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  1. Article ; Online: Endless forms of endless formation - The morphogenesis of organisms and scientific objects.

    Faria, Marcella

    Bio Systems

    2023  Volume 235, Page(s) 105068

    Abstract: The present article proceeds from the premises that living forms and abstract formalization come into being by similar mechanisms (e.g., random variation, selection, conventions) and have similar properties (e.g., semiosis, stasis and complexity). These ... ...

    Abstract The present article proceeds from the premises that living forms and abstract formalization come into being by similar mechanisms (e.g., random variation, selection, conventions) and have similar properties (e.g., semiosis, stasis and complexity). These convergences justify the comparative analysis of form's development, evolution and action in both fields. Here we shall focus on the notion of "endless forms" advanced by Darwin's seminal work in evolutionary biology "On The Origin of Species" to discuss the various ways in which it relates to biological formation. I shall explore the idea of "infinitude of evolved forms" through the lens of the five connotations of the word "endless" provided by the Merriam-Webster Thesaurus dictionary, which are: perpetual; incomputable; manifold; unfinished; steady. From each synonym chosen, a new iteration of dictionary search was made to produce a list of terms that are used in the reviewed literature to describe biological morphogenetic features, which are respectively: reproducible, unpredictable, additive, undetermined, the end of their own formation. In conclusion, I propose a tentative mapping between each of these five connotations and the biological processes at work in their making, which are, respectively: 1) copying organic information; coding organic signs; manufacturing organic meaning 2) natural variation, natural selection, natural conventions; 3) multilevel organization, differentiation/development, complexity; 4) ambiguity, degeneracy, semiotic thresholds; 5) homeostasis, autopoiesis, codepoiesis. The processes discussed here gained salience as developments, additions, or nuances to Darwin's original theory. It must be noted that, even though the discussion is mainly framed by Code Biology as a source of conceptualization, inputs from a wide range of theoretical perspectives will be given emphasis when suitable.
    MeSH term(s) Biological Evolution ; Morphogenesis ; Selection, Genetic
    Language English
    Publishing date 2023-11-19
    Publishing country Ireland
    Document type Journal Article
    ZDB-ID 186234-0
    ISSN 1872-8324 ; 0303-2647
    ISSN (online) 1872-8324
    ISSN 0303-2647
    DOI 10.1016/j.biosystems.2023.105068
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  2. Article ; Online: Two theories of action - Edelman's Neuronal group Selection and the Poetics of Paul Valéry.

    Faria, Marcella

    Bio Systems

    2021  Volume 210, Page(s) 104549

    Abstract: Motivated by two imperatives as they are framed in Code Biology - mechanism and actualization - we have turned to other attempts of modeling life at work. Here, we present two theories devoted to minds in action - one explains neuronal function, and the ... ...

    Abstract Motivated by two imperatives as they are framed in Code Biology - mechanism and actualization - we have turned to other attempts of modeling life at work. Here, we present two theories devoted to minds in action - one explains neuronal function, and the other dissects poetic crafting. Neuronal networks activation and poetic composition, respectively, are seen as the selection of specific connective patterns of either neurons or words, in action. Gerald Edelman, as a scientist, has generalized the Darwinian ideas of variation and selection to the cellular level in his "Sciences of Recognition", a broader theoretical framework that includes the "Theory of Neuronal Group Selection" (TGNS) analyzed here. Paul Valéry, as a poet, has reconciled inspiration and technique in what he has called "works of the mind", the creative processes mediated by sensing and making sense, in the "Poetic Theory" we present here he advances the mechanisms of artistic composition. We have identified the main ideas conveyed in these two theories, i.e., variation and selection, integration and differentiation, ambiguity and degeneracy, binding and blending, stasis and semiosis, by pairing and comparing textual fragments from the authors. We show that TGNS and the Theory of Poetic Action reconcile Sciences and Arts by recognizing that Natural Selection is a mechanism implied by formative acts in both scenarios and discuss to which extent Natural Convention - the main contribution of Code Biology - is integrated by the two thinkers.
    MeSH term(s) Brain/physiology ; Cell Biology ; Humans ; Neurons/physiology ; Poetry as Topic ; Psychophysiology/methods ; Psychophysiology/trends ; Selection, Genetic/physiology ; Thinking/physiology
    Language English
    Publishing date 2021-09-23
    Publishing country Ireland
    Document type Journal Article
    ZDB-ID 186234-0
    ISSN 1872-8324 ; 0303-2647
    ISSN (online) 1872-8324
    ISSN 0303-2647
    DOI 10.1016/j.biosystems.2021.104549
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  3. Article ; Online: Adsorption- and Displacement-Based Approaches for the Removal of Protein-Bound Uremic Toxins.

    Rodrigues, Flávia S C / Faria, Mónica

    Toxins

    2023  Volume 15, Issue 2

    Abstract: End-stage renal disease (ESRD) patients rely on renal replacement therapies to survive. Hemodialysis (HD), the most widely applied treatment, is responsible for the removal of excess fluid and uremic toxins (UTs) from blood, particularly those with low ... ...

    Abstract End-stage renal disease (ESRD) patients rely on renal replacement therapies to survive. Hemodialysis (HD), the most widely applied treatment, is responsible for the removal of excess fluid and uremic toxins (UTs) from blood, particularly those with low molecular weight (MW < 500 Da). The development of high-flux membranes and more efficient treatment modes, such as hemodiafiltration, have resulted in improved removal rates of UTs in the middle molecular weight range. However, the concentrations of protein-bound uremic toxins (PBUTs) remain essentially untouched. Due to the high binding affinity to large proteins, such as albumin, PBUTs form large complexes (MW > 66 kDa) which are not removed during HD and their accumulation has been strongly associated with the increased morbidity and mortality of patients with ESRD. In this review, we describe adsorption- and displacement-based approaches currently being studied to enhance the removal of PBUTs. The development of mixed matrix membranes (MMMs) with selective adsorption properties, infusion of compounds capable of displacing UTs from their binding site on albumin, and competitive binding membranes show promising results, but the road to clinical application is still long, and further investigation is required.
    MeSH term(s) Humans ; Uremic Toxins ; Uremia/metabolism ; Adsorption ; Protein Binding ; Toxins, Biological/metabolism ; Renal Dialysis/methods ; Kidney Failure, Chronic ; Albumins/metabolism
    Chemical Substances Uremic Toxins ; Toxins, Biological ; Albumins
    Language English
    Publishing date 2023-01-28
    Publishing country Switzerland
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 2518395-3
    ISSN 2072-6651 ; 2072-6651
    ISSN (online) 2072-6651
    ISSN 2072-6651
    DOI 10.3390/toxins15020110
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Word games and molecular recognition - The creative control of endothelial cell function.

    Faria, Marcella

    Bio Systems

    2019  Volume 187, Page(s) 104041

    Abstract: In this paper we postulate that figures of language and structural features, which are characteristic of poetic writings and word games, have direct correlates in the cell/cell and cell/matrix recognition processes. We shall discuss the particular ... ...

    Abstract In this paper we postulate that figures of language and structural features, which are characteristic of poetic writings and word games, have direct correlates in the cell/cell and cell/matrix recognition processes. We shall discuss the particular example of endothelial cells engagement into angiogenesis (the making of new blood vessels in adult vertebrates)-an activity that requires intense extracellular matrix (ECM) remodeling and Cell Adhesion Molecules (CAMs) rearrangement-to argue that angiogenesis controls are organized into semiotic dimensions. CAMs attach cells to the ECM; they are mainly composed of integrins (transmembrane receptors) that bind selectively to different ECM components. After ECM binding, the cytoplasmic tails of integrins within the cell will begin to interact with a wide range of recruited factors that, in turn, regulate integrin clustering in the cell membrane. These recruited factors also activate signaling pathways that link activated integrins to later microfilament system remodeling during cell migration. Ultimately CAMs work as functional protein networks-as the adaptor molecules in an organic code, the Adhesion Code-controlling cell migration/proliferation transition through the continual rearrangement of both ECM adhesion and Actin polymerization. Additionally, orchestrating the transition from clonal growth to differentiation, the interaction between CAMs and ECM components will trigger specific Signal Transduction pathways. We shall examine some attempts to conceptualize "somatic cell function" in the recent specialized literature, which introduces the notion of hierarchic organization into levels i.e. molecular, sub-cellular and cellular and describes an informational flow of increasing complexity versus decreasing number of entities through the levels. Beyond the syntactic level-the specific recognition of discrete ECM motifs by integrin heterodimers-we shall examine the semantic and pragmatic levels at which the composition and architecture of multimolecular complexes will dictate cell recognition events and cell fate decisions. These higher-level codes will be compared to the dynamics of the word games of Lewis Carroll, e.g. "doublets" and "magic squares." In such creative games words are subjected to synthetic transformations that have to conform to semantic rules, but are ultimately constrained by meaning, as concrete pragmatics. This gives us a model for analyzing angiogenesis control as a word game.
    MeSH term(s) Animals ; Biomarkers/metabolism ; Cell Adhesion/physiology ; Endothelial Cells/physiology ; Extracellular Matrix/physiology ; Integrins/metabolism ; Language ; Models, Biological ; Neovascularization, Physiologic/physiology ; Poetry as Topic ; Signal Transduction/physiology ; Systems Biology ; Vertebrates/physiology
    Chemical Substances Biomarkers ; Integrins
    Language English
    Publishing date 2019-09-26
    Publishing country Ireland
    Document type Journal Article
    ZDB-ID 186234-0
    ISSN 1872-8324 ; 0303-2647
    ISSN (online) 1872-8324
    ISSN 0303-2647
    DOI 10.1016/j.biosystems.2019.104041
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Equation learning to identify nano-engineered particle-cell interactions: an interpretable machine learning approach.

    Johnston, Stuart T / Faria, Matthew

    Nanoscale

    2022  Volume 14, Issue 44, Page(s) 16502–16515

    Abstract: Designing nano-engineered particles capable of the delivery of therapeutic and diagnostic agents to a specific target remains a significant challenge. Understanding how interactions between particles and cells are impacted by the physicochemical ... ...

    Abstract Designing nano-engineered particles capable of the delivery of therapeutic and diagnostic agents to a specific target remains a significant challenge. Understanding how interactions between particles and cells are impacted by the physicochemical properties of the particle will help inform rational design choices. Mathematical and computational techniques allow for details regarding particle-cell interactions to be isolated from the interwoven set of biological, chemical, and physical phenomena involved in the particle delivery process. Here we present a machine learning framework capable of elucidating particle-cell interactions from experimental data. This framework employs a data-driven modelling approach, augmented by established biological knowledge. Crucially, the model of particle-cell interactions learned by the framework can be interpreted and analysed, in contrast to the 'black box' models inherent to other machine learning approaches. We apply the framework to association data for thirty different particle-cell pairs. This library of data contains both adherent and suspension cell lines, as well as a diverse collection of particles. We consider hyperbranched polymer and poly(methacrylic acid) particles, from 6 nm to 1032 nm in diameter, with small molecule, monoclonal antibody, and peptide surface functionalisations. Despite the diverse nature of the experiments, the learned models of particle-cell interactions for each particle-cell pair are remarkably consistent: out of 2048 potential models, only four unique models are learned. The models reveal that nonlinear saturation effects are a key feature governing particle-cell interactions. Further, the framework provides robust estimates of particle performance, which facilitates quantitative evaluation of particle design choices.
    MeSH term(s) Machine Learning ; Polymers ; Peptides
    Chemical Substances Polymers ; Peptides
    Language English
    Publishing date 2022-11-17
    Publishing country England
    Document type Journal Article
    ZDB-ID 2515664-0
    ISSN 2040-3372 ; 2040-3364
    ISSN (online) 2040-3372
    ISSN 2040-3364
    DOI 10.1039/d2nr04668g
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Efficacy of acupuncture on cancer pain: A systematic review and meta-analysis.

    Faria, Miguel / Teixeira, Mónica / Pinto, Maria João / Sargento, Paulo

    Journal of integrative medicine

    2024  

    Abstract: ... treatment to reduce cancer pain. Please cite this article as: Faria M, Teixeira M, Pinto MJ, Sargento P ...

    Abstract Background: Pain associated with cancer is one of the greatest causes of reduced quality of life in patients. Acupuncture is one of the treatments used to address this issue, with the great advantage of having little or no side effects, especially when compared with pharmacological pain-killers.
    Objective: The aim of this systematic review and meta-analysis was to evaluate the current evidence regarding the efficacy of acupuncture for cancer pain.
    Search strategy: Six electronic databases (PubMed, EBSCO, Cochrane Library, Scielo, b-On and Scopus) were searched for relevant articles about pain relief in cancer patients from their beginning until 2022 using MeSH terms such as "acupuncture," "electroacupuncture," "ear acupuncture," "acupuncture analgesia," ''oncological pain," and "cancer pain."
    Inclusion criteria: Studies included were randomized controlled trials (RCTs) where acupuncture was compared with no treatment, placebo acupuncture or usual care.
    Data extraction and analysis: Three independent reviewers participated in data extraction and evaluation of risk of bias, and a meta-analysis was conducted. The primary outcome was pain intensity, measured with the visual analog scale, numeric rating scale, or brief pain inventory. Secondary outcomes also assessed were quality of life, functionality, xerostomia, pain interference, and analgesic consumption. Results were expressed as standardized mean difference (SMD) with 95% confidence interval (CI).
    Results: Sixteen RCTs with a total of 1124 participants were included in the meta-analysis, with the majority of the studies presenting a low or unclear risk of bias. Acupuncture was more effective in reducing pain than no treatment (SMD = -0.90, 95 % CI [-1.68, -0.12]), sham acupuncture (SMD = -1.10, 95 % CI [-1.59, -0.61]) or usual care (SMD = -1.16, 95 % CI [-1.38, -0.93]).
    Conclusion: The results of this study suggest that acupuncture may be an effective intervention to reduce pain associated with cancer. Despite some limitations due to the low quality and small sample size of some included studies, as well as the different types and stages of cancer, acupuncture might provide an effective and safe treatment to reduce cancer pain. Please cite this article as: Faria M, Teixeira M, Pinto MJ, Sargento P. Efficacy of acupuncture on cancer pain: A systematic review and meta-analysis. J Integr Med. 2024; Epub ahead of print.
    Language English
    Publishing date 2024-03-06
    Publishing country Netherlands
    Document type Journal Article ; Review
    ZDB-ID 2705612-0
    ISSN 2095-4964
    ISSN 2095-4964
    DOI 10.1016/j.joim.2024.03.002
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Aggregating, polarizing, networking - The evolution of cell adhesion codes.

    Faria, Marcella

    Bio Systems

    2017  Volume 164, Page(s) 60–67

    MeSH term(s) Animals ; Cell Adhesion/physiology ; Cell Aggregation/physiology ; Cell Polarity/physiology ; Endoplasmic Reticulum/genetics ; Endoplasmic Reticulum/metabolism ; Evolution, Molecular ; Extracellular Matrix/genetics ; Extracellular Matrix/metabolism ; Gene Regulatory Networks/physiology ; Genetic Code/physiology ; Humans
    Language English
    Publishing date 2017-11-02
    Publishing country Ireland
    Document type Journal Article ; Review
    ZDB-ID 186234-0
    ISSN 1872-8324 ; 0303-2647
    ISSN (online) 1872-8324
    ISSN 0303-2647
    DOI 10.1016/j.biosystems.2017.10.017
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  8. Article ; Online: Microalgal-based industry vs. microplastic pollution: Current knowledge and future perspectives.

    Mendonça, Ivana / Faria, Marisa / Rodrigues, Filipa / Cordeiro, Nereida

    The Science of the total environment

    2023  Volume 909, Page(s) 168414

    Abstract: Microalgae can play a crucial role in the environment due to their efficient capture of ... ...

    Abstract Microalgae can play a crucial role in the environment due to their efficient capture of CO
    MeSH term(s) Microplastics/metabolism ; Plastics/metabolism ; Microalgae/metabolism ; Wastewater ; Biomass ; Water Pollution
    Chemical Substances Microplastics ; Plastics ; Wastewater
    Language English
    Publishing date 2023-11-12
    Publishing country Netherlands
    Document type Journal Article ; Review
    ZDB-ID 121506-1
    ISSN 1879-1026 ; 0048-9697
    ISSN (online) 1879-1026
    ISSN 0048-9697
    DOI 10.1016/j.scitotenv.2023.168414
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    Zs.A 949: Show issues Location:
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  9. Article: Association between Social and Emotional Competencies and Quality of Life in the Context of War, Pandemic and Climate Change.

    Gameiro, Fátima / Ferreira, Paula / Faria, Miguel

    Behavioral sciences (Basel, Switzerland)

    2023  Volume 13, Issue 3

    Abstract: The present context, with an ongoing pandemic situation, war and climate change, seems to play a critical role in both the peoples' perception of their quality of life, and the acquisition and development of social and emotional competencies. In this ... ...

    Abstract The present context, with an ongoing pandemic situation, war and climate change, seems to play a critical role in both the peoples' perception of their quality of life, and the acquisition and development of social and emotional competencies. In this study, our goal was to assess the relationship between social and emotional competencies and peoples' quality of life in a Portuguese sample. Participants were 1139 individuals living in Portugal, aged between 16 and 85 years old, who were mostly (73%) female. An online protocol for data acquisition was used, which included sociodemographic characterization, the Portuguese version of the scale of Social and Emotional Competencies (SEC-Q) and the World Health Organization Quality of Life (WHOQOL-BRIEF). Correlation analysis and a canonical correlation were performed, with results showing a high association between the dimensions of social and emotional competencies and peoples' quality of life. Two significant canonical roots were extracted, and the results show that the first is characterized by internal factors, linking psychological health and self-management and motivation, and the second root evidences the external factors, linking social relations and environment with social awareness and pro-social behavior.
    Language English
    Publishing date 2023-03-12
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2651997-5
    ISSN 2076-328X
    ISSN 2076-328X
    DOI 10.3390/bs13030249
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  10. Article ; Online: Microbial Control of Leptopharsa heveae Drake & Poor (Hemiptera: Tingidae) in Brazilian Rubber Tree Plantations: a Brief Historical Account and Identification of Entomopathogenic Fungi by Means of Multigene Phylogeny.

    Faria, M / de Souza, D A / Lopes, R B

    Neotropical entomology

    2020  Volume 49, Issue 6, Page(s) 864–873

    Abstract: Over the last decades, a few fungal species have been mentioned in the literature associated with the rubber tree lace bug, Leptopharsa heveae Drake & Poor (Hemiptera: Tingidae). The rubber plantation area treated with these biocontrol agents has been ... ...

    Abstract Over the last decades, a few fungal species have been mentioned in the literature associated with the rubber tree lace bug, Leptopharsa heveae Drake & Poor (Hemiptera: Tingidae). The rubber plantation area treated with these biocontrol agents has been steady since the 1990s, estimated in 10,000-15,000 ha per year. A few large-scale rubber operations, one biocontrol company, and three government-owned laboratories were, and currently one still is, involved in their commercialization. One species, currently referred to as Sporothrix insectorum, has been historically deployed in biocontrol applications in Brazilian rubber farms. However, L. heveae-infecting isolates have only been identified through morphological examinations; therefore, proper molecular assessments are needed for accurate identifications. Hence, DNA of six L. heveae-infecting isolates (five of which have been deployed in field applications) were extracted and sequenced. Multigene phylogeny found that both Simplicillium lanosoniveum and Cordyceps (formerly Isaria) sp. have been sprayed on rubber plantations to manage L. heveae populations, although the former is the only one currently applied. Simplicillium lanosoniveum and Cordyceps sp. have no relation whatsoever to true Sporothrix species associated with human and animal diseases. Therefore, our molecular data may encourage biocontrol companies to register mycoinsecticides targeting L. heveae. We also added unpublished historical accounts after contacting key contributors to the launching of this not so well-known biocontrol program in the 1980s.
    MeSH term(s) Animals ; Biological Control Agents ; Brazil ; Fungi/classification ; Heteroptera/microbiology ; Hevea ; Phylogeny
    Chemical Substances Biological Control Agents
    Language English
    Publishing date 2020-09-24
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2105363-7
    ISSN 1678-8052 ; 1519-566X
    ISSN (online) 1678-8052
    ISSN 1519-566X
    DOI 10.1007/s13744-020-00808-4
    Database MEDical Literature Analysis and Retrieval System OnLINE

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