Tuesday, February 25, 2020
Yield Curve
If you think this virus fiasco is bad let's look at the yield curve:
First it inverts and second it is dropping like a brick. Now:
The ten year is less than the 90 day rate! This should be sending shivers through the market. Go to cash, gold, corona virus!
Are We Screaming Fire?
According to CNBC the CDC manager made statements as follows:
The Centers for Disease Control and Prevention stepped up its call Tuesday for the public to start preparing for a possible pandemic outbreak in the U.S. of the coronavirus that’s infected more than 80,000 people killed at least 2,700 overseas in less than two months. “We are asking the American public to work with us to prepare for the expectation that this could be bad,” a top CDC officials told reporters in a conference call outlining what schools and businesses will likely need to do if it will likely need to do if the COVID-19 virus starts to spread throughout the U.S. Schools should consider dividing students into smaller groups or close and use “internet-based teleschooling,” Dr. Nancy Messonnier, director of the CDC’s National Center for Immunization and Respiratory Diseases, told reporters on a conference call.“For adults, businesses can replace in-person meetings with video or telephone conferences and increase teleworking options,” Messonnier said. She said local communities and cities may need to “modify, postpone or cancel mass gatherings.” Hospitals may need to triage patients differently, add more telehealth services and delay elective surgery, she said. ..."I understand this whole situation may seem overwhelming and that disruption to everyday life may be severe. But these are things that people need to start thinking about now,” Messionnier said Tuesday. “You should think about what you would do for child care if schools or day cares closed.”
Then the Market collapsed. Is this yelling Fire in a crowded theater? Frankly you do not tell people this. You tell them what precautions they should take and what the Government is doing. The CDC has only processed some 446 tests to date per their web site. If this is so massive what in God's name are they doing?
"this could be bad" Now just what do we mean by that? Go to the CDC site and try to find her remarks.
In my opinion this discussion was reckless. You do not say things like this. You present facts, what you the CDC are doing, how to protect yourself. You do not just say, "this will be bad".
Or is this all politics?
One must be careful in today's environment on what you say to the masses. One must understand how it can be interpreted and misinterpreted. Is anyone in charge down there in Atlanta? Let's hope and pray there is. Oh by the way, remember Ebola.
The Centers for Disease Control and Prevention stepped up its call Tuesday for the public to start preparing for a possible pandemic outbreak in the U.S. of the coronavirus that’s infected more than 80,000 people killed at least 2,700 overseas in less than two months. “We are asking the American public to work with us to prepare for the expectation that this could be bad,” a top CDC officials told reporters in a conference call outlining what schools and businesses will likely need to do if it will likely need to do if the COVID-19 virus starts to spread throughout the U.S. Schools should consider dividing students into smaller groups or close and use “internet-based teleschooling,” Dr. Nancy Messonnier, director of the CDC’s National Center for Immunization and Respiratory Diseases, told reporters on a conference call.“For adults, businesses can replace in-person meetings with video or telephone conferences and increase teleworking options,” Messonnier said. She said local communities and cities may need to “modify, postpone or cancel mass gatherings.” Hospitals may need to triage patients differently, add more telehealth services and delay elective surgery, she said. ..."I understand this whole situation may seem overwhelming and that disruption to everyday life may be severe. But these are things that people need to start thinking about now,” Messionnier said Tuesday. “You should think about what you would do for child care if schools or day cares closed.”
Then the Market collapsed. Is this yelling Fire in a crowded theater? Frankly you do not tell people this. You tell them what precautions they should take and what the Government is doing. The CDC has only processed some 446 tests to date per their web site. If this is so massive what in God's name are they doing?
"this could be bad" Now just what do we mean by that? Go to the CDC site and try to find her remarks.
In my opinion this discussion was reckless. You do not say things like this. You present facts, what you the CDC are doing, how to protect yourself. You do not just say, "this will be bad".
Or is this all politics?
One must be careful in today's environment on what you say to the masses. One must understand how it can be interpreted and misinterpreted. Is anyone in charge down there in Atlanta? Let's hope and pray there is. Oh by the way, remember Ebola.
Diagnosis by Reporter?
Some ten years ago I wrote a piece critiquing the then recent American and European studies denigrating any use of PSA tests. In my opinion and in my experience they were fatally flawed. I wrote so in this Blog as well.
Simply stated, if one were to perform annual PSA tests which included PSA and %Free PSA and then calculated the Velocity of the PSA increase one can do pretty well in anticipating PCa. The following are two classifiers that we have developed.
The 4K test add a few other variables. Now %Free is a powerful marker because benign cells generate free PSA whereas malignant do not. Also the prostate continues to grwo as one ages and as it grows it generates more PSA. However is %Free remains high, 35% or so, it is a good chance that things are fine. Also velocity demonstrates rate of growth, benign is slow and steady and malignant takes off.
Now some NY Times writer, it seems they are the ones who hold the golden truth about everything, writes:
In the most definitive study done to date to assess the value of PSA screening, the European Randomized Study of Screening for Prostate Cancer concluded that 781 men aged 55 to 69 when they enrolled would have to be screened to prevent one man from dying of prostate cancer after 13 years. In this study, approximately one man in six who were screened was falsely identified as possibly having prostate cancer, and two-thirds of positive PSA results in the first round of screening were false-positives.
However these studies did not reflect actual accepted procedures. The European study was so flawed since it tested men only infrequently, years apart. PSA testing demands annual tests with detailed data analysis. The author continues:
Among older men, screening can be
beneficial to those 70 or over who are very healthy and expected to live
another 10 years or longer. ... urologist at
Johns Hopkins Hospital, noted in an editorial in JAMA
that “older age is associated with more aggressive prostate cancer;
thus, a very healthy older man with the prospects of extended life might
benefit from PSA testing. “Nevertheless,”
he added, “routine screening of average risk men 70 years and older
should be rare, because they are more likely than younger men to
experience the harms of screening, diagnosis and treatment.”
Finally the author notes:
One is the 4Kscore test that combines the
levels of four prostate-specific antigens with clinical information to
estimate a man’s risk of having an aggressive cancer. The other, called
the PHI, for Prostate Health Index, combines three different PSA
measurements to better predict the presence of cancer. Also
under study is the use of an advanced form of M.R.I. that can detect
the presence of cancer with a higher risk of becoming lethal while
overlooking low-risk disease.
1348 Redux
The CDC is allegedly tracking and mitigating the Corona virus. One need look no further than their web page to note:
CDC is closely monitoring an outbreak of respiratory illness caused by a novel (new) coronavirus. The outbreak first started in Wuhan, China, but cases have been identified in a growing number of other international locations, including the United States. This page will be updated regularly on Mondays, Wednesdays, and Fridays.
Yes, they have tested only 426 as of today. One would think that testing would be in the tens of thousands just to get baseline samples epidemiologically. But after all it is our Government. I guess we have to wait for the television documentary on another Government failure. And you want these folks to manage all your health care!
CDC is closely monitoring an outbreak of respiratory illness caused by a novel (new) coronavirus. The outbreak first started in Wuhan, China, but cases have been identified in a growing number of other international locations, including the United States. This page will be updated regularly on Mondays, Wednesdays, and Fridays.
COVID-19: Confirmed Cases in the United States
| Travel-related | 12 |
| Person-to-person spread | 2 |
| Total confirmed cases | 14 |
|---|---|
| Total tested | 426 |
Yes, they have tested only 426 as of today. One would think that testing would be in the tens of thousands just to get baseline samples epidemiologically. But after all it is our Government. I guess we have to wait for the television documentary on another Government failure. And you want these folks to manage all your health care!
| As StatNews relates: The CDC urged American businesses and families to start preparing for the possibility of a bigger outbreak. Messonier said that parents should ask their children’s schools about plans for closures. Businesses should consider whether they can offer tele-commuting options to their employees, while hospitals might need to look into expanding telehealth services, she said. “Disruption to everyday life might be severe,” Messonier said, adding that she talked to her children about the issue Tuesday morning. “While I didn’t think they were at risk right now, we as a family ought to be preparing for significant disruption to our lives.” Messonier said the CDC is in conversation about whether to change the case definition that triggers a sick patient to be tested for the virus. Currently, health officials recommend testing only for people who have respiratory symptoms and have recently traveled to China, or those who have been in close contact with someone who was infected. But as community spread picks up in other countries, the case definition could change. A warning is nice but how about massive distribution of testing kits. Perhaps education, warnings, but then again the trust in the Government has deteriorated so badly that it is not clear that anyone would believe them. One wonders how long before this becomes a massive political football. | |||||||||||||
What Really Counts
Is it the gene or the expression of the gene? Is it the DNA or the RNA? As we progress in understanding cancers we often look for the putative gene. DNA can be read and the presence of absence of the gene is considered dispositive. However, it often is not.
The real is is; does the gene do anything? Namely does it produce an RNA and in turn a protein? In a recent paper Biorxiv, CSHL, we have an interesting result. The authors note:
Disappointing results with genome-based biomarkers have driven calls to look beyond the cancer genome to other possible indicators of cancer-specific vulnerabilities5. A major alternative for tumor characterization is the transcriptome. Although RNA is more difficult to maintain in the clinic than DNA, studies have found that gene expression supplies the most significant predictive features for patient prognosis6. Previous work on predicting cell viability after compound treatment suggests that expression may be more powerful than DNA features for predicting drug response7, but expression-based models are widely treated as undesirable either because they are considered trivial proxies for tissue-type8 or because they are seen as uninterpretable9. These suggestive studies point to the need for a comprehensive comparison of expression and genomic molecular features as predictors of cancer vulnerability and a deeper interrogation of the interpretability of expression models. Here we present the first such study across five large datasets of cancer cell viability including both genetic and chemical perturbations. We find that RNA-Seq expression outperforms DNA-derived features in predicting cell viability response in nearly all cases, including many perturbations with known genomic biomarkers. The best results are typically driven by a small number of interpretable expression features. Our findings suggest that both existing and new cancer targets are frequently better identified using RNA-seq gene expression than any combination of other cancer cell properties.
RNA can be fragile and more difficult to assess. We have seen that RNA-seq does provide a means and have seen this in miRNA analyses. Perhaps this is an added methodology worthy of pursuit.
The real is is; does the gene do anything? Namely does it produce an RNA and in turn a protein? In a recent paper Biorxiv, CSHL, we have an interesting result. The authors note:
Disappointing results with genome-based biomarkers have driven calls to look beyond the cancer genome to other possible indicators of cancer-specific vulnerabilities5. A major alternative for tumor characterization is the transcriptome. Although RNA is more difficult to maintain in the clinic than DNA, studies have found that gene expression supplies the most significant predictive features for patient prognosis6. Previous work on predicting cell viability after compound treatment suggests that expression may be more powerful than DNA features for predicting drug response7, but expression-based models are widely treated as undesirable either because they are considered trivial proxies for tissue-type8 or because they are seen as uninterpretable9. These suggestive studies point to the need for a comprehensive comparison of expression and genomic molecular features as predictors of cancer vulnerability and a deeper interrogation of the interpretability of expression models. Here we present the first such study across five large datasets of cancer cell viability including both genetic and chemical perturbations. We find that RNA-Seq expression outperforms DNA-derived features in predicting cell viability response in nearly all cases, including many perturbations with known genomic biomarkers. The best results are typically driven by a small number of interpretable expression features. Our findings suggest that both existing and new cancer targets are frequently better identified using RNA-seq gene expression than any combination of other cancer cell properties.
RNA can be fragile and more difficult to assess. We have seen that RNA-seq does provide a means and have seen this in miRNA analyses. Perhaps this is an added methodology worthy of pursuit.
Monday, February 24, 2020
Holy Flying Cows, Batman!
In an article in The Atlantic the author notes:
The Harvard epidemiology professor Marc Lipsitch is exacting in his diction, even for an epidemiologist. Twice in our conversation he started to say something, then paused and said, “Actually, let me start again.” So it’s striking when one of the points he wanted to get exactly right was this: “I think the likely outcome is that it will ultimately not be containable.” Containment is the first step in responding to any outbreak. In the case of COVID-19, the possibility (however implausible) of preventing a pandemic seemed to play out in a matter of days. Starting in January, China began cordoning off progressively larger areas, radiating outward from Wuhan City and eventually encapsulating some 100 million people. People were barred from leaving home, and lectured by drones if they were caught outside. Nonetheless, the virus has now been found in 24 countries...
Lipsitch predicts that, within the coming year, some 40 to 70 percent of people around the world will be infected with the virus that causes COVID-19.
But, he clarifies emphatically, this does not mean that all will have severe illnesses. “It’s likely that many will have mild disease, or may be asymptomatic,” he said. As with influenza, which is often life-threatening to people with chronic health conditions and of older age, most cases pass without medical care. (Overall, around 14 percent of people with influenza have no symptoms.)
Yes, he said 70% of the world population will get infected! That is almost 5 billion people. Worse than the 1348 plague. It would concern me to say something like that. That would be 14 million or so in Greater New York.
What is the basis for such a statement. We really know so little at this stage that such a statement in my opinion is reckless at the very least if this is what was really said. We do not really know how it is spread, lots of conjecture, and we do not have adequate clinical experience, in my opinion.
There are time we should just keep our guesses to ourselves.
The Harvard epidemiology professor Marc Lipsitch is exacting in his diction, even for an epidemiologist. Twice in our conversation he started to say something, then paused and said, “Actually, let me start again.” So it’s striking when one of the points he wanted to get exactly right was this: “I think the likely outcome is that it will ultimately not be containable.” Containment is the first step in responding to any outbreak. In the case of COVID-19, the possibility (however implausible) of preventing a pandemic seemed to play out in a matter of days. Starting in January, China began cordoning off progressively larger areas, radiating outward from Wuhan City and eventually encapsulating some 100 million people. People were barred from leaving home, and lectured by drones if they were caught outside. Nonetheless, the virus has now been found in 24 countries...
Lipsitch predicts that, within the coming year, some 40 to 70 percent of people around the world will be infected with the virus that causes COVID-19.
But, he clarifies emphatically, this does not mean that all will have severe illnesses. “It’s likely that many will have mild disease, or may be asymptomatic,” he said. As with influenza, which is often life-threatening to people with chronic health conditions and of older age, most cases pass without medical care. (Overall, around 14 percent of people with influenza have no symptoms.)
Yes, he said 70% of the world population will get infected! That is almost 5 billion people. Worse than the 1348 plague. It would concern me to say something like that. That would be 14 million or so in Greater New York.
What is the basis for such a statement. We really know so little at this stage that such a statement in my opinion is reckless at the very least if this is what was really said. We do not really know how it is spread, lots of conjecture, and we do not have adequate clinical experience, in my opinion.
There are time we should just keep our guesses to ourselves.
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