Relevant bibliographies by topics / Biological mathematic

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  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Academic literature on the topic 'Biological mathematic'

Author: Grafiati
Published: 9 March 2023
Last updated: 10 March 2023

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Journal articles on the topic "Biological mathematic"

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Šorgo, Andrej. "Connecting Biology and Mathematics: First Prepare the Teachers." CBE—Life Sciences Education 9, no. 3 (September 2010): 196–200. http://dx.doi.org/10.1187/cbe.10-03-0014.

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Developing the connection between biology and mathematics is one of the most important ways to shift the paradigms of both established science disciplines. However, adding some mathematic content to biology or biology content to mathematics is not enough but must be accompanied by development of suitable pedagogical models. I propose a model of pedagogical mathematical biological content knowledge as a feasible starting point for connecting biology and mathematics in schools and universities. The process of connecting these disciplines should start as early as possible in the educational process, in order to produce prepared minds that will be able to combine both disciplines at graduate and postgraduate levels of study. Because teachers are a crucial factor in introducing innovations in education, the first step toward such a goal should be the education of prospective and practicing elementary and secondary school teachers.
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Sari, Putri Permata, and Zubaidah Amir MZ. "Pengembangan Lembar Kerja Siswa (LKS) Berbasis Model Pembelajaran Realistic Mathematic Education (RME) Pada Materi Bangun Ruang Sisi Datar." JURING (Journal for Research in Mathematics Learning) 4, no. 3 (November 2, 2021): 269. http://dx.doi.org/10.24014/juring.v4i3.14024.

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Penelitian ini merupakan penelitian pengembangan dengan menggunakan model ADDIE (Analysis, Design, Development, Implementation dan Evaluation ). Penelitian ini bertujuan untuk menghasilkan Lembar Kerja Siswa Berbasis Model Pembelajaran Realistic Mathematic Education (RME) yang valid, praktis dan efektif. Penelitian ini dilakukan di SMP Negeri 2 Rambah Samo, Kab. Rokan Hulu, Riau. Subjek penelitian ini adalah para ahli yang bersala dari dosen, guru dan siswa SMPN 2 Rambah Samo. Objek penelitian ini adalah LKS berbasis Model Pembelajaran Realistic Mathematic Education (RME). Jenis data yang digunakan berupa data kuntitatif dan kualitatif. Berdasarkan uji validitas, LKS berbasis Model Pembelajaran Realistic Mathematic Education (RME) dinyatakan dalam kategori sangat valid dengan tingkat kevalidan 98,45%. Berdasarkan uji kepraktisan, LKS berbasis Model Pembelajaran Realistic Mathematic Education (RME) dinyatakan kategori sangat praktis dengan persentase tingkat kepraktisan 97,08%. Berdasarkan hasil posttest diperoleh nilai sebesar 4,64 dan nilai pada taraf signifikan 5% sebesar 1,73 maka > atau 4,64 > 1,73. Sehingga diterima dan ditolak. Hal tersebut menunjukkan bahwa LKS matematika berbasis Model Pembelajaran Realistic Mathematic Education (RME) yang telah dikembangkan ini memiliki dampak terhadap hasil belajar siswa pada materi bangun ruang sisi datar
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XIE, FEI, PHILLIP C. Y. SHEU, ARTHUR LANDER, and VITTORIO CRISTINI. "SEMANTIC ANALYSIS AND SYNTHESIS OF COMPLEX BIOLOGICAL SYSTEMS." International Journal of Software Engineering and Knowledge Engineering 15, no. 03 (June 2005): 547–69. http://dx.doi.org/10.1142/s0218194005002415.

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In general biologists are not accustomed to formulating biological problems in the precise mathematical terms that are required to solve the problems analytically or numerically. Although many computational tools for systems biology have been developed recently, our observations indicate that many of these tools are powerful only in the hands of those who know a lot about how to use them. For most biologists, the tools have a protracted learning curve and unfriendly user interface that often diminish their likelihood of being used. Our long-term goal is to build a knowledge system that allows biologists to synthesize complex biological systems via natural language interactions, and the system is able to generate the corresponding mathematical descriptions so that the often cumbersome communication process between biologists and mathematicians/engineers in formulating complex biological problems in mathematic terms can be performed more easily. To focus, the first goal in this research is to build a knowledge system prototype that focuses on transport related biological problems that occur from the cellular to tissue level. We address specifically two inter-related problems: (1) Provision of an intelligent system that is capable of automatically synthesizing smaller components into more complex systems; Provision of a user-friendly and natural language interface.
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Li, Xin Yu, Bing Liu, Si Ze Li, and Shu Sen Liu. "Numerical Simulations of Biological Droplet Transport in an Indoor Environment." Advanced Materials Research 356-360 (October 2011): 862–66. http://dx.doi.org/10.4028/www.scientific.net/amr.356-360.862.

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In this paper, the biological droplet transport and deposition in the turbulent airflow inside an indoor environment was studied using the Lagrangian computational method. Meanwhile, as to the mathematic simulation, the Monte Carlo modeling method was coupled into this simulation program to describe the bio-particle transport. Many influent factors such as indoor airflow velocity, the bio-aerosol generator velocity, particle diameter, and evaporation and death were considered synthetically in this paper. Serratia marcescens was used as tracer microorganism to simulate the droplet nuclei exhaled by patients, and the spatial distribution of its concentration was measured. Collected bacteria were quantified using standard cultivating assays. It showed the simulation results were comparable with the data of the experimental findings.
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Zhang, Cheng, Ning Wang, Yu Xu, Hor‐Yue Tan, and Yibin Feng. "Identification of Key Contributive Compounds in a Herbal Medicine: A Novel Mathematic—Biological Evaluation Approach." Advanced Theory and Simulations 4, no. 6 (May 4, 2021): 2000279. http://dx.doi.org/10.1002/adts.202000279.

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Wahyuni, Hanny Indrat, Retno Iswarin Pujaningsih, and Padwi Anwar Sayekti. "Kajian Nilai Energi Metabolis Biji Sorghum Melalui Teknologi Sangrai Pada Ayam Petelur Periode Afkir." Jurnal Agripet 8, no. 1 (April 1, 2008): 25–30. http://dx.doi.org/10.17969/agripet.v8i1.605.

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Evaluation of metabolic energy value of roasted sorghum in culled laying chickens ABSTRACT. Tannin contained in sorghum can be reduced by using technology processing such as roasting. By using this way, husk of sorghum can be removed leading to decrease of tannin content which is reflected by the value of metabolism energy. The purpose of this experiment is to investigate the effect of roasted sorghum on metabolism energy of culled laying chickens. Measurement of metabolic energy as mathematic is used as comparison. The material used in his experiment was red sorghum, water, and 39 culled laying chickens. Equipment used in this experiment was balance, roasting tool, plastic, force feeding equipment, metabolism cages and bomb calori-meter. This experiment used completely randomized design consisting of 4 treatments and 4 replications (each replication 3 chickens). Treatment consisted of T0 = no roasted sorghum, T1 = roasted for 5 minutes and T2 = roasted for 10 minutes. Data collected were metabolism energy of roasted sorghum both biologically (force feeding) and mathematically (proximate analysis) at culled laying chickens. All data were statistically calculated, further statistically was conducted by using Duncan and compression of metabolism energy was calculated by using t-Test. The results show that, no statistically effect (p0, 05) on duration of roasting on metabolism energy of sorghum. Based on t-Test analysis, there was a significantly difference (p0, 05) between biological metabolism and mathematical metabolism. From this experiment, it can be concluded that 10 minutes of roasting cannot increase of sorghum metabolic energy. The average of biological metabolic was lower (3105, 94 kcal/kg) compared to the average of mathematical metabolic energy (3766, 82 kcal/kg).
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Yu, Zhong Hai, Tian Chen, Di Shi Liu, and Jing Wang. "Study on the Optimized Cutting Parameters for the Nuclear Channel Head." Applied Mechanics and Materials 121-126 (October 2011): 3534–40. http://dx.doi.org/10.4028/www.scientific.net/amm.121-126.3534.

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As one of the key components of the nuclear power equipments, the nuclear channel head has a complicated shape and is difficult to be machined. In this paper, the optimal combination of cutting parameters of large-scale nuclear channel head is researched. Considering the machining requirements and machining conditions, the cutting parameters optimized mathematical model is established to achieve the goal of maximum production efficiency. Meanwhile, the target functions and the corresponding constraint functions are analyzed. Finally, by using genetic algorithm of simulating biological evolution, the mathematic models of cutting parameters of CNC machining are compared and optimized. Then the optimized results are compared with the cutting parameters obtained through the trial-producing experience and manual of a small-size channel head. We conclude that the optimized cutting parameters can greatly increase the CNC machining efficiency of Nuclear Channel Head.
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Hayya, Adieba Warda. "The Creative Thinking Skill of Biological Learning Students at Candi Baru High School." Journal Of Biology Education 4, no. 2 (November 18, 2021): 164. http://dx.doi.org/10.21043/jobe.v4i2.10187.

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<p class="Default">The aim of this study was to describe the skill of students to think creatively about Biology at Candi Baru high school (HS). The study used a qualitative approach using a case study method. The population in this study was students of Candi Baru HS from the academic year 2016/2017. This research uses randomized cluster sampling. Samples were XI Mathematic and Science (MIA) 6, 7, and 8 classes. Data collected by observation and document collection, using a human instrument, an observation sheet and a categorization sheet. Data research included the quality of the student's; answers, works, and responses during the learning process. Data analysis was carried out descriptively by comparing the results of the research with information derived from literature or theory. The results showed that students' level of creative thinking skill is still low and the assessment provided by the teacher has not reached the students' creative thinking skill.</p>
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Liang, Xin Li, Dan Lv, Juan Luo, Xue Jing Guan, and Zheng Gen Liao. "Application Research of Lipid Microsphere Biological Carrier Material on Prescription of Tanshinone II a Lipid Microsphere by Central Composite Design-Response Surface Method." Advanced Materials Research 1120-1121 (July 2015): 834–41. http://dx.doi.org/10.4028/www.scientific.net/amr.1120-1121.834.

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To optimize the prescription of tanshinone IIA lipid microspheres by central composite design method, and evaluate the quality. Through evaluating average particle size, stability constant and the encapsulation efficiency of the lipid microsphere to investigate the concentration of the egg yolk lecithin and the poloxamer and the percentage of Soybean oil in the total oil phase which may impact the properties of tanshinone IIA lipid microsphere. Building the mathematic relation between the index and factor by the binomial expression, according to the best mathematical model of the evaluation indicators to describe response surface and then to use response surface method to predict the best prescription which will be analysed. According to the prescription optimization to prepare tanshinone IIA lipid microsphere and evaluate its quality. The results showed that each index of the binomial equation fitting is good, the correlation coefficient of the average particle size, stability constant and the encapsulation efficiency are 0.97, 0.92 and 0.84 respectively. The optimized prescription is as follows: egg yolk lecithin1.38 g, F68 0.19 g, LCT 2 g, MCT 18 g, all the indexes of the optimized prescription are similar to the target values.
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Filipchuk, O. V., and O. M. Gurov. "PECULIARITIES OF APPLYING BALLISTIC GEL AS A SIMULATOR OF HUMAN BIOLOGICAL TISSUES." Theory and Practice of Forensic Science and Criminalistics 15 (November 30, 2016): 367–73. http://dx.doi.org/10.32353/khrife.2015.46.

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The study of a mechanism of gunshot wound formation is the main task of wound ballistics. The damaging effect of the wounding projectile (the regularities in the formation of a temporary pulsating cavity) can be studied the most effectively as part of an experiment on simulators whose physical properties (density, elasticity, the capacity to absorb energy) resemble the tissues of a living human. The article presents modern capacities of applying ballistic gel as the most representative biological simulator of a living human s tissues. The article suggests priority methods ofmaking blocks of gel, the conditions of conducting the experiment and mathematic processing of data from the perspective wounding ballistics. Due to the elastic properties of gel, the temporary pulsating cavity that emerges in the course of the wounding projectile in the same way as the living tissues collapse with the permanent wound tract. In order to evaluate the volume of the damaging effect of the wounding projectile there are used standard calculation methods: the fissure surface area (FSA), wound profile method (WPM), the total crack length method (TCL).
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Dissertations / Theses on the topic "Biological mathematic"

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AFFILI, ELISA. "EVOLUTION EQUATIONS WITH APPLICATIONS TO POPULATION DYNAMICS." Doctoral thesis, Università degli Studi di Milano, 2021. http://hdl.handle.net/2434/820854.

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The main topic of this thesis is the analysis of evolution equations reflecting issues in ecology and population dynamics. In mathematical modelling, the impact of environmental elements and the interaction between species is read into the role of heterogeneity in equations and interactions in coupled systems. In this direction, we investigate three separate problems, each corresponding to a chapter of this thesis. The first problem addresses the evolution of a single population living in a periodic medium with a fast diffusion line; this corresponds to the study of a reaction-diffusion system with equations in different dimensions. We derive results on asymptotic behaviour through the study of some generalised principal eigenvalues. We find that the road has no impact on the survival chances of the population, despite the deleterious effect expected from fragmentation. The second investigation regards a model describing the competition between two populations in a situation of asymmetrically aggressive interactions; this consists of a system of two ODEs. The evolution progresses through two possible scenarios, where only one population survives. Then, the interpretation of one of the parameters as the aggressiveness of the attacker population naturally raises questions of controllability. We characterise the set of initial conditions leading to the victory of the attacker through a suitable (possibly time-dependant) strategy. The third and last part of this thesis analyses the time decay of some evolution equations with classical and fractional time derivatives. Depending on the type of derivative and some degree of non-degeneracy of the spatial operator, quantitative polynomial or exponential estimates are entailed.
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El-Hachem, Maud. "Mathematical models of biological invasion." Thesis, Queensland University of Technology, 2022. https://eprints.qut.edu.au/232864/1/Maud_El-Hachem_Thesis.pdf.

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This thesis studies mathematical models of a population of cells invading the surrounding environment or another living population. A classical single-species model is reformulated using a moving boundary to track the position of the moving front of the invading population. The moving boundary is also used to separate two populations. Other models studied are coupled partial differential equations to describe the interaction of a population with another one. Different types of interaction are represented: the degradation of healthy skin by cancer and the growth of bone tissue on substrate.
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Hodgkinson, Arran. "Mathematical Methods for Modelling Biological Heterogeneity." Thesis, Montpellier, 2019. http://www.theses.fr/2019MONTS119.

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Les processus biologiques sont des phénomènes complexes, multi-échelles, présentant une hétérogénéité importante à travers l’espace, la structure et la fonction. De plus, ils impliquent des événements fortement corrélés et présentent des boucles de rétroaction à travers les échelles. Dans cette thèse, nous utilisons des représentations spatio-structuro-temporelles en grande dimension pour étudier l'hétérogénéité biologique à travers l'espace, la fonction biologique et le temps, et appliquons cette méthode à divers problèmes importants en biologie et en clinique.Nous commençons par introduire un nouveau cadre spatio-structuro-temporel, basé sur équations aux dérivées partielles, pour le cas d’un système biologique dont la fonction dépend de la dynamique dans le temps et l’espace des récepteurs membranaires, des ligands et du métabolisme. Afin d’étudier les solutions de ces équations, nous utilisons un schéma numérique de différences finies ainsi que divers résultats analytiques. Pour tester la validité de nos approches numériques nous prouvons un théorème sur la stabilité de notre schéma.Le cancer est un problème croissant pour la population mondiale, car ses taux d'incidence et sa résistance aux médicaments augmentent. D’abord nous modélisons l’invasion du cancer du sein agressif via sa capacité à produire des enzymes dégradant la matrice extracellulaire, et nous montrons la génération de structures spatiales anatomo-pathologiques difficiles à enlever par la chirurgie. Ensuite, nous développons des modèles mathématiques de tumeurs résistantes au traitement et appliquons ces modèles à la résistance aux thérapies ciblées (inhibiteurs de BRAF et de MEK) du mélanome cutané. Nous constatons que les tumeurs développent une résistance à la fois à travers des processus d'adaptations génétiques ou par le remodelage de leur métabolisme, mais montrons que seules les tumeurs métaboliquement plastiques manifestent une re-sensibilisation à ces thérapies. Enfin, via une approche basée sur des données d’expression en cellule unique (RNA-seq), nous montrons que la dynamique spatiale contribue à l'hétérogénéité tumorale et à la résistante aux traitements de façon liée au statut prolifératif des cellules cancéreuses.Nous appliquons nos méthodes à deux autres systèmes. Dans le contexte de la réponse immunitaire à l’infection virale, nous étudions la production et la dynamique spatiale de l’interféron (IFN) et l’apparent paradoxe de la conservation de molécules d’IFN avec affinités faibles et fortes. Nous constatons que les molécules IFN de faible affinité sont plus capables de se propager dans l'espace, alors que les molécules de haute affinité sont capables de maintenir le signal localement. L’addition de ligands de faible affinité à un système ne comprenant que des ligands de moyenne ou grande affinité peut entraîner une diminution de la charge virale d’environ 23%. Ensuite, nous explorons le contexte de la sélection sexuelle de l'apparence masculine dans l'évolution darwinienne. Nous constatons que les systèmes biologiques conservent les traits sélectionnés sexuellement, même si cela entraîne une diminution générale de la population.Enfin, nous introduisons deux autres techniques de modélisation: pour augmenter la dimensionnalité de notre approche, nous développons une approche pseudo-spectrale basée sur les polynômes de Chebyshev et l’appliquons au même scénario de résistance aux médicaments phénotypiques que ci-dessus. Ensuite, pour étudier un scénario coopératif dans lequel des cellules cancéreuses prolifératives et invasives sont co-injectées, induisant des comportements invasifs dans les cellules prolifératives, nous développons une nouvelle méthode de simulation combinant des automates cellulaires et systèmes d’agents. Nous trouvons que cette méthode est capable de reproduire les résultats de l'expérience de coinjection et d'autres expériences dans lesquelles des cellules ont été placées dans des micropistes de collagène
Biological processes are complex, multi-scale phenomena displaying extensive heterogeneity across space, structure, and function. Moreover, these events are highly correlated and involve feedback loops across scales, with nuclear transcription being effected by protein concentrations and vice versa, presenting a difficulty in representing these through existing mathematical approaches. In this thesis we use higher-dimensional spatio-structuro-temporal representations to study biological heterogeneity through space, biological function, and time and apply this method to various scenarios of significance to the biological and clinical communities.We begin by deriving a novel spatio-structuro-temporal, partial differential equation framework for the general case of a biological system whose function depends upon dynamics in time, space, surface receptors, binding ligands, and metabolism. In order to simulate solutions for this system, we present a numerical finite difference scheme capable of this and various analytic results connected with this system, in order to clarify the validity of our predictions. In addition to this, we introduce a new theorem establishing the stability of the central differences scheme.Despite major recent clinical advances, cancer incidence continues to rise and resistance to newly synthesised drugs represents a major health issue. To tackle this problem, we begin by investigating the invasion of aggressive breast cancer on the basis of its ability to produce extracellular matrix degrading enzymes, finding that the cancer produced a surgically challenging morphology. Next, we produce a novel structure in which models of cancer resistance can be established and apply this computational model to study genetic and phenotypic modes of resistance and re-sensitisation to targeted therapies (BRAF and MEK inhibitors). We find that both genetic and phenotypic heterogeneity drives resistance but that only the metabolically plastic, phenotypically resistant, tumour cells are capable of manifesting re-sensitisation to these therapies. We finally use a data-driven approach for single-cell RNA-seq analysis and show that spatial dynamics fuel tumour heterogeneity, contributing to resistance to treatment accordingly with the proliferative status of cancer cells.In order to expound this method, we look at two further systems: To investigate a case where cell-ligand interaction is particularly important, we take the scenario in which interferon (IFN) is produced upon infection of the cell by a virus and ask why biological systems evolve and retain multiple different affinities of IFN. We find that low affinity IFN molecules are more capable of propagating through space; high affinity molecules are capable of sustaining the signal locally; and that the addition of low affinity ligands to a system with only medium or high affinity ligands can lead to a ~23% decrease in viral load. Next, we explore the non-spatial, structuro-temporal context of male elaboration sexual and natural selection in Darwinian evolution. We find that biological systems will conserve sexually selected traits even in the event where this leads to an overall population decrease, contrary to natural selection.Finally, we introduce two further modelling techniques: To increase the dimensionality of our approach, we develop a pseudo-spectral Chebyshev polynomial-based approach and apply this to the same scenario of phenotypic drug resistance as above. Next, to deal with one scenario in which proliferative and invasive cancer cells are co-injected, inducing invasive behaviours in the proliferative cells, we develop a novel agent-based, cellular automaton method and associated analytic theorems for generating numerical solutions. We find that this method is capable of reproducing the results of the co-injection experiment and further experiments, wherein cells migrate through artificially produced collagen microtracks
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Ohlsson, Henrik. "Mathematical Analysis of a Biological Clock Model." Thesis, Linköping University, Department of Electrical Engineering, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-6750.

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Have you thought of why you get tired or why you get hungry? Something in your body keeps track of time. It is almost like you have a clock that tells you all those things.

And indeed, in the suparachiasmatic region of our hypothalamus reside cells which each act like an oscillator, and together form a coherent circadian rhythm to help our body keep track of time. In fact, such circadian clocks are not limited to mammals but can be found in many organisms including single-cell, reptiles and birds. The study of such rhythms constitutes a field of biology, chronobiology, and forms the background for my research and this thesis.

Pioneers of chronobiology, Pittendrigh and Aschoff, studied biological clocks from an input-output view, across a range of organisms by observing and analyzing their overt activity in response to stimulus such as light. Their study was made without recourse to knowledge of the biological underpinnings of the circadian pacemaker. The advent of the new biology has now made it possible to "break open the box" and identify biological feedback systems comprised of gene transcription and protein translation as the core mechanism of a biological clock.

My research has focused on a simple transcription-translation clock model which nevertheless possesses many of the features of a circadian pacemaker including its entrainability by light. This model consists of two nonlinear coupled and delayed differential equations. Light pulses can reset the phase of this clock, whereas constant light of different intensity can speed it up or slow it down. This latter property is a signature property of circadian clocks and is referred to in chronobiology as "Aschoff's rule". The discussion in this thesis focus on develop a connection and also a understanding of how constant light effect this clock model.

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Magi, Ross. "Dynamic behavior of biological membranes." Thesis, The University of Utah, 2015. http://pqdtopen.proquest.com/#viewpdf?dispub=3680576.

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Biological membranes are important structural units in the cell. Composed of a lipid bilayer with embedded proteins, most exploration of membranes has focused on the proteins. While proteins play a vital role in membrane function, the lipids themselves can behave in dynamic ways which affect membrane structure and function. Furthermore, the dynamic behavior of the lipids can affect and be affected by membrane geometry. A novel fluid membrane model is developed in which two different types of lipids flow in a deforming membrane, modelled as a two-dimensional Riemannian manifold that resists bending. The two lipids behave like viscous Newtonian fluids whose motion is determined by realistic physical forces. By examining the stability of various shapes, it is shown that instability may result if the two lipids forming the membrane possess biophysical qualities, which cause them to respond differently to membrane curvature. By means of numerical simulation of a simplified model, it is shown that this instability results in curvature induced phase separation. Applying the simplified model to the Golgi apparatus, it is hypothesized that curvature induced phase separation may occur in a Golgi cisterna, aiding in the process of protein sorting.

In addition to flowing tangentially in the membrane, lipids also flip back and forth between the two leaflets in the bilayer. While traditionally assumed to occur very slowly, recent experiments have indicated that lipid flip-flop may occur rapidly. Two models are developed that explore the effect of rapid flip-flop on membrane geometry and the effect of a pH gradient on the distribution of charged lipids in the leaflets of the bilayer. By means of a stochastic model, it is shown that even the rapid flip-flop rates observed are unlikely to be significant inducers of membrane curvature. By means of a nonlinear Poisson- Boltzmann model, it is shown that pH gradients are unlikely to be significant inducers of bilayer asymmetry under physiological conditions.

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Chindelevitch, Leonid Alexandrovich. "Extracting information from biological networks." Thesis, Massachusetts Institute of Technology, 2010. http://hdl.handle.net/1721.1/64607.

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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Mathematics, 2010.
Cataloged from PDF version of thesis.
Includes bibliographical references (p. 175-194).
Systems biology, the study of biological systems in a holistic manner, has been catalyzed by a dramatic improvement in experimental techniques, coupled with a constantly increasing availability of biological data. The representation and analysis of this heterogeneous data is facilitated by the powerful abstraction of biological networks. This thesis examines several types of these networks and looks in detail at the kind of information their analysis can yield. The first part discusses protein interaction networks. We introduce a new algorithm for the pairwise alignment of these networks. We show that these alignments can provide important clues to the function of proteins as well as insights into the evolutionary history of the species under examination. The second part discusses regulatory networks. We present an approach for validating putative drug targets based on the information contained in these networks. We show how this approach can also be used to discover drug targets. The third part discusses metabolic networks. We provide new insights into the structure of constraint-based models of cell metabolism and describe a methodology for performing a complete analysis of a metabolic network. We also present an implementation of this methodology and discuss its application to a variety of problems related to the metabolism of bacteria. The final part describes an application of our methodology to Mycobacterium tuberculosis, the pathogen responsible for almost 2 million deaths around the world every year. We introduce a method for reconciling metabolic network reconstructions and apply it to merge the two published networks for tuberculosis. We analyze the merged network and show how it can be refined based on available experimental data to improve its predictive power. We conclude with a list of potential drug targets.
by Leonid Alexandrovich Chindelevitch.
Ph.D.
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Altschul, Stephen Frank. "Aspects of biological sequence comparison." Thesis, Massachusetts Institute of Technology, 1987. http://hdl.handle.net/1721.1/102708.

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Thesis (Ph. D)--Massachusetts Institute of Technology, Dept. of Mathematics, 1987.
This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.
Bibliography: leaves 165-168.
by Stephen Frank Altschul.
Ph.D
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Basse, Britta. "Case studies in mathematical modelling for biological conservation." Thesis, University of Canterbury. Mathematics & Statistics, 1999. http://hdl.handle.net/10092/4804.

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The use of mathematical modelling as a tool for investigating selected topics in conservation biology is the focus of this thesis. A continuous system of partial and ordinary differential equations model the age structured population dynamics of a cohort of endemic, threatened New Zealand North Island brown kiwi, Apteryx mantelli. Critical predation and recruitment rates of immature birds are estimated. Stoats, Mustela erminea, are the main predator of immature kiwi. A refinement to the model allows the calculation of acceptable stoat densities. In order to reduce stoats to this critical density, a linear system of ordinary differential equations, representing an acute secondary poisoning regime, is solved. An optimal secondary poisoning scheme, which minimises the number of prey poisoned and the amount of poison used, is found. The minimum area required for pest control is estimated by simulating the dispersal of sub-adult kiwi using a discrete random walk approach. Simulations and a discrete age structured model are used to investigate pulsed management strategies for both kiwi and kokako, Callaeas cinerea wilsoni. Finally, a two dimensional discrete random walk is generalised and a continuous diffusion equation is derived. A diffusion equation is incorporated into a S1 R (Susceptible, Infected, Recovered) model representing the natural spread of Rabbit Haemorrhagic Disease from a point source in rabbit, Oryctolagus cuniculus cuniculus, populations. The speed for the virus, dependant on certain model parameters, is found and the minimum initial population density, below which the wave of infection will not travel, is estimated. All specific models discussed throughout the thesis are generic by nature and can be applied to a diverse range of subjects.
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Grau, Ribes Alexis. "Mathematical models of transport phenomena in biological tissues." Doctoral thesis, Universite Libre de Bruxelles, 2020. https://dipot.ulb.ac.be/dspace/bitstream/2013/303032/4/contents.pdf.

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Cette thèse est consacrée à l’élaboration et l’étude théorique de modèles de transport décrivant les dynamiques cellulaires et la communication intercellulaire dans les tissus épithéliaux. Nous nous intéressons d’abord à l’influence du transport de microARNs (miRNAs) sur la dynamique spatiotemporelle de réseaux de régulation génétique. Ces courtes séquences d’ARN régulent la synthèse des protéines en bloquant l’activité des ARN messagers et leur sécrétion via des vesicules extracellulaires en font des agents de communication intercellulaire. Différents modèles faisant intervenir des miRNAs extracellulaires ont été construits et étudiés numériquement. Les premiers sont des modèles génériques destinés à mettre en évidence l'effet d'une cellule ayant une production de miRNAs anormale sur l'expression génétique dans les cellules voisines. Nous abordons ensuite des modèles plus complexes et réalistes dans lesquels des oscillations (liées à des rythmes biologiques) et de la bistabilité (liée à une différenciation cellulaire) sont observées. Ces modèles permettent d’étudier des dynamiques de communication complexes observées en biologie, comme la synchronisation de cellules couplées ou la propagation d'un changement de phénotype. Nous mettons également en évidence le rôle de défauts, tels que des mutations génétiques ou encore des variations de densité cellulaire dans les tissus, sur ces phénomènes de propagation. La deuxième partie de la thèse est dédiée à la construction de modèles de réaction-diffusion dans lesquels la dynamique des cellules dépend de leur état interne. Sur base d’études expérimentales montrant l’influence de protéines et de miRNAs sur la mobilité et la prolifération des cellules, nous établissons un modèle multi-échelle dans lequel la dynamique intracellulaire et le mouvement des cellules interagissent. En effet, certaines protéines sont responsables de l’adhésion cellulaire ou régulent la vitesse de prolifération. Dans notre modèle, chaque cellule synthétise ces espèces d’intérêt et les processus cellulaires (migration, prolifération) dépendent de la concentration de ces espèces biochimiques. Ce modèle permet de reproduire des expériences de migration cellulaire et de prédire, notamment, l'influence d'E-cadherin, une protéine clé dans l'adhesion cellulaire, sur la dynamique de régénération d'un tissu.
Doctorat en Sciences
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Orme, Belinda Abigail Amanda. "Biological mixing and chaos." Thesis, University of Birmingham, 2002. http://etheses.bham.ac.uk//id/eprint/7637/.

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We consider a problem from the field of biological fluid mechanics which considers the flow associated with the motion of a flagellum on a sessile micro-organism. Motivation is taken from the movement of fluid around a species of choanoflagellate, \(Salpingoeca\) \(Amphoridium\). Choanoflagellates are a class of organism in the phylum Protozoa. Because the length scales and velocities are very low, the flow is one dominated by viscous forces and the environment is characterised by a low Reynolds number. The flow caused by the flagellum is initially modelled via a point force. These microorganisms operate in more than one location and the motion they create is modelled in a qualitative sense by using two stokeslets (appropriate to Stokes' flow) whose orientation and position is varied with time. The sessile micro-organism resides above a boundary which is modelled, most generally, as an interface between two fluids possessing different properties. Efficiency of feeding currents generated by the flagellum motion is studied. The resulting dynamics are investigated using chaotic measures, which examine the stretching and consequent mixing of elements within the fluid. Different point force locations lead to various eddy structures such that their superposition results in chaotic advection. The model is developed to examine the flow of particles around a three-dimensional realisation of a micro-organism which involves a flagellum and a cell body attached to a substrate. Green's functions are used to satisfy a number of boundary conditions simultaneously. Particle paths of a tracer introduced into the fully three-dimensional model are investigated. Comparisons with experimental data illustrate good agreement between theoretical and experimental results. Further extensions to the model are suggested.
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Books on the topic "Biological mathematic"

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K, Maini Philip, and Othmer H. G. 1943-, eds. Mathematical models for biological pattern formulation: Frontiers in biological mathematics. New York: Springer, 2001.

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Bill, Broadhurst, and Hladky S. B, eds. Mathematics for biological scientists. New York, NY: Garland Science, 2009.

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1960-, Deutsch Andreas, ed. Mathematical modeling of biological systems. Boston: Birkhauser, 2007.

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Lewis, Mark A., Sergei V. Petrovskii, and Jonathan R. Potts. The Mathematics Behind Biological Invasions. Cham: Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-32043-4.

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Banks, H. Thomas. Mathematical and experimental modeling of physical and biological processes. Boca Raton: Chapman & Hall/CRC, 2009.

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Local stereology. Singapore: World Scientific, 1998.

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Friedman, Avner, and Chiu-Yen Kao. Mathematical Modeling of Biological Processes. Cham: Springer International Publishing, 2014. http://dx.doi.org/10.1007/978-3-319-08314-8.

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Ohira, Toru, and Tohru Uzawa, eds. Mathematical Approaches to Biological Systems. Tokyo: Springer Japan, 2015. http://dx.doi.org/10.1007/978-4-431-55444-8.

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Deutsch, Andreas, Lutz Brusch, Helen Byrne, Gerda de Vries, and Hanspeter Herzel, eds. Mathematical Modeling of Biological Systems. Boston, MA: Birkhäuser Boston, 2007. http://dx.doi.org/10.1007/978-0-8176-4558-8.

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Mathematical models of biological systems. Oxford: Oxford University Press, 2011.

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Book chapters on the topic "Biological mathematic"

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Khyar, Omar, Adil Meskaf, and Karam Allali. "Mathematic Analysis of a SIHV COVID-19 Pandemic Model Taking Into Account a Vaccination Strategy." In Trends in Biomathematics: Stability and Oscillations in Environmental, Social, and Biological Models, 211–23. Cham: Springer International Publishing, 2022. http://dx.doi.org/10.1007/978-3-031-12515-7_11.

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Kimmel, Marek, and David E. Axelrod. "Biological Background." In Interdisciplinary Applied Mathematics, 19–36. New York, NY: Springer New York, 2015. http://dx.doi.org/10.1007/978-1-4939-1559-0_2.

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Kimmel, Marek, and David E. Axelrod. "Biological Background." In Interdisciplinary Applied Mathematics, 19–31. New York, NY: Springer New York, 2002. http://dx.doi.org/10.1007/0-387-21639-1_2.

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Britton, Nicholas Ferris. "Biological Motion." In Springer Undergraduate Mathematics Series, 147–73. London: Springer London, 2003. http://dx.doi.org/10.1007/978-1-4471-0049-2_5.

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Voit, Eberhard O. "The Mathematics of Biological Systems." In A First Course in Systems Biology, 83–134. Second edition. | New York : Garland Science, 2017.: Garland Science, 2017. http://dx.doi.org/10.4324/9780203702260-4.

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Stamova, Ivanka, and Gani Stamov. "Impulsive Biological Models." In CMS Books in Mathematics, 41–112. Cham: Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-28061-5_3.

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Lancaster, H. O. "Mathematics and Epidemiology." In Quantitative Methods in Biological and Medical Sciences, 139–51. New York, NY: Springer New York, 1994. http://dx.doi.org/10.1007/978-1-4612-2658-1_12.

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Murray, J. D. "Biological Oscillators and Switches." In Interdisciplinary Applied Mathematics, 218–56. New York, NY: Springer New York, 1993. http://dx.doi.org/10.1007/978-0-387-22437-4_7.

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Lewis, Mark A., Sergei V. Petrovskii, and Jonathan R. Potts. "Dynamics of Biological Invasions." In Interdisciplinary Applied Mathematics, 19–68. Cham: Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-32043-4_2.

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Efendiev, Messoud. "Biological Background." In Mathematical Modeling of Mitochondrial Swelling, 27–35. Cham: Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-319-99100-9_2.

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Conference papers on the topic "Biological mathematic"

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Zakiyah, R. Nur, Ibrohim, and Hadi Suwono. "The influence of science, technology, engineering, mathematic (STEM) based biology learning through inquiry learning models towards students’ critical thinking skills and mastery of biological concepts." In THE 4TH INTERNATIONAL CONFERENCE ON MATHEMATICS AND SCIENCE EDUCATION (ICoMSE) 2020: Innovative Research in Science and Mathematics Education in The Disruptive Era. AIP Publishing, 2021. http://dx.doi.org/10.1063/5.0043361.

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Seipel, Justin. "Mechanistic Model-Based Method for Bio-Inspired Design and Education." In ASME 2011 International Mechanical Engineering Congress and Exposition. ASMEDC, 2011. http://dx.doi.org/10.1115/imece2011-64595.

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Biologically-inspired design is challenging because it requires creative transfer across biological and engineering disciplines. The biologically-inspired design process could therefore be improved with new tools, methods, and pedagogy that enables a smooth transition from a biological example or concept to a conceptual engineering design based on existing engineering components and practices. Two important problems can arise immediately when an engineer or student attempts bioinspired design: I. The practitioner or student of biological inspiration or biomimicry may not understand what the biological mechanism is that underlies a particular function of interest, and may begin engineering conceptual design with a misunderstanding of the essential mechanism required. II. Even when the correct biological mechanism is identified and a conceptual biological model is developed prior to engineering design, it may remain difficult to transition from a biological conceptual model of mechanism to an engineering conceptual design because the way these systems are composed and manufactured can be entirely different. For these reasons a formal process is developed here that links biological science with engineering design: where a biological mechanism of interest is first abstracted to a mechanistic conceptual model that focuses on the scope of the function of interest and removes other levels of biological detail. This results in a physiologically-independent conceptual model that links biological and engineering concepts. Then, subsequently, this inter-disciplinary conceptual model is re-embodied as an engineering design concept utilizing the current state of engineering art, available engineering components, and best practices. An example is presented of an existing class of biologically-inspired legged robots and their relationship to an abstract mathematical model of whole-body animal locomotion. Also, a teaching method is proposed for model-based biologically-inspired engineering design.
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Gaver, Donald P. "The Use of Collaborative Learning in Biomedical Engineering Education." In ASME 2001 International Mechanical Engineering Congress and Exposition. American Society of Mechanical Engineers, 2001. http://dx.doi.org/10.1115/imece2001/bed-23018.

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Abstract At Tulane University, we have developed a course that is intended to bridge the gap between traditional mathematics ‘tools-based’ courses taken by undergraduates and the application of these tools to model biological systems. This course, ‘Mathematical Modeling and Analysis of Biological Systems,’ was developed initially as a graduate-level course, and has migrated to become required of all Biomedical Engineering undergraduates.
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Tregubov, Vladimir, and Gerasim Krivovichev. "Mathematical modelling of biological mobility." In 2014 International Conference on Computer Technologies in Physical and Engineering Applications (ICCTPEA). IEEE, 2014. http://dx.doi.org/10.1109/icctpea.2014.6893353.

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Tregubov, Vladimir. "Mathematical modelling of biological liquids." In 2014 International Conference on Computer Technologies in Physical and Engineering Applications (ICCTPEA). IEEE, 2014. http://dx.doi.org/10.1109/icctpea.2014.6893354.

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Jheng, Yu-Chen, and Chi-Lun Lin. "Fabrication and Testing of Breast Tissue-Mimicking Phantom for Needle Biopsy Cutting: A Pilot Study." In 2017 Design of Medical Devices Conference. American Society of Mechanical Engineers, 2017. http://dx.doi.org/10.1115/dmd2017-3505.

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Breast lesion tissue can be extremely stiff, e.g. calcification or soft, e.g. adipose. When performing needle biopsy, too small or scanty samples can be retrieved due to the tissue is mainly compressed instead of being cut. In order to studying the tissue cutting performance in various cutting conditions, tissue-mimicking phantoms are frequently used as a surrogate of human tissue. The advantage of using tissue phantoms is that their mechanical properties can be controlled. The stiffness of a tissue phantom can be measured by an indentation test. Previous studies have demonstrated mathematic models to estimate Young’s moduli of tissue phantoms from force-displacement data with an adjustable coefficient according to the geometry of the indenter. Tissue force reactions occurred needle insertion has been largely researched [1], but few studies investigated the tissue cutting with a rotational needle, which is a cutting method largely used in the breast needle biopsy. Research has demonstrated that the influence of rotation can significantly reduce the insertion force [2], but the experiment was conducted on a specific formula of silicone-based tissue phantoms. This paper served as a pilot study of a large-scale experiment to study the effect of rotational cutting on various cutting conditions and target materials, including artificial and biological soft tissues. Two most common types of soft tissue phantoms, biopolymers (gelatin gels and agar) and chemically synthesized polymers (polydimethylsiloxane, PDMS) were investigated. Indentation tests were performed to estimate the mechanical properties of tissue phantoms which were then verified by finite element simulations. Tissue cutting tests with and without rotation were conducted to evaluate the effect of needle rotation on the tissue force reactions.
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"Model Composition for Biological Mathematical Systems." In International Conference on Model-Driven Engineering and Software Development. SCITEPRESS - Science and and Technology Publications, 2014. http://dx.doi.org/10.5220/0004699202170224.

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Tregubov, Vladimir. "Mathematical modeling of biological fluid flows." In 2014 2nd International Conference on Emission Electronics (ICEE). IEEE, 2014. http://dx.doi.org/10.1109/emission.2014.6893982.

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Etheridge, Alison M. "Drift, draft and structure: some mathematical models of evolution." In Stochastic Models in Biological Sciences. Warsaw: Institute of Mathematics Polish Academy of Sciences, 2008. http://dx.doi.org/10.4064/bc80-0-7.

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Soetaert, Karline, Dick van Oevelen, Theodore E. Simos, George Psihoyios, Ch Tsitouras, and Zacharias Anastassi. "Modelling Marine Biological and Biogeochemical Data." In NUMERICAL ANALYSIS AND APPLIED MATHEMATICS ICNAAM 2011: International Conference on Numerical Analysis and Applied Mathematics. AIP, 2011. http://dx.doi.org/10.1063/1.3636664.

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Reports on the topic "Biological mathematic"

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Chakraborty, Srijani. Promises and Challenges of Systems Biology. Nature Library, October 2020. http://dx.doi.org/10.47496/nl.blog.09.

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Modern systems biology is essentially interdisciplinary, tying molecular biology, the omics, bioinformatics and non-biological disciplines like computer science, engineering, physics, and mathematics together.
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Heinz, Kevin, Itamar Glazer, Moshe Coll, Amanda Chau, and Andrew Chow. Use of multiple biological control agents for control of western flower thrips. United States Department of Agriculture, 2004. http://dx.doi.org/10.32747/2004.7613875.bard.

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The western flower thrips (WFT), Frankliniella occidentalis (Pergande), is a serious widespread pest of vegetable and ornamental crops worldwide. Chemical control for Frankliniella occidentalis (Pergande) (Thysanoptera: Thripidae) on floriculture or vegetable crops can be difficult because this pest has developed resistance to many insecticides and also tends to hide within flowers, buds, and apical meristems. Predatory bugs, predatory mites, and entomopathogenic nematodes are commercially available in both the US and Israel for control of WFT. Predatory bugs, such as Orius species, can suppress high WFT densities but have limited ability to attack thrips within confined plant parts. Predatory mites can reach more confined habitats than predatory bugs, but kill primarily first-instar larvae of thrips. Entomopathogenic nematodes can directly kill or sterilize most thrips stages, but have limited mobility and are vulnerable to desiccation in certain parts of the crop canopy. However, simultaneous use of two or more agents may provide both effective and cost efficient control of WFT through complimentary predation and/or parasitism. The general goal of our project was to evaluate whether suppression of WFT could be enhanced by inundative or inoculative releases of Orius predators with either predatory mites or entomopathogenic nematodes. Whether pest suppression is best when single or multiple biological control agents are used, is an issue of importance to the practice of biological control. For our investigations in Texas, we used Orius insidiosus(Say), the predatory mite, Amblyseius degeneransBerlese, and the predatory mite, Amblyseius swirskii(Athias-Henriot). In Israel, the research focused on Orius laevigatus (Fieber) and the entomopathogenic nematode, Steinernema felpiae. Our specific objectives were to: (1) quantify the spatial distribution and population growth of WFT and WFT natural enemies on greenhouse roses (Texas) and peppers (Israel), (2) assess interspecific interactions among WFT natural enemies, (3) measure WFT population suppression resulting from single or multiple species releases. Revisions to our project after the first year were: (1) use of A. swirskiiin place of A. degeneransfor the majority of our predatory mite and Orius studies, (2) use of S. felpiaein place of Thripinema nicklewoodi for all of the nematode and Orius studies. We utilized laboratory experiments, greenhouse studies, field trials and mathematical modeling to achieve our objectives. In greenhouse trials, we found that concurrent releases of A.degeneranswith O. insidiosusdid not improve control of F. occidentalis on cut roses over releases of only O. insidiosus. Suppression of WFT by augmentative releases A. swirskiialone was superior to augmentative releases of O. insidiosusalone and similar to concurrent releases of both predator species on cut roses. In laboratory studies, we discovered that O. insidiosusis a generalist predator that ‘switches’ to the most abundant prey and will kill significant numbers of A. swirskiior A. degeneransif WFTbecome relatively less abundant. Our findings indicate that intraguild interactions between Orius and Amblyseius species could hinder suppression of thrips populations and combinations of these natural enemies may not enhance biological control on certain crops. Intraguild interactions between S. felpiaeand O. laevigatus were found to be more complex than those between O. insidiosusand predatory mites. In laboratory studies, we found that S. felpiaecould infect and kill either adult or immature O. laevigatus. Although adult O. laevigatus tended to avoid areas infested by S. felpiaein Petri dish arenas, they did not show preference between healthy WFT and WFT infected with S. felpiaein choice tests. In field cage trials, suppression of WFT on sweet-pepper was similar in treatments with only O. laevigatus or both O. laevigatus and S. felpiae. Distribution and numbers of O. laevigatus on pepper plants also did not differ between cages with or without S. felpiae. Low survivorship of S. felpiaeafter foliar applications to sweet-pepper may explain, in part, the absence of effects in the field trials. Finally, we were interested in how differential predation on different developmental stages of WFT (Orius feeding on WFT nymphs inhabiting foliage and flowers, nematodes that attack prepupae and pupae in the soil) affects community dynamics. To better understand these interactions, we constructed a model based on Lotka-Volterra predator-prey theory and our simulations showed that differential predation, where predators tend to concentrate on one WFT stage contribute to system stability and permanence while predators that tend to mix different WFT stages reduce system stability and permanence.
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Computational Biology: Development in the Field of Medicine. Science Repository, April 2021. http://dx.doi.org/10.31487/sr.blog.31.

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Computational biology involves the development and application of analytical-data and theoretical methods, computational simulation techniques, and mathematical modeling to the study of biological, behavioral, ecological, and social systems.
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Incongruity between biological and chronologic age among the pupils of sports schools and the problem of group lessons effectiveness at the initial stage of training in Greco-Roman wrestling. Aleksandr S. Kuznetsov, March 2021. http://dx.doi.org/10.14526/2070-4798-2021-16-1-19-23.

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Considerable influence and compulsory dropout among those, who go in for GrecoRoman wrestling at the age of 10-13, does not take into account the level of individual biological development and integral demands domination claimed on too high general physical training (GPT) (4) normatives fulfillment. It corresponds with general situation in the system of education (6, 9). In spite of uneven speed of biological development (1, 8, 9), there are general demands claimed on physical training at school for age groups (5) in accordance with chronologic age. The same situation is at sports schools. Technical and physical training lessons at Greco-Roman wrestling school at the stage of initial training are organized according to general group principle. Research methods. Information sources analysis and summarizing, questionnaire survey, coaches’ experience summarizing, methods of mathematical statistics. Results. The received research results led to the following conclusion: it is possible to solve the problem of dropping out of Greco-Roman wrestling sports schools in terms of minimal loss in the quality of sports training by means of dividing the training groups into subgroups. There different normatives of material mastering and set by standard physical qualities development are used. For this purpose we created the training groups and subgroups of the set objectives realization at Greco-Roman wrestling sports schools.
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Methodology of sports working capacity level increase in basketball players on the basis of stimulation and rehabilitation means. Viktor V. Andreev, Igor E. Konovalov, Dmitriy S. Andreev, Aleksandr I. Morozov, March 2021. http://dx.doi.org/10.14526/2070-4798-2021-16-1-5-11.

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The increased level of modern sport development increases the demands claimed on different aspects of the training process with further rehabilitation organization and realization. That is why we still have the problem of an adequate and effective integral system creation. The mentioned direction has a direct connection with the activity of scientists, coaches- practitioners and sports clubs. They have to work within one mechanism of interaction. Materials. Studying the level of working capacity influence stimulation and organism rehabilitation means on an organism of basketball players from higher educational establishments on the basis of a wildgrowing plant root “snowdon rose” (Rhodiola rosea), classical massage with special oils and contrast shower application. Research methods. The following methods were used in the experiment: scientific-methodical sources analysis concerning the level of working capacity and athletes’ functional rehabilitation increase; functional tests; the received video material with the indices analysis; mathematical statistics. The research realization was on the basis of N.F. Katanov State University, Khakassia and Khakassia Technical Institute (branch) of Siberian Federal University in Abakan. Results. During the research work we stated qualitative and quantitative indices of athletes’ coordinating endurance with the help of video together with other mentioned above rehabilitation means; the received results were handled and we revealed positive changes in the studied information values of basketball players’ motor sphere and respiratory system. Conclusion. The results analysis, received after the research, helped to come to the following conclusion: out of the presented components the biological factor in a form of a wild-growing plant root “snowdon rose” (Rhodiola rosea) has the main influence on the working capacity and functional rehabilitation of basketball players’ organisms.
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