Journal articles on the topic 'Multi-organisms approach'
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McFadden, Mary M., Holly White, Beth Christy, and Candace Douglas. "Battling the Bugs: A Multi-Factorial Approach to Reducing Multi-Drug Resistant Organisms in an Academic Teaching Hospital." American Journal of Infection Control 39, no. 5 (June 2011): E15. http://dx.doi.org/10.1016/j.ajic.2011.04.053.
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Teo, Jason, and Hussein A. Abbass. "Automatic Generation of Controllers for Embodied Legged Organisms: A Pareto Evolutionary Multi-Objective Approach." Evolutionary Computation 12, no. 3 (September 2004): 355–94. http://dx.doi.org/10.1162/1063656041774974.
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In this paper, we investigate the use of a self-adaptive Pareto evolutionary multi-objective optimization (EMO) approach for evolving the controllers of virtual embodied organisms. The objective of this paper is to demonstrate the trade-off between quality of solutions and computational cost. We show empirically that evolving controllers using the proposed algorithm incurs significantly less computational cost when compared to a self-adaptive weighted sum EMO algorithm, a self-adaptive single-objective evolutionary algorithm (EA) and a hand-tuned Pareto EMO algorithm. The main contribution of the self-adaptive Pareto EMO approach is its ability to produce sufficiently good controllers with different locomotion capabilities in a single run, thereby reducing the evolutionary computational cost and allowing the designer to explore the space of good solutions simultaneously. Our results also show that self-adaptation was found to be highly beneficial in reducing redundancy when compared against the other algorithms. Moreover, it was also shown that genetic diversity was being maintained naturally by virtue of the system's inherent multi-objectivity.
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Américo, Montiel, Pérez Daniel, and Gorny Matthias. "SELECTION OF TARGET SPECIES FOR MARINE PROTECTED AREAS: A MULTI CRITERIA APPROACH USING BENTHIC ORGANISMS." Arquivos de Ciências do Mar 55, Especial (March 18, 2022): 22–33. http://dx.doi.org/10.32360/acmar.v55iespecial.78210.
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The selection of optimal target species to define and manage protected marine areas (MPAs) has generated a great scientific discussion during the past decades. Benthic invertebrates are commonly less considered as important target species, despite their pivotal role in marine ecosystems. To address this issue, we determined target species among benthic marine organisms using a multi-criteria approach. For this purpose, we used a data base from the Katalalixar National Reserve (RNK) in central Patagonia, Chile. The data were obtained through underwater photography and quantitative sampling by means of scuba diving during three expeditions between 2017 and 2019. Based on the total taxonomical inventory from both methods, a SIMPER analysis was used to determine 10 candidate species, and the Landscape Selection Species program was used for the selection of target species. Finally, eight target species were selected. The black snail Tegula atra, the hermit crab Pagurus comptus, the gastropod Crepipatella dilatata, and the polychaete Platynereis australis were selected among errant species. Among sessile species, the encrusting coralline algae Lithothamnium sp., the sea anemone Actinostola chilensis, the parchment worm Chaetopterus variopedatus, and the encrusting ascidia Didemnum sp. were the selected species. Based on our results we expect that these species will be included as target species in future management plans to improve protection of the marine environment of the Katalalixar National Reserve, one of the most pristine areas of the Chilean fjord region.
Keywords: macroinvertebrates, macroalgae, biodiversity, Patagonia.
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Yavuzcan Yıldız, Hijran, and Serap Pulatsü. "Towards zero waste: Sustainable waste management in aquaculture." Ege Journal of Fisheries and Aquatic Sciences 39, no. 4 (December 15, 2022): 341–48. http://dx.doi.org/10.12714/egejfas.39.4.11.
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Increases in aquaculture production due to higher demand for aquatic foods result in an increase in the amount of aquaculture wastewater. This situation highlights the need for the effective treatment of wastewater in sustainable aquaculture. Today, instead of traditional physical and chemical methods in the treatment of wastewater originating from aquaculture, ecosystem-sensitive and by-product-oriented systems have begun to be adopted. The main principle of the zero-waste approach is the recycling of the nutrients in the wastewater to produce another food. In this new innovative approach, the production of other organisms from the different trophic levels using the wastewater of aquaculture in the integrated multi-trophic systems (such as aquaponics) is possible to recycle the nutrients. It has been considered the integrated multi-trophic systems (IMTA) more valuable as these systems can be used both in environment-friendly wastewater treatment and in the conversion of nutrients in wastewater to biomass. The nutrients such as nitrogen and phosphorus in aquaculture wastewater can be utilized to produce two organisms (i.e. fish+mussel) or three organisms (i.e. fish+mussel+seaweed) through IMTA. Aquaculture wastewater can be used to reduce the nutrients in constructed wetlands and plant lagoons representing the reasonable approach for sustainable aquaculture and wastewater treatment. Here, the innovative approach to sustainable aquaculture wastewater treatment was reviewed for the current and innovative technologies. It was emphasized that the need for environment-friendly wastewater treatment Technologies such as aquaponics, enlargement of constructed wetlands, or increase in using the integrated multi-trophic production systems (IMTA) in practice are recommended for sustainable aquaculture.
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Burton, G. Allen, Marc S. Greenberg, Carolyn D. Rowland, Cameron A. Irvine, Daniel R. Lavoie, John A. Brooker, Laurie Moore, Delia F. N. Raymer, and Ruth A. McWilliam. "In situ exposures using caged organisms: a multi-compartment approach to detect aquatic toxicity and bioaccumulation." Environmental Pollution 134, no. 1 (March 2005): 133–44. http://dx.doi.org/10.1016/j.envpol.2004.07.008.
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ITMI, MHAMED, and ALAIN CARDON. "AUTONOMY AND CONTROL OF ADAPTIVE SYSTEMS OF SYSTEMS." International Journal of Modeling, Simulation, and Scientific Computing 03, no. 01 (March 2012): 1240002. http://dx.doi.org/10.1142/s1793962312400028.
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We propose a unified approach for systems integration and behavior regulation expressing the autonomy of Systems of Systems. For this, we precise the notion of autonomy as a transposition of the living organisms case and we develop the notion of artificial tendencies and behavioral intentions. We present a multi-agent model allowing the implementation with a new multi-scale control.
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Borges, Dérick Gabriel F., Daniel S. Carvalho, Gilberto C. Bomfim, Pablo Ivan P. Ramos, Jerzy Brzozowski, Aristóteles Góes-Neto, Roberto Andrade, and Charbel El-Hani. "On the origin of mitochondria: a multilayer network approach." PeerJ 11 (January 6, 2023): e14571. http://dx.doi.org/10.7717/peerj.14571.
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Backgound The endosymbiotic theory is widely accepted to explain the origin of mitochondria from a bacterial ancestor. While ample evidence supports the intimate connection of Alphaproteobacteria to the mitochondrial ancestor, pinpointing its closest relative within sampled Alphaproteobacteria is still an open evolutionary debate. Many different phylogenetic methods and approaches have been used to answer this challenging question, further compounded by the heterogeneity of sampled taxa, varying evolutionary rates of mitochondrial proteins, and the inherent biases in each method, all factors that can produce phylogenetic artifacts. By harnessing the simplicity and interpretability of protein similarity networks, herein we re-evaluated the origin of mitochondria within an enhanced multilayer framework, which is an extension and improvement of a previously developed method. Methods We used a dataset of eight proteins found in mitochondria (N = 6 organisms) and bacteria (N = 80 organisms). The sequences were aligned and resulting identity matrices were combined to generate an eight-layer multiplex network. Each layer corresponded to a protein network, where nodes represented organisms and edges were placed following mutual sequence identity. The Multi-Newman-Girvan algorithm was applied to evaluate community structure, and bifurcation events linked to network partition allowed to trace patterns of divergence between studied taxa. Results In our network-based analysis, we first examined the topology of the 8-layer multiplex when mitochondrial sequences disconnected from the main alphaproteobacterial cluster. The resulting topology lent firm support toward an Alphaproteobacteria-sister placement for mitochondria, reinforcing the hypothesis that mitochondria diverged from the common ancestor of all Alphaproteobacteria. Additionally, we observed that the divergence of Rickettsiales was an early event in the evolutionary history of alphaproteobacterial clades. Conclusion By leveraging complex networks methods to the challenging question of circumscribing mitochondrial origin, we suggest that the entire Alphaproteobacteria clade is the closest relative to mitochondria (Alphaproteobacterial-sister hypothesis), echoing recent findings based on different datasets and methodologies.
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Rodrigues, Marcelo, Birgit Lengerer, Thomas Ostermann, and Peter Ladurner. "Molecular biology approaches in bioadhesion research." Beilstein Journal of Nanotechnology 5 (July 8, 2014): 983–93. http://dx.doi.org/10.3762/bjnano.5.112.
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The use of molecular biology tools in the field of bioadhesion is still in its infancy. For new research groups who are considering taking a molecular approach, the techniques presented here are essential to unravelling the sequence of a gene, its expression and its biological function. Here we provide an outline for addressing adhesion-related genes in diverse organisms. We show how to gradually narrow down the number of candidate transcripts that are involved in adhesion by (1) generating a transcriptome and a differentially expressed cDNA list enriched for adhesion-related transcripts, (2) setting up a BLAST search facility, (3) perform an in situ hybridization screen, and (4) functional analyses of selected genes by using RNA interference knock-down. Furthermore, latest developments in genome-editing are presented as new tools to study gene function. By using this iterative multi-technologies approach, the identification, isolation, expression and function of adhesion-related genes can be studied in most organisms. These tools will improve our understanding of the diversity of molecules used for adhesion in different organisms and these findings will help to develop innovative bio-inspired adhesives.
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Wang, Mai, Yinyue Wang, and Shu Wang. "A network pharmacology approach to explore Dahuang on colon cancer." E3S Web of Conferences 292 (2021): 03066. http://dx.doi.org/10.1051/e3sconf/202129203066.
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To investigate the mechanism of action of Rhubarb (Dahuang) in the treatment of colon cancer by network pharmacological method. TCMSP database was used to screen the active components and action targets of Rhubarb, Genecards database was used to screen the relevant action targets of colon cancer, Venny 2.1.0 software was used to make the intersection of Rhubarb and colon cancer, and the potential targets of Rhubarb for the treatment of colon cancer were obtained.Cytoscape 3.7.2 software and the STRING database were used to construct the component-target network of Rhubarb active components and colon cancer related targets. The important targets were obtained by analyzing the network, and the GO and KEGG pathway enrichment analysis was performed on them using Metascape database. Sixty active ingredients including EUPATIN, Mutatochrome, Physciondiglucoside, Procyanidin B-5,3’ -o-gallate, rhin were screened from Rhubarb, which could act on 61 colon cancer related targets.Among them, 13 targets, including PTGS2, IL1B and Bax, are important targets, which may be involved in various biological processes such as the response to the regulation of colon cancer nutritional level, the homeostasis of multicellular organisms and the regulation of peptide secretion through the regulation of PI3K and other pathways. Rhubarb can participate in the treatment of colon cancer through multi-target and multi-pathway.
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Araújo, Cristiano V. M., Abdelmourhit Laissaoui, Daniel C. V. R. Silva, Eloisa Ramos-Rodríguez, Enrique González-Ortegón, Evaldo L. G. Espíndola, Francisco Baldó, et al. "Not Only Toxic but Repellent: What Can Organisms’ Responses Tell Us about Contamination and What Are the Ecological Consequences When They Flee from an Environment?" Toxics 8, no. 4 (December 12, 2020): 118. http://dx.doi.org/10.3390/toxics8040118.
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The ability of aquatic organisms to sense the surrounding environment chemically and interpret such signals correctly is crucial for their ecological niche and survival. Although it is an oversimplification of the ecological interactions, we could consider that a significant part of the decisions taken by organisms are, to some extent, chemically driven. Accordingly, chemical contamination might interfere in the way organisms behave and interact with the environment. Just as any environmental factor, contamination can make a habitat less attractive or even unsuitable to accommodate life, conditioning to some degree the decision of organisms to stay in, or move from, an ecosystem. If we consider that contamination is not always spatially homogeneous and that many organisms can avoid it, the ability of contaminants to repel organisms should also be of concern. Thus, in this critical review, we have discussed the dual role of contamination: toxicity (disruption of the physiological and behavioral homeostasis) vs. repellency (contamination-driven changes in spatial distribution/habitat selection). The discussion is centered on methodologies (forced exposure against non-forced multi-compartmented exposure systems) and conceptual improvements (individual stress due to the toxic effects caused by a continuous exposure against contamination-driven spatial distribution). Finally, we propose an approach in which Stress and Landscape Ecology could be integrated with each other to improve our understanding of the threat contaminants represent to aquatic ecosystems.
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Pritsch, Michael, Najib Ben Khaled, Gabriele Liegl, Soeren Schubert, Michael Hoelscher, Christine Woischke, Nathalie Arens, Julia Thorn‐Seshold, Stefan Kammermeier, and Andreas Wieser. "Rapid prototyping vaccine approach in mice against multi‐drug resistant Gram‐negative organisms from clinical isolates based on outer membrane vesicles." Microbiology and Immunology 65, no. 5 (May 2021): 214–27. http://dx.doi.org/10.1111/1348-0421.12882.
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Lofts, Stephen, Peggy Criel, Colin R. Janssen, Koen Lock, Steve P. McGrath, Koen Oorts, Corinne P. Rooney, et al. "Modelling the effects of copper on soil organisms and processes using the free ion approach: Towards a multi-species toxicity model." Environmental Pollution 178 (July 2013): 244–53. http://dx.doi.org/10.1016/j.envpol.2013.03.015.
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Ozen, Mustafa, Tomasz Lipniacki, Andre Levchenko, Effat S. Emamian, and Ali Abdi. "Modeling and measurement of signaling outcomes affecting decision making in noisy intracellular networks using machine learning methods." Integrative Biology 12, no. 5 (May 2020): 122–38. http://dx.doi.org/10.1093/intbio/zyaa009.
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Abstract Characterization of decision-making in cells in response to received signals is of importance for understanding how cell fate is determined. The problem becomes multi-faceted and complex when we consider cellular heterogeneity and dynamics of biochemical processes. In this paper, we present a unified set of decision-theoretic, machine learning and statistical signal processing methods and metrics to model the precision of signaling decisions, in the presence of uncertainty, using single cell data. First, we introduce erroneous decisions that may result from signaling processes and identify false alarms and miss events associated with such decisions. Then, we present an optimal decision strategy which minimizes the total decision error probability. Additionally, we demonstrate how graphing receiver operating characteristic curves conveniently reveals the trade-off between false alarm and miss probabilities associated with different cell responses. Furthermore, we extend the introduced framework to incorporate the dynamics of biochemical processes and reactions in a cell, using multi-time point measurements and multi-dimensional outcome analysis and decision-making algorithms. The introduced multivariate signaling outcome modeling framework can be used to analyze several molecular species measured at the same or different time instants. We also show how the developed binary outcome analysis and decision-making approach can be extended to more than two possible outcomes. As an example and to show how the introduced methods can be used in practice, we apply them to single cell data of PTEN, an important intracellular regulatory molecule in a p53 system, in wild-type and abnormal cells. The unified signaling outcome modeling framework presented here can be applied to various organisms ranging from viruses, bacteria, yeast and lower metazoans to more complex organisms such as mammalian cells. Ultimately, this signaling outcome modeling approach can be utilized to better understand the transition from physiological to pathological conditions such as inflammation, various cancers and autoimmune diseases.
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Zhu, Jisong, Zhaoxia Jing, Tianyao Ji, and Nauman Ali Larik. "Energy–Economy Coupled Simulation Approach and Simulator Based on Invididual-Based Model." Energies 13, no. 11 (June 1, 2020): 2771. http://dx.doi.org/10.3390/en13112771.
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An integrated energy system, referred to specifically as a heterogeneous energy system that combines cooling, heating, power, etc., is a dynamic system containing continuous as well as discrete behaviors on both technical and economic levels. Currently, the comprehensive utilization of multiple forms of energy and the implementation of the energy market have made the simulation of such a system very complicated, which is reflected in two aspects. First, the simulation model becomes complex and varied. Second, the time-varying characteristics of the models are quite diverse. Therefore, a standard and normative modeling and simulation method is urgently needed. This work aims to obtain a compatible modeling and simulation method for the energy economy coupling system. The individual-based model is widely used to describe organisms in an ecology system that are similar to the energy–economy coupled system. Inspired by this, a general simulation approach based on the individual-based model is proposed in this paper to overcome these existing problems. The standard formal expression model is built, then its structure and elements explained in detail, and multi-scale time simulation supported to model and simulate an integrated energy system that is coupled with markets. In addition, a simulator is designed and implemented based on multi-agent framework and model-view-controller architecture. Finally, a simulation case of a conceived scenario was designed and executed, and the results analysis proved the validity and versatility of the proposed approach. The proposed method has the advantages of model standardization, multi-scale time compatibility, distributed simulation capability, and privacy protection. These advantages support and strengthen each other. Through these studies, a systematic approach was formed that could improve the standardization of modeling and simulation in the energy–economy research area.
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CHENG, GUOFENG, and YOUXIN JIN. "MicroRNAs: Potentially important regulators for schistosome development and therapeutic targets against schistosomiasis." Parasitology 139, no. 5 (February 6, 2012): 669–79. http://dx.doi.org/10.1017/s0031182011001855.
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SUMMARYMicroRNAs (miRNAs) are small, endogenous non-coding RNA molecules that regulate gene expression post-transcriptionally by targeting the 3′ untranslated region (3′ UTR) of messenger RNAs. Since the discovery of the first miRNA in Caenorhabditis elegans, important regulatory roles for miRNAs in many key biological processes including development, cell proliferation, cell differentiation and apoptosis of many organisms have been described. Hundreds of miRNAs have been identified in various multicellular organisms and many are evolutionarily conserved. Schistosomes are multi-cellular eukaryotes with a complex life-cycle that require genes to be expressed and regulated precisely. Recently, miRNAs have been identified in two major schistosome species, Schistosoma japonicum and S. mansoni. These miRNAs are likely to play critical roles in schistosome development and gene regulation. Here, we review recent studies on schistosome miRNAs and discuss the potential roles of miRNAs in schistosome development and gene regulation. We also summarize the current status for targeting miRNAs and the potential of this approach for therapy against schistosomiasis.
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Abeysuriya, Kumi, Nadira Khawaja, Freya Mills, Naomi Carrard, Antoinette Kome, and Juliet Willetts. "Faecal sludge reuse in Birendranagar, Nepal: a case study of the world health organisation's multiple barrier approach." Water Practice and Technology 13, no. 1 (March 1, 2018): 1–20. http://dx.doi.org/10.2166/wpt.2018.007.
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Abstract This case study presents an innovative initiative to facilitate safe reuse of faecal sludge (FS) by introducing the World Health Organisation's multi-barrier approach within a Farmer Field Schools framework for participatory experiential learning. A novel FS treatment process based on fermentation by ‘effective organisms’ (EM) was piloted to test the feasibility, safety and acceptability of the resulting fertilizer. Fermented FS in agricultural application was found to perform at least as well as other common fertilizers it was compared with, while its lower cost delivered higher profits per cultivated hectare. Participating farmers found it easy to prepare and use, and viewed it favourably overall. EM-based fermentation was, however, found to be insufficient as an FS treatment to render safe reuse, particularly with respect to helminth inactivation. The paper discusses strengthening the treatment barrier, and improving the application of the multi-barrier approach by the systematic consideration of non-treatment barriers using guidance from the WHO's Sanitation Safety Planning Manual. Further research to enable effective monitoring and support systems for maintaining treatment and non-treatment barriers, and for understanding long term impacts of fermented FS application is recommended. In combination, adequately treated fermented FS may be a candidate for scale up necessary for meeting the Sustainable Development Goals.
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Barreto, Angela, Joana Santos, Mónica J. B. Amorim, and Vera L. Maria. "Is the Synthetic Fungicide Fosetyl-Al Safe for the Ecotoxicological Models Danio rerio and Enchytraeus crypticus?" Applied Sciences 11, no. 16 (August 5, 2021): 7209. http://dx.doi.org/10.3390/app11167209.
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Worldwide, pesticides have contaminated the environment, affecting non-target species. The aim of this work was to evaluate the effects of fosetyl-Al (FOS) on model organisms. Based on the 3 Rs for animal research and described guidelines, the OECD 236 and 220 were applied with some modifications. The FOS test concentrations were 0.02–0.2–2–20–200 mg/L for Danio rerio and 250–500–750–1000–1250 mg/kg for Enchytraeus crypticus. Besides the standard endpoints, additional endpoints were evaluated (D. rerio: behavior and biochemical responses; E. crypticus: extension of exposure duration (28 d (days) + 28 d) and organisms’ sizes). For D. rerio, after 96 h (h), hatching was inhibited (200 mg/L), proteins’ content increased (2 and 20 mg/L), lipids’ content decreased (2 mg/L), glutathione S-transferase activity increased (2 mg/L), and, after 120 h, larvae distance swam increased (20 mg/L). For E. crypticus, after 28 d, almost all the tested concentrations enlarged the organisms’ sizes and, after 56 d, 1250 mg/kg decreased the reproduction. In general, alterations in the organisms’ biochemical responses, behavior, and growth occurred at lower concentrations than the effects observed at the standard endpoints. This ecotoxicological assessment showed that FOS may not be considered safe for the tested species, only at higher concentrations than the predicted environmental concentrations (PECs). This research highlighted the importance of a multi-endpoint approach to assess the (eco)toxic effects of the contaminants.
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Bevilacqua, Dario. "The International Regulation of Genetically Modified Organisms: Uncertainty, Fragmentation, and Precaution." European Energy and Environmental Law Review 16, Issue 12 (December 1, 2007): 314–36. http://dx.doi.org/10.54648/eelr2007037.
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Summary: The regulation of genetically modified organisms (GMOs) is paradigmatic for the study of some of the most interesting features of contemporary international law. The main characteristics of this sector are: scientific uncertainty, multi-sectorality and multi-nationality. There are many different scientific opinions concerning GMOs and at the moment the possibility to determine a sound and common vision on the issue seems quite far from reach. At the same time, GM products affect various interests and goods, of public and private nature, such as agriculture, trade, health and environment protection, and consumer information. This means their diffusion would have a significant impact over a multiplicity of policy areas, often connected, sometimes conflicting. Finally, with the development of global trade, GMOs are a transnational commercial issue, which needs an impartial and agreed solution to their regulation. Starting from the uncertainty and the legal conflicts surrounding the regulation of GMOs, the article will deepen the problematic issues concerning sectorality and fragmentation in international law – taking as an instance the conflict between the Cartagena Biosafety Protocol and the Sanitary and Phytosanitary Agreement of the WTO – and, finally, it will consider the effect of the introduction of a soft version of the precautionary approach at the global level, namely, with reference to international administration of risk.
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Berntson, Gary G., Greg J. Norman, Louise C. Hawkley, and John T. Cacioppo. "Evolution of neuroarchitecture, multi-level analyses and calibrative reductionism." Interface Focus 2, no. 1 (November 30, 2011): 65–73. http://dx.doi.org/10.1098/rsfs.2011.0063.
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Evolution has sculpted the incredibly complex human nervous system, among the most complex functions of which extend beyond the individual to an intricate social structure. Although these functions are deterministic, those determinants are legion, heavily interacting and dependent on a specific evolutionary trajectory. That trajectory was directed by the adaptive significance of quasi-random genetic variations, but was also influenced by chance and caprice. With a different evolutionary pathway, the same neural elements could subserve functions distinctly different from what they do in extant human brains. Consequently, the properties of higher level neural networks cannot be derived readily from the properties of the lower level constituent elements, without studying these elements in the aggregate. Thus, a multi-level approach to integrative neuroscience may offer an optimal strategy. Moreover, the process of calibrative reductionism, by which concepts and understandings from one level of organization or analysis can mutually inform and ‘calibrate’ those from other levels (both higher and lower), may represent a viable approach to the application of reductionism in science. This is especially relevant in social neuroscience, where the basic subject matter of interest is defined by interacting organisms across diverse environments.
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MacManes, Matthew D. "The Oyster River Protocol: a multi-assembler and kmer approach for de novo transcriptome assembly." PeerJ 6 (August 3, 2018): e5428. http://dx.doi.org/10.7717/peerj.5428.
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Characterizing transcriptomes in non-model organisms has resulted in a massive increase in our understanding of biological phenomena. This boon, largely made possible via high-throughput sequencing, means that studies of functional, evolutionary, and population genomics are now being done by hundreds or even thousands of labs around the world. For many, these studies begin with a de novo transcriptome assembly, which is a technically complicated process involving several discrete steps. The Oyster River Protocol (ORP), described here, implements a standardized and benchmarked set of bioinformatic processes, resulting in an assembly with enhanced qualities over other standard assembly methods. Specifically, ORP produced assemblies have higher Detonate and TransRate scores and mapping rates, which is largely a product of the fact that it leverages a multi-assembler and kmer assembly process, thereby bypassing the shortcomings of any one approach. These improvements are important, as previously unassembled transcripts are included in ORP assemblies, resulting in a significant enhancement of the power of downstream analysis. Further, as part of this study, I show that assembly quality is unrelated with the number of reads generated, above 30 million reads. Code Availability: The version controlled open-source code is available at https://github.com/macmanes-lab/Oyster_River_Protocol. Instructions for software installation and use, and other details are available at http://oyster-river-protocol.rtfd.org/.
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Mahmood, Ammar, Ana Giraldo Ospina, Mohammed Bennamoun, Senjian An, Ferdous Sohel, Farid Boussaid, Renae Hovey, Robert B. Fisher, and Gary A. Kendrick. "Automatic Hierarchical Classification of Kelps Using Deep Residual Features." Sensors 20, no. 2 (January 13, 2020): 447. http://dx.doi.org/10.3390/s20020447.
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Across the globe, remote image data is rapidly being collected for the assessment of benthic communities from shallow to extremely deep waters on continental slopes to the abyssal seas. Exploiting this data is presently limited by the time it takes for experts to identify organisms found in these images. With this limitation in mind, a large effort has been made globally to introduce automation and machine learning algorithms to accelerate both classification and assessment of marine benthic biota. One major issue lies with organisms that move with swell and currents, such as kelps. This paper presents an automatic hierarchical classification method local binary classification as opposed to the conventional flat classification to classify kelps in images collected by autonomous underwater vehicles. The proposed kelp classification approach exploits learned feature representations extracted from deep residual networks. We show that these generic features outperform the traditional off-the-shelf CNN features and the conventional hand-crafted features. Experiments also demonstrate that the hierarchical classification method outperforms the traditional parallel multi-class classifications by a significant margin (90.0% vs. 57.6% and 77.2% vs. 59.0%) on Benthoz15 and Rottnest datasets respectively. Furthermore, we compare different hierarchical classification approaches and experimentally show that the sibling hierarchical training approach outperforms the inclusive hierarchical approach by a significant margin. We also report an application of our proposed method to study the change in kelp cover over time for annually repeated AUV surveys.
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Pavlovikj, Natasha, Joao Carlos Gomes-Neto, Jitender S. Deogun, and Andrew K. Benson. "Systems-Based Approach for Optimization of Assembly-Free Bacterial MLST Mapping." Life 12, no. 5 (April 30, 2022): 670. http://dx.doi.org/10.3390/life12050670.
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Epidemiological surveillance of bacterial pathogens requires real-time data analysis with a fast turnaround, while aiming at generating two main outcomes: (1) species-level identification and (2) variant mapping at different levels of genotypic resolution for population-based tracking and surveillance, in addition to predicting traits such as antimicrobial resistance (AMR). Multi-locus sequence typing (MLST) aids this process by identifying sequence types (ST) based on seven ubiquitous genome-scattered loci. In this paper, we selected one assembly-dependent and one assembly-free method for ST mapping and applied them with the default settings and ST schemes they are distributed with, and systematically assessed their accuracy and scalability across a wide array of phylogenetically divergent Public Health-relevant bacterial pathogens with available MLST databases. Our data show that the optimal k-mer length for stringMLST is species-specific and that genome-intrinsic and -extrinsic features can affect the performance and accuracy of the program. Although suitable parameters could be identified for most organisms, there were instances where this program may not be directly deployable in its current format. Next, we integrated stringMLST into our freely available and scalable hierarchical-based population genomics platform, ProkEvo, and further demonstrated how the implementation facilitates automated, reproducible bacterial population analysis.
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Onorato, Lorenzo, Caterina Monari, Salvatore Capuano, Pierantonio Grimaldi, and Nicola Coppola. "Prevalence and Therapeutic Management of Infections by Multi-Drug-Resistant Organisms (MDROs) in Patients with Liver Cirrhosis: A Narrative Review." Antibiotics 11, no. 2 (February 11, 2022): 232. http://dx.doi.org/10.3390/antibiotics11020232.
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Bacterial infections are common events that significantly impact the clinical course of patients with cirrhosis. As in the general population, infections caused by multi-drug-resistant organisms (MDROs) are progressively increasing in cirrhotic patients, accounting for up to 30–35% of all infections. Nosocomial acquisition and prior exposure to antimicrobial treatment or invasive procedures are well-known risk factors for MDRO infections. Several studies have demonstrated that infections due to MDROs have a poorer prognosis and higher rates of treatment failure, septic shock, and hospital mortality. Due to the increasing rate of antimicrobial resistance, the approach to empirical treatment in cirrhotic patients with life-threatening infections has become significantly more challenging. In order to ensure a prompt administration of effective antibiotic therapy while avoiding unnecessary antibiotic exposure at the same time, it is of utmost importance to choose the correct antimicrobial therapy and administration schedule based on individual clinical characteristics and risk factors and rapidly adopt de-escalation strategies as soon as microbiological data are available. In the present paper, we aimed to provide an overview of the most frequent infections diagnosed in cirrhotic patients, the prevalence and impact of antimicrobial resistance, and potential therapeutic options in this population.
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Malic, Sladjana, Katja E. Hill, Anthony Hayes, Steven L. Percival, David W. Thomas, and David W. Williams. "Detection and identification of specific bacteria in wound biofilms using peptide nucleic acid fluorescent in situ hybridization (PNA FISH)." Microbiology 155, no. 8 (August 1, 2009): 2603–11. http://dx.doi.org/10.1099/mic.0.028712-0.
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Biofilms provide a reservoir of potentially infectious micro-organisms that are resistant to antimicrobial agents, and their importance in the failure of medical devices and chronic inflammatory conditions is increasingly being recognized. Particular research interest exists in the association of biofilms with wound infection and non-healing, i.e. chronic wounds. In this study, fluorescent in situ hybridization (FISH) was used in combination with confocal laser scanning microscopy (CLSM) to detect and characterize the spatial distribution of biofilm-forming bacteria which predominate within human chronic skin wounds (Pseudomonas aeruginosa, Staphylococcus aureus, Streptococcus sp. and Micrococcus sp.). In vitro biofilms were prepared using a constant-depth film fermenter and a reconstituted human epidermis model. In vivo biofilms were also studied using biopsy samples from non-infected chronic venous leg ulcers. The specificity of peptide nucleic acid (PNA) probes for the target organisms was confirmed using mixed preparations of planktonic bacteria and multiplex PNA probing. Identification and location of individual bacterial species within multi-species biofilms demonstrated that P. aeruginosa was predominant. CLSM revealed clustering of individual species within mixed-species biofilms. FISH analysis of archive chronic wound biopsy sections showed bacterial presence and allowed bacterial load to be determined. The application of this standardized procedure makes available an assay for identification of single- or multi-species bacterial populations in tissue biopsies. The technique provides a reliable tool to study bacterial biofilm formation and offers an approach to assess targeted biofilm disruption strategies in vivo.
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Williams, Ernest P., Tsvetan R. Bachvaroff, and Allen R. Place. "A Global Approach to Estimating the Abundance and Duplication of Polyketide Synthase Domains in Dinoflagellates." Evolutionary Bioinformatics 17 (January 2021): 117693432110318. http://dx.doi.org/10.1177/11769343211031871.
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Many dinoflagellate species make toxins in a myriad of different molecular configurations but the underlying chemistry in all cases is presumably via modular synthases, primarily polyketide synthases. In many organisms modular synthases occur as discrete synthetic genes or domains within a gene that act in coordination thus forming a module that produces a particular fragment of a natural product. The modules usually occur in tandem as gene clusters with a syntenic arrangement that is often predictive of the resultant structure. Dinoflagellate genomes however are notoriously complex with individual genes present in many tandem repeats and very few synthetic modules occurring as gene clusters, unlike what has been seen in bacteria and fungi. However, modular synthesis in all organisms requires a free thiol group that acts as a carrier for sequential synthesis called a thiolation domain. We scanned 47 dinoflagellate transcriptomes for 23 modular synthase domain models and compared their abundance among 10 orders of dinoflagellates as well as their co-occurrence with thiolation domains. The total count of domain types was quite large with over thirty-thousand identified, 29 000 of which were in the core dinoflagellates. Although there were no specific trends in domain abundance associated with types of toxins, there were readily observable lineage specific differences. The Gymnodiniales, makers of long polyketide toxins such as brevetoxin and karlotoxin had a high relative abundance of thiolation domains as well as multiple thiolation domains within a single transcript. Orders such as the Gonyaulacales, makers of small polyketides such as spirolides, had fewer thiolation domains but a relative increase in the number of acyl transferases. Unique to the core dinoflagellates, however, were thiolation domains occurring alongside tetratricopeptide repeats that facilitate protein-protein interactions, especially hexa and hepta-repeats, that may explain the scaffolding required for synthetic complexes capable of making large toxins. Clustering analysis for each type of domain was also used to discern possible origins of duplication for the multitude of single domain transcripts. Single domain transcripts frequently clustered with synonymous domains from multi-domain transcripts such as the BurA and ZmaK like genes as well as the multi-ketosynthase genes, sometimes with a large degree of apparent gene duplication, while fatty acid synthesis genes formed distinct clusters. Surprisingly the acyl-transferases and ketoreductases involved in fatty acid synthesis (FabD and FabG, respectively) were found in very large clusters indicating an unprecedented degree of gene duplication for these genes. These results demonstrate a complex evolutionary history of core dinoflagellate modular synthases with domain specific duplications throughout the lineage as well as clues to how large protein complexes can be assembled to synthesize the largest natural products known.
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Boulajfene, Wafa, Montassar Lasram, and Sabiha Zouari-Tlig. "Integrated Biomarker Response for Environmental Assessment Using the Gastropod Phorcus turbinatus along the Northern and the Northeastern Coasts of Tunisia." Life 11, no. 6 (June 7, 2021): 529. http://dx.doi.org/10.3390/life11060529.
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This work aims to assess the spatial and temporal variations of four biomarkers activities and to integrate their biological responses in a battery using the gastropod Phorcus turbinatus. The monitoring was carried out during the period between April 2014 and January 2015 at six stations along the northern and the northeastern coasts of Tunisia. The Fulton condition factor was estimated and the activities of catalase, acetylcholinesterase and glutathione-S-transferase were evaluated by spectrophotometry. A multi-biomarker battery approach was used to assess ecosystems’ condition and to identify environmental impacts on the organisms. The results suggest that the enzymatic activities of CAT and GST depend especially on seasons. As for AChE activity, it was similar between seasons and stations. The values of the integrated biological response were maximal at Jarzouna in summer and at Sidi Daoued in winter, indicating the presence of severe stressors suffered by the organisms. This perturbation may be due to the enrichment of the waters by xenobiotics, namely polycyclic aromatic hydrocarbons, insecticides, phosphate wastes, PCBs and pesticides. Thus, P. turbinatus seems to be a good bioindicator of chemical pollution, constituting an adequate tool for a bio-monitoring program.
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Eckmair, Barbara, Chunsheng Jin, Niclas G. Karlsson, Daniel Abed-Navandi, Iain B. H. Wilson, and Katharina Paschinger. "Glycosylation at an evolutionary nexus: the brittle star Ophiactis savignyi expresses both vertebrate and invertebrate N-glycomic features." Journal of Biological Chemistry 295, no. 10 (January 30, 2020): 3173–88. http://dx.doi.org/10.1074/jbc.ra119.011703.
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Echinoderms are among the most primitive deuterostomes and have been used as model organisms to understand chordate biology because of their close evolutionary relationship to this phylogenetic group. However, there are almost no data available regarding the N-glycomic capacity of echinoderms, which are otherwise known to produce a diverse set of species-specific glycoconjugates, including ones heavily modified by fucose, sulfate, and sialic acid residues. To increase the knowledge of diversity of carbohydrate structures within this phylum, here we conducted an in-depth analysis of N-glycans from a brittle star (Ophiactis savignyi) as an example member of the class Ophiuroidea. To this end, we performed a multi-step N-glycan analysis by HPLC and various exoglyosidase and chemical treatments in combination with MALDI-TOF MS and MS/MS. Using this approach, we found a wealth of hybrid and complex oligosaccharide structures reminiscent of those in higher vertebrates as well as some classical invertebrate glycan structures. 70% of these N-glycans were anionic, carrying either sialic acid, sulfate, or phosphate residues. In terms of glycophylogeny, our data position the brittle star between invertebrates and vertebrates and confirm the high diversity of N-glycosylation in lower organisms.
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Leggett, Helen C., Sam P. Brown, and Sarah E. Reece. "War and peace: social interactions in infections." Philosophical Transactions of the Royal Society B: Biological Sciences 369, no. 1642 (May 19, 2014): 20130365. http://dx.doi.org/10.1098/rstb.2013.0365.
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One of the most striking facts about parasites and microbial pathogens that has emerged in the fields of social evolution and disease ecology in the past few decades is that these simple organisms have complex social lives, indulging in a variety of cooperative, communicative and coordinated behaviours. These organisms have provided elegant experimental tests of the importance of relatedness, kin discrimination, cooperation and competition, in driving the evolution of social strategies. Here, we briefly review the social behaviours of parasites and microbial pathogens, including their contributions to virulence, and outline how inclusive fitness theory has helped to explain their evolution. We then take a mechanistically inspired ‘bottom-up’ approach, discussing how key aspects of the ways in which parasites and pathogens exploit hosts, namely public goods, mobile elements, phenotypic plasticity, spatial structure and multi-species interactions, contribute to the emergent properties of virulence and transmission. We argue that unravelling the complexities of within-host ecology is interesting in its own right, and also needs to be better incorporated into theoretical evolution studies if social behaviours are to be understood and used to control the spread and severity of infectious diseases.
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Siembieda, J. L., R. A. Kock, T. A. McCracken, and S. H. Newman. "The role of wildlife in transboundary animal diseases." Animal Health Research Reviews 12, no. 1 (May 27, 2011): 95–111. http://dx.doi.org/10.1017/s1466252311000041.
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AbstractThis paper identifies some of the more important diseases at the wildlife–livestock interface and the role wildlife plays in disease transmission. Domestic livestock, wildlife and humans share many similar pathogens. Pathogens of wild or domestic animal origin that can cause infections in humans are known as zoonotic organisms and the converse are termed as anthroponotic organisms. Seventy-seven percent of livestock pathogens and 91% of domestic carnivore pathogens are known to infect multiple hosts, including wildlife. Understanding this group of pathogens is critical to public health safety, because they infect a wide range of hosts and are most likely to emerge as novel causes of infection in humans and domestic animals. Diseases at the wildlife–livestock interface, particularly those that are zoonotic, must be an area of focus for public health programs and surveillance for emerging infectious diseases. Additionally, understanding wildlife and their role is a vital part of understanding the epidemiology and ecology of diseases. To do this, a multi-faceted approach combining capacity building and training, wildlife disease surveillance, wildlife–livestock interface and disease ecology studies, data and information sharing and outbreak investigation are needed.
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STRANSKY, BEATRIZ, JUNIOR BARRERA, LUCILA OHNO-MACHADO, and SANDRO J. DE SOUZA. "MODELING CANCER: INTEGRATION OF "OMICS" INFORMATION IN DYNAMIC SYSTEMS." Journal of Bioinformatics and Computational Biology 05, no. 04 (August 2007): 977–86. http://dx.doi.org/10.1142/s0219720007002990.
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The last 10 years have seen the rise of many technologies that produce an unprecedented amount of genome-scale data from many organisms. Although the research community has been successful in exploring these data, many challenges still persist. One of them is the effective integration of such data sets directly into approaches based on mathematical modeling of biological systems. Applications in cancer are a good example. The bridge between information and modeling in cancer can be achieved by two major types of complementary strategies. First, there is a bottom–up approach, in which data generates information about structure and relationship between components of a given system. In addition, there is a top–down approach, where cybernetic and systems–theoretical knowledge are used to create models that describe mechanisms and dynamics of the system. These approaches can also be linked to yield multi-scale models combining detailed mechanism and wide biological scope. Here we give an overall picture of this field and discuss possible strategies to approach the major challenges ahead.
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Alcívar, M. Antonella, Marta Sendra, Daniel C. V. R. Silva, Enrique González-Ortegón, Julián Blasco, Ignacio Moreno-Garrido, and Cristiano V. M. Araújo. "Could Contamination Avoidance Be an Endpoint That Protects the Environment? An Overview on How Species Respond to Copper, Glyphosate, and Silver Nanoparticles." Toxics 9, no. 11 (November 11, 2021): 301. http://dx.doi.org/10.3390/toxics9110301.
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The use of non-forced multi-compartmented exposure systems has gained importance in the assessment of the contamination-driven spatial avoidance response. This new paradigm of exposure makes it possible to assess how contaminants fragment habitats, interfering in the spatial distribution and species’ habitat selection processes. In this approach, organisms are exposed to a chemically heterogeneous scenario (a gradient or patches of contamination) and the response is focused on identifying the contamination levels considered aversive for organisms. Despite the interesting results that have been recently published, the use of this approach in ecotoxicological risk studies is still incipient. The current review aims to show the sensitivity of spatial avoidance in non-forced exposure systems in comparison with the traditional endpoints used in ecotoxicology under forced exposure. To do this, we have used the sensitivity profile by biological groups (SPBG) to offer an overview of the highly sensitive biological groups and the species sensitive distribution (SSD) to estimate the hazard concentration for 5% of the species (HC5). Three chemically different compounds were selected for this review: copper, glyphosate, and Ag-NPs. The results show that contamination-driven spatial avoidance is a very sensitive endpoint that could be integrated as a complementary tool to ecotoxicological studies in order to provide an overview of the level of repellence of contaminants. This repellence is a clear example of how contamination might fragment ecosystems, prevent connectivity among populations and condition the distribution of biodiversity.
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Karasawa, Akira, Haijiao Liu, Matthias Quick, Wayne A. Hendrickson, and Qun Liu. "Crystallographic Characterization of Sodium Ions in a Bacterial Leucine/Sodium Symporter." Crystals 13, no. 2 (January 20, 2023): 183. http://dx.doi.org/10.3390/cryst13020183.
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Na+ is the most abundant ion in living organisms and plays essential roles in regulating nutrient uptake, muscle contraction, and neurotransmission. The identification of Na+ in protein structures is crucial for gaining a deeper understanding of protein function in a physiological context. LeuT, a bacterial homolog of the neurotransmitter:sodium symporter family, uses the Na+ gradient to power the uptake of amino acids into cells and has been used as a paradigm for the study of Na+-dependent transport systems. We have devised a low-energy multi-crystal approach for characterizing low-Z (Z ≤ 20) anomalous scattering ions such as Na+, Mg2+, K+, and Ca2+ by combining Bijvoet-difference Fourier syntheses for ion detection and f” refinements for ion speciation. Using the approach, we experimentally identify two Na+ bound near the central leucine binding site in LeuT. Using LeuT microcrystals, we also demonstrate that Na+ may be depleted to study conformational changes in the LeuT transport cycle.
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Ficetola, Gentile Francesco, Claude Miaud, François Pompanon, and Pierre Taberlet. "Species detection using environmental DNA from water samples." Biology Letters 4, no. 4 (April 9, 2008): 423–25. http://dx.doi.org/10.1098/rsbl.2008.0118.
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The assessment of species distribution is a first critical phase of biodiversity studies and is necessary to many disciplines such as biogeography, conservation biology and ecology. However, several species are difficult to detect, especially during particular time periods or developmental stages, potentially biasing study outcomes. Here we present a novel approach, based on the limited persistence of DNA in the environment, to detect the presence of a species in fresh water. We used specific primers that amplify short mitochondrial DNA sequences to track the presence of a frog ( Rana catesbeiana ) in controlled environments and natural wetlands. A multi-sampling approach allowed for species detection in all environments where it was present, even at low densities. The reliability of the results was demonstrated by the identification of amplified DNA fragments, using traditional sequencing and parallel pyrosequencing techniques. As the environment can retain the molecular imprint of inhabiting species, our approach allows the reliable detection of secretive organisms in wetlands without direct observation. Combined with massive sequencing and the development of DNA barcodes that enable species identification, this approach opens new perspectives for the assessment of current biodiversity from environmental samples.
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Boyer, Denis, and Peter D. Walsh. "Modelling the mobility of living organisms in heterogeneous landscapes: does memory improve foraging success?" Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 368, no. 1933 (December 28, 2010): 5645–59. http://dx.doi.org/10.1098/rsta.2010.0275.
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Thanks to recent technological advances, it is now possible to track with an unprecedented precision and for long periods of time the movement patterns of many living organisms in their habitat. The increasing amount of data available on single trajectories offers the possibility of understanding how animals move and of testing basic movement models. Random walks have long represented the main description for micro-organisms and have also been useful to understand the foraging behaviour of large animals. Nevertheless, most vertebrates, in particular humans and other primates, rely on sophisticated cognitive tools such as spatial maps, episodic memory and travel cost discounting. These properties call for other modelling approaches of mobility patterns. We propose a foraging framework where a learning mobile agent uses a combination of memory-based and random steps. We investigate how advantageous it is to use memory for exploiting resources in heterogeneous and changing environments. An adequate balance of determinism and random exploration is found to maximize the foraging efficiency and to generate trajectories with an intricate spatio-temporal order, where travel routes emerge without multi-step planning. Based on this approach, we propose some tools for analysing the non-random nature of mobility patterns in general.
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Dawood, Mahmoud A. O., Mohammed F. El Basuini, Amr I. Zaineldin, Sevdan Yilmaz, Md Tawheed Hasan, Ehsan Ahmadifar, Amel M. El Asely, et al. "Antiparasitic and Antibacterial Functionality of Essential Oils: An Alternative Approach for Sustainable Aquaculture." Pathogens 10, no. 2 (February 9, 2021): 185. http://dx.doi.org/10.3390/pathogens10020185.
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Using synthetic antibiotics/chemicals for infectious bacterial pathogens and parasitic disease control causes beneficial microbial killing, produces multi-drug resistant pathogens, and residual antibiotic impacts in humans are the major threats to aquaculture sustainability. Applications of herbal products to combat microbial and parasitic diseases are considered as alternative approaches for sustainable aquaculture. Essential oils (EOs) are the secondary metabolites of medicinal plants that possess bioactive compounds like terpens, terpenoids, phenylpropenes, and isothiocyanates with synergistic relationship among these compounds. The hydrophobic compounds of EOs can penetrate the bacterial and parasitic cells and cause cell deformities and organelles dysfunctions. Dietary supplementation of EOs also modulate growth, immunity, and infectious disease resistance in aquatic organisms. Published research reports also demonstrated EOs effectiveness against Ichthyophthirius multifiliis, Gyrodactylus sp., Euclinostomum heterostomum, and other parasites both in vivo and in vitro. Moreover, different infectious fish pathogenic bacteria like Aeromonas salmonicida, Vibrio harveyi, and Streptococcus agalactiae destruction was confirmed by plant originated EOs. However, no research was conducted to confirm the mechanism of action or pathway identification of EOs to combat aquatic parasites and disease-causing microbes. This review aims to explore the effectiveness of EOs against fish parasites and pathogenic bacteria as an environment-friendly phytotherapeutic in the aquaculture industry. Moreover, research gaps and future approaches to use EOs for sustainable aquaculture practice are also postulated.
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Marinello, Samuele, and Rita Gamberini. "Multi-Criteria Decision Making Approaches Applied to Waste Electrical and Electronic Equipment (WEEE): A Comprehensive Literature Review." Toxics 9, no. 1 (January 18, 2021): 13. http://dx.doi.org/10.3390/toxics9010013.
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The global demand for electrical and electronic equipment has undergone continuous growth in recent years due to the effect of industrialization and technological development. This indicates substantial quantities of e-waste that need to be managed properly to reduce their environmental impact and to avoid inappropriate forms of disposal. The purpose of this paper is to review the most popular multi-criteria decision-making approaches applied to the management of waste electrical and electronic equipment, analyzing how they are used to contribute to the improvement of management strategies along the entire supply chain. For this purpose, a methodological protocol for the collection, selection, and analysis of the scientific literature was applied, identifying 44 papers on which to conduct this study. The results showed that numerous authors have developed multi-criteria approaches, with particular attention to recycling phase. The analytic hierarchy process is the most widespread multi-criteria approach, often coupled with VIKOR, DELPHI, and TOPSIS methods. The numerous decision making criteria adopted cover different reference dimensions: environmental, economic, social, technical, and legal. Considering environmental aspects also in decision making processes means enhancing the relevance of this dimension, as well as encouraging practices that reduce the impact of toxic substances on the environment and living organisms.
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Maniam, Kranthi Kumar, and Shiladitya Paul. "A Preliminary Assessment of the ‘Greenness’ of Halide-Free Ionic Liquids—An MCDA Based Approach." Processes 9, no. 9 (August 27, 2021): 1524. http://dx.doi.org/10.3390/pr9091524.
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With the growing interests in non-aqueous media for diversified applications, ionic liquids (ILs) are frequently considered as green solvents. While the environmental, health, and safety assessments of the commercially developed ILs and their ‘greenness’ status are in debate, research focus is shifting towards the application of halide-free ILs for diversified applications. To clarify the situation on their greenness, and to understand if they really possess safe characteristics, we performed an initial assessment of 193 halide free ionic liquids composed of four groups of cations (imidazolium, pyridinium, pyrrodilinium, piperidinum) and 5 groups of anions (acetate, propionate, butyrate, alkanesulfonates, alkylsulfates). The ‘Technique for Order of Preference by Similarity to Ideal Solutions’ (TOPSIS), a multi-criteria decision analysis (MCDA) tool that allows ranking many alternatives is applied by carrying out the assessment against 14 criteria that includes hazard statements, precautionary statements, biodegradability, and toxicity towards different organisms. The ranking results obtained against the set of criteria considered show that the halide free ILs placed between recommended polar solvents: methanol and ethanol can be considered to be safer alternatives in terms of ‘greenness’. The study in this work provides an initial assessment of the halide-free ionic liquids evaluated against 14 criteria in terms of their safety characteristics (“green character”) using the MCDA-TOPSIS approach.
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Sheftel, Hila, Pablo Szekely, Avi Mayo, Guy Sella, and Uri Alon. "Evolutionary trade-offs and the structure of polymorphisms." Philosophical Transactions of the Royal Society B: Biological Sciences 373, no. 1747 (April 9, 2018): 20170105. http://dx.doi.org/10.1098/rstb.2017.0105.
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Populations of organisms show genetic differences called polymorphisms. Understanding the effects of polymorphisms is important for biology and medicine. Here, we ask which polymorphisms occur at high frequency when organisms evolve under trade-offs between multiple tasks. Multiple tasks present a problem, because it is not possible to be optimal at all tasks simultaneously and hence compromises are necessary. Recent work indicates that trade-offs lead to a simple geometry of phenotypes in the space of traits: phenotypes fall on the Pareto front, which is shaped as a polytope: a line, triangle, tetrahedron etc. The vertices of these polytopes are the optimal phenotypes for a single task. Up to now, work on this Pareto approach has not considered its genetic underpinnings. Here, we address this by asking how the polymorphism structure of a population is affected by evolution under trade-offs. We simulate a multi-task selection scenario, in which the population evolves to the Pareto front: the line segment between two archetypes or the triangle between three archetypes. We find that polymorphisms that become prevalent in the population have pleiotropic phenotypic effects that align with the Pareto front. Similarly, epistatic effects between prevalent polymorphisms are parallel to the front. Alignment with the front occurs also for asexual mating. Alignment is reduced when drift or linkage is strong, and is replaced by a more complex structure in which many perpendicular allele effects cancel out. Aligned polymorphism structure allows mating to produce offspring that stand a good chance of being optimal multi-taskers in at least one of the locales available to the species. This article is part of the theme issue ‘Self-organization in cell biology’.
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Webb, Joe L., Simon M. Moe, Andrew K. Bolstad, and Elizabeth M. McNeill. "Identification of conserved transcriptome features between humans and Drosophila in the aging brain utilizing machine learning on combined data from the NIH Sequence Read Archive." PLOS ONE 16, no. 8 (August 11, 2021): e0255085. http://dx.doi.org/10.1371/journal.pone.0255085.
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Aging is universal, yet characterizing the molecular changes that occur in aging which lead to an increased risk for neurological disease remains a challenging problem. Aging affects the prefrontal cortex (PFC), which governs executive function, learning, and memory. Previous sequencing studies have demonstrated that aging alters gene expression in the PFC, however the extent to which these changes are conserved across species and are meaningful in neurodegeneration is unknown. Identifying conserved, age-related genetic and morphological changes in the brain allows application of the wealth of tools available to study underlying mechanisms in model organisms such as Drosophila melanogaster. RNA sequencing data from human PFC and fly heads were analyzed to determine conserved transcriptome signatures of age. Our analysis revealed that expression of 50 conserved genes can accurately determine age in Drosophila (R2 = 0.85) and humans (R2 = 0.46). These transcriptome signatures were also able to classify Drosophila into three age groups with a mean accuracy of 88% and classify human samples with a mean accuracy of 69%. Overall, this work identifies 50 highly conserved aging-associated genetic changes in the brain that can be further studied in model organisms and demonstrates a novel approach to uncovering genetic changes conserved across species from multi-study public databases.
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Ollé-Vila, Aina, Luís F. Seoane, and Ricard Solé. "Ageing, computation and the evolution of neural regeneration processes." Journal of The Royal Society Interface 17, no. 168 (July 2020): 20200181. http://dx.doi.org/10.1098/rsif.2020.0181.
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Metazoans gather information from their environments and respond in predictable ways. These computational tasks are achieved with neural networks of varying complexity. Their performance must be reliable over an individual’s lifetime while dealing with the shorter lifespan of cells and connection failure—thus rendering ageing a relevant feature. How do computations degrade over an organism’s lifespan? How reliable can they remain throughout? We tackle these questions with a multi-objective optimization approach. We demand that digital organisms equipped with neural networks solve a computational task reliably over an extended lifespan. Neural connections are costly (as an associated metabolism in living beings). They also degrade over time, but can be regenerated at some expense. We investigate the simultaneous minimization of both these costs and the computational error. Pareto optimal trade-offs emerge with designs displaying a broad range of solutions: from small networks with high regeneration rate, to large, redundant circuits that regenerate slowly. The organism’s lifespan and the external damage act as evolutionary pressures. They improve the exploration of the space of solutions and impose tighter optimality constraints. Large damage rates can also constrain the space of possibilities, forcing the commitment of organisms to unique strategies for neural systems maintenance.
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Zhang, Weiwen, Feng Li, and Lei Nie. "Integrating multiple ‘omics’ analysis for microbial biology: application and methodologies." Microbiology 156, no. 2 (February 1, 2010): 287–301. http://dx.doi.org/10.1099/mic.0.034793-0.
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Recent advances in various ‘omics’ technologies enable quantitative monitoring of the abundance of various biological molecules in a high-throughput manner, and thus allow determination of their variation between different biological states on a genomic scale. Several popular ‘omics’ platforms that have been used in microbial systems biology include transcriptomics, which measures mRNA transcript levels; proteomics, which quantifies protein abundance; metabolomics, which determines abundance of small cellular metabolites; interactomics, which resolves the whole set of molecular interactions in cells; and fluxomics, which establishes dynamic changes of molecules within a cell over time. However, no single ‘omics’ analysis can fully unravel the complexities of fundamental microbial biology. Therefore, integration of multiple layers of information, the multi-‘omics’ approach, is required to acquire a precise picture of living micro-organisms. In spite of this being a challenging task, some attempts have been made recently to integrate heterogeneous ‘omics’ datasets in various microbial systems and the results have demonstrated that the multi-‘omics’ approach is a powerful tool for understanding the functional principles and dynamics of total cellular systems. This article reviews some basic concepts of various experimental ‘omics’ approaches, recent application of the integrated ‘omics’ for exploring metabolic and regulatory mechanisms in microbes, and advances in computational and statistical methodologies associated with integrated ‘omics’ analyses. Online databases and bioinformatic infrastructure available for integrated ‘omics’ analyses are also briefly discussed.
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Manzalini, Antonio, and Bruno Galeazzi. "Explaining Homeopathy with Quantum Electrodynamics." Homeopathy 108, no. 03 (March 22, 2019): 169–76. http://dx.doi.org/10.1055/s-0039-1681037.
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Background Every living organism is an open system operating far from thermodynamic equilibrium and exchanging energy, matter and information with an external environment. These exchanges are performed through non-linear interactions of billions of different biological components, at different levels, from the quantum to the macro-dimensional. The concept of quantum coherence is an inherent property of living cells, used for long-range interactions such as synchronization of cell division processes. There is support from recent advances in quantum biology, which demonstrate that coherence, as a state of order of matter coupled with electromagnetic (EM) fields, is one of the key quantum phenomena supporting life dynamics. Coherent phenomena are well explained by quantum field theory (QFT), a well-established theoretical framework in quantum physics. Water is essential for life, being the medium used by living organisms to carry out various biochemical reactions and playing a fundamental role in coherent phenomena. Methods Quantum electrodynamics (QED), which is the relativistic QFT of electrodynamics, deals with the interactions between EM fields and matter. QED provides theoretical models and experimental frameworks for the emergence and dynamics of coherent structures, even in living organisms. This article provides a model of multi-level coherence for living organisms in which fractal phase oscillations of water are able to link and regulate a biochemical reaction. A mathematical approach, based on the eigenfunctions of Laplace operator in hyper-structures, is explored as a valuable framework to simulate and explain the oneness dynamics of multi-level coherence in life. The preparation process of a homeopathic medicine is analyzed according to QED principles, thus providing a scientific explanation for the theoretical model of “information transfer” from the substance to the water solution. A subsequent step explores the action of a homeopathic medicine in a living organism according to QED principles and the phase-space attractor's dynamics. Results According to the developed model, all levels of a living organism—organelles, cells, tissues, organs, organ systems, whole organism—are characterized by their own specific wave functions, whose phases are perfectly orchestrated in a multi-level coherence oneness. When this multi-level coherence is broken, a disease emerges. An example shows how a homeopathic medicine can bring back a patient from a disease state to a healthy one. In particular, by adopting QED, it is argued that in the preparation of homeopathic medicines, the progressive dilution/succussion processes create the conditions for the emergence of coherence domains (CDs) in the aqueous solution. Those domains code the original substance information (in terms of phase oscillations) and therefore they can transfer said information (by phase resonance) to the multi-level coherent structures of the living organism. Conclusions We encourage that QED principles and explanations become embodied in the fundamental teachings of the homeopathic method, thus providing the homeopath with a firm grounding in the practice of rational medicine. Systematic efforts in this direction should include multiple disciplines, such as quantum physics, quantum biology, conventional and homeopathic medicine and psychology.
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Couch, Alan J., Fiona Dyer, and Mark Lintermans. "Multi-year pair-bonding in Murray cod (Maccullochella peelii)." PeerJ 8 (December 10, 2020): e10460. http://dx.doi.org/10.7717/peerj.10460.
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Mating strategies in fishes are known to include polygyny, polyandry and monogamy and provide valuable insights regarding powerful evolutionary forces such as sexual selection. Monogamy is a complex of mating systems that has been relatively neglected. Previous work on mating strategies in fishes has often been based on observation and focused on marine species rather than freshwater fishes. SNPs are increasingly being used as a molecular ecology tool in non-model organisms, and methods of probabilistic genetic analysis of such datasets are becoming available for use in the absence of parental genotypes. This approach can be used to infer mating strategies. The long-term pair bonding seen in mammals, reptiles and birds has not been recorded in freshwater fishes—in every other respect an extremely diverse group. This study shows that multi-year pair bonding occurs in an Australian Percichthyid fish that exhibits paternal care of eggs and larvae. Using SNPs, full sibling pairs of larvae were found over multiple years in a three-year study. Stable isotope signatures of the larvae support the genetic inference that full sibling pairs shared a common mother, the ultimate source of that isotopic signature during oogenesis. Spatial and temporal clustering also suggests that the full sibling larvae are unlikely to be false positive identifications of the probabilistic identification of siblings. For the first time, we show multi-year pair bonding in a wild freshwater fish. This will have important conservation and management implications for the species. This approach could provide insights into many behavioural, ecological and evolutionary questions, particularly if this is not a unique case. Our findings are likely to initiate interest in seeking more examples of monogamy and alternative mating strategies in freshwater fishes, particularly if others improve methods of analysis of SNP data for identification of siblings in the absence of parental genotypes.
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Austigard, Mari Sand, and Johan Mattsson. "Monitoring climate change related biodeterioration of protected historic buildings." International Journal of Building Pathology and Adaptation 38, no. 4 (November 11, 2019): 529–38. http://dx.doi.org/10.1108/ijbpa-11-2018-0094.
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Purpose Expected rates of biodeterioration in heritage buildings under historic conditions are well known. Deteriorating organisms will benefit from a warmer and wetter climate, giving faster and less predictable rates of deterioration. The Directorate for Cultural Heritage in Norway has requested development of a programme for long-term monitoring of climate change impacts to historic buildings. The development process and resulting monitoring system are previously described. The paper aims to discuss this issue. Design/methodology/approach An initial conditions survey is performed, and reference points are chosen in each building. Two microclimatic biodeterioration monitoring panels (MBM panels) are mounted in every building. The MBM panels monitor temperature, relative humidity and wood moisture content, and have standard wooden blocks for investigation of mould growth. The panels will show both the influence of outdoor climate on microclimate inside the building, and the connection between microclimate and activity of degrading organisms. Findings High competence and multi-disciplinary approach from the personnel involved are essential to balance flexibility and rigidity and decide the damages that are probably influenced by climate change. Extensive knowledge and experience in surveys of biodeterioration damages in heritage buildings is necessary to distinguish “normal” biodeterioration from biodeterioration caused by climate changes. The MBM panels are essential for possible establishment of causality between damages and climate change. Originality/value The authors believe that the methods described give the best possible grounds for future evaluation of damages and microclimatic conditions in buildings compared to changes in regional climatic conditions. Establishment of causality between climate change and development in biological deterioration is still a challenging task.
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CALCINAI, B., M. BERTOLINO, G. BAVESTRELLO, S. MONTORI, M. MORI, D. PICA, L. VALISANO, and C. CERRANO. "Comparison between the sponge fauna living outside and inside the coralligenous bioconstruction. A quantitative approach." Mediterranean Marine Science 16, no. 2 (June 26, 2015): 413. http://dx.doi.org/10.12681/mms.900.
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Coralligenous habitat results from a multi-stratified accumulation of crustose coralline algae and animal builders in a dynamic equilibrium with disruptive agents. The result is a complex architecture crossed by crevices and holes. Due to this three-dimensional structure, coralligenous may host a rich and diversified fauna, more abundant than any other Mediterranean habitat. Unfortunately, very few data are available about the cryptic fauna that lives inside the conglomerate. As already reported for coral reefs, the cryptic fauna plays an important role in the exchange of material and energy between water column and benthic assemblages. Here we compare the sponge community present inside and outside the coralligenous framework of Portofino Promontory (Ligurian Sea) at different depths (15 and 30 meters) not only in terms of taxonomic diversity but for the first time also in term of biomass. Sponges present on the surface of each block were collected, weighed and identified; after blocks dissolution in HCl, target cryptic sponges were separated from other organisms, weighed, and identified. We recorded a total of 62 sponge species. The average number of sponge taxa occurring outside the coralligenous accretions is lower than the number of taxa identified inside. This pattern is confirmed also regarding sponge biomass. These results underlines that studies focused on coralligenous functioning should take in account the important contribution of cryptic fauna, as recently evidenced also for tropical reef habitats.
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Mongkoldhumrongkul, Napachanok, Suresh C. Swain, Suwan N. Jayasinghe, and Stephen Stürzenbaum. "Bio-electrospraying the nematode Caenorhabditis elegans : studying whole-genome transcriptional responses and key life cycle parameters." Journal of The Royal Society Interface 7, no. 45 (September 23, 2009): 595–601. http://dx.doi.org/10.1098/rsif.2009.0364.
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Bio-electrospray, the direct jet-based cell handling approach, is able to handle a wide range of cells (spanning immortalized, primary to stem cells). Studies at the genomic, genetic and the physiological levels have shown that, post-treatment, cellular integrity is unperturbed and a high percentage (more than 70%, compared with control) of cells remain viable. Although, these results are impressive, it may be argued that cell-based systems are oversimplistic. Therefore, it is important to evaluate the bio-electrospray technology using sensitive and dynamically developing multi-cellular organisms that share, at least some, similarities with multi-cell microenviorments encountered with tissues and organs. This study addressed this issue by using a well-characterized model organism, the non-parasitic nematode Caenorhabditis elegans . Nematode cultures were subjected to bio-electrospraying and compared with positive (heat shock) and negative controls (appropriate laboratory culture controls). Overall, bio-electrospraying did not modulate the reproductive output or induce significant changes in in vivo stress-responsive biomarkers (heat shock proteins). Likewise, whole-genome transcriptomics could not identify any biological processes, cellular components or molecular functions (gene ontology terms) that were significantly enriched in response to bio-electrospraying. This demonstrates that bio-electrosprays can be safely applied directly to nematodes and underlines its potential future use in the creation of multi-cellular environments within clinical applications.
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Ventegodt, Søren, Tyge Dahl Hermansen, Trine Flensborg-Madsen, Maj Lyck Nielsen, and Joav Merrick. "Human Development VIII: A Theory of Deep Quantum Chemistry and Cell Consciousness: Quantum Chemistry Controls Genes and Biochemistry to Give Cells and Higher Organisms Consciousness and Complex Behavior." Scientific World JOURNAL 6 (2006): 1441–53. http://dx.doi.org/10.1100/tsw.2006.257.
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Deep quantum chemistry is a theory of deeply structured quantum fields carrying the biological information of the cell, making it able to remember, intend, represent the inner and outer world for comparison, understand what it “sees”, and make choices on its structure, form, behavior and division. We suggest that deep quantum chemistry gives the cell consciousness and all the qualities and abilities related to consciousness. We use geometric symbolism, which is a pre-mathematical and philosophical approach to problems that cannot yet be handled mathematically. Using Occams razor we have started with the simplest model that works; we presume this to be a many-dimensional, spiral fractal. We suggest that all the electrons of the large biological molecules orbitals make one huge “cell-orbital”, which is structured according to the spiral fractal nature of quantum fields. Consciousness of single cells, multi cellular structures as e.g. organs, multi-cellular organisms and multi-individual colonies (like ants) and human societies can thus be explained by deep quantum chemistry. When biochemical activity is strictly controlled by the quantum-mechanical super-orbital of the cell, this orbital can deliver energetic quanta as biological information, distributed through many fractal levels of the cell to guide form and behavior of an individual single or a multi-cellular organism. The top level of information is the consciousness of the cell or organism, which controls all the biochemical processes. By this speculative work inspired by Penrose and Hameroff we hope to inspire other researchers to formulate more strict and mathematically correct hypothesis on the complex and coherence nature of matter, life and consciousness.
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Menna, F., E. Nocerino, S. Malek, F. Remondino, and S. Schiaparelli. "A COMBINED APPROACH FOR LONG-TERM MONITORING OF BENTHOS IN ANTARCTICA WITH UNDERWATER PHOTOGRAMMETRY AND IMAGE UNDERSTANDING." International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences XLIII-B2-2022 (May 30, 2022): 935–43. http://dx.doi.org/10.5194/isprs-archives-xliii-b2-2022-935-2022.
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Abstract. Long-term monitoring projects are becoming more than ever crucial in assessing the effects of climate change on marine communities, especially in Antarctica, where these changes are expected to be particularly dramatic. Detailed studies of the Antarctic benthos are in fact particularly important for a better understanding of benthos dynamics and potential climate-driven shifts. Here, due to the extreme fragility of benthic communities, non-destructive techniques represent the best solution in long-term monitoring programs. In this paper we report new results from 2017, 2018, 2019 photogrammetric campaigns within the Italian National Antarctic Research Program (PNRA). A new protocol of data acquisition and multi-temporal processing that provides co-registered 3D point clouds between the three years without control points nor direct georeferencing methods is presented. This is achieved by adding a level of image understanding leveraging semantic segmentation with convolutional neural network (CNN) of the benthic features. Slow growing (estimated less than a mm per year) organisms, such as Corallinales (Rhodophyta algae), represent a natural stable pattern, leveraged to automatically orient in the same reference system the photogrammetric surveys of different epochs. This approach is also proved to be effective in improving the orientation of adjacent strips acquired within the same campaign. Within the paper an in depth analysis of the achieved results shows the effectiveness of the implemented procedure.
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Lausser, Ludwig, Lea Siegle, Wolfgang Rottbauer, Derk Frank, Steffen Just, and Hans Kestler. "Semantic Multi-Classifier Systems Identify Predictive Processes in Heart Failure Models across Species." Biomolecules 8, no. 4 (November 26, 2018): 158. http://dx.doi.org/10.3390/biom8040158.
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Genetic model organisms have the potential of removing blind spots from the underlying gene regulatory networks of human diseases. Allowing analyses under experimental conditions they complement the insights gained from observational data. An inevitable requirement for a successful trans-species transfer is an abstract but precise high-level characterization of experimental findings. In this work, we provide a large-scale analysis of seven weak contractility/heart failure genotypes of the model organism zebrafish which all share a weak contractility phenotype. In supervised classification experiments, we screen for discriminative patterns that distinguish between observable phenotypes (homozygous mutant individuals) as well as wild-type (homozygous wild-types) and carriers (heterozygous individuals). As the method of choice we use semantic multi-classifier systems, a knowledge-based approach which constructs hypotheses from a predefined vocabulary of high-level terms (e.g., Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways or Gene Ontology (GO) terms). Evaluating these models leads to a compact description of the underlying processes and guides the screening for new molecular markers of heart failure. Furthermore, we were able to independently corroborate the identified processes in Wistar rats.
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Rossi, P., S. Righi, L. Parente, C. Castagnetti, S. Cattini, G. Di Loro, E. Falvo, et al. "PHOTOGRAMMETRIC AND FLUORESCENCE SOLUTIONS FOR MONITORING OF HABITAT FORMING ORGANISMS." International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences XLIII-B2-2022 (May 30, 2022): 877–83. http://dx.doi.org/10.5194/isprs-archives-xliii-b2-2022-877-2022.
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Abstract. The development and testing of innovative technologies and automated data analysis methodologies offer tools for the monitoring of complex marine ecosystems and the direct and indirect effects of climate change on natural heritage. Photogrammetric methods allow precise mapping of the underwater landscape as well as detailed three-dimensional (3D) reconstruction of marine structures, improving the study of complex marine ecosystems. Moreover, fluorescence analyses can provide critical information about the health status of marine organisms. Analysing the variations in their self-fluorescence, allow for early detect changes in their physiological state. These applications provide very useful data to evaluate the health state of biodiversity-rich 3D biogenic structures and make measurements of fine-scale changes, with greater precision than existing methodologies. This contribution shows a multidisciplinary approach to the design, development, and implementation of a technological solution based on the above-mentioned optical measuring systems. Such a system is characterized by a reflex camera, LED-based light sources, and filters to allow the analysis of the self-fluorescence signal. The proposed solution aspires to improve the standardization of monitoring plans through non-destructive fine-scale accurate data collection for image analysis and multi-temporal comparisons, providing challenging stepping-stones for habitat-forming anthozoan management and restoration activities. Initial results of tests carried out in controlled conditions are shown. The photogrammetric approach resulted in 3D reconstructions that allow the monitoring of deformations at millimetre scale. The fluorimetry methodology allowed to obtain high-resolution images with great repeatability, which enabled the identification of stressful status even in absence of geometric deformations. The proposed approaches and obtained results are discussed, together with potential issues related to their implementation in a real-world context adopting remotely operative vehicles.