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  1. Article: Machine learning of cellular metabolic rewiring.

    Xavier, Joao B

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Metabolic rewiring allows cells to adapt their metabolism in response to evolving environmental conditions. Traditional metabolomics techniques, whether targeted or untargeted, often struggle to interpret these adaptive shifts. Here, we ... ...

    Abstract Metabolic rewiring allows cells to adapt their metabolism in response to evolving environmental conditions. Traditional metabolomics techniques, whether targeted or untargeted, often struggle to interpret these adaptive shifts. Here, we introduce
    Language English
    Publishing date 2023-10-10
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.08.11.552957
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  2. Article ; Online: Unclouding Clostridiodes difficile virulence with systems biology.

    Mishra, Vishwas / Xavier, Joao B

    Cell host & microbe

    2021  Volume 29, Issue 11, Page(s) 1608–1610

    Abstract: Systems biology studies how complex dynamics emerge from many elements interacting with each other in biological systems. This definition might sound abstract, but the applications are concrete. In this issue of Cell Host & Microbe, two studies apply ... ...

    Abstract Systems biology studies how complex dynamics emerge from many elements interacting with each other in biological systems. This definition might sound abstract, but the applications are concrete. In this issue of Cell Host & Microbe, two studies apply systems biology to study Clostridioides difficile, a major cause of hospital-acquired infections.
    MeSH term(s) Clostridioides ; Clostridioides difficile ; Metabolic Networks and Pathways ; Systems Analysis ; Systems Biology ; Virulence
    Language English
    Publishing date 2021-12-10
    Publishing country United States
    Document type Journal Article ; Comment
    ZDB-ID 2278004-X
    ISSN 1934-6069 ; 1931-3128
    ISSN (online) 1934-6069
    ISSN 1931-3128
    DOI 10.1016/j.chom.2021.10.005
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 6578: Show issues Location:
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  3. Article ; Online: Optimizing the future: how mathematical models inform treatment schedules for cancer.

    Mathur, Deepti / Barnett, Ethan / Scher, Howard I / Xavier, Joao B

    Trends in cancer

    2022  Volume 8, Issue 6, Page(s) 506–516

    Abstract: For decades, mathematical models have influenced how we schedule chemotherapeutics. More recently, mathematical models have leveraged lessons from ecology, evolution, and game theory to advance predictions of optimal treatment schedules, often in a ... ...

    Abstract For decades, mathematical models have influenced how we schedule chemotherapeutics. More recently, mathematical models have leveraged lessons from ecology, evolution, and game theory to advance predictions of optimal treatment schedules, often in a personalized medicine manner. We discuss both established and emerging therapeutic strategies that deviate from canonical standard-of-care regimens, and how mathematical models have contributed to the design of such schedules. We first examine scheduling options for single therapies and review the advantages and disadvantages of various treatment plans. We then consider the challenge of scheduling multiple therapies, and review the mathematical and clinical support for various conflicting treatment schedules. Finally, we propose how a consilience of mathematical and clinical knowledge can best determine the optimal treatment schedules for patients.
    MeSH term(s) Humans ; Models, Theoretical ; Neoplasms/drug therapy ; Precision Medicine
    Language English
    Publishing date 2022-03-09
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 2852626-0
    ISSN 2405-8025 ; 2405-8033 ; 2405-8033
    ISSN (online) 2405-8025 ; 2405-8033
    ISSN 2405-8033
    DOI 10.1016/j.trecan.2022.02.005
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  4. Book ; Online: PATSMA

    Fernandes, Joao B. / da Silva, Felipe H. S. / Xavier-de-Souza, Samuel / Assis, Italo A. S.

    Parameter Auto-tuning for Shared Memory Algorithms

    2024  

    Abstract: Programs with high levels of complexity often face challenges in adjusting execution parameters, particularly when these parameters vary based on the execution context. These dynamic parameters significantly impact the program's performance, such as loop ...

    Abstract Programs with high levels of complexity often face challenges in adjusting execution parameters, particularly when these parameters vary based on the execution context. These dynamic parameters significantly impact the program's performance, such as loop granularity, which can vary depending on factors like the execution environment, program input, or the choice of compiler. Given the expensive nature of testing each case individually, one viable solution is to automate parameter adjustments using optimization methods. This article introduces PATSMA, a parameter auto-tuning tool that leverages Coupled Simulated Annealing (CSA) and Nelder-Mead (NM) optimization methods to fine-tune existing parameters in an application. We demonstrate how auto-tuning can contribute to the real-time optimization of parallel algorithms designed for shared memory systems. PATSMA is a C++ library readily available under the MIT license.
    Keywords Computer Science - Distributed ; Parallel ; and Cluster Computing
    Subject code 004
    Publishing date 2024-01-15
    Publishing country us
    Document type Book ; Online
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  5. Article ; Online: Sociomicrobiology and Pathogenic Bacteria.

    Xavier, Joao B

    Microbiology spectrum

    2016  Volume 4, Issue 3

    Abstract: The study of microbial pathogenesis has been primarily a reductionist science since Koch's principles. Reductionist approaches are essential to identify the causal agents of infectious disease, their molecular mechanisms of action, and potential drug ... ...

    Abstract The study of microbial pathogenesis has been primarily a reductionist science since Koch's principles. Reductionist approaches are essential to identify the causal agents of infectious disease, their molecular mechanisms of action, and potential drug targets, and much of medicine's success in the treatment of infectious disease stems from that approach. But many bacteria-caused diseases cannot be explained by a single bacterium. Several aspects of bacterial pathogenesis will benefit from a more holistic approach that takes into account social interaction among bacteria of the same species and between species in consortia such as the human microbiome. The emerging discipline of sociomicrobiology provides a framework to dissect microbial interactions in single and multi-species communities without compromising mechanistic detail. The study of bacterial pathogenesis can benefit greatly from incorporating concepts from other disciplines such as social evolution theory and microbial ecology, where communities, their interactions with hosts, and with the environment play key roles.
    MeSH term(s) Bacteria/pathogenicity ; Bacterial Infections/microbiology ; Host-Pathogen Interactions ; Humans ; Microbial Consortia ; Microbial Interactions
    Language English
    Publishing date 2016-06-23
    Publishing country United States
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 2807133-5
    ISSN 2165-0497 ; 2165-0497
    ISSN (online) 2165-0497
    ISSN 2165-0497
    DOI 10.1128/microbiolspec.VMBF-0019-2015
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  6. Article ; Online: Fatty acid oxidation fuels natural killer cell responses against infection and cancer.

    Sheppard, Sam / Srpan, Katja / Lin, Wendy / Lee, Mariah / Delconte, Rebecca B / Owyong, Mark / Carmeliet, Peter / Davis, Daniel M / Xavier, Joao B / Hsu, Katharine C / Sun, Joseph C

    Proceedings of the National Academy of Sciences of the United States of America

    2024  Volume 121, Issue 11, Page(s) e2319254121

    Abstract: Natural killer (NK) cells are a vital part of the innate immune system capable of rapidly clearing mutated or infected cells from the body and promoting an immune response. Here, we find that NK cells activated by viral infection or tumor challenge ... ...

    Abstract Natural killer (NK) cells are a vital part of the innate immune system capable of rapidly clearing mutated or infected cells from the body and promoting an immune response. Here, we find that NK cells activated by viral infection or tumor challenge increase uptake of fatty acids and their expression of carnitine palmitoyltransferase I (CPT1A), a critical enzyme for long-chain fatty acid oxidation. Using a mouse model with an NK cell-specific deletion of CPT1A, combined with stable
    MeSH term(s) Humans ; Lipid Metabolism ; Killer Cells, Natural ; Neoplasms ; Fatty Acids ; Virus Diseases
    Chemical Substances Fatty Acids
    Language English
    Publishing date 2024-03-05
    Publishing country United States
    Document type Journal Article
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2319254121
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    Zs.A 1148: Show issues Location:
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  7. Article: Diel biochemical and photosynthetic monitorization of Skeletonema costatum and Phaeodactylum tricornutum grown in outdoor pilot-scale flat panel photobioreactors

    Maia, Inês B. / Carneiro, Mariana / Magina, Tânia / Malcata, F. Xavier / Otero, Ana / Navalho, João / Varela, João / Pereira, Hugo

    Journal of biotechnology. 2022 Jan. 10, v. 343

    2022  

    Abstract: Diatoms are currently considered valuable feedstocks for different biotechnological applications. To deepen the knowledge on the production of these microalgae, the diel pattern of batch growth, photosystem II performance, and accumulation of target ... ...

    Abstract Diatoms are currently considered valuable feedstocks for different biotechnological applications. To deepen the knowledge on the production of these microalgae, the diel pattern of batch growth, photosystem II performance, and accumulation of target metabolites of two commercially relevant diatoms, Phaeodactylum tricornutum and Skeletonema costatum, were followed outdoors in 100-L flat panel photobioreactors. S. costatum presented a higher light-to-biomass conversion resulting in higher growth than P. tricornutum. Both fluorescence data and principal component analysis pointed to temperature as a limiting factor for the growth of P. tricornutum. Higher protein and carbohydrate contents were found in P. tricornutum, whereas S. costatum fatty acids were characterized by a higher unsaturation degree. Higher productivities were found at 1 p.m. for protein, lipid, and ash in the case of S. costatum. Overall, S. costatum showed great potential for outdoor cultivation, revealing a broader temperature tolerance and increased biomass productivity than P. tricornutum.
    Keywords Phaeodactylum tricornutum ; Skeletonema costatum ; biomass production ; carbohydrates ; feedstocks ; fluorescence ; metabolites ; microalgae ; photobioreactors ; principal component analysis ; temperature
    Language English
    Dates of publication 2022-0110
    Size p. 110-119.
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 843647-2
    ISSN 1873-4863 ; 0168-1656 ; 1389-0352
    ISSN (online) 1873-4863
    ISSN 0168-1656 ; 1389-0352
    DOI 10.1016/j.jbiotec.2021.11.008
    Database NAL-Catalogue (AGRICOLA)

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    Zs.A 2299: Show issues Location:
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  8. Article ; Online: Listening in on the conversation between the human gut microbiome and its host.

    Lin, Wendy / Djukovic, Ana / Mathur, Deepti / Xavier, Joao B

    Current opinion in microbiology

    2021  Volume 63, Page(s) 150–157

    Abstract: The gut microbiome is an ecosystem. Natural selection favored microbes fit for the gut, which can utilize and convert molecules produced by the host for their own benefit. But natural selection also favored the host's mechanisms to sense and respond to ... ...

    Abstract The gut microbiome is an ecosystem. Natural selection favored microbes fit for the gut, which can utilize and convert molecules produced by the host for their own benefit. But natural selection also favored the host's mechanisms to sense and respond to the microbial ecosystem for its own benefit. We can listen in on the host-microbiome 'conversation' in the simultaneous responses of the microbiome and the host to strong perturbations. In laboratory animals a perturbation can be done for research; in human patients a perturbation can be caused by disease or therapy. Advances in metagenomics, metabolomics and computation amplify our means to listen in on the conversation between the gut microbiome and its host.
    MeSH term(s) Animals ; Gastrointestinal Microbiome/genetics ; Humans ; Metabolomics ; Metagenomics ; Microbiota
    Language English
    Publishing date 2021-08-02
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 1418474-6
    ISSN 1879-0364 ; 1369-5274
    ISSN (online) 1879-0364
    ISSN 1369-5274
    DOI 10.1016/j.mib.2021.07.009
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    Zs.A 5514: Show issues Location:
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    Zs.MG 51: Show issues

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  9. Article ; Online: Assessing Engraftment Following Fecal Microbiota Transplant.

    Herman, Chloe / Barker, Bridget M / Bartelli, Thais F / Chandra, Vidhi / Krajmalnik-Brown, Rosa / Jewell, Mary / Li, Le / Liao, Chen / McAllister, Florencia / Nirmalkar, Khemlal / Xavier, Joao B / Caporaso, J Gregory

    ArXiv

    2024  

    Abstract: Fecal Microbiota Transplant (FMT) is an FDA approved treatment for recurrent Clostridium difficile infections, and is being explored for other clinical applications, from alleviating digestive and neurological disorders, to priming the microbiome for ... ...

    Abstract Fecal Microbiota Transplant (FMT) is an FDA approved treatment for recurrent Clostridium difficile infections, and is being explored for other clinical applications, from alleviating digestive and neurological disorders, to priming the microbiome for cancer treatment, and restoring microbiomes impacted by cancer treatment. Quantifying the extent of engraftment following an FMT is important in determining if a recipient didn't respond because the engrafted microbiome didn't produce the desired outcomes (a successful FMT, but negative treatment outcome), or the microbiome didn't engraft (an unsuccessful FMT and negative treatment outcome). The lack of a consistent methodology for quantifying FMT engraftment extent hinders the assessment of FMT success and its relation to clinical outcomes, and presents challenges for comparing FMT results and protocols across studies. Here we review 46 studies of FMT in humans and model organisms and group their approaches for assessing the extent to which an FMT engrafts into three criteria: 1) Chimeric Asymmetric Community Coalescence investigates microbiome shifts following FMT engraftment. 2) Donated Microbiome Indicator Features tracks donated microbiome features as a signal of engraftment with methods such as differential abundance testing based on the current sample collection, or tracking changes in feature abundances that have been previously identified. 3) Temporal Stability examines how resistant post-FMT recipient's microbiomes are to reverting back to their baseline microbiome. Investigated together, these criteria provide a clear assessment of microbiome engraftment. We discuss the pros and cons of each of these criteria, providing illustrative examples of their application. We also introduce key terminology and recommendations on how FMT studies can be analyzed for rigorous engraftment extent assessment.
    Language English
    Publishing date 2024-04-10
    Publishing country United States
    Document type Preprint
    ISSN 2331-8422
    ISSN (online) 2331-8422
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Determinação da produção de metalo-b-lactamases em amostras de Pseudomonas aeruginosa isoladas em João Pessoa, Paraíba

    Santos Filho Lauro / Santos Isabele Beserra / Assis Alexandro Mangueira Lima de / Xavier Danilo Elias

    Jornal Brasileiro de Patologia e Medicina Laboratorial, Vol 38, Iss 4, Pp 291-

    2002  Volume 296

    Abstract: Bactérias produtoras de metalo-beta-lactamases (MBLs) são em grande parte resistentes aos betalactâmicos de largo espectro, incluindo oximino-aminotiazol cefalosporinas e também aos carbapenens. O objetivo deste trabalho foi detectar cepas de Pseudomonas ...

    Abstract Bactérias produtoras de metalo-beta-lactamases (MBLs) são em grande parte resistentes aos betalactâmicos de largo espectro, incluindo oximino-aminotiazol cefalosporinas e também aos carbapenens. O objetivo deste trabalho foi detectar cepas de Pseudomonas aeruginosa resistentes ao imipenem e à ceftazidima, assim como identificar aquelas produtoras de MBLs. Foram estudadas 198 linhagens não-repetitivas isoladas de diversas amostras clínicas, hospitalares e comunitárias, identificadas bioquimicamente por técnicas de rotina. A triagem para a detecção de amostras produtoras de MBLs foi realizada pelo método de dupla difusão proposto por Arakawa et al. (2000) e modificado por Nakajima et al. (2001), utilizando discos contendo mercaptoacetato de sódio. Foi detectado um percentual de resistência de 19,7% (39/198) ao imipenem e de 15,2% (30/198) à ceftazidima, com 10,1% (20/198) de resistência cruzada aos dois antimicrobianos. Entre estas amostras, 2% (4/198) demonstraram produção de MBLs e padrão de multirresistência. A detecção destas amostras configura um problema emergente, com importantes implicações na terapêutica antimicrobiana, necessitando, portanto, de maior investigação através de metodologia molecular, para melhor caracterizar a extensão do problema.
    Keywords Pseudomonas aeruginosa ; Resistência ; Metalo-beta-lactamases ; Pathology ; RB1-214 ; Medicine ; R ; DOAJ:Pathology ; DOAJ:Medicine (General) ; DOAJ:Health Sciences
    Language English
    Publishing date 2002-01-01T00:00:00Z
    Publisher Sociedade Brasileira de Patologia Clínica
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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