CharonY

There are numerous publications investigating the decline of terrorism. While there is not necessary broad agreement on how to fight terrorism and how unique each case might be, there is evidence that repressive military force has little evidence for being a solution. Most effects were found to temporary, counterproductive or export the issue to other countries. Targeted elimination of leadership will (hopefully) reduce Hamas' capabilities in the short term. In the long-term only a lasting peace agreement can end the conflict. And this has to include violence in the West Bank (again, where Hamas is not a major player). How do you remove Hamas? Present the Palestinian people a viable alternative. Something that promises peace and self-determination. Netanyahu understood that, which is why he bolstered Hamas. And who comes after him? If folks are sufficiently afraid the idea of suppression is likely to continue. And where does it leave the option for peace?

OK, this result is really weird, as it might suggest that ROX is dependent on your sample, rather than the MM. Not sure if it is related, but I do wonder whether the position plays a role. Your Positivkontrolle is on top and your NTC is on the bottom of the plate (and the increase affects all samples in the middle). Perhaps a silly question, but in your method, ROX is selected as the reference dye, rather than target? Generally speaking an increase in the reference tends to be indicative of evaporation and concentrating the MM. Quenching could affect ROX, too, in theory, but in your case I fail to see how that would work. I am especially unclear sure why you see all three effects in the same run in a seemingly well or template-dependent way. One thing to check is whether the ROX traces are similar in all your runs. Also ROX seems a bit on the low end (close to 0) though I don't know if your software normalizes the values somewhat. At this point I would check your reference runs/SOP to see what your expectation of the raw fluorescence levels are and/or discuss the issue with the manufacturer (after checking that the software settings are correct, of course).

We can start a new thread, but I just wanted to mention that the economic model is not what necessarily creates dictatorships (as evidenced that we have basically five countries left that call themselves communist, but far more dictatorships), so I would not be particularly interested in rehashing that argument. One could make a thread discussing the difference between ideologies (which is structured in Marxism, but fairly empty in Fascism) and contrast it to the respective movements (which both were autocratic either from inception or increasingly became thus). But I suspect that neither of us has the background to fully flesh those discussions out in detail. To move things on topic, a fourth reich or whatever is certainly hyperbole, but there have been active discussions in Israel (prior to the current events) regarding a possible slide towards fascism. Following the election in 2022 some have argued that despite a right-wing slide (far right bloc with 11%, Israel is still lagging behind Europe in that regard with the far (not sure whether that is reassuring, though) https://www.nytimes.com/2022/11/08/opinion/israel-election-fascism.html. Other articles in a similar vein claim that fascist characteristics in Europe are not present in Israel. Conversely, some folks, including former prime minister Ehud Barak have argued that the the government under Netanyahu are indeed showing signs of fascism https://www.timesofisrael.com/ehud-barak-govt-shows-signs-of-fascism-mass-non-violent-revolt-may-be-needed/ Also: https://www.theatlantic.com/ideas/archive/2023/03/israel-benjamin-netanyahu-democracy-rule-of-law/673469/ I.e. if one focuses on the end points, it is easy enough to find distinctions, and some are probably trivial (such as anti-Semitism). However, looking at the mechanisms, such as dismantling of judiciary systems, the similarities start to show. Not only in Israel, but also in countries with increasingly powerful right-wing populist movements. It is detrimental to use terms such as fourth reich or concentration camps, as those are loaded and inevitably invite a rather meaningless discussion in semantics. The real questions here in my mind is what happens to democratic safeguards with the rise of populism, what are the reasons for that rise and are the long-term consequences. I do think that this is a global challenge and relying of the relative peace in the Western world after WWII as evidence that all is going to go well forever, is somewhat shortsighted. To be sure, the events in OP are not necessarily connected to this particular issue, but the jingoist sentiments that put Netanyahu in power and encouraged him to support Hamas to further weaken the two-state solution shows the risks of such sentiments. Peace should not be taken for granted.

Sound like a red herring to me. There are more than two autocratic governments and neither of those two actually have a communist economic system. Moreover, there are many good arguments that have argued that Russia is in fact fascist. https://theconversation.com/yes-putin-and-russia-are-fascist-a-political-scientist-shows-how-they-meet-the-textbook-definition-179063 My point is that because we have all this long history, one would expect that no one sane would ever want to even dip their toes into this mess ever again. Yet here we are discussing trends and nuances and the best we can come up is that it ain't that bad as before? Before the Great Depression the Germany economy was in recovery after reigning in hyperinflation. And basically it means that economic hardship (plus threats from black and brown folks in Europe) and we all goose-step right into the abyss.

I noticed that your wells say 10CFU MO. Is your template dilute to about 10 CFU? If so the Ct range makes much more sense to me. But as you can see in your multicomponent plot, you have got technical issues. See the ROX signal? For some the signal increases, which could be an evaporation issues and for two it actually drops into the negative (i.e. below initial baseline). There are really only two samples that show the expected flat line. Considering the very low amount of template, these issues can compound the result a fair bit. Also, to check the amplification curve shape, it often helps to plot the signal over ct rather than the delta rn. But even there you can see that it barely passes the threshold, aside from the positive controls. But first I would check the plates/tubes. Are they properly sealed, for instance, are there droplets/bubbles etc. Also is the cover heating activated?

Many things are comparable and it is dangerous to only focus on the most extreme outcomes. Keep in mind, we have a examples what happened when fascism reigned (in its various forms) and the fact that folks look at it and think, yeah, we want something like that is dangerous in itself. In fact, you could argue that due to the social upheaval at that time (after WWI, oppression of the working class and associated rise of socialist and communist ideals, Russian revolution, Great depression, novelty of democratic systems etc.) it was excusable that folks desired a strong leader type and were susceptible to populist appeals. Now with that lesson learned, even inching toward that again, is a huge backslide, especially for the Germans (for historic reasons- heck courts have verified that the leader of the potentially second strongest party is a Nazi). What we do see is that once in power those parties start to erode checks and balances. Not at the rate nor necessarily as brutally as in the interwar period, but it is like putting your small finger on the hot stove after burning your whole hand and thinking this is so much better. The reasons are quite similar to a large degree. Fear, misinformation, and the associated desire to be ruled by a strong ordering hand that make things great again. If we only focus on the genocidal aspects, we won't notice the erosion of democracy right under our noses. Well fascisms was a new thing, but in both countries the groups were originally "just" agitators, and while Mussolini had a rather fast rise and was asked by Italy's king to form a government after they basically incited an uprising. Hitler at the same time was seen more like an upstart and after the failed putsch was seen as a controllable asset for the establishment right. They were wrong, of course. Now today folks still find whatever that was appealing, but aside from a much smaller militant wing most cannot be arsed to perform violent actions. And the nice thing is they don't have to. Instead of firebombing press and political opponents, they can do that now from home on their cell phones (Luegenpresse, anyone?). Again, the bad thing is not (only) that they are making a comeback. The bad thing is that I don't think we are learning from our past and are also forgetting things at an incredible pace.

This is also very much the lesson you get, growing up in Germany (well perhaps not anymore, things are changing, unfortunately). But ultimately the perpetrator were the the (great)grandparents of the folks in class. It is trivially easy to understand that Nazis are not something alien and evil. And over the last decade or so we have seen the allure of fascism in the Western world, suggesting that lessons were not learned.

Well, it has been described (by Jewish journalists and researchers) as Jewish supremacist and fascist group. That's two for two already.

There are difficult paths and none that are obvious. If the war has any chance of securing long lasting peace one might make the tenuous argument that the civilian deaths might have been worth it. Yet everything points to further escalation, so my question is now what purpose does it serve besides ringing the bell for the next round of deaths. Ehud Barak has discussed the need for a path toward a two state solution, which includes opening lines with Palestinian Authority and showing that there is an alternative to Hamas. Instead, the settler violence I the West Bannk tells folks that whatever you do, you are screwed. And at that point a blaze of glory might just sound right. And off we go to another round of bloodshed. Because we cannot think beyond an eye for an eye. Unfortunately we have been blind for some time now.

Just to clarify, what you indicate as standard in your list are the extracts from counted cells? And the difference you see is e.g. between B1 and B2, which contains template from the same sample? If the difference are all >35, you are likely looking at noise (again, check the curve to verify). However if they are e.g. 30 and 35, and nothing is suspicious with your MM, then the most likely candidate are pipetting errors of the template. Is there a trend (i.e. is the first typically higher/lower than the other) or is it random? As part of your SOP, are you using low-biding filter tips?

Well, ultimately what has to happen is that the voices of consensus builders are elevated. I.e. having the Likud and Hamas in power (and by now it has been extensively discussed how Netanyahu's anti-two state strategy has empowered Hamas) the cycle of violence is likely only to continue. The other aspect is the one of outcome. Sure killing folks now eliminates them as immediate risk, but with a longer view it is abundantly clear that this also creates a vast (international) recruitment ground for Hamas and their allies. I am not saying that doing nothing is a great strategy, but we also know that a violent outburst is not solving things easier (just take a look at the US wars in the Middle East). I think the Israeli policy of isolating the West Bank is also not to be underestimated as an issue, specifically the state-supported settler violence: https://www.npr.org/2023/11/14/1212836719/ex-idf-soldier-calls-for-international-intervention-to-stop-settler-violence In other word, the discussion cannot only be about the current violence, but also the paths leading to it. Again, a blame game about who is justified to what level of violence just reinforces bloodshed. The system that has been implemented supposedly to protect Israel, clearly have failed and there is little reason to assume that escalating the violence will improve situations. As many folks have stated, this is similar to the US lashing out after 9/11 and as expected, we fail to learn from past lessons.

Normally some standard DNA/QC for QA/QC is in place to ensure that the qPCR works as expected. However, rather than just looking at pos/neg, it is often worthwhile to have a more concentrated standard (e.g. synthetic target DNA) and run a dilution series to establish PCR efficiency. This is more important for quantitative approaches, but variation in batches of master mixes or probes are not that rare. So if you have minor changes in PCR efficiency, and you are operating near detection limits anyway it might not be that unusual that you dip in and out of the detection range (and anything >40 is almost certainly a false positive). In that context it is important to consider is that we are not looking at a normal, but rather a Poisson distribution which is limited by sample volume (roughly speaking you might have have somewhere between 1-20 copies in your reaction). Since you use FAM you won't have melt curves, but you could plot the fluorescence data to see whether you amplification or perhaps issues with noise which might justify a shift in thresholding. I.e. check the whether you can see an exponential signal and where it sits relative to the noise. Considering that you are using a fixed starting material and have established protocols, one would expect fairly consistent results, but of your Ct of your actual samples also is around 30-35 it suggests that out of 13 million host cells you get somewhere around 1-100 Mycos, if I understand you correctly. Is that expected?

Seems like a convoluted way to state that all extant species have a common ancestor somewhere. And the helping hand is a combination of selection and chance. The main issue is the direction, i.e. the assumption that it is guided toward something.

*Sigh* need to make faster progress on the time machine, then.

This is also highlighted in the New Yorker piece here: https://www.newyorker.com/magazine/2023/12/11/the-inside-story-of-microsofts-partnership-with-openai It is a bit worrisome that a company initially set up for ethical AI development combats attempts to develop a governance system for it. It looks like openai is going down the Google "don't be evil" path. Move fast, break things and let others pay for it.

You can read up the interpretation of CIs here https://en.wikipedia.org/wiki/Confidence_interval Specifically: A 95% confidence level does not mean that 95% of the sample data lie within the confidence interval. A 95% confidence level does not mean that there is a 95% probability of the parameter estimate from a repeat of the experiment falling within the confidence interval computed from a given experiment.[16] Because a) in terms of safety we only look for certain defined endpoints (e.g. death, cancer, etc.) so potential other effects can be easily missed, and b) experiments are set up to test the null (i.e. no effect) so it is not really possible to calculate the likelihood of no effect. For the extremes and for short term you can establish a measure of safety (i.e. no one dying within 6 months of taking a medication). But if you want to look all effects (liver, kidney, inflammation, immune modulation, cardiovascular health, and so on) or for effects in the long term, confounders will have an increasingly bigger role (such as diet, lifestyle, age, health status etc.). Controlling for all these factors is near impossible (there would be a near infinite list to track for each person). I brought up the issue of diet, which had over the years huge cohorts and long-time data, but the effects have not been reproducible.

Yes. Normalization generally means adjusting the value to a certain scale. In this case to 100,000 person-years. Because you constantly claim that you understood things perfectly, yet your questions clearly show that you don't (especially basic definitions). While I am happy to teach, it is very difficult if you do not realize that you have to revise your basic assumptions. And frankly I do have enough entitlement from my students, and a direct challenge often shortens things a fair bit. No, if a difference is not significant it means that the distributions are not distinguishable from each other. It does not matter if the means or CI is skewed in one direction or another, that is not something the test can tell us. If there was a trend, the statistical power of the cohort is insufficient to show it (and/or the effect size is too small). Also, one thing to consider is that the cohort over 15 years is likely older, and increasingly other confounders influence cancer risk, as acknowledged in the study. As noted, there are not really many studies that set up to prove a non-effect (safety is usually assessed in clinical trials) and there is basically no way for any treatment to do that conclusively, especially when looking at long-term effects. What studies can do, is try to see effects (as this one does) while controlling for a set number of factors. The complexity of the matter is also why we do not have figured out the perfect healthy food, for example. Likewise, there won't be risk-free medication. All we have is the weight of available evidence and never certainty. Also, it is often the case for weak effects that some studies show an effect and others don't. So evidence of one or the other side of argument will pile up over time until a tipping point for action is reached. So far the available studies show no outsized role of metronidazole in short-term harm (compared to other antibiotics), increasing evidence of general carcinogenic effects of long-term treatment with antibiotics, but also no true alternatives to antibiotic treatment.

It is not strange, do you understand what person-years are and why that number is going to be larger than persons (specifically look how many person years are there in aggregate and what they normalized it against). If you did, then there is no reason to be confused about it. So either you did not understand and got confused, or you understood and pretend to be confused. Which is it? Again, these are person-years not numbers of cancer incidences. What they calculate are proportionate hazard ratios and likely age stratified (I do not recall). So the attributable risk ratio (as you acknowledge) had a huge spread, looking at the CI. So obviously the P is going to be high. This is the whole purpose of statistical tests, so that we just don't just look at the higher number and make inappropriate assumptions. Remember, these are matched pairs, and what it suggests is that there is going to be a big spread, which is really expected for rare conditions such as cancer (with a big impact on the age bracket of the matched pairs). But if you are genuinely interested in statistical analyses I suggest to dig out a good textbook (and to be honest in order to fully recapitulate the methodology I would need to so, too to avoid errors- I rarely use risk ratio calculations in matched cohorts). With regard to the other antibiotics, tetracycline, penicillin and nitrofuran have have some history in being associated with breast cancer specifically. There have been discussions of how microflora disruptions can influence the immune system and modulate estrogen levels. But as mentioned before, there is also increasing awareness that especially long-term disruptions of gut microbiota, really with any antibiotic, are likely to have some impact (though the effects are likely to be very complicated, in some cases antibiotics are part of the cancer therapy). Ultimately, you won't find a perfectly safe antibiotic, they all carry risks. And trying to quantify them is not going to be terribly useful, unless there is a huge effect size to be measure. The reason is also clear, our bodies (and microbiota) are dependent on an uncountable number of things that we accumulate over our lifetime. Some antibiotics might be fairly safe for some individuals but if the same individuals take a certain drug, have a certain lifestyle or happened to have a specific type of infections, the risk on the individual level might skyrocket. There is simply no reasonable way to capture all this diversity. So all we can do is looking at rough aggregates and there, small differences rarely matter as the spread (or CI) is going to be very broad, anyway. With regard to AB, the most important aspect is whether they work in the first place. I.e. folks look at local resistance profiles and prescribe ABs that work. The secondary aspect is then to look whether the patient has any immediate adverse reactions to them. Long-term concerns are not unimportant, but are generally secondary unless a smoking gun study emerges. But that will take time. And if we wait for them before treating immediate issues, we will do more harm then good.

No you misread the metric. The measure is per 100,000 person-years, not persons. The second thing you likely missed is reading through the study design, where they describe their follow up. Specifically the start date is when they get their first dose dispensed (for the user group). The follow-up ends either with the latest known consultation or the first diagnosed case of cancer. Because the result was statistically insignificant (.11). The statistical power of that cohort (i.e. folks that were cancer-free for over 15 years and remained enrolled in the program) is just too low to be sure that it was not a statistical fluke. The caveats are pretty much standard, having more data is of course better, but often not feasible and often nearly impossible for multi-year studies. Keeping folks in these programs is very, very difficult.

No, there is far more evidence of that, dating back to the 80s. The effect size is overall weak, but shows up fairly persistently in multiple human cohorts. A review summarizing some of those studies: https://doi.org/10.3390/cancers11081174 A random selection of papers: Breast cancer and antibiotics early study here: doi:10.1001/jama.291.7.827 Other studies found mild effects, but there are mechanistic hypotheses underpinning this relationship: https://doi.org/10.3390/cells8121642 Relationship of AB use and colon cancer: http://dx.doi.org/10.1136/gutjnl-2016-313413; https://doi.org/10.1007/s10620-015-3828-0; Discussion of the role of microbiota, antibiotics and cancer https://doi.org/10.1016/j.ejca.2015.08.015 And the list goes on. Stating that there are only two papers are seriously misunderstanding the literature information. Also considering that these effects keep popping up in various studies, the link between AB and cancer in humans is far stronger than any short-term effect exclusive to metronidazole. I echo this sentiment. It is unclear how this particular AB is assumed to be vastly different in risk compared to all the others.

Yet their conclusion remains that sensible use of metronidazole is backed by evidence, in part because there is no strong evidence of added metronidazole over other antibiotics for short-term use: Also from the same paper:

OK, you are doing purity checks, high cutoffs make sense here. I assumed you had the issue even when using pure standards with higher concentration. High CT beyond 40 are generally unspecific signals. I.e. hon-targets could be amplified, probes break down etc. First thing is to check the amplification curves for shape, do the thresholds make sense? If running SYBR check melt curves. One can also run a gel to see what has been amplified or send for sequencing.

At that stage we would still think of it as correlation. We need to have a model first to explain why A causes B at minimum.

Perhaps no rights for them unless they are one of the good ones? Nudge nudge wink wink?

The first thing to do is to talk to your supervisor to check what kind of quality control you are using and what the expected results are. From your description it is not clear for example whether your standards are extracted DNA with known quantity, for example. A Ct of 45 is pretty much unspecific and 35 is close to what is generally the detection limit (so roughly <10 genomic copies). It is advisable to start with pure DNA standards and establish a calibration curve or at least detection limit and PCR efficiency so that you have an idea what to expect. Then work your way backward to the isolation steps.