scholarly journals Comparative Study of Metaheuristics for the Curve-Fitting Problem: Modeling Neurotransmitter Diffusion and Synaptic Receptor Activation

2015 ◽  
Vol 2015 ◽  
pp. 1-16
Author(s):  
Jesús Montes ◽  
Antonio LaTorre ◽  
Santiago Muelas ◽  
Ángel Merchán-Pérez ◽  
José M. Peña

Synapses are key elements in the information transmission in the nervous system. Among the different approaches to study them, the use of computational simulations is identified as the most promising technique. Simulations, however, do not provide generalized models of the underlying biochemical phenomena, but a set of observations, or time-series curves, displaying the behavior of the synapse in the scenario represented. Finding a general model of these curves, like a set of mathematical equations, could be an achievement in the study of synaptic behavior. In this paper, we propose an exploratory analysis in which selected curve models are proposed, and state-of-the-art metaheuristics are used and compared to fit the free coefficients of these curves to the data obtained from simulations. Experimental results demonstrate that several models can fit these data, though a deeper analysis from a biological perspective reveals that some are better suited for this purpose, as they represent more accurately the biological process. Based on the results of this analysis, we propose a set of mathematical equations and a methodology, adequate for modeling several aspects of biochemical synaptic behavior.

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 760 ◽  
Author(s):  
Alysson R. Muotri

Human brain organoids, generated from pluripotent stem cells, have emerged as a promising technique for modeling early stages of human neurodevelopment in controlled laboratory conditions. Although the applications for disease modeling in a dish have become routine, the use of these brain organoids as evolutionary tools is only now getting momentum. Here, we will review the current state of the art on the use of brain organoids from different species and the molecular and cellular insights generated from these studies. Besides, we will discuss how this model might be beneficial for human health and the limitations and future perspectives of this technology.


2016 ◽  
Vol 2016 ◽  
pp. 1-9 ◽  
Author(s):  
Fayçal Ait Aoudia ◽  
Matthieu Gautier ◽  
Olivier Berder

Opportunistic forwarding has emerged as a promising technique to address the problem of unreliable links typical in wireless sensor networks and improve energy efficiency by exploiting multiuser diversity. Timer-based solutions, such as timer-based contention, form promising schemes to allow opportunistic next hop relay selection. However, they can incur significant idle listening and thus reduce the lifetime of the network. To tackle this problem, we propose to exploit emerging wake-up receiver technologies that have the potential to considerably reduce the power consumption of wireless communications. A careful design of MAC protocols is required to efficiently employ these new devices. In this work, we propose Opportunistic Wake-Up MAC (OPWUM), a novel multihop MAC protocol using timer-based contention. It enables the opportunistic selection of the best receiver among its neighboring nodes according to a given metric (e.g., the remaining energy), without requiring any knowledge about them. Moreover, OPWUM exploits emerging wake-up receivers to drastically reduce nodes power consumption. Through analytical study and exhaustive networks simulations, we show the effectiveness of OPWUM compared to the current state-of-the-art protocols using timer-based contention.


2020 ◽  
pp. 107385842096011
Author(s):  
Alexios A. Panoutsopoulos

In neuroscience research, the efforts to find the model through which we can mimic the in vivo microenvironment of a developing or defective brain have been everlasting. While model organisms are used for over a hundred years, many more methods have been introduced with immortalized or primary cell lines and later induced pluripotent stem cells and organoids to be some of these. As the use of organoids becomes more and more common by many laboratories in biology and neuroscience in particular, it is crucial to deeper understand the challenges and possible pitfalls of their application in research, many of which can be surpassed with the support of state-of-the art bioengineering solutions. In this review, after a brief chronicle of the path to the discovery of organoids, we focus on the latest approaches to study neuroscience related topics with organoids, such as the use of assembloids, CRISPR technology, patch-clamp and optogenetics techniques and discuss how modern 3-dimensional biomaterials, miniaturized bioreactors and microfluidic chips can help to overcome the disadvantages of their use.


2020 ◽  
Vol 34 (05) ◽  
pp. 9490-9497
Author(s):  
Ke Yuan ◽  
Dafang He ◽  
Zhuoren Jiang ◽  
Liangcai Gao ◽  
Zhi Tang ◽  
...  

Mathematical equations are an important part of dissemination and communication of scientific information. Students, however, often feel challenged in reading and understanding math content and equations. With the development of the Web, students are posting their math questions online. Nevertheless, constructing a concise math headline that gives a good description of the posted detailed math question is nontrivial. In this study, we explore a novel summarization task denoted as geNerating A concise Math hEadline from a detailed math question (NAME). Compared to conventional summarization tasks, this task has two extra and essential constraints: 1) Detailed math questions consist of text and math equations which require a unified framework to jointly model textual and mathematical information; 2) Unlike text, math equations contain semantic and structural features, and both of them should be captured together. To address these issues, we propose MathSum, a novel summarization model which utilizes a pointer mechanism combined with a multi-head attention mechanism for mathematical representation augmentation. The pointer mechanism can either copy textual tokens or math tokens from source questions in order to generate math headlines. The multi-head attention mechanism is designed to enrich the representation of math equations by modeling and integrating both its semantic and structural features. For evaluation, we collect and make available two sets of real-world detailed math questions along with human-written math headlines, namely EXEQ-300k and OFEQ-10k. Experimental results demonstrate that our model (MathSum) significantly outperforms state-of-the-art models for both the EXEQ-300k and OFEQ-10k datasets.


2004 ◽  
Vol 57 (5) ◽  
pp. 345-384 ◽  
Author(s):  
William L Oberkampf ◽  
Timothy G Trucano ◽  
Charles Hirsch

Developers of computer codes, analysts who use the codes, and decision makers who rely on the results of the analyses face a critical question: How should confidence in modeling and simulation be critically assessed? Verification and validation (V&V) of computational simulations are the primary methods for building and quantifying this confidence. Briefly, verification is the assessment of the accuracy of the solution to a computational model. Validation is the assessment of the accuracy of a computational simulation by comparison with experimental data. In verification, the relationship of the simulation to the real world is not an issue. In validation, the relationship between computation and the real world, ie, experimental data, is the issue. This paper presents our viewpoint of the state of the art in V&V in computational physics. (In this paper we refer to all fields of computational engineering and physics, eg, computational fluid dynamics, computational solid mechanics, structural dynamics, shock wave physics, computational chemistry, etc, as computational physics.) We describe our view of the framework in which predictive capability relies on V&V, as well as other factors that affect predictive capability. Our opinions about the research needs and management issues in V&V are very practical: What methods and techniques need to be developed and what changes in the views of management need to occur to increase the usefulness, reliability, and impact of computational physics for decision making about engineering systems? We review the state of the art in V&V over a wide range of topics, for example, prioritization of V&V activities using the Phenomena Identification and Ranking Table (PIRT), code verification, software quality assurance (SQA), numerical error estimation, hierarchical experiments for validation, characteristics of validation experiments, the need to perform nondeterministic computational simulations in comparisons with experimental data, and validation metrics. We then provide an extensive discussion of V&V research and implementation issues that we believe must be addressed for V&V to be more effective in improving confidence in computational predictive capability. Some of the research topics addressed are development of improved procedures for the use of the PIRT for prioritizing V&V activities, the method of manufactured solutions for code verification, development and use of hierarchical validation diagrams, and the construction and use of validation metrics incorporating statistical measures. Some of the implementation topics addressed are the needed management initiatives to better align and team computationalists and experimentalists in conducting validation activities, the perspective of commercial software companies, the key role of analysts and decision makers as code customers, obstacles to the improved effectiveness of V&V, effects of cost and schedule constraints on practical applications in industrial settings, and the role of engineering standards committees in documenting best practices for V&V. There are 207 references cited in this review article.


2015 ◽  
Vol 26 (2) ◽  
pp. 1-13
Author(s):  
Fabio Porto ◽  
Ramon G. Costa ◽  
Ana Maria de C. Moura ◽  
Bernardo Gonçalves

Computational Simulations are important tools that enable scientists to study complex phenomena about which few data is available or that require dangerous human interventions. They involve complex and heterogeneous components, including: mathematical equations, hypothesis, computational models and data. In order to support in-silico scientific research this complex environment needs to be modeled and have its data and metadata managed enabling model evolution, prediction analysis and decision-making. This paper proposes a scientific hypothesis conceptual model that allows scientists to represent the phenomenon been investigated, the hypotheses formulated in the attempt to explain it, and provides the ability to store results of experiment simulations with their corresponding provenance metadata. The proposed model supports scientific life-cycle through: provenance management, exchange of hypothesis as data, experiment reproducibility, model steering and simulation result analyses. A cardiovascular numerical simulation illustrates the applicability of the model and an initial implementation using SciDB is discussed.


2007 ◽  
Vol 146 (1) ◽  
pp. 85-92 ◽  
Author(s):  
M. KOZAK ◽  
J. BOCIANOWSKI ◽  
W. RYBIŃSKI

SUMMARYThe objective of the present paper was to propose a statistical approach to support selection of the most promising genotypes in a breeding programme. The approach is based on applying two state-of-the-art statistical methodologies, likelihood-based path analysis and model-based cluster analysis. The first method is applied to find a causal mechanism lying behind a biological process of development of final crop yield. These results are then used for weighting traits to be used in cluster analysis, which helps select genotypes possessing a desirable level of yield and yield-contributing traits. An application of the approach is presented for a 2-year study on 22 grasspea genotypes, two cultivars (Derek and Krab) and 20 mutants from those cultivars. Seed yield/plant and seven yield-related traits were studied. Among these, plant height, number of branches/plant, pod length and number of seeds/plant determined seed yield; number of pods/plant influenced seed yield only for 2002. These results were used for appropriate weighting in cluster analysis, which indicated that cultivar Krab and its two mutants, K3 and K64, had the best level of the traits and were the most stable genotypes.


2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Barbara Zdrazil ◽  
Lars Richter ◽  
Nathan Brown ◽  
Rajarshi Guha

AbstractDrug Discovery is a lengthy and costly process and has faced a period of declining productivity within the last two decades resulting in increasing importance of integrative data-driven approaches. In this paper, data mining and integration is leveraged to inspect target innovation trends in drug discovery. The study highlights protein families and classes that have received more attention and those that have just emerged in the scientific literature, thus highlighting novel opportunities for drug intervention. In order to delineate the evolution of target-driven research interest from a biological perspective, trends in biological process annotations from Gene Ontology and disease annotations from DisGeNET are captured. The analysis reveals an increasing interest in targets related to immune system processes, and a recurrent trend for targets involved in circulatory system processes. At the level of diseases, targets associated with cancer-related pathologies, intellectual disability, and schizophrenia are increasingly investigated in recent years. The methodology enables researchers to capture trends in research attention in target space at an early stage during the drug discovery process. Workflows, scripts, and data used in this study are publicly available from https://github.com/BZdrazil/Moving_Targets. An interactive web application allows the customized exploration of target, biological process, and disease trends (available at https://rguha.shinyapps.io/MovingTargets/).


2012 ◽  
Vol 2012 ◽  
pp. 1-12 ◽  
Author(s):  
Sofie Van Landeghem ◽  
Kai Hakala ◽  
Samuel Rönnqvist ◽  
Tapio Salakoski ◽  
Yves Van de Peer ◽  
...  

Technological advancements in the field of genetics have led not only to an abundance of experimental data, but also caused an exponential increase of the number of published biomolecular studies. Text mining is widely accepted as a promising technique to help researchers in the life sciences deal with the amount of available literature. This paper presents a freely available web application built on top of 21.3 million detailed biomolecular events extracted from all PubMed abstracts. These text mining results were generated by a state-of-the-art event extraction system and enriched with gene family associations and abstract generalizations, accounting for lexical variants and synonymy. The EVEX resource locates relevant literature on phosphorylation, regulation targets, binding partners, and several other biomolecular events and assigns confidence values to these events. The search function accepts official gene/protein symbols as well as common names from all species. Finally, the web application is a powerful tool for generating homology-based hypotheses as well as novel, indirect associations between genes and proteins such as coregulators.


2021 ◽  
Vol 26 (1) ◽  
pp. 32-38
Author(s):  
Toluwase Hezekiah Fatoki

Abstract This work provides a cogent review of biomarketing. Biomarketing is an emerging discipline that crisscross the fields of management and science. Biomarketing is defined as the marketing of bio-relevant products and services within the global biosphere. Biomarketing pose that the interactions between salespeople and customers can be studied from a biological perspective. The emerging research in marketing studying buyer–seller interactions has explored the role of genes, hormones, and pleasure and pain processes. Clarity in health communication aid customer understanding of brand information. Brand management is explicitly focused on the application of all relevant marketing techniques in order to boost the perceived value of bio-relevant product to the customers. Biomarketing companies are different from regular marketing agency in that they know the physician and the science.


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