All Relations between bottom-up and matrix compartment

Publication Sentence Publish Date Extraction Date Species
Deanna L Plubell, Eric Huang, Sandra E Spencer, Kathleen Poston, Thomas J Montine, Michael J MacCos. Data Independent Acquisition to Inform the Development of Targeted Proteomics Assays Using a Triple Quadrupole Mass Spectrometer. bioRxiv : the preprint server for biology. 2024-06-10. PMID:38853953. to develop a targeted bottom-up proteomics assay, peptides must be evaluated as proxies for the measurement of a protein or proteoform in a biological matrix. 2024-06-10 2024-06-14 Not clear
J Rudolf-Scholik, D Lilek, M Maier, T Reischenböck, C Maisl, J Allram, B Herbinger, J Rechthale. Increasing protein identifications in bottom-up proteomics of T. castaneum - Exploiting synergies of protein biochemistry and bioinformatics. Journal of chromatography. B, Analytical technologies in the biomedical and life sciences. vol 1240. 2024-05-17. PMID:38759531. our work with tribolium castaneum larvae demonstrates that sometimes - depending on matrix and research question - more complex and time-consuming sample preparation can be advantageous for isolation and identification of additional proteins in bottom-up proteomics. 2024-05-17 2024-05-27 Not clear
Asunción Fernández, Vanda Godinho, José Ávila, M Carmen Jiménez de Haro, Dirk Hufschmidt, Jennifer López-Viejobueno, G Eduardo Almanza-Vergara, F Javier Ferrer, Julien L Colaux, Stephane Lucas, M Carmen Asensi. Synergistic Effect of He for the Fabrication of Ne and Ar Gas-Charged Silicon Thin Films as Solid Targets for Spectroscopic Studies. Nanomaterials (Basel, Switzerland). vol 14. issue 8. 2024-04-26. PMID:38668221. sputtering of silicon in a he magnetron discharge (ms) has been reported as a bottom-up procedure to obtain he-charged silicon films (i.e., he nanobubbles encapsulated in a silicon matrix). 2024-04-26 2024-04-28 Not clear
Annachiara Scalzone, Giorgia Imparato, Francesco Urciuolo, Paolo Antonio Nett. Bioprinting of human dermal microtissues precursors as building blocks for endogenous in vitro connective tissue manufacturing. Biofabrication. 2024-04-04. PMID:38574552. building upon our expertise in developing competent three-dimensional tissue equivalents (e.g., skin, gut, cervix), we established a two-step bottom-up approach involving the dynamic assembly of microtissue precursors (μtps) to generate macroscopic functional tissue composed of cell-secreted extracellular matrix (ecm). 2024-04-04 2024-04-07 human
Hao Dong, Fen Hu, Xuehe Ma, Jianyu Yang, Leiting Pan, Jingjun X. Collective Cell Radial Ordered Migration in Spatial Confinement. Advanced science (Weinheim, Baden-Wurttemberg, Germany). 2024-03-23. PMID:38520715. combining bottom-up cell-to-extracellular matrix (ecm) interaction strategy, numerical simulations based on a developed mechanical model well reproduce and explain above observations. 2024-03-23 2024-03-26 Not clear
Oliver Cameron, Joana F Neves, Eileen Gentlema. Listen to Your Gut: Key Concepts for Bioengineering Advanced Models of the Intestine. Advanced science (Weinheim, Baden-Wurttemberg, Germany). 2023-11-27. PMID:38009508. this review dissects the cellular and matrix components of the intestine and discusses strategies to replicate them in vitro using principles drawing from bottom-up biological self-organization and top-down bioengineering. 2023-11-27 2023-11-29 human
Siqi Wang, Xiaosheng Yu, Wenzhuo Jia, Jianning Chi, Pengfei Lv, Junxiang Wang, Chengdong W. Optic disc detection based on fully convolutional network and weighted matrix recovery model. Medical & biological engineering & computing. 2023-09-05. PMID:37668892. secondly, the top-down semantic prior information provided by fcn and bottom-up background prior information of the optic disc region are used to jointly construct the prior information weighting matrix, which more accurately guides the decomposition of the feature matrix into a sparse matrix representing the optic disc and a low-rank matrix representing the background. 2023-09-05 2023-09-07 human
Ashley Beasley-Green, N Alan Hecker. Estimation of measurement uncertainty for the quantification of protein by ID-LC-MS/MS. Analytical and bioanalytical chemistry. 2023-05-25. PMID:37231301. using a bottom-up approach, which is the model outlined in the "guide to the expression of uncertainty of measurement" (gum), we evaluated the uncertainty components of a ms-based measurement procedure for a protein biomarker in a complex matrix. 2023-05-25 2023-08-14 human
Anna Luparelli, Ilario Losito, Elisabetta De Angelis, Rosa Pilolli, Linda Monac. Multi-Target Detection of Nuts and Peanuts as Hidden Allergens in Bakery Products through Bottom-Up Proteomics and High-Resolution Mass Spectrometry. Foods (Basel, Switzerland). vol 12. issue 4. 2023-02-25. PMID:36832800. specifically, allergenic proteins of the six ingredients were used as the analytical targets, and the lc-ms responses of selected peptides resulting from their tryptic digestion, after extraction from the bakery product matrix, were exploited for quantification, following a bottom-up approach typical of proteomics. 2023-02-25 2023-08-14 Not clear
C Russo, L Wyld, M Da Costa Aubreu, C S Bury, C Heaton, L M Cole, S Frances. Non-invasive screening of breast cancer from fingertip smears-a proof of concept study. Scientific reports. vol 13. issue 1. 2023-02-01. PMID:36725900. this proof-of-concept study, combining bottom-up proteomics with matrix assisted laser desorption ionisation mass spectrometry (maldi ms) detection, explores the potential for a non-invasive technique for the early detection of breast cancer from fingertip smears. 2023-02-01 2023-08-14 Not clear
Sara Molinari, Robert F Tesoriero, Dong Li, Swetha Sridhar, Rong Cai, Jayashree Soman, Kathleen R Ryan, Paul D Ashby, Caroline M Ajo-Frankli. A de novo matrix for macroscopic living materials from bacteria. Nature communications. vol 13. issue 1. 2022-09-21. PMID:36130968. while bottom-up assembly of macroscopic elms with a de novo matrix would offer the greatest control over material properties, we lack the ability to genetically encode a protein matrix that leads to collective self-organization. 2022-09-21 2023-08-14 Not clear
Jinwoo Kim, Ji Young Kim, Eun Soo Par. Pushing the Boundaries of Multicomponent Alloy Nanostructures: Hybrid Approach of Liquid Phase Separation and Selective Leaching Processes. Accounts of chemical research. 2022-06-17. PMID:35713467. extracting those alloy nanophases from the matrix could provide an alternative way to fabricate novel mca nanostructures.in this account, we describe a hybrid approach of metallurgical bottom-up and chemical top-down processes for fabricating mca nanostructures including nanoparticles and nanofoams. 2022-06-17 2023-08-14 Not clear
Huie Zhu, Shunsuke Yamamoto, Jun Matsui, Tokuji Miyashita, Masaya Mitsuish. Resistive non-volatile memories fabricated with poly(vinylidene fluoride)/poly(thiophene) blend nanosheets. RSC advances. vol 8. issue 15. 2022-05-11. PMID:35542040. because of the precisely controllable bottom-up construction, semiconductive p3cpent were well dispersed into the ferroelectric pvdf matrix. 2022-05-11 2023-08-13 Not clear
Katie Kennedy, Laura Cole, Matthias Witt, Mark Sealey, Simona Frances. Forensic Discrimination of Differentially Sourced Animal Blood Using a Bottom-Up Proteomics Based MALDI MS Approach. Molecules (Basel, Switzerland). vol 27. issue 7. 2022-04-12. PMID:35408438. recently published work has reported the development and application of a bottom-up proteomic approach to distinguish between human and animal blood (down to animal species level), by rapid screening using matrix assisted laser desorption ionisation mass spectrometry (maldi ms). 2022-04-12 2023-08-13 human
Maxime den Ridder, Ewout Knibbe, Wiebeke van den Brandeler, Pascale Daran-Lapujade, Martin Pabs. A systematic evaluation of yeast sample preparation protocols for spectral identifications, proteome coverage and post-isolation modifications. Journal of proteomics. 2022-03-30. PMID:35351659. here, we performed a systematic comparison of sample preparation protocols using a matrix of different conditions commonly applied in whole cell lysate, bottom-up proteomics experiments. 2022-03-30 2023-08-13 Not clear
Piotr Szefer, Kenneth Molem, Austin Sau, Vojtech Novotn. Weak effects of birds, bats, and ants on their arthropod prey on pioneering tropical forest gap vegetation. Ecology. 2022-03-24. PMID:35322403. possible explanations are strong bottom-up control, a low activity of the higher order predators, especially birds, possibly also bats, in gaps, and continuous influx of herbivores from surrounding mature forest matrix. 2022-03-24 2023-08-13 Not clear
Benjamin J Bielajew, Ryan P Donahue, Elliott K Lamkin, Jerry C Hu, Vincent C Hascall, Kyriacos A Athanasio. Proteomic, Mechanical, and Biochemical Characterization of Cartilage Development. Acta biomaterialia. 2022-03-02. PMID:35235865. this analysis shows that bottom-up proteomics is a critical tool in tissue characterization, especially toward developing a deeper understanding of matrix composition and development in tissue engineering studies. 2022-03-02 2023-08-13 Not clear
Kiheon Baek, Alexander D Noblett, Pengyu Ren, Laura J Sugg. Design and Characterization of Nucleopeptides for Hydrogel Self-Assembly. ACS applied bio materials. vol 2. issue 7. 2022-01-15. PMID:35030815. self-assembling peptides can be used in a bottom-up approach to build hydrogels that are similar to the extracellular matrix at both structural and functional levels. 2022-01-15 2023-08-13 Not clear
Philip Boucher, Clair Goug. Mapping the ethical landscape of carbon capture and storage. Poiesis & praxis : international journal of ethics of science and technology assessment. vol 9. issue 3-4. 2021-10-21. PMID:23226998. this imitates a bottom-up analytic structure in the absence of the direct participation of actors, culminating in the construction of a map of the ethical landscape; a high-resolution ethical matrix of coded interpretations of various actors' ethical framings of the technology. 2021-10-21 2023-08-12 Not clear
Hai-Jun Su, Hongliang Shi, Jingjun Y. A Symbolic Formulation for Analytical Compliance Analysis and Synthesis of Flexure Mechanisms. Journal of mechanical design (New York, N.Y. : 1990). vol 134. issue 5. 2021-10-21. PMID:23904747. at last, we use a bottom-up approach to obtain the compliance/stiffness matrix for the overall mechanism. 2021-10-21 2023-08-12 Not clear