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OT: Tracking Current Developments in Coronavirus Science and Public Health

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Comments

  • Important article discussing what is known and not so far about immunity gained from COVID-19 infection:

    https://www.nytimes.com/2020/04/13/opinion/coronavirus-immunity.html

  • @espiegel123 said:

    @richardyot said:
    Interesting read about infection rates in the US:

    http://systrom.com/blog/the-metric-we-need-to-manage-covid-19/

    Thanks for posting, but something that I didn't see mentioned (but perhaps I overlooked it) is that there is not enough testing nor consistent levels of testing in various regions to know how many cases there are or how rapidly case loads are changing. In California, for instance, there is still a test shortage and not all people suspected of being infected are being tested.

    Epidemiologists here chatter about which metrics they can use to gauge the changes in case rate in a useful way. Some extrapolate from some combimation of hospital admission data and deaths and test results.

    It is one of the biggest frustrations of the public health folks that there hasn't been a effect centralized effort to get the testing in place to accurately assess the viral spread. It is essential for knowing when it is safe to loosen restrictions and when to lock down hot spots.

    In Northern California, they ratcheted up restrictions about 20 days ago because while curve has flattened , the transmission rate was still too high.

    Agree, but the combination of the two things (adequate testing informing Rt) would be a decent way forward in terms of policy.

  • @lukesleepwalker said:

    @espiegel123 said:

    @richardyot said:
    Interesting read about infection rates in the US:

    http://systrom.com/blog/the-metric-we-need-to-manage-covid-19/

    Thanks for posting, but something that I didn't see mentioned (but perhaps I overlooked it) is that there is not enough testing nor consistent levels of testing in various regions to know how many cases there are or how rapidly case loads are changing. In California, for instance, there is still a test shortage and not all people suspected of being infected are being tested.

    Epidemiologists here chatter about which metrics they can use to gauge the changes in case rate in a useful way. Some extrapolate from some combimation of hospital admission data and deaths and test results.

    It is one of the biggest frustrations of the public health folks that there hasn't been a effect centralized effort to get the testing in place to accurately assess the viral spread. It is essential for knowing when it is safe to loosen restrictions and when to lock down hot spots.

    In Northern California, they ratcheted up restrictions about 20 days ago because while curve has flattened , the transmission rate was still too high.

    Agree, but the combination of the two things (adequate testing informing Rt) would be a decent way forward in terms of policy.

    And that’s what epidemiologists have been doing but, as they keep saying, you can’t get a decent Rt estimate without adequate testing. You need to be able to test everyone who either has any sort of possibly related symptoms AND every person that person has had contact with. Until then Rt is just a guess of unknown accuracy.

  • People who are having difficulties breathing should be put in a prone position (lying flat on their stomach):

  • @richardyot said:
    People who are having difficulties breathing should be put in a prone position (lying flat on their stomach):

    Good advice, I'm off for a nap....

  • @richardyot said:
    From an ICU doctor:

    Also, many patients suffering severe kidney failure:

    Even though I can’t be sure I have had the virus for the two days I was bedridden, I was laying on my front because it was the most comfortable position and I also felt pain in both sides of my lower back.

  • An interesting article about vaccine development. A bit of a slog to read but very worthwhile

    https://www.pnas.org/content/early/2020/03/27/2005456117

    @LinearLineman : this may give some insight as to why you don’t just start using the first vaccine candidate en masse ... it isn’t just bureaucratic obstacles.

  • edited April 2020

    I came across these articles today which explains an immune reaction called a "cytokine storm".

    https://www.knowablemagazine.org/article/health-disease/2020/what-cytokine-storm

    https://www.latimes.com/world-nation/story/2020-04-13/coworkers-save-coronavirus-doctor

    As I understand the theory.... Certain covid-19 patients develop this "cytokine storm" type immune reaction when their body's attempt to fight off the virus. Instead of the immune system reacting in a measured way that targets only the virus. The immune system instead floods the body with proteins called cytokines.

    This "cytokine Flood" causes the immune system to loose the ability to target just the virus, and the result is essentially a virus induced autoimmune disease type reaction where the immune system targets healthy cells.

    The immune system targeting healthy cells results in a systemic inflammatory response, and the resulting cellular damage causes blood vessel to leak fluid which fills the lungs. There is also mention of this "runaway immune response" causing scaring of the lung tissue which further impairs the lungs ability to uptake oxygen.

    Fortunately there is an existing Immunosuppressive drug called Tocilizumab (Actemra), which was designed to treat rheumatoid arthritis (an autoimmune disease).

    There have been successful recoveries believed to have been made posable by the drug Tocilizumab's ability to suppress this "cytokine storm" reaction, thus allowing the body to fight off the virus using a measured level of immune response.

    I think this theory might help provide one explanation for why certain covid-19 patients may have such life threatening reactions to infection, while others suffer only a lessor degree of symptoms.

  • McDMcD
    edited April 2020

    For anyone with the background in the "maths" to follow one of the current
    models being discussed:

    https://www.sas.upenn.edu/~jesusfv/slides-covid.pdf

    It is created by Jesus (and Chad). So, probably contains the word of God too.
    I like the little Greek lower case Delta that looks like a Quail to me.
    I keep seeing Jesus and the death quail negotiating in God's Mysterious Ways.

  • edited April 2020

    This is a really great explanation of the shortcomings of modelling by FiveThirtyEight, in comic book form, I've embedded the first page but it's well worth reading the whole thing:

    https://fivethirtyeight.com/features/a-comic-strip-tour-of-the-wild-world-of-pandemic-modeling/

  • Pre-symptomatic transmission may account for a large percentage of COVID-19 infections:

    https://www.nature.com/articles/s41591-020-0869-5

  • @richardyot said:
    This is a really great explanation of the shortcomings of modelling by FiveThirtyEight, in comic book form, I've embedded the first page but it's well worth reading the whole thing:

    Thanks for this Mister Yot. I'd missed it....

  • Possibly of interest as people think about how the mortality data we are seeing compares to flu epidemics. The death tolls for COVID-19 that we are seeing are merely deaths were COVID causality was ascertained. When we see flu death statistics for prior years, we are seeing "excess mortality" statistics NOT just the deaths of people that tested positive for the flu.

    As has been documented, the excess mortality statistics can only be done in retrospect as they require comparisons of a current period to past periods. That data is only starting to emerge. And in places where they are examining it, it is looking like depending on the location the excess mortality figures are ranging from 1.25 to 4 or more times the number of identified COVID-19 deaths. The multipliers seem to be particularly higher in places (like New York City and Bergamo, Italy) where the surge is large enough to impact health care services generally and where many have died at home without having been tested. It also can be high in rural areas where the epidemic has spread because people may not have easy access to health care.

    In the current situation, there are also concerns that some places are intentionally undercounting deaths (Florida has been up to some shenanigans by not reporting deaths for people dying in Florida who are not official state residents).

  • edited April 2020

    @horsetrainer said:
    I came across these articles today which explains an immune reaction called a "cytokine storm".

    https://www.knowablemagazine.org/article/health-disease/2020/what-cytokine-storm

    https://www.latimes.com/world-nation/story/2020-04-13/coworkers-save-coronavirus-doctor

    As I understand the theory.... Certain covid-19 patients develop this "cytokine storm" type immune reaction when their body's attempt to fight off the virus. Instead of the immune system reacting in a measured way that targets only the virus. The immune system instead floods the body with proteins called cytokines.

    This "cytokine Flood" causes the immune system to loose the ability to target just the virus, and the result is essentially a virus induced autoimmune disease type reaction where the immune system targets healthy cells.

    The immune system targeting healthy cells results in a systemic inflammatory response, and the resulting cellular damage causes blood vessel to leak fluid which fills the lungs. There is also mention of this "runaway immune response" causing scaring of the lung tissue which further impairs the lungs ability to uptake oxygen.

    Fortunately there is an existing Immunosuppressive drug called Tocilizumab (Actemra), which was designed to treat rheumatoid arthritis (an autoimmune disease).

    There have been successful recoveries believed to have been made posable by the drug Tocilizumab's ability to suppress this "cytokine storm" reaction, thus allowing the body to fight off the virus using a measured level of immune response.

    I think this theory might help provide one explanation for why certain covid-19 patients may have such life threatening reactions to infection, while others suffer only a lessor degree of symptoms.

    This article details the cytokine storm phenomenon, as it relates to covid 9 and the medicine available to treat it

    https://medium.com/@noorchashm/a-covid-19-vaccine-is-not-coming-anytime-soon-herd-immunity-will-have-to-do-after-we-turn-off-47117cdaeafd

  • @espiegel123 said:
    Possibly of interest as people think about how the mortality data we are seeing compares to flu epidemics. The death tolls for COVID-19 that we are seeing are merely deaths were COVID causality was ascertained. When we see flu death statistics for prior years, we are seeing "excess mortality" statistics NOT just the deaths of people that tested positive for the flu.

    As has been documented, the excess mortality statistics can only be done in retrospect as they require comparisons of a current period to past periods. That data is only starting to emerge. And in places where they are examining it, it is looking like depending on the location the excess mortality figures are ranging from 1.25 to 4 or more times the number of identified COVID-19 deaths. The multipliers seem to be particularly higher in places (like New York City and Bergamo, Italy) where the surge is large enough to impact health care services generally and where many have died at home without having been tested. It also can be high in rural areas where the epidemic has spread because people may not have easy access to health care.

    In the current situation, there are also concerns that some places are intentionally undercounting deaths (Florida has been up to some shenanigans by not reporting deaths for people dying in Florida who are not official state residents).

    Yes and in the meantime the denialists are going to be doing everything they can to underplay the death counts.

  • Paper out today that estimates that in the neighboring county in Northern California that there may have been 90 times as many infected people in early April as were indicated by blood tests. The paper has not yet completed the peer-review process. If it is accurate, it indicates that mortality rate is a lot lower than we've thought and that a much higher percentage of cases are asymptomatic than have been realized. I haven't seen any analyses of the paper yet by the epidemiologists that I follow.

    https://www.medrxiv.org/content/10.1101/2020.04.14.20062463v1?cf_chl_jschl_tk=3994fd33b88b7643bc24978c5bda66db9c792784-1587140719-0-ATt5KciAQ4OMW-W73PMdxvUda7AhOB6U9r52Xa9PPyrooMejvf8lJlBEXjazLk9hTsKf3E_s9WGra0wsLh6YUVE4P1WSk0dseqg6c24Wj-A_MpDLOi7IqEaalWWRxiXErcqUF7uS_0vk6DyUJb7Ii_8oWEpqw0ssv8TD39t30u3IFcOIhKCj3MHKxyxOl5vbjF30ANDz3pS4iQ4OMv0QrtPFgPcYMqqMnXB4Z3cP_CLF80cxmD8fOHLN7NxVFmU33YDxFERBZ_9kezS0VivNznMXUmYJddI_VBtjTkAeJFTeReVVFyDiKAiCV9aHlGbRtey3Ky2YH8GiP9ed5hlOm3I

  • @espiegel123 said:
    Paper out today that estimates that in the neighboring county in Northern California that there may have been 90 times as many infected people in early April as were indicated by blood tests. The paper has not yet completed the peer-review process. If it is accurate, it indicates that mortality rate is a lot lower than we've thought and that a much higher percentage of cases are

    I've seen a lot of people saying something similar: up to 50% of cases are completely asymptomatic, and suffer no ill effects at all. Once those cases are counted the death rate falls to around 1.5%, similar to what was found on the Diamond Princess and the Italian town of Vo where almost everyone was tested.

    So while the mortality rate is similar to a very bad flu, the infection rate is much higher which means that more people end up dying. This is what was witnessed in Lombardy and New York (and Wuhan obviously).

  • edited April 2020

    @richardyot said:

    @espiegel123 said:
    Paper out today that estimates that in the neighboring county in Northern California that there may have been 90 times as many infected people in early April as were indicated by blood tests. The paper has not yet completed the peer-review process. If it is accurate, it indicates that mortality rate is a lot lower than we've thought and that a much higher percentage of cases are

    I've seen a lot of people saying something similar: up to 50% of cases are completely asymptomatic, and suffer no ill effects at all. Once those cases are counted the death rate falls to around 1.5%, similar to what was found on the Diamond Princess and the Italian town of Vo where almost everyone was tested.

    So while the mortality rate is similar to a very bad flu, the infection rate is much higher which means that more people end up dying. This is what was witnessed in Lombardy and New York (and Wuhan obviously).

    I think it’s nigh on impossible to get any kind of accurate figures for this thing. For example the mortality rate in the UK has risen to 5% for those with ‘no underlying health conditions’. But that only includes previously diagnosed issues - there’s no knowing if the patient had an undiagnosed problem, so that figure could be totally misleading.

    Without testing everyone, and even then the reliability of the tests is in question, we’ve no idea how many have had it, and so can’t work out a reliable mortality rate.

    It’s obviously a lot more contagious than flu, but whether it’s more of a risk than flu or pneumonia is another matter. My cousin died of pneumonia a few months back - reasonably healthy (though a smoker) and only in his 60’s, suddenly within a couple of days he was gone. Ditto his brother, younger, non-smoker a year before.

    The scale of the new virus is the thing, but pneumonia and flu can be just as deadly.

  • @richardyot said:

    @espiegel123 said:
    Paper out today that estimates that in the neighboring county in Northern California that there may have been 90 times as many infected people in early April as were indicated by blood tests. The paper has not yet completed the peer-review process. If it is accurate, it indicates that mortality rate is a lot lower than we've thought and that a much higher percentage of cases are

    I've seen a lot of people saying something similar: up to 50% of cases are completely asymptomatic, and suffer no ill effects at all. Once those cases are counted the death rate falls to around 1.5%, similar to what was found on the Diamond Princess and the Italian town of Vo where almost everyone was tested.

    So while the mortality rate is similar to a very bad flu, the infection rate is much higher which means that more people end up dying. This is what was witnessed in Lombardy and New York (and Wuhan obviously).

    I said quite some time ago, that in Italy the underlying amount of infections were asymptomatic due to the ‘early’ explosion, exponential growth rate in cases, also due to the mass seeding of other countries mainly in Europe at this time

  • For sure there's a lot of unknowns, and it might take years before any kind of reliable data is established. In the meantime it's impossible to establish any kind of consensus due to competing narratives driven by political agendas.

    The only sensible approach is to use the precautionary principle when faced with an asymmetric risk: try and avoid becoming Lombardy or New York by social distancing measures and encouraging the use of masks etc. alongside widespread testing and contact tracing, but the politics make this very difficult if you have a vocal minority noisily protesting that it's all a hoax. Any flaw in policy response, or modelling predictions, or testing, or attributing cause of death, will be used to drive the narrative that it's all been overblown.

  • edited April 2020

    @richardyot said:
    For sure there's a lot of unknowns, and it might take years before any kind of reliable data is established. In the meantime it's impossible to establish any kind of consensus due to competing narratives driven by political agendas.

    The only sensible approach is to use the precautionary principle when faced with an asymmetric risk: try and avoid becoming Lombardy or New York by social distancing measures and encouraging the use of masks etc. alongside widespread testing and contact tracing, but the politics make this very difficult if you have a vocal minority noisily protesting that it's all a hoax. Any flaw in policy response, or modelling predictions, or testing, or attributing cause of death, will be used to drive the narrative that it's all been overblown.

    I doubt many are taking the hoax theory seriously, but yeah, politics will make the difference in numbers of deaths. The slow response from some governments, lack of protective gear, lack of testing, ending lockdowns too early will all contribute to a higher death toll.

    I can't see anyone seriously defending a stance that it's overblown either, the infection rates speak for themselves. What we don't know for certain though, is whether it's more lethal than similar viruses, since we don't have an accurate death rate. More infectious, yes. More lethal - maybe, but we don't know. Viral 'load' seems to play a big role in the seriousness of a patients condition, and so lots of exposure may be playing a big factor in how lethal it can be.

    Since a large number of my relatives have been wiped out suddenly by pneumonia over the years, I'm aware this isn't the only scary dude stalking the old and vulnerable with no apparent cure at hand.

    What we all should be agreeing on is that healthcare has been woefully neglected in a lot of so-called 'rich' countries, and deaths from a whole host of conditions are unecessary, and could have been prevented.

    In the meantime one of my friends is going in to work today as a nurse, with no proper protective equipment, putting her and her family at risk while Johnson & Co. announce £35 billion for the HS2 project that will shave 15 minutes off a train journey.

    At the end of all this I'd like to see criminal charges against the government, and proper investment in the NHS and care sector.

  • edited April 2020

    Another puzzle is why some areas seem to be affected so much more drastically than others: why is the death rate (and also the all-cause mortality rate) in Lombardy, New York, and London so high whereas in other places such as Germany and Japan it's much lower.

    Is it because the health service was overrun? Is it because of some other factor such as genetic predisposition?

    We have to assume that any area has the potential to become another Lombardy or New York if mitigation measures are not enforced, but the truth is that's actually entirely unknown. Again the precautionary principle should take precedent until we know more.

  • @MonzoPro said:
    I doubt many are taking the hoax theory seriously, but yeah, politics will make the difference in numbers of deaths. The slow response from some governments, lack of protective gear, lack of testing, ending lockdowns too early will all contribute to a higher death toll.

    In Europe not many people are buying into the hoax narrative, but in the US a significant minority on the right and far-right definitely are. That's why there have been protests in Michigan, Ohio, Virginia etc...

  • edited April 2020

    @richardyot said:
    Another puzzle is why some areas seem to be affected so much more drastically than others: why is the death rate (and also the all-cause mortality rate) in Lombardy, New York, and London so high whereas in other places such as Germany and Japan it's much lower.

    Is it because the health service was overrun? Is it because of some other factor such as genetic predisposition?

    We have to assume that any area has the potential to become another Lombardy or New York if mitigation measures are not enforced, but the truth is that's actually entirely unknown. Again the precautionary principle should take precedent until we know more.

    That’s the problem though, without sound knowledge of how this thing works, we can’t be sure if precautionary measures aren’t actually making some things worse. For example the close proximity of neighbours, everyone home, normally quiet roads packed with cyclists and joggers due to travel restrictions means my chances of catching it here are much higher than before. Cancelled appointments of other conditions means my sisters cancer treatment has stopped, increasing her risk of dying from that. People with mental health issues freaking out. Treatable conditions not being assessed and caught early due to people scared to visit their GP. A nurse friend having to make a series of home visits as the normal health centre venue no longer available.

    If we knew the implications of viral load on the severity of symptoms, maybe restrictions could be managed more effectively to allow some form of normality to continue, and lower deaths and other problems that are side effects of a total shutdown.

    If a vaccine becomes available it’s not going to appear until late next year. The world can’t stay on lockdown for that long, so governments need to get their acts in gear and do proper testing and find out exactly what a viable exit strategy looks like.

    The problem is, most governments are run by idiots.

    @richardyot said:

    @MonzoPro said:
    I doubt many are taking the hoax theory seriously, but yeah, politics will make the difference in numbers of deaths. The slow response from some governments, lack of protective gear, lack of testing, ending lockdowns too early will all contribute to a higher death toll.

    In Europe not many people are buying into the hoax narrative, but in the US a significant minority on the right and far-right definitely are. That's why there have been protests in Michigan, Ohio, Virginia etc...

    Darwin’s waiting room. Natural selection etc.

  • @espiegel123 said:
    Paper out today that estimates that in the neighboring county in Northern California that there may have been 90 times as many infected people in early April as were indicated by blood tests. The paper has not yet completed the peer-review process. If it is accurate, it indicates that mortality rate is a lot lower than we've thought and that a much higher percentage of cases are asymptomatic than have been realized. I haven't seen any analyses of the paper yet by the epidemiologists that I follow.

    https://www.medrxiv.org/content/10.1101/2020.04.14.20062463v1?cf_chl_jschl_tk=3994fd33b88b7643bc24978c5bda66db9c792784-1587140719-0-ATt5KciAQ4OMW-W73PMdxvUda7AhOB6U9r52Xa9PPyrooMejvf8lJlBEXjazLk9hTsKf3E_s9WGra0wsLh6YUVE4P1WSk0dseqg6c24Wj-A_MpDLOi7IqEaalWWRxiXErcqUF7uS_0vk6DyUJb7Ii_8oWEpqw0ssv8TD39t30u3IFcOIhKCj3MHKxyxOl5vbjF30ANDz3pS4iQ4OMv0QrtPFgPcYMqqMnXB4Z3cP_CLF80cxmD8fOHLN7NxVFmU33YDxFERBZ_9kezS0VivNznMXUmYJddI_VBtjTkAeJFTeReVVFyDiKAiCV9aHlGbRtey3Ky2YH8GiP9ed5hlOm3I

    So, any easing of restrictions will put the asymptotic into circulation leading to a rise in infections. Until a vaccine then we will be living with outbreaks... unless testing is available like a pregnancy test. Results in minutes and, hopefully, self isolation.

  • @richardyot said:
    Another puzzle is why some areas seem to be affected so much more drastically than others: why is the death rate (and also the all-cause mortality rate) in Lombardy, New York, and London so high whereas in other places such as Germany and Japan it's much lower.

    Btw, Germany's success is not on the same scale as Japan's. It is doing well compared to Western Europe but the response was not nearly as effective as in Japan.

    In Japan, there have been 2 deaths per million people. Germany is at 55. California is at 27.

    japan is doing literally 20 times better than Germany.

    Germany has managed it with less extreme measures than California but we should be looking at Japan as an example of success more than anywhere in the west.

  • @espiegel123 said:

    @richardyot said:
    Another puzzle is why some areas seem to be affected so much more drastically than others: why is the death rate (and also the all-cause mortality rate) in Lombardy, New York, and London so high whereas in other places such as Germany and Japan it's much lower.

    Btw, Germany's success is not on the same scale as Japan's. It is doing well compared to Western Europe but the response was not nearly as effective as in Japan.

    In Japan, there have been 2 deaths per million people. Germany is at 55. California is at 27.

    japan is doing literally 20 times better than Germany.

    Germany has managed it with less extreme measures than California but we should be looking at Japan as an example of success more than anywhere in the west.

    Japan just starting to struggle:

    https://www.japantimes.co.jp/news/2020/04/07/national/science-health/hospital-beds-gear-coronavirus/#.Xpr98C94Xmo

    https://www.theguardian.com/world/live/2020/apr/18/coronavirus-live-news-global-deaths-pass-150000-trump-china-china-denies-any-concealment-pence-origins-europe-germany?page=with:block-5e9a72228f08bade1f29576d#block-5e9a72228f08bade1f29576d

  • Maybe the best examples to follow would be South Korea, which has done a great job of flattening the curve, or New Zealand which completely crushed its curve.

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