, whereas each chord of the diagram stands for one interaction for Watson-Crick base pairs between two nonconsecutive nucleotides. A chord diagram is an oriented circle with a set of n pairs of distinct points, considered up to orientation preserving diffeomorphisms of the circle. A linear chord diagram (LCD) is a special kind of graph obtained cutting the oriented circle of a chord diagram. It consists of a line segment, called its backbone, to which are attached a number of chords with distinct endpoints. There is a natural fattening on any linear chord diagram; the backbone lies on the real axis, while all the chords are in the upper half-plane. Each linear chord diagram has a natural genus of its associated surface. To each chord diagram and linear chord diagram, it is possible to associate the intersection graph. It consists of a graph whose vertices correspond to the chords of the diagram, whereas the chord intersections are represented by a connection between the vertices. Such intersection graph carries a lot of information about the diagram. Our goal is to define an LCD equivalence class in terms of identity of intersection graphs, from which many chord diagram invariants depend. For studying these invariants, we introduce a new representation of Linear Chord Diagrams based on a set of appropriate topological operators that permits to model LCD in terms of the relations among chords. Such set is composed of: crossing, nesting, and concatenations. The crossing operator is able to generate the whole space of linear chord diagrams, and a multiple context free grammar able to uniquely generate each LDC starting from a linear chord diagram adding a chord for each production of the grammar is defined. In other words, it allows to associate a unique algebraic term to each linear chord diagram, while the remaining operators allow to rewrite the term throughout a set of appropriate rewriting rules. Such rules define an LCD equivalence class in terms of the identity of intersection graphs. Starting from a modelled RNA molecule and the linear chord, some authors proposed a topological classification and folding. Our LCD equivalence class could contribute to the RNA folding problem leading to the definition of an algorithm that calculates the free energy of the molecule more accurately respect to the existing ones. Such LCD equivalence class could be useful to obtain a more accurate estimate of link between the crossing number and the topological genus and to study the relation among other invariants.

Keywords: chord diagrams, linear chord diagram, equivalence class, topological language

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Authors: André Melo Franco Lorena De Barros, Elida Geralda Campos

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The bilingual education has just started in Brazils public schools. This paper is a didactic sequence of biology bilingual lessons about biologic control in the Brazilian Savana. This sequence has been applied in the first year of a bilingual education program in the only public English and Portuguese bilingual high school in Brazil. The aim of this work is to develop and apply a didactic sequence capable of developing the scientific literacy through the bilingual education associated with Problem Based Learning. This didactic sequence was applied in a class of 30 students. It was divided in three lessons. In the first lesson the students were divided in groups and received a fiction Letter from a mayor explaining the problem and asking students for help. The organic soy plantation of the mayor’s is been attacked by caterpillars. The students read the text then raised hypothesis of how they could solve the problem. In the second lesson the students searched online to verify if theirs hypothesis were correct and to find answers for the question proposed. In the third lesson the groups got together and discussed about their results and wrote a final essay with the answers for the problem proposed. The tools used to acquire information about the didactic sequence were: researcher’s diary, survey, interview and essay developed by the students. Most of the initial hypothesis couldn’t answer the problem properly. By the second lesson most of the students could answer properly. During the third lesson all the groups figured out suitable answers. The forms of biological control, birds habits and transgenic were deeply studied by the students. This methodology was successful for developing the scientific literacy with most of the students and also concluded that the quality of learning is directly associated with the effort of each student during the process. [ARAÚJO, Denise Lino de. O que é (e como se faz) sequência didática. Entrepalavras, Fortaleza, v. 3, n. 3, p.322-334, jul. 2013.] [FRANCO, Aline Aparecida et al. Preferência alimentar de Anticarsia gemmatalis Hübner (Lepidoptera: Noctuidae) por cultivares de soja. Científica: Revista de Ciências Agrárias, Jaboticabal, v. 1, n. 42, p.32-38, 29 jan. 2014.] [RIBEIRO, Luis Roberto de Camargo. Aprendizagem baseada em problemas (PBL): Uma experiência no ensino superior. São Carlos: Editora da Universidade Federal de São Carlos Ribeiro, 2008. 151 p.] [TRIVELATO, Sílvia L. Frateschi; TONIDANDEL, Sandra M. Rudella. Ensino Por Investigação: Eixos Organizadores Para Sequências De Ensino De Biologia. Ensaio Pesquisa em Educação em Ciências, Belo Horizonte, v. 17, n. especial, p.97-114, nov. 2015.].

Keywords: Bilingual Education, Environmental Education, Problem Based Learning, Science education

Procedia PDF Downloads 151

Authors: Bruno C. Schimming, Leandro L. Martins, PatríCia F. F. Pinheiro, Raquel F. Domeniconi, FabríCio S. Oliveira

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The agouti is a wildlife rodent that can be used as an alternative source of animal protein and this species has been raised in captivity in Brazil with the aim of providing meat. Thus, the knowledge of their reproductive biology and morphology of the reproductive organs is important. The objective of this study was to describe the morphology of epididymis in the Azara’s agouti, by light microscopy. Samples of epididymis were obtained from five adult Azara’s agouti (Dasyprocta azarae) during castration surgery performed at the Municipal Zoo of Catanduva, Brazil. Fragments of the epididymal regions (initial segment, caput, corpus and cauda) were collected. The biological samples were immediately fixed in paraformaldehyde for 24 hours, followed by histologic procedures comprising embedding in ParaplastTM (Sigma, St. Louis, MO, USA), sections of 5 µm, and staining with HE and Masson’s trichrome. The epididymis was a highly convoluted tubule that links the testis to the vas deferens. The epithelium lining was pseudostratified columnar surrounded by a periductal stroma. The epithelium contains several cell types: principal, basal, apical, clear, and hallo cells. Principal cells were the most abundant cell type. There were observed also migratory cells named halo cells. The caput epididymis was divided into two different regions: initial segment and caput. The initial segment has a very wide lumen, a high epithelium with conspicuous microvilli and the lumen was wide with exfoliated material. The other region of the caput epididymis, showed a lower epithelium when compared with the initial segment, large amounts of spermatozoa in the lumen, and a cytoplasmic vacuolization. This region presented many narrows cells. Many spermatozoa appeared in the lumen of corpus epididymis. The cauda region had a lower epithelium than the other epididymal regions in the agouti. The cauda epithelium presented plicae protruding into the lumen. Large amounts of spermatozoa are also present in the lumen. Small microvilli uniformly arranged so as to form a kind of “brush border” are observed on the apical surface of the cauda epithelium. The pattern of the epithelium lining the duct of the agouti epididymis does not differ greatly from that reported to other mammals, such as domestic and wildlife animals. These findings can cooperate with future investigations especially those related to rational exploration of these animals. All experimental procedures were approved by the institutional ethics committee (CEUA 796/2015). This study was supported by FAPESP (Grants 2015/23822-1).

Keywords: wildlife, testis excurrent ducts, epididymis, morphology

Procedia PDF Downloads 209

Authors: Mahmoud M. S. Farrag, Alaa A. K. Elhaweet, El-Sayed Kh. A. Akel, Mohsen A. Moustafa

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The present work aimed to study the reproductive strategy of the common lessepsian puffer fish Lagocephalus sceleratus (Gmelin, 1879) from the Egyptian Mediterranean Waters. It is a famous migratory species plays an important role in the field of fisheries and ecology of aquatic ecosystem. The specimens were collected monthly from the landing centers along the Egyptian Mediterranean coast during 2012. Six maturity stages were recorded: (I) Thread like stage, (II) Immature stage (Virgin stage), (III) Maturing stage (Developing Virgin and recovering spent), (IV) Nearly ripe stage, (V) Fully ripe, (VI) Spawning stage, (VII) Spent stage. According to sex ratio, males exhibited higher number than females representing 52.44 % of the total fishes with sex ratio 1: 0.91. Fish length corresponding to 50% maturation was 38.5 cm for males and 41 cm for females. The corresponding ages (age at first maturity) are equal to 2.14 and 2.27 years for male and female respectively. The ova diameter ranged from 0.02mm to 0.85mm, the mature ova ranged from 0.16mm to 0.85mm and showed progressive increase from April towards September. Also, the presences of ova diameter in one peak of mature and ripe eggs in the ovaries were observed during spawning period. The relationship between gutted weight and absolute fecundity indicated that that fecundity increased as the fish grew in weight. The absolute fecundity ranged from 260288 to 2372931 for fish weight ranged from 698 to 3285 cm with an average of 1449522±720975. The relative fecundity ranged from 373 to 722 for fish weight ranged from 698 to 3285 cm with an average of 776±231. The spawning season of L. sceleratus was investigated from the data of gonado-somatic index and monthly distribution of maturity stages along the year as well as sequence of ova diameter for mature stages and exhibited a relatively prolong spawning season extending from April for both sexes and ends in August for male while ends in September for female. Fish releases its ripe ova in one batch during the spawning season. Histologically, the ovarian cycle of L. sceleratus was classified into six stages and the testicular cycle into five stages. Histological characters of gonads of L. sceleratus during the year of study had confirmed the previous results of distribution of maturity stages, gonado-somatic index and ova diameter, indicating this fish species has prolonged spawning season from April to September. This species is considered totally or uni spawner with synchronous group as it contained one to two developmental stages at the same gonad.

Keywords: Lagocephalus sceleratus, reproductive biology, oogenesis, histology

Procedia PDF Downloads 277

Authors: Debjit Ray

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Horizontal gene transfer (HGT) and recombination leads to the emergence of bacterial antibiotic resistance and pathogenic traits. HGT events can be identified by comparing a large number of fully sequenced genomes across a species or genus, define the phylogenetic range of HGT, and find potential sources of new resistance genes. In-depth comparative phylogenomics can also identify subtle genome or plasmid structural changes or mutations associated with phenotypic changes. Comparative phylogenomics requires that accurately sequenced, complete and properly annotated genomes of the organism. Assembling closed genomes requires additional mate-pair reads or “long read” sequencing data to accompany short-read paired-end data. To bring down the cost and time required of producing assembled genomes and annotating genome features that inform drug resistance and pathogenicity, we are analyzing the performance for genome assembly of data from the Illumina NextSeq, which has faster throughput than the Illumina HiSeq (~1-2 days versus ~1 week), and shorter reads (150bp paired-end versus 300bp paired end) but higher capacity (150-400M reads per run versus ~5-15M) compared to the Illumina MiSeq. Bioinformatics improvements are also needed to make rapid, routine production of complete genomes a reality. Modern assemblers such as SPAdes 3.6.0 running on a standard Linux blade are capable in a few hours of converting mixes of reads from different library preps into high-quality assemblies with only a few gaps. Remaining breaks in scaffolds are generally due to repeats (e.g., rRNA genes) are addressed by our software for gap closure techniques, that avoid custom PCR or targeted sequencing. Our goal is to improve the understanding of emergence of pathogenesis using sequencing, comparative genomics, and machine learning analysis of ~1000 pathogen genomes. Machine learning algorithms will be used to digest the diverse features (change in virulence genes, recombination, horizontal gene transfer, patient diagnostics). Temporal data and evolutionary models can thus determine whether the origin of a particular isolate is likely to have been from the environment (could it have evolved from previous isolates). It can be useful for comparing differences in virulence along or across the tree. More intriguing, it can test whether there is a direction to virulence strength. This would open new avenues in the prediction of uncharacterized clinical bugs and multidrug resistance evolution and pathogen emergence.

Keywords: genomics, pathogens, genome assembly, superbugs

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Authors: Miguel Contreras, David Long, Will Bachman

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Background: Microscopy plays a central role in cell and developmental biology. In particular, fluorescence microscopy can be used to visualize specific cellular components and subsequently quantify their morphology through development of virtual-cell models for study of effects of mechanical forces on cells. However, there are challenges with these imaging experiments, which can make it difficult to quantify cell morphology: inconsistent results, time-consuming and potentially costly protocols, and limitation on number of labels due to spectral overlap. To address these challenges, the objective of this project is to develop an automatic computational machine learning pipeline to predict cellular components morphology for virtual-cell generation based on fluorescence cell membrane confocal z-stacks. Methods: Registered confocal z-stacks of nuclei and cell membrane of endothelial cells, consisting of 20 images each, were obtained from fluorescence confocal microscopy and normalized through software pipeline for each image to have a mean pixel intensity value of 0.5. An open source machine learning algorithm, originally developed to predict fluorescence labels on unlabeled transmitted light microscopy cell images, was trained using this set of normalized z-stacks on a single CPU machine. Through transfer learning, the algorithm used knowledge acquired from its previous training sessions to learn the new task. Once trained, the algorithm was used to predict morphology of nuclei using normalized cell membrane fluorescence images as input. Predictions were compared to the ground truth fluorescence nuclei images. Results: After one week of training, using one cell membrane z-stack (20 images) and corresponding nuclei label, results showed qualitatively good predictions on training set. The algorithm was able to accurately predict nuclei locations as well as shape when fed only fluorescence membrane images. Similar training sessions with improved membrane image quality, including clear lining and shape of the membrane, clearly showing the boundaries of each cell, proportionally improved nuclei predictions, reducing errors relative to ground truth. Discussion: These results show the potential of pre-trained machine learning algorithms to predict cell morphology using relatively small amounts of data and training time, eliminating the need of using multiple labels in immunofluorescence experiments. With further training, the algorithm is expected to predict different labels (e.g., focal-adhesion sites, cytoskeleton), which can be added to the automatic machine learning pipeline for direct input into Principal Component Analysis (PCA) for generation of virtual-cell mechanical models.

Keywords: cell morphology prediction, computational machine learning, fluorescence microscopy, virtual-cell models

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Authors: Sharmeen Rahman, Daniel Schmidt, Jane Hughes

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Paratya australiensis Kemp (Decapoda: Atyidae) is a widely distributed indigenous freshwater shrimp, highly abundant in eastern Australia. This species has been considered as a model stream organism to study genetics, dispersal, biology, behaviour and evolution in Atyids. Paratya has a filter feeding and scavenging habit which plays a significant role in the formation of lotic community structure. It has been shown to reduce periphyton and sediment from hard substrates of coastal streams and hence acts as a strongly-interacting ecosystem macroconsumer. Besides, Paratya is one of the major food sources for stream dwelling fishes. Paratya australiensis is a cryptic species complex consisting of 9 highly divergent mitochondrial DNA lineages. Among them, one lineage has been observed to favour upstream sites at higher altitudes, with cooler water temperatures. This study aims to identify local adaptation in upstream and downstream populations of this lineage in three streams in the Conondale Range, North-eastern Brisbane, Queensland, Australia. Two populations (up and down stream) from each stream have been chosen to test for local adaptation, and a parallel pattern of adaptation is expected across all streams. Six populations each consisting of 24 individuals were sequenced using the Restriction Site Associated DNA-seq (RAD-seq) technique. Genetic markers (SNPs) were developed using double digest RAD sequencing (ddRAD-seq). These were used for de novo assembly of Paratya genome. De novo assembly was done using the STACKs program and produced 56, 344 loci for 47 individuals from one stream. Among these individuals, 39 individuals shared 5819 loci, and these markers are being used to test for local adaptation using Fst outlier tests (Arlequin) and Bayesian analysis (BayeScan) between up and downstream populations. Fst outlier test detected 27 loci likely to be under selection and the Bayesian analysis also detected 27 loci as under selection. Among these 27 loci, 3 loci showed evidence of selection at a significance level using BayeScan program. On the other hand, up and downstream populations are strongly diverged at neutral loci with a Fst =0.37. Similar analysis will be done with all six populations to determine if there is a parallel pattern of adaptation across all streams. Furthermore, multi-locus among population covariance analysis will be done to identify potential markers under selection as well as to compare single locus versus multi-locus approaches for detecting local adaptation. Adaptive genes identified in this study can be used for future studies to design primers and test for adaptation in related crustacean species.

Keywords: Paratya australiensis, rainforest streams, selection, single nucleotide polymorphism (SNPs)

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Authors: Ujjwall Sai Sunder Uppuluri

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Group theory is a powerful tool that researchers can use to provide a structural foundation for their Agent Based Models. These Agent Based models are argued by this paper to be the future of the Social Science Disciplines. More specifically, researchers can use them to apply evolutionary theory to the study of complex social systems. This paper illustrates one such example of how theoretically an Agent Based Model can be formulated from the application of Group Theory, Systems Dynamics, and Evolutionary Biology to analyze the strategies pursued by states to mitigate risk and maximize usage of resources to achieve the objective of economic growth. This example can be applied to other social phenomena and this makes group theory so useful to the analysis of complex systems, because the theory provides the mathematical formulaic proof for validating the complex system models that researchers build and this will be discussed by the paper. The aim of this research, is to also provide researchers with a framework that can be used to model political entities such as states on a 3-dimensional plane. The x-axis representing resources (tangible and intangible) available to them, y the risks, and z the objective. There also exist other states with different constraints pursuing different strategies to climb the mountain. This mountain’s environment is made up of risks the state faces and resource endowments. This mountain is also layered in the sense that it has multiple peaks that must be overcome to reach the tallest peak. A state that sticks to a single strategy or pursues a strategy that is not conducive to the climbing of that specific peak it has reached is not able to continue advancement. To overcome the obstacle in the state’s path, it must innovate. Based on the definition of a group, we can categorize each state as being its own group. Each state is a closed system, one which is made up of micro level agents who have their own vectors and pursue strategies (actions) to achieve some sub objectives. The state also has an identity, the inverse being anarchy and/or inaction. Finally, the agents making up a state interact with each other through competition and collaboration to mitigate risks and achieve sub objectives that fall within the primary objective. Thus, researchers can categorize the state as an organism that reflects the sum of the output of the interactions pursued by agents at the micro level. When states compete, they employ a strategy and that state which has the better strategy (reflected by the strategies pursued by her parts) is able to out-compete her counterpart to acquire some resource, mitigate some risk or fulfil some objective. This paper will attempt to illustrate how group theory combined with evolutionary theory and systems dynamics can allow researchers to model the long run development, evolution, and growth of political entities through the use of a bottom up approach.

Keywords: complex systems, evolutionary theory, group theory, international political economy

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Authors: Nir Nissim, Ran Yahalom, Tomer Lancewiki, Yuval Elovici, Boaz Lerner

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Background: Attackers increasingly take advantage of innocent users who tend to use USB devices casually, assuming these devices benign when in fact they may carry an embedded malicious behavior or hidden malware. USB devices have many properties and capabilities that have become the subject of malicious operations. Many of the recent attacks targeting individuals, and especially organizations, utilize popular and widely used USB devices, such as mice, keyboards, flash drives, printers, and smartphones. However, current detection tools, techniques, and solutions generally fail to detect both the known and unknown attacks launched via USB devices. Significance: We propose USBWARE, a project that focuses on the vulnerabilities of USB devices and centers on the development of a comprehensive detection framework that relies upon a crucial attack repository. USBWARE will allow researchers and companies to better understand the vulnerabilities and attacks associated with USB devices as well as providing a comprehensive platform for developing detection solutions. Methodology: The framework of USBWARE is aimed at accurate detection of both known and unknown USB-based attacks by a process that efficiently enhances the framework's detection capabilities over time. The framework will integrate two main security approaches in order to enhance the detection of USB-based attacks associated with a variety of USB devices. The first approach is aimed at the detection of known attacks and their variants, whereas the second approach focuses on the detection of unknown attacks. USBWARE will consist of six independent but complimentary detection modules, each detecting attacks based on a different approach or discipline. These modules include novel ideas and algorithms inspired from or already developed within our team's domains of expertise, including cyber security, electrical and signal processing, machine learning, and computational biology. The establishment and maintenance of the USBWARE’s dynamic and up-to-date attack repository will strengthen the capabilities of the USBWARE detection framework. The attack repository’s infrastructure will enable researchers to record, document, create, and simulate existing and new USB-based attacks. This data will be used to maintain the detection framework’s updatability by incorporating knowledge regarding new attacks. Based on our experience in the cyber security domain, we aim to design the USBWARE framework so that it will have several characteristics that are crucial for this type of cyber-security detection solution. Specifically, the USBWARE framework should be: Novel, Multidisciplinary, Trusted, Lightweight, Extendable, Modular and Updatable and Adaptable. Major Findings: Based on our initial survey, we have already found more than 23 types of USB-based attacks, divided into six major categories. Our preliminary evaluation and proof of concepts showed that our detection modules can be used for efficient detection of several basic known USB attacks. Further research, development, and enhancements are required so that USBWARE will be capable to cover all of the major known USB attacks and to detect unknown attacks. Conclusion: USBWARE is a crucial detection framework that must be further enhanced and developed.

Keywords: USB, device, cyber security, attack, detection

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Authors: Magdalena Zabrocka

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The terror of women throughout the governance of the current populist ruling party in Poland, PiS, has been a subject of a heated debate alongside the issues of minorities’ rights, the rule of law, and democracy in the country. The challenges that women and other vulnerable groups are currently facing, however, come down to more than just a lack of comprehensive equality laws, severely limited reproductive rights, hateful slogans, and messages propagated by the central authority and its sympathisers, or a common disregard for women’s fundamental rights. Many sources and media reports are available only in Polish, while international rapporteurs fail to acknowledge the whole picture of the tragedy happening in the country and the variety of factors affecting it. Starting with the authorities’ and Polish catholic church’s propaganda concerning CEDAW and the Istanbul Convention Action against Violence against Women and Domestic Violence by spreading strategic disinformation that it codifies ‘gender ideology’ and ‘anti-Christian values’ in order to convince the electorate that the legal instruments should be ‘abandoned’. Alongside severely restricted abortion rights, bullying medical professionals helping women exercise their reproductive rights, violating women’s privacy by introducing a mandatory registry of pregnancies (so that one’s pregnancy or its ‘loss’ can be tracked and traced), restricting access to the ‘day after pill’ and real sex education at schools (most schools have a subject of ‘knowledge of living in a family’), introducing prison punishment for teachers accused of spreading ‘sex education’, and many other, the current tyrant government, has now decided to target the youngest with its misinformation and indoctrination, via strategically designed textbooks and curriculum. Biology books have seen a big restriction on the size of the chapters devoted to evolution, reproductive system, and sexual health. Approved religion books (which are taught 2-3 times a week as compared to 1 a week sciences) now cover false information about Darwin’s theory and arguments ‘against it’. Most recently, however, the public spoke up against the absurd messages contained in the politically rewritten history books, where the material about some figures not liked by the governing party has already been manipulated. In the recently approved changes to the history textbook, one can find a variety of strongly biased and politically-charged views representative of the conservatives in the states, most notably, equating the ‘gender ideology’ and feminism with Nazism. Thus, this work, by employing a human rights approach, would focus on the right to education and development as well as the considerate obstacles to access to scientific information by the youth.

Keywords: Poland, right to education, right to development, authoritarianism, access to information

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Authors: Sofia Papadimitriou

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INTRODUCTION: The differential diagnosis between acute viral and bacterial infections is an important cost-effectiveness parameter at the stage of the treatment process in order to achieve the maximum benefits in therapeutic intervention by combining the minimum cost to ensure the proper use of antibiotics.The discovery of sensitive and robust molecular diagnostic tests in response to the role of the host in infections has enhanced the accurate diagnosis and differentiation of infections. METHOD: The study used a sample of six independent blood samples (total=756) which are associated with human proteins-proteins, each of which at the transcription stage expresses a different response in the host network between viral and bacterial infections.Τhe individual blood samples are subjected to a sequence of computer filters that identify a gene panel corresponding to an autonomous diagnostic score. The data set and the correspondence of the gene panel to the diagnostic patents a new Bangalore -Viral Bacterial (BL-VB). FINDING: We use a biomarker based on the blood of 10 genes(Panel-VB) that are an important prognostic value for the detection of viruses from bacterial infections with a weighted average AUROC of 0.97(95% CL:0.96-0.99) in eleven independent samples (sets n=898). We discovered a base with a patient score (VB 10 ) according to the table, which is a significant diagnostic value with a weighted average of AUROC 0.94(95% CL: 0.91-0.98) in 2996 patient samples from 56 public sets of data from 19 different countries. We also studied VB 10 in a new cohort of South India (BL-VB,n=56) and found 97% accuracy in confirmed cases of viral and bacterial infections. We found that VB 10 (a)accurately identifies the type of infection even in unspecified cases negative to the culture (b) shows its clinical condition recovery and (c) applies to all age groups, covering a wide range of acute bacterial and viral infectious, including non-specific pathogens. We applied our VB 10 rating to publicly available COVID 19 data and found that our rating diagnosed viral infection in patient samples. RESULTS: Τhe results of the study showed the diagnostic power of the biomarker VB 10 as a diagnostic test for the accurate diagnosis of acute infections in recovery conditions. We look forward to helping you make clinical decisions about prescribing antibiotics and integrating them into your policies management of antibiotic stewardship efforts. CONCLUSIONS: Overall, we are developing a new property of the RNA-based biomarker and a new blood test to differentiate between viral and bacterial infections to assist a physician in designing the optimal treatment regimen to contribute to the proper use of antibiotics and reduce the burden on antimicrobial resistance, AMR.

Keywords: acute infections, antimicrobial resistance, biomarker, blood transcriptome, systems biology, classifier diagnostic score

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Authors: Mohamed Fawzy Elzarei, Yousef Mohammed Al-Dakheel, Ali Mohamed Alseaf

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Modern molecular techniques, like single marker analysis for linked traits to these markers, can provide us with rapid and accurate genetic results. In the last two decades of the last century, the applications of molecular techniques were reached a faraway point in cattle, sheep, and pig. In goats, especially in our region, the application of molecular techniques is still far from other species. As reported by many researchers, microsatellites marker is one of the suitable markers for lie studies. The single marker linked to traits of interest is one technique allowed us to early select animals without the necessity for mapping the entire genome. Simplicity, applicability, and low cost of this technique gave this technique a wide range of applications in many areas of genetics and molecular biology. Also, this technique provides a useful approach for evaluating genetic differentiation, particularly in populations that are poorly known genetically. The expected breeding value (EBV) and yield deviation (YD) are considered as the most parameters used for studying the linkage between quantitative characteristics and molecular markers, since these values are raw data corrected for the non-genetic factors. A total of 17 microsatellites markers (from chromosomes 6, 14, 18, 20 and 23) were used in this study to search for areas that could be responsible for genetic variability for some milk traits and search of chromosomal regions that explain part of the phenotypic variance. Results of single-marker analyses were used to identify the linkage between microsatellite markers and variation in EBVs of these traits, Milk yield, Protein percentage, Fat percentage, Litter size and weight at birth, and litter size and weight at weaning. The estimates of the parameters from forward and backward solutions using stepwise regression procedure on milk yield trait, only two markers, OARCP9 and AGLA29, showed a highly significant effect (p≤0.01) in backward and forward solutions. The forward solution for different equations conducted that R2 of these equations were highly depending on only two partials regressions coefficient (βi,) for these markers. For the milk protein trait, four marker showed significant effect BMS2361, CSSM66 (p≤0.01), BMS2626, and OARCP9 (p≤0.05). By the other way, four markers (MCM147, BM1225, INRA006, andINRA133) showed highly significant effect (p≤0.01) in both backward and forward solutions in association with milk fat trait. For both litter size at birth and at weaning traits, only one marker (BM143(p≤0.01) and RJH1 (p≤0.05), respectively) showed a significant effect in backward and forward solutions. The estimates of the parameters from forward and backward solution using stepwise regression procedure on litter weight at birth (LWB) trait only one marker (MCM147) showed highly significant effect (p≤0.01) and two marker (ILSTS011, CSSM66) showed a significant effect (p≤0.05) in backward and forward solutions.

Keywords: microsatellites marker, estimated breeding value, stepwise regression, milk traits

Procedia PDF Downloads 55

Authors: Chahad P. Alexandre

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PIBID-Institutional Program of Scholarships to Encourage Teaching - is a Brazilian government program that counts today with 48.000 students. It's goal is to motivate the students to stay in the teaching undergraduate programs and to help fill the gap of 100.000 teachers that are needed today in the under graduated schools. The major lack of teachers today is in physics, chemistry, mathematics, and biology. At IFSP-Itapetininga we formatted our physics PIBID based on practical activities. Our students are divided in two São Paulo state government high schools in the same city. The project proposes class activities based on experimentation, observation and understanding of physical phenomena. The didactical experiments are always in relation with the content that the teacher is working, he is the supervisor of the program in the school. Always before an experiment is proposed a little questionnaire to learn about the students preconceptions and one is filled latter to evaluate if now concepts have been created. This procedure is made in order to compare their previous knowledge and how it changed after the experiment is developed. The primary goal of our project is to make the Physics class more attractive to the students and to develop in high school students the interest in learning physics and to show the relation of Physics to the day by day and to the technological world. The objective of the experimental activities is to facilitate the understanding of the concepts that are worked on classes because under experimentation the PIBID scholarship student stimulate the curiosity of the high school student and with this he can develop the capacity to understand and identify the physical phenomena with concrete examples. Knowing how to identify this phenomena and where they are present at the high school student life makes the learning process more significant and pleasant. This proposal make achievable to the students to practice science, to appropriate of complex, in the traditional classes, concepts and overcoming the common preconception that physics is something distant and that is present only on books. This preconception is extremely harmful in the process of scientific knowledge construction. This kind of learning – through experimentation – make the students not only accumulate knowledge but also appropriate it, also to appropriate experimental procedures and even the space that is provided by the school. The PIBID scholarship students, as future teachers also have the opportunity to try experimentation classes, to intervene in the classes and to have contact with their future career. This opportunity allows the students to make important reflection about the practices realized and consequently about the learning methods. Due to this project, we found out that the high school students stay more time focused in the experiment compared to the traditional explanation teachers´ class. As a result in a class, as a participative activity, the students got more involved and participative. We also found out that the physics under graduated students drop out percentage is smaller in our Institute than before the PIBID program started.

Keywords: innovation, projects, PIBID, physics, pre-service teacher experiences

Procedia PDF Downloads 319

Authors: Sukran Karatas

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Authentic energy network interrelations between the Creator and the creations as well as from creations to creations are the most important points for the worlds of physics and metaphysic to unite together and work in harmony, both within human beings, on the other hand, have the ability to choose their own life style voluntarily. However, it includes the automated involuntary spirit, soul and body working systems together with the voluntary actions, which involve personal, cultural and universal, rational or irrational variable values. Therefore, it is necessary for human beings to know the methods of existing authentic energy network connections to be able to communicate correlate and accommodate the physical and metaphysical entities as a proper functioning unity; this is essential for complete human psychological, biological and social well-being. Authentic knowledge is necessary for human beings to verify the position of self within self and with others to regulate conscious and voluntary actions accordingly in order to prevent oppressions and frictions within self and between self and others. Unfortunately, the absence of genuine individual and universal basic knowledge about how to establish an authentic energy network connection within self, with the deity and the environment is the most problematic issue even in the twenty-first century. The second most problematic issue is how to maintain freedom, equality and justice among human beings during these strictly interwoven network connections, which naturally involve physical, metaphysical and behavioral actions of the self and the others. The third and probably the most complicated problem is the scientific identification and the authentication of the deity. This not only provides the whole power and control over the choosers to set their life orders but also to establish perfect physical and metaphysical links as fully coordinated functional energy network. This thus indicates that choosing an authentic deity is the key-point that influences automated, emotional, and behavioral actions altogether, which shapes human perception, personal actions, and life orders. Therefore, we will be considering the existing ‘four types of energy wave end boundary behaviors’, comprising, free end, fixed end boundary behaviors, as well as boundary behaviors from denser medium to less dense medium and from less dense medium to denser medium. Consequently, this article aims to demonstrate that the authentication and the choice of deity has an important effect on individual psychological, biological and social health. It is hoped that it will encourage new researches in the field of authentic energy network connections to establish the best position and the most correct interrelation connections with self and others without violating the authorized orders and the borders of one another to live happier and healthier lives together. In addition, the book ‘Deity and Freedom, Equality, Justice in History, Philosophy, Science’ has more detailed information for those interested in this subject.

Keywords: deity, energy network, power, freedom, equality, justice, happiness, sadness, hope, fear, psychology, biology, sociology

Procedia PDF Downloads 327

Authors: A. S. Vidyashree, C. M. Kalleshwaraswamy, R. Asokan, H. M. Mahadevaswamy

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Termites are very vital ecological thespians in tropical ecosystem, having been designated as “ecosystem engineers”, due to their significant role in providing soil ecosystem services. Despite their importance, our understanding of a number of their basic biological processes in termites is extremely limited. Developing a better understanding of termite biology is closely dependent upon consistent species identification. At present, identification of termites is relied on soldier castes. But for many species, soldier caste is not reported, that creates confusion in identification. The use of molecular markers may be helpful in estimating phylogenetic relatedness between the termite species and estimating genetic differentiation among local populations within each species. To understand this, termites samples were collected from various places of Western Ghats covering four states namely Karnataka, Kerala, Tamil Nadu, Maharashtra during 2013-15. Termite samples were identified based on their morphological characteristics, molecular characteristics, or both. Survey on the termite fauna in Karnataka, Kerala, Maharashtra and Tamil Nadu indicated the presence of a 16 species belongs to 4 subfamilies under two families viz., Rhinotermitidae and Termitidae. Termititidae was the dominant family which was belonging to 4 genera and four subfamilies viz., Macrotermitinae, Amitermitinae, Nasutitermitinae and Termitinae. Amitermitinae had three species namely, Microcerotermes fletcheri, M. pakistanicus and Speculitermes sinhalensis. Macrotermitinae had the highest number of species belonging two genera, namely Microtermes and Odontotermes. Microtermes genus was with only one species i.e., Microtermes obesi. The genus Odontotermes was represented by the highest number of species (07), namely, O. obesus was the dominant (41 per cent) and the most widely distributed species in Karnataka, Karala, Maharashtra and Tamil nadu followed by O. feae (19 per cent), O.assmuthi (11 per cent) and others like O. bellahunisensis O. horni O. redemanni, O. yadevi. Nasutitermitinae was represented by two genera namely Nasutitermes anamalaiensis and Trinervitermes biformis. Termitinae subfamily was represented by Labiocapritermes distortus. Rhinotermitidae was represented by single subfamily Heterotermetinae. In Heterotermetinae, two species namely Heterotermes balwanthi and H. malabaricus were recorded. Genetic relationship among termites collected from various locations of Western Ghats of India was characterized based on mitochondrial DNA sequences (12S, 16S, and COII). Sequence analysis and divergence among the species was assessed. These results suggest that the use of both molecular and morphological approaches is crucial in ensuring accurate species identification. Efforts were made to understand their evolution and to address the ambiguities in morphological taxonomy. The implication of the study in revising the taxonomy of Indian termites, their characterization and molecular comparisons between the sequences are discussed.

Keywords: isoptera, mitochondrial DNA sequences, rhinotermitidae, termitidae, Western ghats

Procedia PDF Downloads 245

Authors: Kalaya Sribuddhachart, Mayuree Pumipaiboon, Mayuva Youngsabanant-Areekijseree

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The ultrastructure of 20 species of pheasant eggshells in Thailand, (Simese Fireback, Lophura diardi), (Silver Pheasant, Lophura nycthemera), (Kalij Pheasant, Lophura leucomelanos crawfurdii), (Kalij Pheasant, Lophura leucomelanos lineata), (Red Junglefowl, Gallus gallus spadiceus), (Crested Fireback, Lophura ignita rufa), (Green Peafowl, Pavo muticus), (Indian Peafowl, Pavo cristatus), (Grey Peacock Pheasant, Polyplectron bicalcaratum bicalcaratum), (Lesser Bornean Fireback, Lophura ignita ignita), (Green Junglefowl, Gallus varius), (Hume's Pheasant, Syrmaticus humiae humiae), (Himalayan Monal, Lophophorus impejanus), Golden Pheasant, Chrysolophus pictus, (Ring-Neck Pheasant, Phasianus sp.), (Reeves’s Pheasant, Syrmaticus reevesi), (Polish Chicken, Gallus sp.), (Brahma Chicken, Gallus sp.), (Yellow Golden Pheasant, Chrysolophus pictus luteus), and (Lady Amhersts Pheasant, Chrysolophus amherstiae) were studied by Secondary electron imaging (SEI) and Energy dispersive X-ray analysis (EDX) detectors of scanning electron microscope. Generally, all pheasant eggshells showed 3 layers of cuticle, palisade, and mammillary. The total thickness was ranging from 190.28±5.94-838.96±16.31µm. The palisade layer is the most thickness layer following by mammillary and cuticle layers. The palisade layer in all pheasant eggshells consisted of numerous vesicle holes that were firmly forming as network thorough the layer. The vesicle holes in all pheasant eggshells had difference porosity ranging from 0.44±0.11-0.23±0.05 µm. While the mammillary layer was the most compact layer with a variable shape (broad-base V and U-shape) connect to shell membrane. Elemental analysis by of 20 specie eggshells showed 9 apparent elements including carbon (C), oxygen (O), calcium (Ca), phosphorous (P), sulfur (S), magnesium (Mg), silicon (Si), aluminum (Al), and copper (Cu) at the percentage of 28.90- 8.33%, 60.64-27.61%, 55.30-14.49%, 1.97-0.03%, 0.08-0.03%, 0.50-0.16%, 0.30-0.04%, 0.06-0.02%, and 2.67-1.73%, respectively. It was found that Ca, C, and O showed highest elemental compositions, which essential for pheasant embryonic development, mainly presented as composited structure of calcium carbonate (CaCO3) more than 97%. Meanwhile, Mg, S, Si, Al, and P were major inorganic constituents of the eggshells which directly related to an increase of the shell hardness. Finally, the percentage of heavy metal copper (Cu) has been observed in 4 eggshell species. There are Golden Pheasant (2.67±0.16%), Indian Peafowl (2.61±0.13%), Green Peafowl (1.97±0.74%), and Silver Pheasant (1.73±0.11%), respectively. A non-significant difference was found in the percentages of 9 elements in all pheasant eggshells. This study is useful to provide the information of biology and taxonomic of pheasant study in Thailand for conservation.

Keywords: pheasants eggshells, secondary electron imaging (SEI) and energy dispersive X-ray analysis (EDX), morphology, Thailand

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Authors: Georgi Y. Georgiev, Matthew Brouillet

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This research applies the power of agent-based modeling to a pivotal question at the intersection of biology, computer science, physics, and complex systems theory about the self-organization processes in open, complex, non-equilibrium thermodynamic systems. Central to this investigation is the principle of Maximum Entropy Production (MEP). This principle suggests that such systems evolve toward states that optimize entropy production, leading to the formation of structured environments. It is hypothesized that guided by the least action principle, open thermodynamic systems identify and follow the shortest paths to transmit energy and matter, resulting in maximal entropy production, internal structure formation, and a decrease in internal entropy. Concurrently, it is predicted that there will be an increase in system information as more information is required to describe the developing structure. To test this, an agent-based model is developed simulating an ant colony's formation of a path between a food source and its nest. Utilizing the Netlogo software for modeling and Python for data analysis and visualization, self-organization is quantified by calculating the decrease in system entropy based on the potential states and distribution of the ants within the simulated environment. External entropy production is also evaluated for information increase and efficiency improvements in the system's action. Simulations demonstrated that the system begins at maximal entropy, which decreases as the ants form paths over time. A range of system behaviors contingent upon the number of ants are observed. Notably, no path formation occurred with fewer than five ants, whereas clear paths were established by 200 ants, and saturation of path formation and entropy state was reached at populations exceeding 1000 ants. This analytical approach identified the inflection point marking the transition from disorder to order and computed the slope at this point. Combined with extrapolation to the final path entropy, these parameters yield important insights into the eventual entropy state of the system and the timeframe for its establishment, enabling the estimation of the self-organization rate. This study provides a novel perspective on the exploration of self-organization in thermodynamic systems, establishing a correlation between internal entropy decrease rate and external entropy production rate. Moreover, it presents a flexible framework for assessing the impact of external factors like changes in world size, path obstacles, and friction. Overall, this research offers a robust, replicable model for studying self-organization processes in any open thermodynamic system. As such, it provides a foundation for further in-depth exploration of the complex behaviors of these systems and contributes to the development of more efficient self-organizing systems across various scientific fields.

Keywords: complexity, self-organization, agent based modelling, efficiency

Procedia PDF Downloads 43

Authors: Ibtissem Hosni, Lilia Bennaceur Farah, Saber Mohamed Naceur

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In order to assess the water availability in the soil, it is crucial to have information about soil distributed moisture content; this parameter helps to understand the effect of humidity on the exchange between soil, plant cover and atmosphere in addition to fully understanding the surface processes and the hydrological cycle. On the other hand, aerodynamic roughness length is a surface parameter that scales the vertical profile of the horizontal component of the wind speed and characterizes the surface ability to absorb the momentum of the airflow. In numerous applications of the surface hydrology and meteorology, aerodynamic roughness length is an important parameter for estimating momentum, heat and mass exchange between the soil surface and atmosphere. It is important on this side, to consider the atmosphere factors impact in general, and the natural erosion in particular, in the process of soil evolution and its characterization and prediction of its physical parameters. The study of the induced movements by the wind over soil vegetated surface, either spaced plants or plant cover, is motivated by significant research efforts in agronomy and biology. The known major problem in this side concerns crop damage by wind, which presents a booming field of research. Obviously, most models of soil surface require information about the aerodynamic roughness length and its temporal and spatial variability. We have used a bi-dimensional multi-scale (2D MLS) roughness description where the surface is considered as a superposition of a finite number of one-dimensional Gaussian processes each one having a spatial scale using the wavelet transform and the Mallat algorithm to describe natural surface roughness. We have introduced multi-layer aspect of the humidity of the soil surface, to take into account a volume component in the problem of backscattering radar signal. As humidity increases, the dielectric constant of the soil-water mixture increases and this change is detected by microwave sensors. Nevertheless, many existing models in the field of radar imagery, cannot be applied directly on areas covered with vegetation due to the vegetation backscattering. Thus, the radar response corresponds to the combined signature of the vegetation layer and the layer of soil surface. Therefore, the key issue of the numerical estimation of soil moisture is to separate the two contributions and calculate both scattering behaviors of the two layers by defining the scattering of the vegetation and the soil blow. This paper presents a synergistic methodology, and it is for estimating roughness and soil moisture from C-band radar measurements. The methodology adequately represents a microwave/optical model which has been used to calculate the scattering behavior of the aerodynamic vegetation-covered area by defining the scattering of the vegetation and the soil below.

Keywords: aerodynamic, bi-dimensional, vegetation, synergistic

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Authors: Yakup Ulusu, Faruk Ozel, Numan Eczacioglu, Abdurrahman Ozen, Sabriye Acikgoz

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GFP discovered in the mid-1970s, has been used as a marker after replicated genetic study by scientists. In biotechnology, cell, molecular biology, the GFP gene is frequently used as a reporter of expression. In modified forms, it has been used to make biosensors. Many animals have been created that express GFP as an evidence that a gene can be expressed throughout a given organism. Proteins labeled with GFP identified locations are determined. And so, cell connections can be monitored, gene expression can be reported, protein-protein interactions can be observed and signals that create events can be detected. Additionally, monitoring GFP is noninvasive; it can be detected by under UV-light because of simply generating fluorescence. Moreover, GFP is a relatively small and inert molecule, that does not seem to treat any biological processes of interest. The synthesis of GFP has some steps like, to construct the plasmid system, transformation in E. coli, production and purification of protein. GFP carrying plasmid vector pBAD–GFPuv was digested using two different restriction endonuclease enzymes (NheI and Eco RI) and DNA fragment of GFP was gel purified before cloning. The GFP-encoding DNA fragment was ligated into pET28a plasmid using NheI and Eco RI restriction sites. The final plasmid was named pETGFP and DNA sequencing of this plasmid indicated that the hexa histidine-tagged GFP was correctly inserted. Histidine-tagged GFP was expressed in an Escherichia coli BL21 DE3 (pLysE) strain. The strain was transformed with pETGFP plasmid and grown on LuiraBertoni (LB) plates with kanamycin and chloramphenicol selection. E. coli cells were grown up to an optical density (OD 600) of 0.8 and induced by the addition of a final concentration of 1mM isopropyl-thiogalactopyranoside (IPTG) and then grown for additional 4 h. The amino-terminal hexa-histidine-tag facilitated purification of the GFP by using a His Bind affinity chromatography resin (Novagen). Purity of GFP protein was analyzed by a 12 % sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE). The concentration of protein was determined by UV absorption at 280 nm (Varian Cary 50 Scan UV/VIS spectrophotometer). Synthesis of GFP-Polymer composite nanofibers was produced by using GFP solution (10mg/mL) and polymer precursor Polyvinylpyrrolidone, (PVP, Mw=1300000) as starting materials and template, respectively. For the fabrication of nanofibers with the different fiber diameter; a sol–gel solution comprising of 0.40, 0.60 and 0.80 g PVP (depending upon the desired fiber diameter) and 100 mg GFP in 10 mL water: ethanol (3:2) mixtures were prepared and then the solution was covered on collecting plate via electro spinning at 10 kV with a feed-rate of 0.25 mL h-1 using Spellman electro spinning system. Results show that GFP-based nano-fiber can be used plenty of biomedical applications such as bio-imaging, bio-mechanic, bio-material and tissue engineering.

Keywords: biomaterial, GFP, nano-fibers, protein expression

Procedia PDF Downloads 286

Authors: Eashwar V. Somasundaram, Raoul R. Wadhwa, Jacob G. Scott

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The use of radiomics in measuring geometric properties of tumor images such as size, surface area, and volume has been invaluable in assessing cancer diagnosis, treatment, and prognosis. In addition to analyzing geometric properties, radiomics would benefit from measuring topological properties using persistent homology. Intuitively, features uncovered by persistent homology may correlate to tumor structural features. One example is necrotic cavities (corresponding to 2D topological features), which are markers of very aggressive tumors. We develop a data pipeline in R that clusters tumors images based on persistent homology is used to identify meaningful clinical distinctions between tumors and possibly new relationships not captured by established clinical categorizations. A preliminary analysis was performed on 16 Magnetic Resonance Imaging (MRI) breast tissue segments downloaded from the 'Investigation of Serial Studies to Predict Your Therapeutic Response with Imaging and Molecular Analysis' (I-SPY TRIAL or ISPY1) collection in The Cancer Imaging Archive. Each segment represents a patient’s breast tumor prior to treatment. The ISPY1 dataset also provided the estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2) status data. A persistent homology matrix up to 2-dimensional features was calculated for each of the MRI segmentation. Wasserstein distances were then calculated between all pairwise tumor image persistent homology matrices to create a distance matrix for each feature dimension. Since Wasserstein distances were calculated for 0, 1, and 2-dimensional features, three hierarchal clusters were constructed. The adjusted Rand Index was used to see how well the clusters corresponded to the ER/PR/HER2 status of the tumors. Triple-negative cancers (negative status for all three receptors) significantly clustered together in the 2-dimensional features dendrogram (Adjusted Rand Index of .35, p = .031). It is known that having a triple-negative breast tumor is associated with aggressive tumor growth and poor prognosis when compared to non-triple negative breast tumors. The aggressive tumor growth associated with triple-negative tumors may have a unique structure in an MRI segmentation, which persistent homology is able to identify. This preliminary analysis shows promising results in the use of persistent homology on tumor imaging to assess the severity of breast tumors. The next step is to apply this pipeline to other tumor segment images from The Cancer Imaging Archive at different sites such as the lung, kidney, and brain. In addition, whether other clinical parameters, such as overall survival, tumor stage, and tumor genotype data are captured well in persistent homology clusters will be assessed. If analyzing tumor MRI segments using persistent homology consistently identifies clinical relationships, this could enable clinicians to use persistent homology data as a noninvasive way to inform clinical decision making in oncology.

Keywords: cancer biology, oncology, persistent homology, radiomics, topological data analysis, tumor imaging

Procedia PDF Downloads 106

Authors: Zsolt Kotroczó, Katalin Juhos, Áron Béni, Gábor Várbíró, Tamás Kocsis, István Fekete

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Soil organic matter plays an extremely important role in the functioning and regulation processes of ecosystems. It follows that the C content of organic matter in soil is one of the most important indicators of soil fertility. Part of the carbon stored in them is returned to the atmosphere during soil respiration. Climate change and inappropriate land use can accelerate these processes. Our work aimed to determine how soil CO2 emissions change over ten years as a result of organic matter manipulation treatments. With the help of this, we were able to examine not only the effects of the different organic matter intake but also the effects of the different microclimates that occur as a result of the treatments. We carried out our investigations in the area of the Síkfőkút DIRT (Detritus Input and Removal Treatment) Project. The research area is located in the southern, hilly landscape of the Bükk Mountains, northeast of Eger (Hungary). GPS coordinates of the project: 47°55′34′′ N and 20°26′ 29′′ E, altitude 320-340 m. The soil of the area is Luvisols. The 27-hectare protected forest area is now under the supervision of the Bükki National Park. The experimental plots in Síkfőkút were established in 2000. We established six litter manipulation treatments each with three 7×7 m replicate plots established under complete canopy cover. There were two types of detritus addition treatments (Double Wood and Double Litter). In three treatments, detritus inputs were removed: No Litter No Roots plots, No Inputs, and the Controls. After the establishment of the plots, during the drier periods, the NR and NI treatments showed the highest CO2 emissions. In the first few years, the effect of this process was evident, because due to the lack of living vegetation, the amount of evapotranspiration on the NR and NI plots was much lower, and transpiration practically ceased on these plots. In the wetter periods, the NL and NI treatments showed the lowest soil respiration values, which were significantly lower compared to the Co, DW, and DL treatments. Due to the lower organic matter content and the lack of surface litter cover, the water storage capacity of these soils was significantly limited, therefore we measured the lowest average moisture content among the treatments after ten years. Soil respiration is significantly influenced by temperature values. Furthermore, the supply of nutrients to the soil microorganisms is also a determining factor, which in this case is influenced by the litter production dictated by the treatments. In the case of dry soils with a moisture content of less than 20% in the initial period, litter removal treatments showed a strong correlation with soil moisture (r=0.74). In very dry soils, a smaller increase in moisture does not cause a significant increase in soil respiration, while it does in a slightly higher moisture range. In wet soils, the temperature is the main regulating factor, above a certain moisture limit, water displaces soil air from the soil pores, which inhibits aerobic decomposition processes, and so heterotrophic soil respiration also declines.

Keywords: soil biology, organic matter, nutrition, DIRT, soil respiration

Procedia PDF Downloads 42

Authors: Jeet Chakraborty, Sanjay Dutta

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Antibiotic resistance by bacteria has proved to be a severe threat to mankind in recent times, and this fortifies an urgency to design and develop potent antibacterial small molecules/compounds with nonconventional mechanisms than the conventional ones. DNA carries the genetic signature of any organism, and bacteria maintain their genomic DNA inside the cell in a well-regulated compact form with the help of various nucleoid associated proteins like HU, HNS, etc. These proteins control various fundamental processes like gene expression, replication, etc., inside the cell. Alteration of the native DNA structure of bacteria can lead to severe consequences in cellular processes inside the bacterial cell that ultimately result in the death of the organism. The change in the global DNA structure by small molecules initiates a plethora of cellular responses that have not been very well investigated. Echinomycin and Triostin-A are biologically active Quinoxaline small molecules that typically consist of a quinoxaline chromophore attached with an octadepsipeptide ring. They bind to double-stranded DNA in a sequence-specific way and have high activity against a wide variety of bacteria, mainly against Gram-positive ones. To date, few synthetic quinoxaline scaffolds were synthesized, displaying antibacterial potential against a broad scale of pathogenic bacteria. QNOs (Quinoxaline N-oxides) are known to target DNA and instigate reactive oxygen species (ROS) production in bacteria, thereby exhibiting antibacterial properties. The divergent role of Quinoxaline small molecules in medicinal research qualifies them for the evaluation of their antimicrobial properties as a potential candidate. The previous study from our lab has given new insights on a 6-nitroquinoxaline derivative 1d as an intercalator of DNA, which induces conformational changes in DNA upon binding.7 The binding event observed was dependent on the presence of a crucial benzyl substituent on the quinoxaline moiety. This was associated with a large induced CD (ICD) appearing in a sigmoidal pattern upon the interaction of 1d with dsDNA. The induction of DNA superstructures by 1d at high Drug:DNA ratios was observed that ultimately led to DNA condensation. Eviction of invitro-assembled nucleosome upon treatment with a high dose of 1d was also observed. In this work, monoquinoxaline derivatives of 1d were synthesized by various modifications of the 1d scaffold. The set of synthesized 6-nitroquinoxaline derivatives along with 1d were all subjected to antibacterial evaluation across five different bacteria species. Among the compound set, 3a displayed potent antibacterial activity against Staphylococcus aureus bacteria. 3a was further subjected to various biophysical studies to check whether the DNA structural alteration potential was still intact. The biological response of S. aureus cells upon treatment with 3a was studied using various cell biology processes, which led to the conclusion that 3d can initiate DNA damage in the S. aureus cells. Finally, the potential of 3a in disrupting preformed S.aureus and S.epidermidis biofilms was also studied.

Keywords: DNA structural change, antibacterial, intercalator, DNA superstructures, biofilms

Procedia PDF Downloads 146

Authors: Luci V. Hyett

Abstract:

The criminal law of England and Wales currently deems that a person cannot consent to the infliction of injury upon their own body, where the level of harm is considered to be Actual or Grevious. This renders the defence of consent of the victim as being unavailable to those persons carrying out an Alternative Body Modification procedure. However, the criminalization of consensual injury is more appropriately deemed as being categorized as an offense against public morality and not one against the person, which renders the State’s involvement in the autonomous choices of a consenting adult, when determining what can be done to one’s own body, an arbitrary one. Furthermore, to recognise in law that a person is capable of giving a valid consent to socially acceptable cosmetic interventions that largely consist of procedures designed to aesthetically please men and, not those of people who want to modify their bodies for other reasons means that patriarchal attitudes are continuing to underpin public repulsion and inhibit social acceptance of such practices. Theoretical analysis will begin with a juridical examination of R v M(B) [2019] QB 1 where the High Court determined that Alternative Body Modification was not a special category exempting a person so performing from liability for Grevious Bodily Harm using the defence of consent. It will draw from its reasoning which considered that ‘the removal of body parts were medical procedures being carried out for no medical reason by someone not qualified to carry them out’ which will form the basis of this enquiry. It will consider the philosophical work of Georgio Agamben when analysing whether the biopolitical climate in the UK, which places the optimization of the perfect, healthy body at the centre of political concern can explain why those persons who wish to engage in Alternative Body Modification are treated as the ‘Exception’ to that which is normal using the ‘no medical reason’ canon to justify criminalisation, rather than legitimising the industry through regulation. It will consider, through a feminist lens, the current conflict in law between traditional cosmetic interventions which alter one’s physical appearance for socially accepted aesthetic purposes such as those to the breast, lip and buttock and, modifications described as more outlandish such as earlobe stretching, tooth filing and transdermal implants to create horns and spikes under the skin. It will assert that ethical principles relating to the psychological impact of body modification described as ‘alternative’ is used as a means to exclude person’s seeking such a procedure from receiving safe and competent treatment via a registered cosmetic surgeon which leads to these increasingly popular surgery’s being performed in Tattoo parlours throughout the UK as an extension to other socially acceptable forms of self-modification such as piercings. It will contend that only by ‘inclusive exclusion’ will those ‘othered’ through ostracisation be welcomed into the fold of normality and this can only be achieved through recognition of alternative body modification as a legitimate cosmetic intervention, subject to the same regulatory framework as existing practice. This would assist in refocusing the political landscape by erring on the side of liberty rather than that of biology.

Keywords: biopolitics, body modification, consent, criminal law

Procedia PDF Downloads 87

Authors: Sandra Arango-Caro, Kristine Callis-Duehl

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The Education Research and Outreach Lab at the Donald Danforth Plant Science Center established the Plant and Agriculture Augmented and Virtual Reality Learning Laboratory (PAVRLL) to promote science education through professional development, school programs, internships, and outreach events. Professional development is offered to high school and college science and agriculture educators on the use and applications of zSpace and Oculus platforms. Educators learn to use, edit, or create lesson plans in the zSpace platform that are aligned with the Next Generation Science Standards. They also learn to use virtual reality experiences created by the PAVRLL available in Oculus (e.g. The Soybean Saga). Using a cost-free loan rotation system, educators can bring the AVR units to the classroom and offer AVR activities to their students. Each activity has user guides and activity protocols for both teachers and students. The PAVRLL also offers activities for 3D plant modeling. High school students work in teams of art-, science-, and technology-oriented students to design and create 3D models of plant species that are under research at the Danforth Center and present their projects at scientific events. Those 3D models are open access through the zSpace platform and are used by PAVRLL for professional development and the creation of VR activities. Both teachers and students acquire knowledge of plant and agriculture content and real-world problems, gain skills in AVR technology, 3D modeling, and science communication, and become more aware and interested in plant science. Students that participate in the PAVRLL activities complete pre- and post-surveys and reflection questions that evaluate interests in STEM and STEM careers, students’ perceptions of three design features of biology lab courses (collaboration, discovery/relevance, and iteration/productive failure), plant awareness, and engagement and learning in AVR environments. The PAVRLL was established in the fall of 2019, and since then, it has trained 15 educators, three of which will implement the AVR programs in the fall of 2021. Seven students have worked in the 3D plant modeling activity through a virtual internship. Due to the COVID-19 pandemic, the number of teachers trained, and classroom implementations have been very limited. It is expected that in the fall of 2021, students will come back to the schools in person, and by the spring of 2022, the PAVRLL activities will be fully implemented. This will allow the collection of enough data on student assessments that will provide insights on benefits and best practices for the use of AVR technologies in the classrooms. The PAVRLL uses cutting-edge educational technologies to promote science education and assess their benefits and will continue its expansion. Currently, the PAVRLL is applying for grants to create its own virtual labs where students can experience authentic research experiences using real Danforth research data based on programs the Education Lab already used in classrooms.

Keywords: assessment, augmented reality, education, plant science, virtual reality

Procedia PDF Downloads 148

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

Abstract:

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

Procedia PDF Downloads 124

Authors: Petra Gruber, Ariana Rupp, Peter Niewiarowski

Abstract:

This paper presents a concept for a biomimetic fablab as a physical space for education, research and development of innovation inspired by nature. Biomimetics as a discipline finds increasing recognition in academia and has started to be institutionalized at universities in programs and centers. The Biomimicry Research and Innovation Center was founded in 2012 at the University of Akron as an interdisciplinary venture for the advancement of innovation inspired by nature and is part of a larger community fostering the approach of bioimimicry in the Great Lakes region of the US. With 30 faculty members the center has representatives from Colleges of Arts and Sciences (e.g., biology, chemistry, geoscience, and philosophy) Engineering (e.g., mechanical, civil, and biomedical), Polymer Science, and Myers School of Arts. A platform for training PhDs in Biomimicry (17 students currently enrolled) is co-funded by educational institutions and industry partners. Research at the center touches on many areas but is also currently biased towards materials and structures, with highlights being materials based on principles found in spider silk and gecko attachment mechanisms. As biomimetics is also a novel scientific discipline, there is little standardisation in programming and the equipment of research facilities. As a field targeting innovation, design and prototyping processes are fundamental parts of the developments. For experimental design and prototyping, MIT's maker space concept seems to fit well to the requirements, but facilities need to be more specialised in terms of accessing biological systems and knowledge, specific research, production or conservation requirements. For the education and research facility BRIC we conceptualize the concept of a biomimicry fablab, that ties into the existing maker space concept and creates the setting for interdisciplinary research and development carried out in the program. The concept takes on the process of biomimetics as a guideline to define core activities that shall be enhanced by the allocation of specific spaces and tools. The limitations of such a facility and the intersections to further specialised labs housed in the classical departments are of special interest. As a preliminary proof of concept two biomimetic design courses carried out in 2016 are investigated in terms of needed tools and infrastructure. The spring course was a problem based biomimetic design challenge in collaboration with an innovation company interested in product design for assisted living and medical devices. The fall course was a solution based biomimetic design course focusing on order and hierarchy in nature with the goal of finding meaningful translations into art and technology. The paper describes the background of the BRIC center, identifies and discusses the process of biomimetics, evaluates the classical maker space concept and explores how these elements can shape the proposed research facility of a biomimetic fablab by examining two examples of design courses held in 2016.

Keywords: biomimetics, biomimicry, design, biomimetic fablab

Procedia PDF Downloads 251