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  Subjects -> BIOLOGY (Total: 3153 journals)
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    - BIOLOGY (1504 journals)
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BIOLOGY (1504 journals)                  1 2 3 4 5 6 7 8 | Last

Showing 1 - 200 of 1720 Journals sorted alphabetically
AAPS Journal     Hybrid Journal   (Followers: 22)
Achievements in the Life Sciences     Open Access   (Followers: 5)
ACS Synthetic Biology     Hybrid Journal   (Followers: 25)
Acta Biologica Colombiana     Open Access   (Followers: 7)
Acta Biologica Hungarica     Full-text available via subscription   (Followers: 4)
Acta Biologica Sibirica     Open Access   (Followers: 1)
Acta Biomaterialia     Hybrid Journal   (Followers: 27)
Acta Biotheoretica     Hybrid Journal   (Followers: 4)
Acta Chiropterologica     Full-text available via subscription   (Followers: 6)
acta ethologica     Hybrid Journal   (Followers: 4)
Acta Fytotechnica et Zootechnica     Open Access   (Followers: 1)
Acta Limnologica Brasiliensia     Open Access   (Followers: 3)
Acta Médica Costarricense     Open Access   (Followers: 2)
Acta Musei Silesiae, Scientiae Naturales     Open Access  
Acta Neurobiologiae Experimentalis     Open Access  
Acta Parasitologica     Hybrid Journal   (Followers: 10)
Acta Scientiarum. Biological Sciences     Open Access   (Followers: 2)
Acta Scientifica Naturalis     Open Access   (Followers: 3)
Acta Universitatis Agriculturae et Silviculturae Mendelianae Brunensis     Open Access  
Actualidades Biológicas     Open Access   (Followers: 1)
Advanced Health Care Technologies     Open Access   (Followers: 4)
Advanced Journal of Graduate Research     Open Access  
Advanced Studies in Biology     Open Access  
Advances in Antiviral Drug Design     Full-text available via subscription   (Followers: 2)
Advances in Bioinformatics     Open Access   (Followers: 17)
Advances in Biological Regulation     Hybrid Journal   (Followers: 4)
Advances in Biology     Open Access   (Followers: 9)
Advances in Biosensors and Bioelectronics     Open Access   (Followers: 7)
Advances in Cell Biology/ Medical Journal of Cell Biology     Open Access   (Followers: 25)
Advances in Cellular and Molecular Biology of Membranes and Organelles     Full-text available via subscription   (Followers: 12)
Advances in Developmental Biology     Full-text available via subscription   (Followers: 12)
Advances in DNA Sequence-Specific Agents     Full-text available via subscription   (Followers: 5)
Advances in Ecological Research     Full-text available via subscription   (Followers: 44)
Advances in Environmental Sciences - International Journal of the Bioflux Society     Open Access   (Followers: 17)
Advances in Enzyme Research     Open Access   (Followers: 10)
Advances in Experimental Biology     Full-text available via subscription   (Followers: 7)
Advances in Genome Biology     Full-text available via subscription   (Followers: 8)
Advances in High Energy Physics     Open Access   (Followers: 19)
Advances in Human Biology     Open Access   (Followers: 3)
Advances in Life Science and Technology     Open Access   (Followers: 16)
Advances in Life Sciences     Open Access   (Followers: 6)
Advances in Marine Biology     Full-text available via subscription   (Followers: 17)
Advances in Molecular and Cell Biology     Full-text available via subscription   (Followers: 22)
Advances in Organ Biology     Full-text available via subscription   (Followers: 1)
Advances in Planar Lipid Bilayers and Liposomes     Full-text available via subscription   (Followers: 3)
Advances in Regenerative Biology     Open Access   (Followers: 1)
Advances in Space Biology and Medicine     Full-text available via subscription   (Followers: 6)
Advances in Structural Biology     Full-text available via subscription   (Followers: 5)
Advances in Virus Research     Full-text available via subscription   (Followers: 5)
African Journal of Range & Forage Science     Hybrid Journal   (Followers: 6)
AFRREV STECH : An International Journal of Science and Technology     Open Access   (Followers: 1)
Ageing Research Reviews     Hybrid Journal   (Followers: 11)
Aging Cell     Open Access   (Followers: 16)
Agrokémia és Talajtan     Full-text available via subscription   (Followers: 2)
Agrokreatif Jurnal Ilmiah Pengabdian kepada Masyarakat     Open Access  
AJP Cell Physiology     Hybrid Journal   (Followers: 15)
AJP Endocrinology and Metabolism     Hybrid Journal   (Followers: 24)
AJP Lung Cellular and Molecular Physiology     Hybrid Journal   (Followers: 3)
Al-Kauniyah : Jurnal Biologi     Open Access  
Alasbimn Journal     Open Access   (Followers: 1)
Alces : A Journal Devoted to the Biology and Management of Moose     Open Access  
AMB Express     Open Access   (Followers: 1)
Ambix     Hybrid Journal   (Followers: 3)
American Biology Teacher     Full-text available via subscription   (Followers: 14)
American Fern Journal     Full-text available via subscription   (Followers: 1)
American Journal of Agricultural and Biological Sciences     Open Access   (Followers: 8)
American Journal of Bioethics     Hybrid Journal   (Followers: 12)
American Journal of Human Biology     Hybrid Journal   (Followers: 14)
American Journal of Medical and Biological Research     Open Access   (Followers: 8)
American Journal of Plant Sciences     Open Access   (Followers: 19)
American Journal of Primatology     Hybrid Journal   (Followers: 15)
American Malacological Bulletin     Full-text available via subscription   (Followers: 3)
American Naturalist     Full-text available via subscription   (Followers: 74)
Amphibia-Reptilia     Hybrid Journal   (Followers: 6)
Anadolu University Journal of Science and Technology : C Life Sciences and Biotechnology     Open Access  
Anaerobe     Hybrid Journal   (Followers: 4)
Analytical Methods     Full-text available via subscription   (Followers: 11)
Anatomical Science International     Hybrid Journal   (Followers: 3)
Animal Cells and Systems     Hybrid Journal   (Followers: 4)
Animal Models and Experimental Medicine     Open Access  
Annales de Limnologie - International Journal of Limnology     Hybrid Journal   (Followers: 1)
Annales françaises d'Oto-rhino-laryngologie et de Pathologie Cervico-faciale     Full-text available via subscription   (Followers: 3)
Annales Henri Poincaré     Hybrid Journal   (Followers: 3)
Annals of Applied Biology     Hybrid Journal   (Followers: 7)
Annals of Biomedical Engineering     Hybrid Journal   (Followers: 18)
Annals of Human Biology     Hybrid Journal   (Followers: 5)
Annals of Science and Technology     Open Access  
Annual Review of Biomedical Engineering     Full-text available via subscription   (Followers: 14)
Annual Review of Biophysics     Full-text available via subscription   (Followers: 23)
Annual Review of Cancer Biology     Full-text available via subscription   (Followers: 2)
Annual Review of Cell and Developmental Biology     Full-text available via subscription   (Followers: 37)
Annual Review of Food Science and Technology     Full-text available via subscription   (Followers: 13)
Annual Review of Genomics and Human Genetics     Full-text available via subscription   (Followers: 23)
Annual Review of Phytopathology     Full-text available via subscription   (Followers: 12)
Anthropological Review     Open Access   (Followers: 23)
Anti-Infective Agents     Hybrid Journal   (Followers: 3)
Antibiotics     Open Access   (Followers: 9)
Antioxidants     Open Access   (Followers: 4)
Antioxidants & Redox Signaling     Hybrid Journal   (Followers: 8)
Antonie van Leeuwenhoek     Hybrid Journal   (Followers: 5)
Anzeiger für Schädlingskunde     Hybrid Journal   (Followers: 1)
Apidologie     Hybrid Journal   (Followers: 4)
Apmis     Hybrid Journal   (Followers: 1)
APOPTOSIS     Hybrid Journal   (Followers: 8)
Applied Bionics and Biomechanics     Open Access   (Followers: 8)
Applied Vegetation Science     Full-text available via subscription   (Followers: 10)
Aquaculture Environment Interactions     Open Access   (Followers: 3)
Aquaculture International     Hybrid Journal   (Followers: 24)
Aquaculture Reports     Open Access   (Followers: 3)
Aquaculture, Aquarium, Conservation & Legislation - International Journal of the Bioflux Society     Open Access   (Followers: 7)
Aquatic Biology     Open Access   (Followers: 5)
Aquatic Ecology     Hybrid Journal   (Followers: 34)
Aquatic Ecosystem Health & Management     Hybrid Journal   (Followers: 15)
Aquatic Science and Technology     Open Access   (Followers: 3)
Aquatic Toxicology     Hybrid Journal   (Followers: 23)
Archaea     Open Access   (Followers: 3)
Archiv für Molluskenkunde: International Journal of Malacology     Full-text available via subscription   (Followers: 3)
Archives of Biological Sciences     Open Access  
Archives of Microbiology     Hybrid Journal   (Followers: 8)
Archives of Natural History     Hybrid Journal   (Followers: 6)
Archives of Oral Biology     Hybrid Journal   (Followers: 2)
Archives of Virology     Hybrid Journal   (Followers: 5)
Archivum Immunologiae et Therapiae Experimentalis     Hybrid Journal   (Followers: 2)
Arid Ecosystems     Hybrid Journal   (Followers: 2)
Arquivos do Instituto Biológico     Open Access   (Followers: 1)
Arquivos do Museu Dinâmico Interdisciplinar     Open Access  
Arthropod Structure & Development     Hybrid Journal   (Followers: 2)
Arthropods     Open Access   (Followers: 1)
Artificial DNA: PNA & XNA     Hybrid Journal   (Followers: 3)
Asian Bioethics Review     Full-text available via subscription   (Followers: 3)
Asian Journal of Biodiversity     Open Access   (Followers: 4)
Asian Journal of Biological Sciences     Open Access   (Followers: 3)
Asian Journal of Cell Biology     Open Access   (Followers: 5)
Asian Journal of Developmental Biology     Open Access   (Followers: 2)
Asian Journal of Medical and Biological Research     Open Access   (Followers: 4)
Asian Journal of Nematology     Open Access   (Followers: 4)
Asian Journal of Poultry Science     Open Access   (Followers: 4)
Atti della Accademia Peloritana dei Pericolanti - Classe di Scienze Medico-Biologiche     Open Access  
Australian Life Scientist     Full-text available via subscription   (Followers: 2)
Australian Mammalogy     Hybrid Journal   (Followers: 6)
Autophagy     Hybrid Journal   (Followers: 2)
Avian Biology Research     Full-text available via subscription   (Followers: 4)
Avian Conservation and Ecology     Open Access   (Followers: 11)
Bacteriology Journal     Open Access   (Followers: 1)
Bacteriophage     Full-text available via subscription   (Followers: 3)
Bangladesh Journal of Bioethics     Open Access  
Bangladesh Journal of Plant Taxonomy     Open Access  
Bangladesh Journal of Scientific Research     Open Access   (Followers: 1)
Batman Üniversitesi Yaşam Bilimleri Dergisi     Open Access  
Berita Biologi     Open Access   (Followers: 1)
Between the Species     Open Access   (Followers: 1)
Bio Tribune Magazine     Hybrid Journal  
BIO Web of Conferences     Open Access  
BIO-Complexity     Open Access  
Bio-Grafía. Escritos sobre la Biología y su enseñanza     Open Access  
Bioanalytical Reviews     Hybrid Journal   (Followers: 2)
Biocatalysis and Biotransformation     Hybrid Journal   (Followers: 6)
BioCentury Innovations     Full-text available via subscription   (Followers: 1)
Biochemistry and Cell Biology     Hybrid Journal   (Followers: 15)
Biochimie     Hybrid Journal   (Followers: 7)
BioControl     Hybrid Journal   (Followers: 5)
Biocontrol Science and Technology     Hybrid Journal   (Followers: 5)
Biodemography and Social Biology     Hybrid Journal  
BioDiscovery     Open Access   (Followers: 2)
Biodiversitas : Journal of Biological Diversity     Open Access  
Biodiversity Data Journal     Open Access   (Followers: 4)
Biodiversity Informatics     Open Access   (Followers: 1)
Biodiversity Information Science and Standards     Open Access  
Biodiversity: Research and Conservation     Open Access   (Followers: 26)
Bioedukasi : Jurnal Pendidikan Biologi FKIP UM Metro     Open Access  
Bioeksperimen : Jurnal Penelitian Biologi     Open Access  
Bioelectrochemistry     Hybrid Journal   (Followers: 2)
Bioelectromagnetics     Hybrid Journal   (Followers: 1)
Bioenergy Research     Hybrid Journal   (Followers: 2)
Bioengineering and Bioscience     Open Access   (Followers: 1)
BioEssays     Hybrid Journal   (Followers: 10)
Bioethics     Hybrid Journal   (Followers: 15)
BioéthiqueOnline     Open Access  
Biofabrication     Hybrid Journal   (Followers: 5)
Biofilms     Full-text available via subscription   (Followers: 1)
Biogeosciences (BG)     Open Access   (Followers: 10)
Biogeosciences Discussions (BGD)     Open Access   (Followers: 2)
Bioinformatics     Hybrid Journal   (Followers: 305)
Bioinformatics and Biology Insights     Open Access   (Followers: 11)
Bioinspiration & Biomimetics     Hybrid Journal   (Followers: 7)
Biointerphases     Open Access   (Followers: 1)
Biojournal of Science and Technology     Open Access  
BioLink : Jurnal Biologi Lingkungan, Industri, Kesehatan     Open Access  
Biologia     Hybrid Journal  
Biologia on-line : Revista de divulgació de la Facultat de Biologia     Open Access  
Biological Bulletin     Partially Free   (Followers: 6)
Biological Control     Hybrid Journal   (Followers: 4)
Biological Invasions     Hybrid Journal   (Followers: 20)
Biological Journal of the Linnean Society     Hybrid Journal   (Followers: 18)
Biological Letters     Open Access   (Followers: 5)
Biological Procedures Online     Open Access  
Biological Psychiatry     Hybrid Journal   (Followers: 48)
Biological Psychology     Hybrid Journal   (Followers: 6)
Biological Research     Open Access  
Biological Rhythm Research     Hybrid Journal   (Followers: 2)

        1 2 3 4 5 6 7 8 | Last

Journal Cover
Acta Biotheoretica
Journal Prestige (SJR): 0.284
Citation Impact (citeScore): 1
Number of Followers: 4  
 
  Hybrid Journal Hybrid journal (It can contain Open Access articles)
ISSN (Print) 1572-8358 - ISSN (Online) 0001-5342
Published by Springer-Verlag Homepage  [2351 journals]
  • An Inverse Problem: Trappers Drove Hares to Eat Lynx
    • Authors: Bo Deng
      Abstract: The Canadian lynx and snowshoe hare pelt data by the Hudson Bay Company did not fit the classical predator–prey theory. Rather than following the peak density of the hare, that of the lynx leads it, creating the hares-eat-lynx (HEL) paradox. Although trappers were suspected to play a role, no mathematical model has ever demonstrated the HEL effect. Here we show that the long-held assumption that the pelt number is a proxy of the wild populations is false and that when the data are modeled by the harvest rates by the trappers, the problem is finally resolved: both the HEL paradox and the classical theory are unified in our mechanistic hare-lynx-competitor-trapper (HLCT) model where competitor stands for all predators of the hares other than the lynx. The result is obtained by systematically fitting the data to various models using Newton’s inverse problem method. Main findings of this study include: the prey-eats-predator paradox in kills by an intraguild top-predator can occur if the top-predator prefers the predator to the prey; the benchmark HLCT model is more sensitive to all lynx-trapper interactions than to the respective hare-trapper interactions; the Hudson Bay Company’s hare pelt number maybe under-reported; and, the most intriguing of all, the trappers did not interfere in each other’s trapping activities.
      PubDate: 2018-05-30
      DOI: 10.1007/s10441-018-9333-z
       
  • Permanence and Extinction of a Diffusive Predator–Prey Model with
           Robin Boundary Conditions
    • Authors: M. A. Aziz-Alaoui; M. Daher Okiye; A. Moussaoui
      Abstract: The main concern of this paper is to study the dynamic of a predator–prey system with diffusion. It incorporates the Holling-type-II and a modified Leslie–Gower functional responses under Robin boundary conditions. More concretely, we study the dissipativeness of the system by using the comparison principle, and we derive a criteria for permanence and for predator extinction.
      PubDate: 2018-05-28
      DOI: 10.1007/s10441-018-9332-0
       
  • Descriptive Modeling of the Dynamical Systems and Determination of
           Feedback Homeostasis at Different Levels of Life Organization
    • Authors: G. N. Zholtkevych; K. V. Nosov; Yu. G. Bespalov; L. I. Rak; M. Abhishek; E. V. Vysotskaya
      Abstract: The state-of-art research in the field of life’s organization confronts the need to investigate a number of interacting components, their properties and conditions of sustainable behaviour within a natural system. In biology, ecology and life sciences, the performance of such stable system is usually related to homeostasis, a property of the system to actively regulate its state within a certain allowable limits. In our previous work, we proposed a deterministic model for systems’ homeostasis. The model was based on dynamical system’s theory and pairwise relationships of competition, amensalism and antagonism taken from theoretical biology and ecology. However, the present paper proposes a different dimension to our previous results based on the same model. In this paper, we introduce the influence of inter-component relationships in a system, wherein the impact is characterized by direction (neutral, positive, or negative) as well as its (absolute) value, or strength. This makes the model stochastic which, in our opinion, is more consistent with real-world elements affected by various random factors. The case study includes two examples from areas of hydrobiology and medicine. The models acquired for these cases enabled us to propose a convincing explanation for corresponding phenomena identified by different types of natural systems.
      PubDate: 2018-05-24
      DOI: 10.1007/s10441-018-9321-3
       
  • Importance of Initial Concentration of Factor VIII in a Mechanistic Model
           of In Vitro Coagulation
    • Authors: M. Susree; M. Anand
      Abstract: This computational study generates a hypothesis for the coagulation protein whose initial concentration greatly influences the course of coagulation. Many clinical malignancies of blood coagulation arise due to abnormal initial concentrations of coagulation factors. Sensitivity analysis of mechanistic models of blood coagulation is a convenient method to assess the effect of such abnormalities. Accordingly, the study presents sensitivity analysis, with respect to initial concentrations, of a recently developed mechanistic model of blood coagulation. Both the model and parameters to which model sensitivity is being analyzed provide newer insights into blood coagulation: the model incorporates distinct equations for plasma-phase and platelet membrane-bound species, and sensitivity to initial concentrations is a new dimension in sensitivity analysis. The results show that model predictions are most uncertain with respect to changes in initial concentration of factor VIII, and this hypothesis is supported by results from other models developed independently.
      PubDate: 2018-05-14
      DOI: 10.1007/s10441-018-9329-8
       
  • Natural Selection and Drift as Individual-Level Causes of Evolution
    • Authors: Pierrick Bourrat
      Abstract: In this paper I critically evaluate Reisman and Forber’s (Philos Sci 72(5):1113–1123, 2005) arguments that drift and natural selection are population-level causes of evolution based on what they call the manipulation condition. Although I agree that this condition is an important step for identifying causes for evolutionary change, it is insufficient. Following Woodward, I argue that the invariance of a relationship is another crucial parameter to take into consideration for causal explanations. Starting from Reisman and Forber’s example on drift and after having briefly presented the criterion of invariance, I show that once both the manipulation condition and the criterion of invariance are taken into account, drift, in this example, should better be understood as an individual-level rather than a population-level cause. Later, I concede that it is legitimate to interpret natural selection and drift as population-level causes when they rely on genuinely indeterministic events and some cases of frequency-dependent selection.
      PubDate: 2018-05-14
      DOI: 10.1007/s10441-018-9331-1
       
  • Systems Biology, Systems Medicine, Systems Pharmacology: The What and The
           Why
    • Authors: Angélique Stéphanou; Eric Fanchon; Pasquale F. Innominato; Annabelle Ballesta
      Abstract: Systems biology is today such a widespread discipline that it becomes difficult to propose a clear definition of what it really is. For some, it remains restricted to the genomic field. For many, it designates the integrated approach or the corpus of computational methods employed to handle the vast amount of biological or medical data and investigate the complexity of the living. Although defining systems biology might be difficult, on the other hand its purpose is clear: systems biology, with its emerging subfields systems medicine and systems pharmacology, clearly aims at making sense of complex observations/experimental and clinical datasets to improve our understanding of diseases and their treatments without putting aside the context in which they appear and develop. In this short review, we aim to specifically focus on these new subfields with the new theoretical tools and approaches that were developed in the context of cancer. Systems pharmacology and medicine now give hope for major improvements in cancer therapy, making personalized medicine closer to reality. As we will see, the current challenge is to be able to improve the clinical practice according to the paradigm shift of systems sciences.
      PubDate: 2018-05-09
      DOI: 10.1007/s10441-018-9330-2
       
  • Theoretical Assessment of the Impact of Climatic Factors in a Vibrio
           Cholerae Model
    • Authors: G. Kolaye; I. Damakoa; S. Bowong; R. Houe; D. Békollè
      Abstract: A mathematical model for Vibrio Cholerae (V. Cholerae) in a closed environment is considered, with the aim of investigating the impact of climatic factors which exerts a direct influence on the bacterial metabolism and on the bacterial reservoir capacity. We first propose a V. Cholerae mathematical model in a closed environment. A sensitivity analysis using the eFast method was performed to show the most important parameters of the model. After, we extend this V. cholerae model by taking account climatic factors that influence the bacterial reservoir capacity. We present the theoretical analysis of the model. More precisely, we compute equilibria and study their stabilities. The stability of equilibria was investigated using the theory of periodic cooperative systems with a concave nonlinearity. Theoretical results are supported by numerical simulations which further suggest the necessity to implement sanitation campaigns of aquatic environments by using suitable products against the bacteria during the periods of growth of aquatic reservoirs.
      PubDate: 2018-05-04
      DOI: 10.1007/s10441-018-9322-2
       
  • The Origin of Species by Means of Mathematical Modelling
    • Authors: Nikolai Bessonov; Natalia Reinberg; Malay Banerjee; Vitaly Volpert
      Abstract: Darwin described biological species as groups of morphologically similar individuals. These groups of individuals can split into several subgroups due to natural selection, resulting in the emergence of new species. Some species can stay stable without the appearance of a new species, some others can disappear or evolve. Some of these evolutionary patterns were described in our previous works independently of each other. In this work we have developed a single model which allows us to reproduce the principal patterns in Darwin’s diagram. Some more complex evolutionary patterns are also observed. The relation between Darwin’s definition of species, stated above, and Mayr’s definition of species (group of individuals that can reproduce) is also discussed.
      PubDate: 2018-04-30
      DOI: 10.1007/s10441-018-9328-9
       
  • Drug Repositioning by Integrating Known Disease-Gene and Drug-Target
           Associations in a Semi-supervised Learning Model
    • Authors: Duc-Hau Le; Doanh Nguyen-Ngoc
      Abstract: Computational drug repositioning has been proven as a promising and efficient strategy for discovering new uses from existing drugs. To achieve this goal, a number of computational methods have been proposed, which are based on different data sources of drugs and diseases. These methods approach the problem using either machine learning- or network-based models with an assumption that similar drugs can be used for similar diseases to identify new indications of drugs. Therefore, similarities between drugs and between diseases are usually used as inputs. In addition, known drug-disease associations are also needed for the methods as prior information. It should be noted that those associations are still not well established due to the fact that many of marketed drugs have been withdrawn and this could affect the outcome of the methods. In this study, we propose a novel method named RLSDR (Regularized Least Square for Drug Repositioning) to find new uses of drugs. More specifically, it relies on a semi-supervised learning model, Regularized Least Square, thus it does not require definition of non-drug-disease associations as previously proposed machine learning-based methods. In addition, the similarity between drugs measured by chemical structures of drug compounds and the similarity between diseases which share phenotypes can be represented in a form of either similarity network or similarity matrix as inputs of the method. Moreover, instead of using a gold-standard set of known drug-disease associations, we construct an artificial set of the associations based on known disease-gene and drug-target associations. Experiment results demonstrate that RLSDR achieves better prediction performance on the artificial set of drug-disease associations than that on the gold-standard ones in terms of area under the Receiver Operating Characteristic (ROC) curve (AUC). In addition, it outperforms two representative network-based methods irrespective of the prior information of drug-disease associations. Novel indications for a number of drugs are also identified and validated by evidences from a different data resource.
      PubDate: 2018-04-26
      DOI: 10.1007/s10441-018-9325-z
       
  • Mathematical Basis of Predicting Dominant Function in Protein Sequences by
           a Generic HMM–ANN Algorithm
    • Authors: Siddhartha Kundu
      Abstract: The accurate annotation of an unknown protein sequence depends on extant data of template sequences. This could be empirical or sets of reference sequences, and provides an exhaustive pool of probable functions. Individual methods of predicting dominant function possess shortcomings such as varying degrees of inter-sequence redundancy, arbitrary domain inclusion thresholds, heterogeneous parameterization protocols, and ill-conditioned input channels. Here, I present a rigorous theoretical derivation of various steps of a generic algorithm that integrates and utilizes several statistical methods to predict the dominant function in unknown protein sequences. The accompanying mathematical proofs, interval definitions, analysis, and numerical computations presented are meant to offer insights not only into the specificity and accuracy of predictions, but also provide details of the operatic mechanisms involved in the integration and its ensuing rigor. The algorithm uses numerically modified raw hidden markov model scores of well defined sets of training sequences and clusters them on the basis of known function. The results are then fed into an artificial neural network, the predictions of which can be refined using the available data. This pipeline is trained recursively and can be used to discern the dominant principal function, and thereby, annotate an unknown protein sequence. Whilst, the approach is complex, the specificity of the final predictions can benefit laboratory workers design their experiments with greater confidence.
      PubDate: 2018-04-26
      DOI: 10.1007/s10441-018-9327-x
       
  • Adaptive Control Based Harvesting Strategy for a Predator–Prey
           Dynamical System
    • Authors: Moitri Sen; Ashutosh Simha; Soumyendu Raha
      Abstract: This paper deals with designing a harvesting control strategy for a predator–prey dynamical system, with parametric uncertainties and exogenous disturbances. A feedback control law for the harvesting rate of the predator is formulated such that the population dynamics is asymptotically stabilized at a positive operating point, while maintaining a positive, steady state harvesting rate. The hierarchical block strict feedback structure of the dynamics is exploited in designing a backstepping control law, based on Lyapunov theory. In order to account for unknown parameters, an adaptive control strategy has been proposed in which the control law depends on an adaptive variable which tracks the unknown parameter. Further, a switching component has been incorporated to robustify the control performance against bounded disturbances. Proofs have been provided to show that the proposed adaptive control strategy ensures asymptotic stability of the dynamics at a desired operating point, as well as exact parameter learning in the disturbance-free case and learning with bounded error in the disturbance prone case. The dynamics, with uncertainty in the death rate of the predator, subjected to a bounded disturbance has been simulated with the proposed control strategy.
      PubDate: 2018-04-23
      DOI: 10.1007/s10441-018-9323-1
       
  • A Possible Role for Philosophy: Bridging the Conceptual Divide in Cancer
           Research
    • Authors: Silvia Caianiello
      PubDate: 2018-04-19
      DOI: 10.1007/s10441-018-9326-y
       
  • Graphical Representation and Similarity Analysis of DNA Sequences Based on
           Trigonometric Functions
    • Authors: Guo-Sen Xie; Xiao-Bo Jin; Chunlei Yang; Jiexin Pu; Zhongxi Mo
      Abstract: In this paper, we propose two four-base related 2D curves of DNA primary sequences (termed as F-B curves) and their corresponding single-base related 2D curves (termed as A-related, G-related, T-related and C-related curves). The constructions of these graphical curves are based on the assignments of individual base to four different sinusoidal (or tangent) functions; then by connecting all these points on these four sinusoidal (tangent) functions, we can get the F-B curves; similarly, by connecting the points on each of the four sinusoidal (tangent) functions, we get the single-base related 2D curves. The proposed 2D curves are all strictly non degenerate. Then, a 8-component characteristic vector is constructed to compare similarity among DNA sequences from different species based on a normalized geometrical centers of the proposed curves. As examples, we examine similarity among the coding sequences of the first exon of beta-globin gene from eleven species, similarity of cDNA sequences of beta-globin gene from eight species, and similarity of the whole mitochondrial genomes of 18 eutherian mammals. The experimental results well demonstrate the effectiveness of the proposed method.
      PubDate: 2018-04-19
      DOI: 10.1007/s10441-018-9324-0
       
  • Culture and the Trajectories of Developmental Pathology: Insights from
           Control and Information Theories
    • Authors: Rodrick Wallace
      Abstract: Cognition in living entities—and their social groupings or institutional artifacts—is necessarily as complicated as their embedding environments, which, for humans, includes a particularly rich cultural milieu. The asymptotic limit theorems of information and control theories permit construction of a new class of empirical ‘regression-like’ statistical models for cognitive developmental processes, their dynamics, and modes of dysfunction. Such models may, as have their simpler analogs, prove useful in the study and re-mediation of cognitive failure at and across the scales and levels of organization that constitute and drive the phenomena of life. These new models particularly focus on the roles of sociocultural environment and stress, in a large sense, as both trigger for the failure of the regulation of bio-cognition and as ‘riverbanks’ determining the channels of pathology, with implications across life-course developmental trajectories. We examine the effects of an embedding cultural milieu and its socioeconomic implementations using the ‘lenses’ of metabolic optimization, control system theory, and an extension of symmetry-breaking appropriate to information systems. A central implication is that most, if not all, human developmental disorders are fundamentally culture-bound syndromes. This has deep implications for both individual treatment and public health policy.
      PubDate: 2018-04-03
      DOI: 10.1007/s10441-018-9320-4
       
  • Quaternion-Based Texture Analysis of Multiband Satellite Images:
           Application to the Estimation of Aboveground Biomass in the East Region of
           Cameroon
    • Authors: Cedrigue Boris Djiongo Kenfack; Olivier Monga; Serge Moto Mpong; René Ndoundam
      Abstract: Within the last decade, several approaches using quaternion numbers to handle and model multiband images in a holistic manner were introduced. The quaternion Fourier transform can be efficiently used to model texture in multidimensional data such as color images. For practical application, multispectral satellite data appear as a primary source for measuring past trends and monitoring changes in forest carbon stocks. In this work, we propose a texture-color descriptor based on the quaternion Fourier transform to extract relevant information from multiband satellite images. We propose a new multiband image texture model extraction, called FOTO++, in order to address biomass estimation issues. The first stage consists in removing noise from the multispectral data while preserving the edges of canopies. Afterward, color texture descriptors are extracted thanks to a discrete form of the quaternion Fourier transform, and finally the support vector regression method is used to deduce biomass estimation from texture indices. Our texture features are modeled using a vector composed with the radial spectrum coming from the amplitude of the quaternion Fourier transform. We conduct several experiments in order to study the sensitivity of our model to acquisition parameters. We also assess its performance both on synthetic images and on real multispectral images of Cameroonian forest. The results show that our model is more robust to acquisition parameters than the classical Fourier Texture Ordination model (FOTO). Our scheme is also more accurate for aboveground biomass estimation. We stress that a similar methodology could be implemented using quaternion wavelets. These results highlight the potential of the quaternion-based approach to study multispectral satellite images.
      PubDate: 2018-03-21
      DOI: 10.1007/s10441-018-9317-z
       
  • A 3D Individual-Based Model to Study Effects of Chemotaxis, Competition
           and Diffusion on the Motile-Phytoplankton Aggregation
    • Authors: Ilhem Bouderbala; Nadjia El Saadi; Alassane Bah; Pierre Auger
      Abstract: In this paper, we develop a 3D-individual-based model (IBM) to understand effect of various small-scale mechanisms in phytoplankton cells, on the cellular aggregation process. These mechanisms are: spatial interactions between cells due to their chemosensory abilities (chemotaxis), a molecular diffusion and a demographical process. The latter is considered as a branching process with a density-dependent death rate to take into account the local competition on resources. We implement the IBM and simulate various scenarios under real parameter values for phytoplankton cells. To quantify the effects of the different processes quoted above on the spatial and temporal distribution of phytoplankton, we used two spatial statistics: the Clark–Evans index and the group belonging percentage. Our simulation study highlights the role of the branching process with a weak-to-medium competition in reinforcing the aggregating structure that forms from attraction mechanisms (under suitable conditions for diffusion and attraction forces), and shows by contrast that aggregations cannot form when competition is high.
      PubDate: 2018-03-15
      DOI: 10.1007/s10441-018-9318-y
       
  • Prediction of Apoptosis Protein’s Subcellular Localization by Fusing Two
           Different Descriptors Based on Evolutionary Information
    • Authors: Yunyun Liang; Shengli Zhang
      Abstract: The apoptosis protein has a central role in the development and the homeostasis of an organism. Obtaining information about the subcellular localization of apoptosis protein is very helpful to understand the apoptosis mechanism and the function of this protein. Prediction of apoptosis protein’s subcellular localization is a challenging task, and currently the existing feature extraction methods mainly rely on the protein’s primary sequence. In this paper we develop a feature extraction model based on two different descriptors of evolutionary information, which contains the 192 frequencies of triplet codons (FTC) in the RNA sequence derived from the protein’s primary sequence and the 190 features from a detrended forward moving-average cross-correlation analysis (DFMCA) based on a position-specific scoring matrix (PSSM) generated by the PSI-BLAST program. Hence, this model is called FTC-DFMCA-PSSM. A 382-dimensional (382D) feature vector is constructed on the ZD98, ZW225 and CL317 datasets. Then a support vector machine is adopted as classifier, and the jackknife cross-validation test method is used for evaluating the accuracy. The overall prediction accuracies are further improved by an objective and rigorous jackknife test. Our model not only broadens the source of the feature information, but also provides a more accurate and reliable automated calculation method for the prediction of apoptosis protein’s subcellular localization.
      PubDate: 2018-03-12
      DOI: 10.1007/s10441-018-9319-x
       
  • In the Future There Will Be No Genes
    • Authors: Oren Harman
      PubDate: 2018-02-19
      DOI: 10.1007/s10441-018-9316-0
       
  • R 0 : Host Longevity Matters
    • Authors: L. M. Viljoen; L. Hemerik; J. Molenaar
      Abstract: The basic reproduction ratio, R0, is a fundamental concept in epidemiology. It is defined as the total number of secondary infections brought on by a single primary infection, in a totally susceptible population. The value of R0 indicates whether a starting epidemic reaches a considerable part of the population and causes a lot of damage, or whether it remains restricted to a relatively small number of individuals. To calculate R0 one has to evaluate an integral that ranges over the duration of the infection of the host. This duration is, of course, limited by remaining host longevity. So, R0 depends on remaining host longevity and in this paper we show that for long-lived hosts this aspect may not be ignored for long-lasting infections. We investigate in particular how this epidemiological measure of pathogen fitness depends on host longevity. For our analyses we adopt and combine a generic within- and between-host model from the literature. To find the optimal strategy for a pathogen from an evolutionary point of view, we focus on the indicator \(R_0^{{opt}}\) , i.e., the optimum of R0 as a function of its replication and mutation rates. These are the within-host parameters that the pathogen has at its disposal to optimize its strategy. We show that \(R_0^{{opt}}\) is highly influenced by remaining host longevity in combination with the contact rate between hosts in a susceptible population. In addition, these two parameters determine whether a killer-like or a milker-like strategy is optimal for a given pathogen. In the killer-like strategy the pathogen has a high rate of reproduction within the host in a short time span causing a relatively short disease, whereas in the milker-like strategy the pathogen multiplies relatively slowly, producing a continuous small amount of offspring over time with a small effect on host health. The present research allows for the determination of a bifurcation line in the plane of host longevity versus contact rate that forms the boundary between the milker-like and killer-like regions. This plot shows that for short remaining host longevities the killer-like strategy is optimal, whereas for very long remaining host longevities the milker-like strategy is advantageous. For in-between values of host longevity, the contact rate determines which of both strategies is optimal.
      PubDate: 2018-02-19
      DOI: 10.1007/s10441-018-9315-1
       
  • A Model of Isotope Separation in Plants
    • Authors: A. V. Melkikh; A. O. Bokunyaeva
      Pages: 271 - 284
      Abstract: A model representing isotope separation during water evaporation in plants was constructed. The model accounts for substance diffusion, convective transfer and evaporation from the surface of the leaves. The dependence of the system’s separation and enrichment coefficients on various parameters (liquid velocity, diffusion coefficient, and potential barriers for molecules and their thermal velocities) was determined. A comparison was made between the enrichment coefficients calculated from experimental data from different plants and those based on the model. Qualitative agreement between the experimental and theoretical values was obtained for the case of \(\frac{uh}{D} {\gg} 1\) , where u is the average velocity of water in the plant, h is the height of the plant, and D is the diffusion coefficient of the substance.
      PubDate: 2017-11-24
      DOI: 10.1007/s10441-017-9314-7
      Issue No: Vol. 65, No. 4 (2017)
       
 
 
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