420 Matching Annotations
  1. Jan 2022
  2. Dec 2021
    1. Heitmann, J. S., Bilich, T., Tandler, C., Nelde, A., Maringer, Y., Marconato, M., Reusch, J., Jäger, S., Denk, M., Richter, M., Anton, L., Weber, L. M., Roerden, M., Bauer, J., Rieth, J., Wacker, M., Hörber, S., Peter, A., Meisner, C., … Walz, J. S. (2021). A COVID-19 peptide vaccine for the induction of SARS-CoV-2 T cell immunity. Nature, 1–9. https://doi.org/10.1038/s41586-021-04232-5

  3. Nov 2021
  4. Oct 2021
    1. Andreano, E., Paciello, I., Piccini, G., Manganaro, N., Pileri, P., Hyseni, I., Leonardi, M., Pantano, E., Abbiento, V., Benincasa, L., Giglioli, G., De Santi, C., Fabbiani, M., Rancan, I., Tumbarello, M., Montagnani, F., Sala, C., Montomoli, E., & Rappuoli, R. (2021). Hybrid immunity improves B cells and antibodies against SARS-CoV-2 variants. Nature, 1–7. https://doi.org/10.1038/s41586-021-04117-7

  5. Sep 2021
    1. Lee, J. W., Su, Y., Baloni, P., Chen, D., Pavlovitch-Bedzyk, A. J., Yuan, D., Duvvuri, V. R., Ng, R. H., Choi, J., Xie, J., Zhang, R., Murray, K., Kornilov, S., Smith, B., Magis, A. T., Hoon, D. S. B., Hadlock, J. J., Goldman, J. D., Price, N. D., … Heath, J. R. (2021). Integrated analysis of plasma and single immune cells uncovers metabolic changes in individuals with COVID-19. Nature Biotechnology, 1–11. https://doi.org/10.1038/s41587-021-01020-4

    1. Each cubic cell has 8 atoms in each corner of the cube, and that atom is shared with 8 neighboring cells. In the Body Centered Cubic Cell (BCC) there is an additional atom in the center of the cube, and in the face centered cubic cell, an atom is shared between two unit cells along the face.
    1. John Burn-Murdoch. (2021, August 23). NEW: in the last couple of weeks there have a lot of new studies out assessing vaccine efficacy, many of which have touched on the question of waning immunity. Unsurprisingly, these have prompted a lot of questions. Time for a thread to summarise what we do and don’t know: [Tweet]. @jburnmurdoch. https://twitter.com/jburnmurdoch/status/1429878189011111936

  6. Aug 2021
  7. Jul 2021
    1. Keerthivasan, S., Şenbabaoğlu, Y., Martinez-Martin, N., Husain, B., Verschueren, E., Wong, A., Yang, Y. A., Sun, Y., Pham, V., Hinkle, T., Oei, Y., Madireddi, S., Corpuz, R., Tam, L., Carlisle, S., Roose-Girma, M., Modrusan, Z., Ye, Z., Koerber, J. T., & Turley, S. J. (2021). Homeostatic functions of monocytes and interstitial lung macrophages are regulated via collagen domain-binding receptor LAIR1. Immunity, 54(7), 1511-1526.e8. https://doi.org/10.1016/j.immuni.2021.06.012

  8. Jun 2021
    1. Parry, H. M., Tut, G., Faustini, S., Stephens, C., Saunders, P., Bentley, C., Hilyard, K., Brown, K., Amirthalingam, G., Charlton, S., Leung, S., Chiplin, E., Coombes, N. S., Bewley, K. R., Penn, E. J., Rowe, C., Otter, A., Watts, R., D’Arcangelo, S., … Moss, P. (2021). BNT162b2 Vaccination in People Over 80 Years of Age Induces Strong Humoral Immune Responses with Cross Neutralisation of P.1 Brazilian Variant. SSRN Electronic Journal. https://doi.org/10.2139/ssrn.3816840

  9. May 2021
  10. Apr 2021
  11. Feb 2021
  12. Nov 2020
  13. Oct 2020
    1. messenger RNA (mRNA)

      This is a single strand on an RNA molecule that leaves the the nucleus of a cell in order to relocate to the cytoplasm. This is where the mRNA can help create the protein for the cell in a process known as protein synthesis. The mRNA takes in information passed into it by DNA and decode it for the ribosomes to make more protein for the cell to live on.

  14. Sep 2020
    1. Le Bert, N., Tan, A. T., Kunasegaran, K., Tham, C. Y. L., Hafezi, M., Chia, A., Chng, M. H. Y., Lin, M., Tan, N., Linster, M., Chia, W. N., Chen, M. I.-C., Wang, L.-F., Ooi, E. E., Kalimuddin, S., Tambyah, P. A., Low, J. G.-H., Tan, Y.-J., & Bertoletti, A. (2020). SARS-CoV-2-specific T cell immunity in cases of COVID-19 and SARS, and uninfected controls. Nature, 584(7821), 457–462. https://doi.org/10.1038/s41586-020-2550-z

  15. Aug 2020
    1. Mateus, J., Grifoni, A., Tarke, A., Sidney, J., Ramirez, S. I., Dan, J. M., Burger, Z. C., Rawlings, S. A., Smith, D. M., Phillips, E., Mallal, S., Lammers, M., Rubiro, P., Quiambao, L., Sutherland, A., Yu, E. D., Antunes, R. da S., Greenbaum, J., Frazier, A., … Weiskopf, D. (2020). Selective and cross-reactive SARS-CoV-2 T cell epitopes in unexposed humans. Science. https://doi.org/10.1126/science.abd3871

    1. Ferretti, A. P., Kula, T., Wang, Y., Nguyen, D. M., Weinheimer, A., Dunlap, G. S., Xu, Q., Nabilsi, N., Perullo, C. R., Cristofaro, A. W., Whitton, H. J., Virbasius, A., Olivier, K. J., Baiamonte, L. B., Alistar, A. T., Whitman, E. D., Bertino, S. A., Chattopadhyay, S., & MacBeath, G. (2020). COVID-19 Patients Form Memory CD8+ T Cells that Recognize a Small Set of Shared Immunodominant Epitopes in SARS-CoV-2. MedRxiv, 2020.07.24.20161653. https://doi.org/10.1101/2020.07.24.20161653

    1. Unterman, A., Sumida, T. S., Nouri, N., Yan, X., Zhao, A. Y., Gasque, V., Schupp, J. C., Asashima, H., Liu, Y., Cosme, C., Deng, W., Chen, M., Raredon, M. S. B., Hoehn, K., Wang, G., Wang, Z., Deiuliis, G., Ravindra, N. G., Li, N., … Cruz, C. S. D. (2020). Single-Cell Omics Reveals Dyssynchrony of the Innate and Adaptive Immune System in Progressive COVID-19. MedRxiv, 2020.07.16.20153437. https://doi.org/10.1101/2020.07.16.20153437

  16. Jul 2020
  17. Jun 2020
    1. Governments’ use of purchased location data has exploded in recent months, as officials around the world have sought insights on how people are moving around during the Covid-19 pandemic. In general, governments have assured their citizens that any location data collected by the marketing industry and used by public health entities is anonymous. But the movements of a phone give strong clues to its ownership—for example, where the phone is located during the evenings and overnight is likely where the phone owner lives. The identity of the phone’s owner can further be corroborated if their workplace, place of worship, therapist’s office or other information about their real-world activities are known to investigators.

      private data is not anonymous as is purported

  18. May 2020
    1. Grifoni, A., Weiskopf, D., Ramirez, S. I., Mateus, J., Dan, J. M., Moderbacher, C. R., Rawlings, S. A., Sutherland, A., Premkumar, L., Jadi, R. S., Marrama, D., de Silva, A. M., Frazier, A., Carlin, A., Greenbaum, J. A., Peters, B., Krammer, F., Smith, D. M., Crotty, S., & Sette, A. (2020). Targets of T cell responses to SARS-CoV-2 coronavirus in humans with COVID-19 disease and unexposed individuals. Cell, S0092867420306103. https://doi.org/10.1016/j.cell.2020.05.015

  19. Dec 2019
  20. Nov 2019
    1. in Figure 1A,B: (I) The NP reaches the membrane surface via diffusion. (II) The NP diffuses over the water–membrane interface

      In fact, in the simulation a potential is applied to drive the particles towards the membrane so neither (I) nor (II) can be described as free diffusion.

  21. Oct 2019
    1. Based on the values of the partition function as well as the difference in time scale between the leakage process and the entry process (seconds or minutes vs nanoseconds), we assume that a steady-state condition is rapidly reached. Therefore, by comparing eq 5 with eq 4, we find that

      These words are confusing. If they assume that I(t) is proportional to [GDQ]m then equations 4 and 5 are simply identical with two different notations. I can see no reasonable reason to assume that though.

  22. Sep 2019
    1. biolabeling

      Ref 6 (2013) does not demonstrate wide use in biolabelling. It is a synthesis and proof of principle paper. 6 years later, no biologist are using these materials for their imaging needs. However there are tons more of papers about the "emerging" carbon nanomaterials for imaging. The paper has a figure about uptake in cells. It says nothing about the mechanisms of uptake and it is not possible to conclude from the data provided.

    2. cancer therapy

      "widely used in cancer therapy" I know that this kind of poetic license is common in scientific writing but it is nevertheless wrong. Carbonaceous NPs have not been used in cancer therapy. Those two references are materials synthesis papers that claim that they could be used in the future for this purpose. Reference 5 is about pegylated graphene oxide which is fundamentally different from anything modelled here (and the PEG is to make it water soluble). Reference 5 also concludes the nanoparticles enter by endocytosis.

    3. like drug delivery

      Reference 2 is a paper about micron-size particles that can be opened by ultrasounds. It does not have any experiments with membranes nor living things. Reference 3 is mostly a materials synthesis and characterization paper. The little it has about interaction with cells, figure 8 and 9, concludes unambiguously that the particles enter by endocytosis, i.e. nothing to do with the kind of mechanisms modelled in this paper. Reference 4 is about particles which are ~75 nm diameter so very different from the materials modelled in this paper. Like for Ref 3, the paper concludes unambiguously that entry into the cells is by endocytosis (that's even visible from TOC visual abstract).

    4. Figure 9. Measured GQD leakage from different lipid vesicles. (A) Experimental images of photoluminescence change over a 1 h period. Images were taken every 15 min. White scale bar is 50 μm. (B) Photoluminescence intensity over a 1 h period for GQD-encapsulated vesicles with different lipid compositions is indicated. (C) Comparison of the model’s predictions to the permeability measured from experiment (error bars correspond to one standard deviation).

      The partition coefficient tell us that it should be 100% in the membrane (see table 1). Why don't we see any accumulation in the membranes at all?

    5. Specifically, a buckminsterfullerene, a curved OH-terminated graphene quantum dot (GQD), and GQD functionalized with two cysteine groups (cys-GQD) were used.(40) This selection covers NPs of similar size but different shape and hydrophilicity

      So all of the intro (and title) is a general blurb about nanoparticles going through membranes, but these three examples are tiny hydrophobic objects.

    6. ller nanoparticles can instead cross the membrane by passive transport, that is, by displacing, sometimes irreversibly, the lipids or by diffusing in the hydrophobic region of the membrane and then on the other side

      This is an extraordinary assertion that is not backed up by references.

    7. For particles with the smallest dimension larger than the membrane thickness, approximately above 10–15 nm, the permeation is generally controlled by membrane deformation(23) and endocytosis.(24)

      This gives the impression that particles generally permeate. This is contradiction with earlier statements that correctly indicate that they don't.

    8. an effective barrier. Nonetheless,

      That apparent contradiction is missing a crucial point. What is the proportion of material getting "cytoplasmic access"? The Cell Penetrating Peptides field is a right mess. One thing is sure: most (maybe all) CPPs enter via endocytotic pathways and for any CPP only a tiny proportion reaches the cytosol. My own experience with the TAT-HA2 peptide was not particularly encouraging. Importantly, when "access to the cytosol" is measured by a biological outcome (e.g. transfection or toxicity), this can be achieved by a rare event. In other words, depending on the conditions, efficient transfection (e.g. 75% of cells transfected) can be achieved with very low percentage of particles reaching the cytosol (e.g. 99.9% in endosomes; 0.1% escape).

    9. ensing of cellular behavior.(6−10)

      Again, all of these papers are chemistry papers describing the synthesis of new materials which, according to their authors, could be useful for deep tissue imaging etc. Some of these are 5+ years old. These are indeed examples of "engineering for applications" but not of applications. Essentially no biologists use these materials for their imaging or sensing needs.

    10. such as drug delivery,(2−4)

      It enables engineering for applications... But it does not enable applications. None of these examples of drug delivery are remotely realistic. These are examples of chemistry papers not of drug delivery applications. The first paper (ref 2) is so far from drug delivery application that it does not even have cell culture experiments (not to mention preclinical or clinical work). Ref 3-4 are also mostly materials synthesis/characterization papers ; they do have some cell uptake/toxicity experiments. Still million miles away from "applications in drug delivery".

    11. However, this is not the case for most macromolecules, such as proteins or nanoparticles (NPs), whose hydrophilicity and large size hamper direct diffusion through the membrane lipid bilayer.(1)

      Exactly. Nanoparticles large size and hydrophilicity hamper direct diffusion through the membrane bylayer. So far so good.