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Everything posted by CharonY

  1. The next step is usually generating a list based on the references in the initial screen and expand the search. But abstracts give me a good sense whether I got good coverage. Obviously one also need to apply ones own expertise. For students or laypersons a guided approach is usually better.
  2. Depends on what I am writing. For a technique paper I'd go for methods. Otherwise intro and discussion provide context and relevance.
  3. There is also several fundamental misunderstandings of the methods, it is a RT-PCR (which along with viral cultivation is considered a gold standard but has mostly replaced the latter),primers provide target specificity, detection of antibodies is useful for rapid testing (but suffers more false negatives than RT-PCR), current tests look at two targets and inconclusive tests are validated via Sanger sequencing.
  4. I found to rely on keywords more than, say two decades ago (where I would read whole journals more often). When writing reviews I often use pubmed to create a document with all the abstracts and tag those that warrant a closer read. Among those I check intro and maybe a bit of the discussion to see if it is relevant to my topic. In contrast to some of my colleagues I try to avoid relying on known authors too much to avoid biasing against newer or less well known authors (but they can be a positive control yo make sure my search strategy did not suck). But overall it is true that it is difficult to keep track of things.
  5. ! Moderator Note This is not a medical topic and inches towards rather unsavory subjects. I am going to shut it down pending review by other modes.
  6. The issue is that it seems rather sweeping with little details. It is, in theory fairly easy to be non-compliant and blame it on the outbreak. E.g. the folks responsible for sampling could not go out (or were let go) due to coronavirus related worker shortages. Therefore spills were not detected until it was too late (or perhaps will not be detected, if one cannot determine it retroactively). It is not clear whether that would be enough or not, per the directives. Specifically the EPA does say that it does not expect catch-up monitoring for certain cases, which could complicate matters. So there is a potential time frame where stuff (especially non acute) things could happening, but essentially stay invisible. There is no indication that it only applies to operations that are actually being suspended during the outbreak (because if they were, they probably would not need a waiver in the first place, depending on the type of operations). In other cases waivers could be provided based but what is currently implemented is (or looks) like a wide-ranging suspension. Previous EPA officials have been quite critical of that move though current spokespersons have defended it, of course (but then it should be noted that the EPA has been stripped of many scientists and experts so who knows on what they base their policies on nowadays).
  7. I think by now interactions will or should be severely limited. As others have said, it should be taken seriously, if not a a risk to yourself it poses to those you interact with. There are already a ton of good advise posted basically everywhere (keep distance, wash hands, do not touch your face etc.). Trying to remove infectious material should also help. One should try to avoid touching things with our hands (e.g. opening doors hands-free if possible, use elbows to operate switches or doors etc.). One of the habits I picked up during lab work is to use the non-dominant hand as designated "dirty" hand (assuming that you are less likely to touch yourself with that hand, which might not be true for everyone) and then make a fist with that hand whenever you are not using it (I often imagine holding something in the fist). I try to keep it up until I disinfect/glove/whatever needs to be done. What I also train students is to lock their hands when they are not supposed to touch anything (e.g. when they are gloved) to keep them from touching themselves, their clothes and so on.
  8. While alleviating certain rules may have been necessary in an emergency, this looks like a blanket waiver which can lead to rather unfortunate issues down the road. The EPA contests that it is a blanket waiver and reserves the right to interfere to save human lives. Though it says nothing about e.g. about ongoing issues that can cost human lives in the future (which, I think, is often the bigger issue than acute dangers). https://thehill.com/policy/energy-environment/489753-epa-suspends-enforcement-of-environmental-laws-amid-coronavirus
  9. So there is a preprint that predicts about 80k deaths in the USA over the next 4 months with large uncertainties, though (MEDRXIV/2020/043752). See also https://www.reuters.com/video/?videoId=OVC6U1U23&jwsource=cl Edit: If true, it be more deaths than the deaths attributed to influenza (at least since 2010).
  10. Yes it is a possible treatment. If the recovered patients produced enough antibodies against the pathogen, it can help in alleviating the disease. It has been attempted with SARS and Ebola, mostly with modest success. And there are ongoing trials (i.e. treatments of patients with this approach) in China and Italy. (side note- antibodies should be directed toward external targets, such as viruses and bacteria. Sometimes they react to host cell components, which can result in auto-immune diseases). I think that this is useful to limit. However, even conditions that we consider sanitary, we run risk of spreading zoonotic diseases. Animal farming is not a sterile process and pathogens are constantly evolving. In my mind, better processes can slow down the rate, but not stop the process.
  11. No, I am not sure whether the community actually proposed a name (I think the evidence is not strong enough to warrant it, but folks still may have done so). Radiata is a historic term deep in the animal group. The idea was to group all animals with radial symmetry. However, as it turned out, animals with such body plans are not monophyletic (i.e. share the same common recent ancestor). On the comment I made above, when we go away from viruses, I should also add that the various Cholera epidemics throughout history (including the one that is going since the 60s) have origins largely in India. Though due to the mode of transmission this is actually a sanitary issue (specifically lack of access to clean water).
  12. I think there may a couple of wrong assumptions but I am not read enough in those areas to provide an immediate in-depth response. Let's talk about zoonotic diseases first. One thing of note is that at high population densities and contacts with animals there is a higher likelihood of a pathogen crossing species barriers. But even then they may not cause large outbreaks, as they may have low transmission or low virulence and either exist invisibly in a given population or do otherwise do not garner a lot of traction. Many viruses re-assort in pigs transfer to humans and then change further (e.g. by grabbing genes from other viruses in their hosts) before they cause outbreaks. Take the H1N1pdm09 (swine-flu) pandemic, for example. That particular strain has a bit of a mosaic structure, probably originating from three parental pig viruses and emerged into humans somewhere in North America, some assume in Mexico. There is also the MERS epidemic, that came likely from camels but were sufficiently contained not to cause an epidemic. Hantavirus is a deadly virus that has a case fatality of ca. 40%. However, it is spread by mice and not human to human (luckily) and was found in the USA. There are also plenty of zoonotic diseases found in India, such NIpah virus and has been slowly spreading. However as there is no human-human transmission the spread is not as rapid. Likewise, we had a Zika pandemic not so long ago, a mosquito borne disease, originating from Africa. Japanese encephalitis likely originated in the Indonesia-Malaysia region and while it is also transmitted by mosquitos, it causes outbreaks every couple of years with about 13-20 thousand deaths each year. Again, lucky break that they need mosquitos as vectors. So in a way to me the question is whether it is by chance that those originating from China have larger impact on global health and economy or whether there are factors contributing to it. I think one needs to think beyond sanitary issues, as you mentioned. One question could be for example how connected China is compared to India. But also for example how the meat industry looks like. Another perhaps simple question is also what types of potential zoonotic diseases are there that could for example mix with animals that come into close contact with humans. In India many are mosquito borne, but perhaps they are less relevant in China. In Europe and US industrial pig farming has a huge potential to recombine and spread viruses in pigs, but there are perhaps fewer animals around that can spread novel viruses into pigs. Regulating or closing those market can likely close some of the risk factors. However, ultimately my thinking is that the world is shrinking, for better or for worse. There will be more contact between each of us and there are diseases that not zoonotic. What it means is that otherwise local disease have a much easier to become epidemic and even pandemic. Without the willingness for rapid responses to detect human-human spread, I think that most of the measures will be insufficient. And I think it is somewhat wrong to think that in the Western world our measures will keep us safe indefinitely. We had prion disease entering the food chain (sure it is not an infectious disease per se, but still). Farm animals often have to be culled due to various disease outbreaks. So far those have not managed to jump the species barrier, but it is not something that may so forever. On the other hand of course there is the tendency of diseases to become less virulent over time (as killing the host is generally not a good long-term strategy) but in the meantime a lot of harm can be done. Other man-made reasons for outbreak are for example anti-vaccination campaigns. HIV/AIDS now is well controlled, and we get complacent again (in the 90s it was for a time the leading cause of death in young adults). We have tons of pathogens that can mix, mutate and while there may be area with larger reservoirs than others, I do think it is dangerous to think it as an "elsewhere" problem. I think this is what lead to complacency when China was facing COVID-19 and that is why despite ample warnings the Western world only reacted when they had deaths in their midst. It may not be quite what you are thinking of, but I do think that this change in mentality is necessary to combat the inevitable occurrence and re-occurrence of diseases (and I apologize for all the typo and rantiness, it is more flow of thoughts without proper editing, may try to express it clearer when I got time again). Edit: had so many unfinished thoughts but wanted to include that global warming is going to increase the likelihood of many, especially mosquito borne diseases, so that has to go in there also somewhere.
  13. I think a good start would be to discuss how ventilators work and why they are needed, to get a better idea what functions a different system would need to have. In addition a better idea of the pathological profile of patients requiring ventilators would be needed. I am sure there is a range from folks having trouble breathing to those that are entirely dependent on mechanical ventilators as the lung does not compress properly anymore.
  14. Yes, cardiovascular issues are associated with worse outcomes, for example (based on Wuhan data). But also note that all age groups can have more severe outcomes requiring hospitalization. The US is still undersampled but initial info shows almost all brackets affected except 19 and younger based on CDC data a couple of days ago:
  15. Well, there are recommendations for decontamination of hospital bedding and clothing. Heat alone is seemingly insufficient for full decontamination based on above data, but a combination of heat/detergent/bleach might be. For sun light one might calculate the output for UVC and see whether that may be high enough, I suppose.
  16. I am not sure, ozonation, UV treatment and disinfectant fogging are being used in certain biocontainment facilities, but I don't know whether they would work and/or may be harmful in patient care facilities. The latter are often more crowded than biological workspaces and patients are more vulnerable to ozone, for example. I know that fogging is not allowed but I don't think that there are recommendations regarding UV and ozone in patient care (to my knowledge). Theoretically one could establish a protocol with thorough ozonation followed by quantitative ventilation or quenching to ensure safe levels. But again, I do not know if folks have tried or studied that.
  17. I vaguely remember such data but am not sure whether it was about viruses. I am going to have a look. Edit, took a quick look and while it is not the paper I had in mind, but there is one on SARS-CoV-1. UV radiation source was placed 3 cm above the sample. UVA (365nm) emitted 2133 µW/cm2, UVC(254nm) 4016 µW/cm2. Note TCID50 is a measure of viral titer (by assessing the titer at which 50% of the host cells show cytopathic effects). So it looks that in most cases a short exposure will result in incomplete inactivation, especially under less ideal conditions. Edit forgot to add: Darnell et al. 2004 J Vir Met 121:1 85-91. They also looked at temperature: at 56 C much was inactivated after 20 min, but active viral particles could still be found for at least 60 min. 60C most inactivated after 4 min, but still incomplete after 60 min. 75C authors claim full inactivation after 40 min.
  18. I think it is because it is roughly the recommended time to run the UV light on bio benches. Kind of a default setting.
  19. Surgical masks are basically used for that, i.e. as a temporary barrier. The important bit is safe handling of such masks. I have seen a couple of folks wearing masks around their chin while chatting and then putting them on and then adjusting them after walking through a door outside. That, of course is not helpful at all, as folks are touching their faces after touching potentially contaminated surfaces. Adjusting them or taken them on and off increases contamination risk. In biological safety situation masks usually go on only once and then off once. This is probably why there is little data showing usefulness of masks wearing for infection protection. However the reverse seems to be true. When specifically sick folks wear masks it seems to reduce transmission a bit, I guess because folks keep their distance and it gets harder to sneeze at somebody with mask on.
  20. You mean the origins? That is part of a large discussion with quite a bit of unknowns. I think most think that they are a version of mobile genetic elements, like transposons or plasmid, but more autonomous. However another line of thinking, especially among folks working on giant viruses think that they might be stripped-down cells from an unrecognized domain of life. I think the latter has some traction in certain areas but is still considered the less likely narrative by most folks, I would say. Or do you mean how viruses are formed by their host cells? There are different pathways, but in all cases essentially the viral genetic load is transferred into the host cell which is then used to produce viral proteins as well as propagate its genetic material. There can be steps in between (such as reverse transcribing the RNA in case of retroviruses, for example). At some point the virus particles are packaged with the genetic material and they then escape the cells. This can e.g. happen by lysing the host cells, budding or exocytosis. The two latter processes result in enveloped viral particles.
  21. The graph shows trajectories in the number of cases and it does show that in most cases they will rise further.
  22. Yes, that is what you normally do as an impact statement. However, such studies have been conducted since at least the 2000s. While it does not mean that it is not worthwhile pursuing, it probably does mean that it is difficult to translate it into an effective treatment. I have not checked whether any trials have been conducted but it is not uncommon (actually far more common) that promising preliminary studies do not translate well into clinical utility.
  23. Sorry genetics and evolution does not work like that and I suggest opening up a new thread if you want to discuss that further (we have hijacked quite a bit already).
  24. That is not the how the terminology is usually used. The gene pool for humans has precisely the same age. There is difference in diversity or gene flow (e.g. due to isolation) but there is nothing that is older or newer per se. Increase in genetic determinants of resistance to certain disease stems from selection for that (e.g. by pathogens but also co-selection) within a given population but you can have higher susceptibility e.g. in Africans and lower elsewhere. The higher genetic variance is a different factor and only means if a selective sweep happens, there is a higher chance of finding individuals with higher fitness (but does not mean that a given individual in a given population is actually a carrier).
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