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Journal articles on the topic 'Organisms'

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Author: Grafiati
Published: 4 June 2021
Last updated: 1 August 2024

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1

Pandey, Shiv Shanker, Samer Singh, Chandramani Pathak, and Budhi Sagar Tiwari. "“Programmed Cell Death: A Process of Death for Survival” – How Far Terminology Pertinent for Cell Death in Unicellular Organisms." Journal of Cell Death 11 (January 2018): 117906601879025. http://dx.doi.org/10.1177/1179066018790259.

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Programmed cell death (PCD) is genetically regulated phenomenon of selective elimination of target cells that are either under pathological conditions or unwanted for organism’s normal growth and development due to other reasons. The process although being genetically controlled is physiological in nature that renders some hallmarks like blebs in the cell membrane, lobe formation in nuclear membrane, DNA nicks resulting to DNA ladder of 200 bp, and downstream activation of caspases. Moreover, as the process refers to the death of “targeted cell”, the term is exclusively suitable for multicellular organisms. Number of reports advocate similar type of cell death process in unicellular organisms. As cell death in unicellular organisms is also reflected by the signature of PCD obtained in metazoans, such cell death has been grouped under the broad category of PCD. It is pertinent to mention that by definition a unicellular organism is made of a single cell wherein it carries out all of its life processes. Using the term “Programmed Cell Death” with a preset “survival strategy of the organism” for unicellular organisms looks misnomer. Therefore, this correspondence argues and requests recommendation committee on cell death to revisit for the nomenclature of the cell death process in the unicellular organisms.
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2

Holm, Sune. "Organism and artifact: Proper functions in Paley organisms." Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 44, no. 4 (December 2013): 706–13. http://dx.doi.org/10.1016/j.shpsc.2013.05.018.

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3

Wetherick, Norman. "On the basis of ‘scientific’ psychology." History & Philosophy of Psychology 18, no. 1 (2017): 43–48. http://dx.doi.org/10.53841/bpshpp.2017.18.1.43.

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The object of scientific psychology is to give us a better understanding of the capacity to do anything we know a human organism can do, and is at the same time capable of instantiation in the mechanism described by brain physiology. Such potential is, in turn, capable of developing from a genetic point-source, regulated by the Personal Environment made available in the course of its life by its sensory capacities. Personal Environment must be distinguished from ‘Environment’ which may include objects/events that have not yet figured in any individual Personal Environment. Psychology resembles physical science in many respects but the latter can legitimately claim to have achieved a near complete account of the material, physical world whereas psychology is open-ended. It must cover whatever is/was/will be, in the course of the organism’s life, observable in its behaviour. Sub-human organisms are regularly reported to have more extensive Personal Environments than had been assumed. In particular, argument still rages whether any but human organisms have consciousness. The evidence that lower organisms (e.g. insects, etc.) can find their way home with minimal CNS (central nervous system) shows that neurons, when active, must constitute pictorial consciousness for them, and there is no reason to doubt that higher organisms also have this capacity, or that mammals (including ourselves) have an additional capacity to reason which vastly increases their chance of survival. Possession of consciousness can only be confirmed by the verbal testimony of the organism whose consciousness it is, and only the human organism has evolved language. It appears that experience of rewarded approach is sufficient for describing the behaviour observed in sub-human organisms. They learn little or nothing from failure. Mammals learn from both success and failure, vastly increasing their chances of survival.
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4

Hull, David L., Rodney E. Langman, and Sigrid S. Glenn. "A general account of selection: Biology, immunology, and behavior." Behavioral and Brain Sciences 24, no. 3 (June 2001): 511–28. http://dx.doi.org/10.1017/s0140525x01004162.

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Authors frequently refer to gene-based selection in biological evolution, the reaction of the immune system to antigens, and operant learning as exemplifying selection processes in the same sense of this term. However, as obvious as this claim may seem on the surface, setting out an account of “selection” that is general enough to incorporate all three of these processes without becoming so general as to be vacuous is far from easy. In this target article, we set out such a general account of selection to see how well it accommodates these very different sorts of selection. The three fundamental elements of this account are replication, variation, and environmental interaction. For selection to occur, these three processes must be related in a very specific way. In particular, replication must alternate with environmental interaction so that any changes that occur in replication are passed on differentially because of environmental interaction.One of the main differences among the three sorts of selection that we investigate concerns the role of organisms. In traditional biological evolution, organisms play a central role with respect to environmental interaction. Although environmental interaction can occur at other levels of the organizational hierarchy, organisms are the primary focus of environmental interaction. In the functioning of the immune system, organisms function as containers. The interactions that result in selection of antibodies during a lifetime are between entities (antibodies and antigens) contained within the organism. Resulting changes in the immune system of one organism are not passed on to later organisms. Nor are changes in operant behavior resulting from behavioral selection passed on to later organisms. But operant behavior is not contained in the organism because most of the interactions that lead to differential replication include parts of the world outside the organism. Changes in the organism's nervous system are the effects of those interactions. The role of genes also varies in these three systems. Biological evolution is gene-based (i.e., genes are the primary replicators). Genes play very different roles in operant behavior and the immune system. However, in all three systems, iteration is central. All three selection processes are also incredibly wasteful and inefficient. They can generate complexity and novelty primarily because they are so wasteful and inefficient.
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5

Aminatun, Tien, Siti Umniyatie, Anna Rakhmawati, Aji Suhandy, Nrangwesthi Widyaningrum, and Kurnia Cahyani. "KEANEKARAGAMAN ORGANISME PADA RHIZOSFER GULMA SIAM DI LAHAN VULKANIK, PESISIR, DAN KARST." Jurnal Penelitian Saintek 26, no. 1 (April 26, 2021): 1–16. http://dx.doi.org/10.21831/jps.v26i1.38754.

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Penelitian ini bertujuan untuk membandingkan kondisi edafik, hubungan antara kondisi edafik dan keanekaragaman organisme tanah, serta perbedaan keanekaragaman organisme tanah pada berbagai ekosistem rhizosfer gulma Siam (Chromolaena odorata) yang tumbuh di lahan vulkanik, pesisir, dan karst. Penelitian dilakukan dengan mengambil sampel tanah dari ekosistem rhizosfer gulma Siam di lahan vulkanik, karst, dan pesisir Daerah Istimewa Yogyakarta; mengamati komposisi organisme tanah di laboratorium, yaitu collembola, nematoda, dan mikoriza. Hasil penelitian menunjukkan bahwa tanah pada rhizosfer gulma Siam yang tumbuh di lahan karst menunjukkan tingkat kesuburan tertinggi yang ditunjukkan oleh kandungan N, K, dan C-organik tanah, sedangkan tanah pesisir memiliki kandungan P tertinggi. Tekstur tanah pada rhizosfer gulma Siam lebih berpengaruh terhadap keanekaragaman organisme tanah dibandingkan kandungan hara tanah dan sifat tanah lainnya yang diteliti. Keragaman organisme tanah rhizosfer gulma Siam lebih besar di lahan pesisir dibandingkan di lahan karst dan vulkanik. Implikasi dari hasil tersebut adalah bahwa tanah dengan tekstur berpasir akan lebih bermanfaat bagi pertumbuhan gulma Siam dengan keanekaragaman organisme rhizosfer yang lebih tinggi.ORGANISM DIVERSITY IN THE RHIZOSPHERE OF SIAM WEEDS IN VOLCANIC, COASTAL AND KARST LANDThe research aims to compare the edaphic condition, the relationship between the edaphic condition and soil organism diversity, and the differences of soil organism diversity in different rhizosphere ecosystems of Siam weed growing in volcanic, coastal and karts areas. The research was conducted by taking soil samples from the Siam weed rhizosphere ecosystems in volcanic, karst and coastal areas of the Special Region of Yogyakarta and observing the composition of the soil organisms in the laboratory, including collembola, nematode, and mycorrhiza. The results find that soil from rhizosphere of Siam weed growing in karst area shows the highest level of fertility indicated by the N, K, and C-organic contents of the soil, whereas soil from coastal area has the highest P content. Soil texture in the rhizosphere of Siam weed has more effect on the diversity of soil organisms than the soil nutrient content and other soil properties investigated. The diversity of soil organisms of Siam weed rhizosphere is greater in coastal area than those in karst and volcanic areas. The implication of the results is that soil with a sandy texture will be more beneficial for the growth of Siam weed with a higher diversity of rhizosphere organisms
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6

McMahan, Jeff. "An Alternative to Brain Death." Journal of Law, Medicine & Ethics 34, no. 1 (2006): 44–48. http://dx.doi.org/10.1111/j.1748-720x.2006.00007.x.

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Most contributors to the debate about brain death, including Dr. James Bernat, share certain assumptions. They believe that the concept of death is univocal, that death is a biological phenomenon, that it is necessarily irreversible, that it is paradigmatically something that happens to organisms, that we are human organisms, and therefore that our deaths will be deaths of organisms. These claims are supposed to have moral significance. It is, for example, only when a person dies that it is permissible to extract her organs for transplantation.It is also commonly held that our univocal notion of death is the permanent cessation of integrated functioning in an organism and that the criterion for determining when this has occurred in animals with brains is the death of the brain as a whole – that is, brain death. The reason most commonly given for this is that the brain is the irreplaceable master control of the organism's integration.
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7

Hellmuth, Kathrin, Christian Klingenberg, Qin Li, and Min Tang. "Multiscale Convergence of the Inverse Problem for Chemotaxis in the Bayesian Setting." Computation 9, no. 11 (November 11, 2021): 119. http://dx.doi.org/10.3390/computation9110119.

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Chemotaxis describes the movement of an organism, such as single or multi-cellular organisms and bacteria, in response to a chemical stimulus. Two widely used models to describe the phenomenon are the celebrated Keller–Segel equation and a chemotaxis kinetic equation. These two equations describe the organism’s movement at the macro- and mesoscopic level, respectively, and are asymptotically equivalent in the parabolic regime. The way in which the organism responds to a chemical stimulus is embedded in the diffusion/advection coefficients of the Keller–Segel equation or the turning kernel of the chemotaxis kinetic equation. Experiments are conducted to measure the time dynamics of the organisms’ population level movement when reacting to certain stimulation. From this, one infers the chemotaxis response, which constitutes an inverse problem. In this paper, we discuss the relation between both the macro- and mesoscopic inverse problems, each of which is associated with two different forward models. The discussion is presented in the Bayesian framework, where the posterior distribution of the turning kernel of the organism population is sought. We prove the asymptotic equivalence of the two posterior distributions.
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8

van Baalen, Minus, and Philippe Huneman. "Organisms as Ecosystems/Ecosystems as Organisms." Biological Theory 9, no. 4 (October 21, 2014): 357–60. http://dx.doi.org/10.1007/s13752-014-0194-7.

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9

Kingma, Elselijn. "Lady Parts: The Metaphysics of Pregnancy." Royal Institute of Philosophy Supplement 82 (July 2018): 165–87. http://dx.doi.org/10.1017/s1358246118000115.

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AbstractWhat is the metaphysical relationship between the fetus/embryo and the pregnant organism? In this paper I apply a substance metaphysics view developed by Barry Smith and Berit Brogaard to argue, on the basis of topological connectedness, that fetuses/embryos are Lady-Parts: part of the maternal organism up until birth. This leaves two options. Either mammalian organisms begin at birth, or we revise our conception of organisms such that mammalian organisms can be part of other mammals. The first option has some advantages: it is numerically neat; aligns with an intuitive picture of organisms as physically distinct individuals; and ties ‘coming into existence’ to a suitably recognisable and important event: birth. But it denies that the fetus survives birth, or that human organisms existed prior to their birth. The second option allows us to recognise that human organisms exist prior to and survive their birth, but at a cost: it leaves the question of when an organism comes into existence unanswered, and demands potentially far-reaching conceptual revision across a range of domains.
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10

Manrique, Pedro, Mason Klein, Yao Sheng Li, Chen Xu, Pak Ming Hui, and Neil Johnson. "Decentralized Competition Produces Nonlinear Dynamics Akin to Klinotaxis." Complexity 2018 (July 22, 2018): 1–8. http://dx.doi.org/10.1155/2018/9803239.

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One of the biggest challenges in unravelling the complexity of living systems, is to fully understand the neural logic that translates sensory input into the highly nonlinear motor outputs that are observed when simple organisms crawl. Recent work has shown that organisms such as larvae that exhibit klinotaxis (i.e., orientation through lateral movements of portions of the body) can perform normal exploratory practices even in the absence of a brain. Abdominal and thoracic networks control the alternation between crawls and turns. This motivates the search for decentralized models of movement that can produce nonlinear outputs that resemble the experiments. Here, we present such a complex system model, in the form of a population of decentralized decision-making components (agents) whose aggregate activity resembles that observed in klinotaxis organisms. Despite the simplicity of each component, the complexity created by their collective feedback of information and actions akin to proportional navigation, drives the model organism towards a specific target. Our model organism’s nonlinear behaviors are consistent with empirically observed reorientation rate measures for Drosophila larvae as well as nematode C. elegans.
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11

Pineda-Krch, Mario, and Alistair G. B. Poore. "Spatial interactions within modular organisms: genetic heterogeneity and organism fitness." Theoretical Population Biology 66, no. 1 (August 2004): 25–36. http://dx.doi.org/10.1016/j.tpb.2004.03.002.

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12

Prados, Carlos, Miguel Hernando, Ernesto Gambao, and Alberto Brunete. "MoCLORA—An Architecture for Legged-and-Climbing Modular Bio-Inspired Robotic Organism." Biomimetics 8, no. 1 (December 27, 2022): 11. http://dx.doi.org/10.3390/biomimetics8010011.

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MoCLORA (Modular Climbing-and-Legged Robotic Organism Architecture) is a software framework for climbing bio-inspired robotic organisms composed of modular robots (legs). It is presented as a modular low-level architecture that coordinates the modules of an organism with any morphology, at the same time allowing exchanges between the physical robot and its digital twin. It includes the basic layers to control and coordinate all the elements, while allowing adding new higher-level components to improve the organism’s behavior. It is focused on the control of both the body and the legs of the organism, allowing for position and velocity control of the whole robot. Similarly to insects, which are able to adapt to new situations after the variation on the capacity of any of their legs, MoCLORA allows the control of organisms composed of a variable number of modules, arranged in different ways, giving the overall system the versatility to tackle a wide range of tasks in very diverse environments. The article also presents ROMERIN, a modular climbing and legged robotic organism, and its digital twin, which allows the creation of different module arrangements for testing. MoCLORA has been tested and validated with both the physical robot and its digital twin.
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13

Haggerty, Leanne S., Fergal J. Martin, David A. Fitzpatrick, and James O. McInerney. "Gene and genome trees conflict at many levels." Philosophical Transactions of the Royal Society B: Biological Sciences 364, no. 1527 (August 12, 2009): 2209–19. http://dx.doi.org/10.1098/rstb.2009.0042.

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Horizontal gene transfer (HGT) plays a significant role in microbial evolution. It can accelerate the adaptation of an organism, it can generate new metabolic pathways and it can completely remodel an organism's genome. We examine 27 closely related genomes from the YESS group of gamma proteobacteria and a variety of four-taxon datasets from a diverse range of prokaryotes in order to explore the kinds of effects HGT has had on these organisms.
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14

Pietraszewski, David, Annie E. Wertz, Gregory A. Bryant, and Karen Wynn. "Three-month-old human infants use vocal cues of body size." Proceedings of the Royal Society B: Biological Sciences 284, no. 1856 (June 7, 2017): 20170656. http://dx.doi.org/10.1098/rspb.2017.0656.

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Differences in vocal fundamental ( F 0 ) and average formant ( F n ) frequencies covary with body size in most terrestrial mammals, such that larger organisms tend to produce lower frequency sounds than smaller organisms, both between species and also across different sex and life-stage morphs within species. Here we examined whether three-month-old human infants are sensitive to the relationship between body size and sound frequencies. Using a violation-of-expectation paradigm, we found that infants looked longer at stimuli inconsistent with the relationship—that is, a smaller organism producing lower frequency sounds, and a larger organism producing higher frequency sounds—than at stimuli that were consistent with it. This effect was stronger for fundamental frequency than it was for average formant frequency. These results suggest that by three months of age, human infants are already sensitive to the biologically relevant covariation between vocalization frequencies and visual cues to body size. This ability may be a consequence of developmental adaptations for building a phenotype capable of identifying and representing an organism's size, sex and life-stage.
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15

Vieglais, C. M. C., and L. Harrison. "Conditional release of new organisms in New Zealand." New Zealand Plant Protection 57 (August 1, 2004): 161–65. http://dx.doi.org/10.30843/nzpp.2004.57.6897.

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New organisms are defined as species not present in New Zealand prior to 29 July 1998 the date the New Organisms component of the Hazardous Substances and New Organisms (HSNO) Act 1996 came into effect New organisms also include genetically modified (GM) organisms organisms that have been approved for containment or conditional release and exotic organisms that have been eradicated There are three ways a new organism can occur in New Zealand accidental incursions deliberate but illegal introductions and legal introductions Applications for introductions are evaluated by the Environmental Risk Management Authority (ERMA New Zealand) In October 2003 the HSNO Act was amended to allow for the conditional release of new organisms including GM organisms This paper describes the process for the introduction of new organisms into New Zealand with an emphasis on conditional release to assess the risks costs and benefits of new organisms to human health the environment and the economy
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16

Ivashov, Anatolij, and Andriy Simchuk. "Ecological Consortium as an Elementary Ecosystem." Journal of Vasyl Stefanyk Precarpathian National University 8, no. 4 (January 20, 2022): 34–44. http://dx.doi.org/10.15330/jpnu.8.4.34-44.

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Each of the large autotrophic or heterotrophic organisms reproduces an environment for many organisms, living in, on and around it. This central organism and all other organisms, living in the sphere of its influence, constitute together an elementary community or ecosystem if to take into the consideration soil, air and other elements, which are included into the sphere. In East European ecological tradition such the elementary ecosystems are named individual consortia. Population and species consortia integrate individual consortia of population and species representatives correspondingly. Each central organism has unique genotype, and, thus, reproduces unique environment for its inhabitants. In this reason, the result of interaction between consorters and their host depend both from the genotype of central organism from one side and from genetic structures of the consorters from another side. Thus, autotrophic or heterotrophic individual consortium is a spatially limited unity of different organisms, zone of life concentration, in which specific composition of living and non-living components with peculiar energetic and informative exchange is forming arround the determinant, anough large central organism.
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17

Kahn, Rachel E., Andone C. Lavery, and Annette F. Govindarajan. "Broadband backscattering from scyphozoan jellyfish." Journal of the Acoustical Society of America 153, no. 5 (May 1, 2023): 3075. http://dx.doi.org/10.1121/10.0019577.

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As the ecological importance of gelatinous organisms becomes increasingly appreciated, so has the need for improved knowledge of their abundance and distribution. Acoustic backscattering measurements are routine for fisheries assessments but are not yet widely used to survey populations of gelatinous zooplankton. The use of acoustic backscattering techniques to understand the distribution and abundance of organisms requires an understanding of their target strength (TS). This study presents a framework for a sound scattering model for jellyfish based on the Distorted Wave Born Approximation that incorporates size, shape, and material properties of individual organisms. This model, with a full three-dimensional shape rendition, is applied to a common species of scyphomedusa (Chrysaora chesapeakei) and verified experimentally with broadband (52–90 and 93–161 kHz) laboratory TS measurements of live individuals. Cyclical changes in the organism's shape due to swimming kinematics were examined, as well as averages over swimming position and comparisons with scattering from simpler shapes. The model predicts overall backscattering levels and broad spectral behavior within <2 dB. Measured TS exhibits greater variability than is predicted by scaling the size of the organism in the scattering model, showing that density and sound speed vary among individuals.
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18

Cascarina, Sean M., and Eric D. Ross. "Identification of Low-Complexity Domains by Compositional Signatures Reveals Class-Specific Frequencies and functions across the domains of life." PLOS Computational Biology 20, no. 5 (May 15, 2024): e1011372. http://dx.doi.org/10.1371/journal.pcbi.1011372.

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Low-complexity domains (LCDs) in proteins are typically enriched in one or two predominant amino acids. As a result, LCDs often exhibit unusual structural/biophysical tendencies and can occupy functional niches. However, for each organism, protein sequences must be compatible with intracellular biomolecules and physicochemical environment, both of which vary from organism to organism. This raises the possibility that LCDs may occupy sequence spaces in select organisms that are otherwise prohibited in most organisms. Here, we report a comprehensive survey and functional analysis of LCDs in all known reference proteomes (>21k organisms), with added focus on rare and unusual types of LCDs. LCDs were classified according to both the primary amino acid and secondary amino acid in each LCD sequence, facilitating detailed comparisons of LCD class frequencies across organisms. Examination of LCD classes at different depths (i.e., domain of life, organism, protein, and per-residue levels) reveals unique facets of LCD frequencies and functions. To our surprise, all 400 LCD classes occur in nature, although some are exceptionally rare. A number of rare classes can be defined for each domain of life, with many LCD classes appearing to be eukaryote-specific. Certain LCD classes were consistently associated with identical functions across many organisms, particularly in eukaryotes. Our analysis methods enable simultaneous, direct comparison of all LCD classes between individual organisms, resulting in a proteome-scale view of differences in LCD frequencies and functions. Together, these results highlight the remarkable diversity and functional specificity of LCDs across all known life forms.
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19

McEachern, Lori A. "Transgenic Epigenetics: Using Transgenic Organisms to Examine Epigenetic Phenomena." Genetics Research International 2012 (March 27, 2012): 1–14. http://dx.doi.org/10.1155/2012/689819.

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Non-model organisms are generally more difficult and/or time consuming to work with than model organisms. In addition, epigenetic analysis of model organisms is facilitated by well-established protocols, and commercially-available reagents and kits that may not be available for, or previously tested on, non-model organisms. Given the evolutionary conservation and widespread nature of many epigenetic mechanisms, a powerful method to analyze epigenetic phenomena from non-model organisms would be to use transgenic model organisms containing an epigenetic region of interest from the non-model. Interestingly, while transgenic Drosophila and mice have provided significant insight into the molecular mechanisms and evolutionary conservation of the epigenetic processes that target epigenetic control regions in other model organisms, this method has so far been under-exploited for non-model organism epigenetic analysis. This paper details several experiments that have examined the epigenetic processes of genomic imprinting and paramutation, by transferring an epigenetic control region from one model organism to another. These cross-species experiments demonstrate that valuable insight into both the molecular mechanisms and evolutionary conservation of epigenetic processes may be obtained via transgenic experiments, which can then be used to guide further investigations and experiments in the species of interest.
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20

Málik-Roffa, Hajnalka, Dávid Tőzsér, Béla Tóthmérész, and Tibor Magura. "BugTracker: Software for Tracking and Measuring Arthropod Activity." Diversity 15, no. 7 (July 10, 2023): 846. http://dx.doi.org/10.3390/d15070846.

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The automated video tracking of the activity/movement of an experimental organism is essential for reliable, repeatable quantitative analyses in behavioral ecology and also in other disciplines. There are only some open-access, open-source automated tracking software applications that can track unmarked organisms. Moreover, several of these software applications are substantially affected by brightness and differences in the lighting conditions of the video recording. Our Python-based software, called BugTracker, uses the latest innovations in computer vision technologies to solve these problems. By analyzing videos with considerably different lighting conditions with BugTracker and other available software, we demonstrate that our software could reliably track the studied organisms of any size and speed. Additionally, the results provide accurate measures of the organism’s movements. BugTracker is the most reliable currently available, easy-to-use, and automated tracking software compatible with the Windows, Linux, and MacOS operating systems.
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Okajima, Kei, Shunsuke Shigaki, Takanobu Suko, Duc-Nhat Luong, Cesar Hernandez Reyes, Yuya Hattori, Kazushi Sanada, and Daisuke Kurabayashi. "A novel framework based on a data-driven approach for modelling the behaviour of organisms in chemical plume tracing." Journal of The Royal Society Interface 18, no. 181 (August 2021): 20210171. http://dx.doi.org/10.1098/rsif.2021.0171.

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We propose a data-driven approach for modelling an organism's behaviour instead of conventional model-based strategies in chemical plume tracing (CPT). CPT models based on this approach show promise in faithfully reproducing organisms’ CPT behaviour. To construct the data-driven CPT model, a training dataset of the odour stimuli input toward the organism is needed, along with an output of the organism’s CPT behaviour. To this end, we constructed a measurement system comprising an array of alcohol sensors for the measurement of the input and a camera for tracking the output in a real scenario. Then, we determined a transfer function describing the input–output relationship as a stochastic process by applying Gaussian process regression, and established the data-driven CPT model based on measurements of the organism’s CPT behaviour. Through CPT experiments in simulations and a real environment, we evaluated the performance of the data-driven CPT model and compared its success rate with those obtained from conventional model-based strategies. As a result, the proposed data-driven CPT model demonstrated a better success rate than those obtained from conventional model-based strategies. Moreover, we considered that the data-driven CPT model could reflect the aspect of an organism’s adaptability that modulated its behaviour with respect to the surrounding environment. However, these useful results came from the CPT experiments conducted in simple settings of simulations and a real environment. If making the condition of the CPT experiments more complex, we confirmed that the data-driven CPT model would be less effective for locating an odour source. In this way, this paper not only poses major contributions toward the development of a novel framework based on a data-driven approach for modelling an organism’s CPT behaviour, but also displays a research limitation of a data-driven approach at this stage.
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22

Pribadi, Teguh. "Bagaimana Rayap dapat Digunakan sebagai Bioindikator." Anterior Jurnal 14, no. 1 (December 1, 2014): 20–28. http://dx.doi.org/10.33084/anterior.v14i1.219.

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Ecosystem alterations not only affect habitat conditions but also have an impact on biotic components. The presence of organisms provides a response of habitat alteration can be used as indication organism. Indication organisms or bioindicator are key components in ecosystem management. This paper aims to evaluate and review the role of termites as bioindicator. Bioindicator defined as organisms or group of organism reflect and inform the ecosystem circumstance; environmental, ecological and biodiversity status as well as. Main criteria of bioindicator are as follow: taxonomical and biological characters of these organisms well-knew, cosmopolitan organisms, they have a well-response to habitat alteration, and their responses are closed correlated to all communities or properties of stress factors. Termites showed responses to environmental change, especially in habitat alteration. Termites responded to habitat alteration on termites composition change and termites richness decrease. Furthermore, termite�s richness strong correlated with another taxon in their community. Biological and taxonomical termites are well-known. In addition, a standard survey of termites has been developed to explore termite�s richness in tropics ecosystems. This implication, termites can be applied as one of the indicator organisms or bioindicator, notably their relation in ecological indicator and biodiversity indicator.
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Matta-Gutiérrez, Gianmarco, Esther García-Morales, Yolanda García-Álvarez, Francisco Javier Álvaro-Afonso, Raúl Juan Molines-Barroso, and José Luis Lázaro-Martínez. "The Influence of Multidrug-Resistant Bacteria on Clinical Outcomes of Diabetic Foot Ulcers: A Systematic Review." Journal of Clinical Medicine 10, no. 9 (May 1, 2021): 1948. http://dx.doi.org/10.3390/jcm10091948.

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Multidrug-resistant organism infections have become important in recent years due to the increased prevalence of diabetic foot ulcers and their possible consequences. This study aimed to systematically review and evaluate ulcer duration, healing time, hospital stay, amputation, and mortality rates in patients with diabetic foot ulcers caused by infection with multidrug-resistant organisms. PubMed, the Cochrane Library, and Web of Science were searched in May 2020 to find observational studies in English about the clinical outcomes of multidrug-resistant organism infection in diabetic foot ulcers. Eight studies met the inclusion criteria, and these studies included 923 patients. The overall methodological quality of the study was moderate. Ulcer duration was described in six studies, and there was no practical association with multidrug-resistant organisms. Two out of three studies reported a longer healing time in multidrug-resistant organism infections than in non-multidrug-resistant organism infections. Clinical outcomes included the duration of hospitalisation, surgeries, amputations, and deaths. Lower limb amputation was the most reported clinical outcome in the included studies, and was more prevalent in the multidrug-resistant organism infections. We concluded that there was not enough evidence that multidrug-resistant organisms hindered the healing of diabetic foot ulcers. In contrast to the clinical outcomes, multidrug-resistant organisms affect both amputation rates and mortality rates.
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Bechtel, William, and Leonardo Bich. "Grounding cognition: heterarchical control mechanisms in biology." Philosophical Transactions of the Royal Society B: Biological Sciences 376, no. 1820 (January 25, 2021): 20190751. http://dx.doi.org/10.1098/rstb.2019.0751.

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We advance an account that grounds cognition, specifically decision-making, in an activity all organisms as autonomous systems must perform to keep themselves viable—controlling their production mechanisms. Production mechanisms, as we characterize them, perform activities such as procuring resources from their environment, putting these resources to use to construct and repair the organism's body and moving through the environment. Given the variable nature of the environment and the continual degradation of the organism, these production mechanisms must be regulated by control mechanisms that select when a production is required and how it should be carried out. To operate on production mechanisms, control mechanisms need to procure information through measurement processes and evaluate possible actions. They are making decisions. In all organisms, these decisions are made by multiple different control mechanisms that are organized not hierarchically but heterarchically. In many cases, they employ internal models of features of the environment with which the organism must deal. Cognition, in the form of decision-making, is thus fundamental to living systems which must control their production mechanisms. This article is part of the theme issue ‘Basal cognition: conceptual tools and the view from the single cell’.
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25

Choi, JaeJin, and Sung-Hou Kim. "Whole-proteome tree of life suggests a deep burst of organism diversity." Proceedings of the National Academy of Sciences 117, no. 7 (February 4, 2020): 3678–86. http://dx.doi.org/10.1073/pnas.1915766117.

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An organism tree of life (organism ToL) is a conceptual and metaphorical tree to capture a simplified narrative of the evolutionary course and kinship among the extant organisms. Such a tree cannot be experimentally validated but may be reconstructed based on characteristics associated with the organisms. Since the whole-genome sequence of an organism is, at present, the most comprehensive descriptor of the organism, a whole-genome sequence-based ToL can be an empirically derivable surrogate for the organism ToL. However, experimentally determining the whole-genome sequences of many diverse organisms was practically impossible until recently. We have constructed three types of ToLs for diversely sampled organisms using the sequences of whole genome, of whole transcriptome, and of whole proteome. Of the three, whole-proteome sequence-based ToL (whole-proteome ToL), constructed by applying information theory-based feature frequency profile method, an “alignment-free” method, gave the most topologically stable ToL. Here, we describe the main features of a whole-proteome ToL for 4,023 species with known complete or almost complete genome sequences on grouping and kinship among the groups at deep evolutionary levels. The ToL reveals 1) all extant organisms of this study can be grouped into 2 “Supergroups,” 6 “Major Groups,” or 35+ “Groups”; 2) the order of emergence of the “founders” of all of the groups may be assigned on an evolutionary progression scale; 3) all of the founders of the groups have emerged in a “deep burst” at the very beginning period near the root of the ToL—an explosive birth of life’s diversity.
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26

Rose, Laura J., Hollis Houston, Marla Martinez-Smith, Amanda K. Lyons, Carrie Whitworth, Sujan C. Reddy, and Judith Noble-Wang. "Factors influencing environmental sampling recovery of healthcare pathogens from non-porous surfaces with cellulose sponges." PLOS ONE 17, no. 1 (January 13, 2022): e0261588. http://dx.doi.org/10.1371/journal.pone.0261588.

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Results from sampling healthcare surfaces for pathogens are difficult to interpret without understanding the factors that influence pathogen detection. We investigated the recovery of four healthcare-associated pathogens from three common surface materials, and how a body fluid simulant (artificial test soil, ATS), deposition method, and contamination levels influence the percent of organisms recovered (%R). Known quantities of carbapenemase-producing KPC+ Klebsiella pneumoniae (KPC), Acinetobacter baumannii, vancomycin-resistant Enterococcus faecalis, and Clostridioides difficile spores (CD) were suspended in Butterfield’s buffer or ATS, deposited on 323cm2 steel, plastic, and laminate surfaces, allowed to dry 1h, then sampled with a cellulose sponge wipe. Bacteria were eluted, cultured, CFU counted and %R determined relative to the inoculum. The %R varied by organism, from <1% (KPC) to almost 60% (CD) and was more dependent upon the organism’s characteristics and presence of ATS than on surface type. KPC persistence as determined by culture also declined by >1 log10 within the 60 min drying time. For all organisms, the %R was significantly greater if suspended in ATS than if suspended in Butterfield’s buffer (p<0.05), and for most organisms the %R was not significantly different when sampled from any of the three surfaces. Organisms deposited in multiple droplets were recovered at equal or higher %R than if spread evenly on the surface. This work assists in interpreting data collected while investigating a healthcare infection outbreak or while conducting infection intervention studies.
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Lyakh, Anton. "Minimal Structure of the Database for Storing Organisms’ Biodiversity Data." SPIIRAS Proceedings 19, no. 4 (September 7, 2020): 855–79. http://dx.doi.org/10.15622/sp.2020.19.4.6.

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To date, a huge amount of data on organisms diversity has been accumulated. Databases help to store and use these data for scientific purposes. There exists several dozens of databases for storing biodiversity data that were described in publications. Each has an original structure which badly correlates with the structures of other databases. This complicates data exchange and the formation of big biodiversity data array. The cause of this situation is the lack of the formal definitions of universal data components, which allow to build the database with any data on the diversity of organisms. The analysis of publications and author’s experience show that such universal components are present in the characteristics of any organisms. For example, it is an organism taxonomic name and a location where it was found. There are six such components and they answer to one of the six questions: what, where, when, who, where from and where to. What determines the name of an organism; where determines the location where it was found; when indicates the date of finding; who enumerates the persons, who found and analyzed an organism; where from refers to publications, where data about an organism are extracted or published; where to shows in which biological collection an organism is put in. Each component corresponds to a separate database table. These tables are linked to the table with data about organism (individual) and they are not linked with each other. Attributes of the links between the organism table and the component tables are stored in intermediate tables. They are used, for example, to store bibliographic facts, descriptions of collection items or geographical points. They also act as docking stations to which tables with any other information are attached. The creation of any database about the diversity of living organisms begins with the definition of the table of organism specimens. It must be used even if there is no explicit data on organisms. In that case virtual organisms should be introduced and the other components should be linked with them by means of intermediate tables. The latter are docked to other data. Minimal structures of all the tables, links between them and examples of databases construction are described in the work.
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Leonelli, Sabina, and Rachel A. Ankeny. "Re-thinking organisms: The impact of databases on model organism biology." Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 43, no. 1 (March 2012): 29–36. http://dx.doi.org/10.1016/j.shpsc.2011.10.003.

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29

Peck, Lloyd S. "Ecology of Articulated Brachiopods." Paleontological Society Papers 7 (November 2001): 171–84. http://dx.doi.org/10.1017/s1089332600000954.

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Ecology is the study of the relationships between organisms and their environments. For brachiopods living in marine habitats the main external factors of interest are temperature, water chemistry, light characteristics, and oxygen availability. However, organisms also modify their environments and in many cases the biotic environment may dictate changes or organism responses. Factors of importance here for animals are resources consumed (usually food items), predators that consume the species under study, organisms that compete for resources, organisms that provide benefits such as symbiotic arrangements or new habitat for colonisation, and those organisms which reduce the quality of the environment such as pathogens or parasites.
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30

Hershenov, David B. "Soulless Organisms?" American Catholic Philosophical Quarterly 85, no. 3 (2011): 465–82. http://dx.doi.org/10.5840/acpq201185331.

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31

Fulton, Chandler. "Favored Organisms." Science 245, no. 4924 (September 22, 1989): 1311. http://dx.doi.org/10.1126/science.245.4924.1311.a.

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32

Padian, Kevin. "Ordering Organisms." Science 265, no. 5175 (August 19, 1994): 1017. http://dx.doi.org/10.1126/science.265.5175.1017.b.

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Chapman, Michael, and John Roberts. "Industrial Organisms." Fabrications 24, no. 1 (January 2, 2014): 72–91. http://dx.doi.org/10.1080/10331867.2014.901137.

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34

Fulton, C. "Favored Organisms." Science 245, no. 4924 (September 22, 1989): 1311. http://dx.doi.org/10.1126/science.245.4924.1311.

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35

Iyengar, Erika. "Marine Organisms." American Biology Teacher 77, no. 1 (January 1, 2015): 80. http://dx.doi.org/10.1525/abt.2015.77.1.12b.

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36

Bradley, Ryan. "Transparent Organisms." Scientific American 311, no. 6 (November 18, 2014): 48. http://dx.doi.org/10.1038/scientificamerican1214-48a.

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37

Padian, K. "Ordering Organisms." Science 265, no. 5175 (August 19, 1994): 1017. http://dx.doi.org/10.1126/science.265.5175.1017-a.

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38

Dixon, Bernard. "Uncultivated organisms." Lancet Infectious Diseases 3, no. 6 (June 2003): 390. http://dx.doi.org/10.1016/s1473-3099(03)00664-9.

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39

Tintara, Supisara, Sean Rice, and Dhyanesh Patel. "Sarcina Organisms." American Journal of Gastroenterology 114, no. 6 (June 2019): 859. http://dx.doi.org/10.14309/ajg.0000000000000124.

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40

Nicholson, Daniel J. "Organisms≠Machines." Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 44, no. 4 (December 2013): 669–78. http://dx.doi.org/10.1016/j.shpsc.2013.05.014.

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41

Song, Can, ShaoJun Liu, Jun Xiao, WeiGuo He, Yi Zhou, QinBo Qin, Chun Zhang, and Yun Liu. "Polyploid organisms." Science China Life Sciences 55, no. 4 (April 2012): 301–11. http://dx.doi.org/10.1007/s11427-012-4310-2.

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42

O’Malley, Maureen A. "Molecular organisms." Biology & Philosophy 31, no. 4 (March 20, 2015): 571–89. http://dx.doi.org/10.1007/s10539-015-9482-2.

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43

Iten, Laurie. "Animated organisms." Trends in Cell Biology 8, no. 10 (October 1998): 423. http://dx.doi.org/10.1016/s0962-8924(98)01345-2.

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44

Napier, Stephen. "Identifying Organisms." Linacre Quarterly 84, no. 2 (May 2017): 145–54. http://dx.doi.org/10.1080/00243639.2017.1306678.

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Defenders of human, embryonic, destructive stem-cell research and early abortion typically argue for their position by showing that you and I do not come into existence at conception but rather at some point after. Eugene Mills has provided an ingenious argument that you and I could not have come into existence at conception. I argue against Mills's argument on two counts: first, his argument depends upon a cursory limning of human conception, and when fuller details are considered, a premise in his argument is undercut. Second, Mills's argument invites us to ask questions about how to identify individual organisms. Given a fuller description of human conception and some plausible metaphysical principles, I argue that Mills should hold instead that you and I do in fact come into being at conception. Summary One way to argue that early abortions are permissible is to argue against the view that you and I come into existence at conception. Most abortion rights defenders argue for this conclusion by noting that in order for you and I to exist, there must be developed psychological capacities. Eugene Mills takes a different route and argues that you and I could not come into existence at conception because that would mean being identical to an egg – which he rightly notes we cannot be. I argue against Mills in this article.
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45

Callebaut, Werner. "Modeling Organisms." Biological Theory 2, no. 2 (June 2007): 209–10. http://dx.doi.org/10.1162/biot.2007.2.2.209.

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46

Bastian, Joseph. "Electrosensory Organisms." Physics Today 47, no. 2 (February 1994): 30–37. http://dx.doi.org/10.1063/1.881411.

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47

Bargmann, Cornelia. "Simple Organisms." Neurobiology of Disease 7, no. 5 (October 2000): 520–22. http://dx.doi.org/10.1006/nbdi.2000.0345.

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48

Maurin, M., and Didier Raoult. "Intracellular organisms." International Journal of Antimicrobial Agents 9, no. 1 (June 1997): 61–70. http://dx.doi.org/10.1016/s0924-8579(97)00028-9.

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49

Liang, Tong, and Braden A. W. Brinkman. "Evolution of innate behavioral strategies through competitive population dynamics." PLOS Computational Biology 18, no. 3 (March 14, 2022): e1009934. http://dx.doi.org/10.1371/journal.pcbi.1009934.

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Many organism behaviors are innate or instinctual and have been “hard-coded” through evolution. Current approaches to understanding these behaviors model evolution as an optimization problem in which the traits of organisms are assumed to optimize an objective function representing evolutionary fitness. Here, we use a mechanistic birth-death dynamics approach to study the evolution of innate behavioral strategies in a simulated population of organisms. In particular, we performed agent-based stochastic simulations and mean-field analyses of organisms exploring random environments and competing with each other to find locations with plentiful resources. We find that when organism density is low, the mean-field model allows us to derive an effective objective function, predicting how the most competitive phenotypes depend on the exploration-exploitation trade-off between the scarcity of high-resource sites and the increase in birth rate those sites offer organisms. However, increasing organism density alters the most competitive behavioral strategies and precludes the derivation of a well-defined objective function. Moreover, there exists a range of densities for which the coexistence of many phenotypes persists for evolutionarily long times.
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Sylvia, Chatrine, Thiofani Maureen Tjandra, and Rizka Nurhudami. "RANCANG BANGUN APLIKASI BUDIDAYA PERIKANAN BERBASIS MOBILE “NUFARM”." Jurnal Teknik Informasi dan Komputer (Tekinkom) 4, no. 1 (2021): 25–31. http://dx.doi.org/10.37600/tekinkom.v4i1.234.

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The NUFARM application is a mobile application that delivers online aquaculture management services for aquaculture cultivators by providing information / news about aquaculture, cultivated organism’s growth monitoring by delivering real-time information about cultivation condition, and providing a marketplace for buying and selling transactions for business entrepreneurs or aquaculture cultivators.several problems have been found in the aquaculture industry which is comprise of the lack of reliableinformation sources on aquaculture management, the unavailability of media that able to assist farmers on accessing information about the place’s conditions and organisms that being cultivated, there is no place for buying and selling transactions specialized on aquaculture for farmers. entrepreneur in the aquaculture business sector. The application design provides various online aquaculture management services which are manifested in the several main features. NUMonitor which provides information about the condition of the organism in real-time (in the form of temperature, dissolved oxygen levels, and pH) for the user. NUFeed which able to feed organisms with variety of settings which is able to be scheduled, automatic feeding and manual feeding. NUPeep which is a camera sensor that able to display organism condition tothe user visually. NULight as an additional feature with its function for adjusting the illumination level of for example the aquarium lights. NUShop that serves a place for trading transactions for cultivated organisms and their equipment. As well as the NUpdate feature that able to provide the latest information / news about aquaculture along with tips and tricks for aquaculture management. Keywords: aquaculture, aquaculture management, mobile applications
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