Remove secreted beta-lactamase from the starter cultures. This can be done by pelleting and re-suspending the starter culture in fresh, antibiotic-free medium before innoculating the main culture.
- May 2020
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bitesizebio.com bitesizebio.com
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royalsocietypublishing.org royalsocietypublishing.org
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These and other breakthroughs promoted a feeling of optimism that, with the tools of quantum mechanics, the secrets of life could finally be laid bare.
What is the connection between the microscope, X-ray mutagenesis, ultracentrifugation and quantum mechanics? It should be made more clear
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www.edwardtufte.com www.edwardtufte.com
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Scientist's Guide to Poster Presentations, by Peter J. Gosling; Preparing Scientific Illustrations: A Guide to Better Posters, Presentations, and Publications, by Mary Helen Briscoe; Displaying Your Findings: A Practical Guide for Presenting Figures, Posters, and Presentations, by Adelheid A. M. Nicol, et.al.
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www-ncbi-nlm-nih-gov.ezproxy.rice.edu www-ncbi-nlm-nih-gov.ezproxy.rice.edu
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Fourth, a minimal insert region (amino acids 310 to 518) was found to be sufficient to convert the SL-CoV S from non-ACE2 binding to human ACE2 binding, indicating that the SL-CoV S is largely compatible with SARS-CoV S protein both in structure and in function
193 amino acids in a 510 amino acid protein is by no means minimal. It constitutes 40% of the protein
- Also there seems to be a typo here. The paragraph below says 318 - 510 is the receptor binding domain
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project-evidence.github.io project-evidence.github.io
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a minimal insert region (amino acids 310 to 518)
193 amino acids in a 510 amino acid protein is by no means minimal. It constitutes 40% of the protein
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It only takes a few changes ("exchange of a relatively small sequence segment") between two coronaviruses to result in a third coronavirus that can infect other animals ("host-switching")
This cannot be said based on the above paper since one of the recombining fragments was the human infecting SARS-CoV itself.
It should instead read as "it only takes a few changes to a coronavirus to result in a novel variant that can infect other animals"
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The odds of this happening are pretty good!
There is no mention of the odds of such an even happening in the paper so this conclusion is misleading and not based on evidence
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it is equally possible that the virus originated somewhere else entirely
If this is equally possible then why is the seafood market origin "unlikely" in the rest of this article?
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While Mr. Fu here seems to believe the virus originated from the market, we know from the Lancet study that it is unlikely
It should not be struck down as unlikely, just because there is another possibility that is equally likely (stated 2 paragraphs above)
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Because 34% of cases did not have exposure to the market yet were exposed to the virus, it is highly unlikely the market is the origin point of SARS-CoV-2
This claim is poorly made and not backed up by alternative explanations. It is quite plausible that the 66% who were exposed in the market transmitted to others through asymptomatic contacts who could not be epidemiologically traced
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meaning that the first patient at the market was not responsible for spreading the virus to other cases
hasty generalization
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pubs.rsc.org pubs.rsc.org
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Research on enveloped virus presence and fate in water is hindered by the lack of proven detection methods. Detecting and quantifying viruses in environmental samples requires first concentrating the viruses in the sample into a smaller volume to improve detection limits
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link-springer-com.ezproxy.rice.edu link-springer-com.ezproxy.rice.edu
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virus-loaded filters were rinsed with an acidic solution to eliminate remaining cations before elution with NaOH or other alkaline buffers
Elution with alkaline buffer only works when using negatively charged membranes. ion exchange chromatography?
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www-sciencedirect-com.ezproxy.rice.edu www-sciencedirect-com.ezproxy.rice.edu
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The 1MDS-method and the HA-method did not provide as high recovery yields of the virions as the Mg-method.
The reason for this could be the beef extract used to elute the virions from both these membranes. The other two successful methods (Mg and Al) used H2SO4 for elution.
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mbio-asm-org.ezproxy.rice.edu mbio-asm-org.ezproxy.rice.edu
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low-pathogenic viruses often acquire multiple basic amino acids at the HA cleavage site, which is recognized by ubiquitous cellular proteases such as furin and PC6
Why the emphasis on basic amino acids, are they more prone to protease activity?
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- Apr 2020
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www.mdpi.com www.mdpi.com
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. When E. coli metabolizes Collilert-18’s nutrient-indicator, MUG, the sample also fluoresces. It is reported that the method is able to detect a single viable coliform or E. coli per sample
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pdf.sciencedirectassets.com pdf.sciencedirectassets.com
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The daily flow rate of wastewater was calculated as a point estimate using the product of the at-home population in the catchmentofapproximately 600,000 persons(capita), andthe observed average per capita wastewater rate of 250 L/person/day
Isn't the daily flow rate of wastewater directly measurable in the treatment plant?
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www-ncbi-nlm-nih-gov.ezproxy.rice.edu www-ncbi-nlm-nih-gov.ezproxy.rice.edu
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a defined quantity of a nonhuman control virus (seal herpes virus [SHV], kindly provided by H. G. M. Niesters, University of Rotterdam, The Netherlands) was spiked into each sample prior to DNA and RNA extraction. Since constant DNA quantities of the control virus are coextracted even when RNA isolation kits are used (H. G. M. Niesters, personal communication; our own unpublished observations), the virus can also serve as a control in RNA virus detection assays.
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blogs.rsc.org blogs.rsc.org
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on the topic of working with sewage to detect viruses, there are new guidelines from the US CDC that require BSL-3 PPE.
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jamanetwork-com.ezproxy.rice.edu jamanetwork-com.ezproxy.rice.edu
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We investigated the biodistribution of SARS-CoV-2 among different tissues of inpatients with coronavirus disease 2019 (COVID-19)
It would have been good to include 2-3 negative control samples in the data
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Four SARS-CoV-2 positive fecal specimens with high copy numbers were cultured
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www-sciencemag-org.ezproxy.rice.edu www-sciencemag-org.ezproxy.rice.edu
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scientists have found limited instances of infectious virus in fecal matter
Did people test in spit or nasal secretions which would also be inside wastewater?
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wastewater monitoring in Israel, for example, picked up a polio outbreak before any clinical cases appeared at all, according to a 2018 study.
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www-nature-com.ezproxy.rice.edu www-nature-com.ezproxy.rice.edu
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transfer
transformation might be a better word
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www-ncbi-nlm-nih-gov.ezproxy.rice.edu www-ncbi-nlm-nih-gov.ezproxy.rice.edu
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However, using metabolites as reporters requires more precise control than what is necessary for most metabolic engineering applications, since small amounts of enzyme can produce visible amounts of pigment and overproduction of certain metabolites can be toxic to the cell.
Is this amplification the result of the multi-step pathway? Is beta-galactosidase + x-gal not a good single step substitute for generating blue colouration?
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In this paper, we designed a system that could fully repress lycopene production in the absence of an inducer and produce visible lycopene within two hours of induction. We engineered Lac, Ara, and T7 systems to be up to 10 times more repressible, but these improved systems could still not fully repress lycopene. Translational modifications proved much more effective in controlling lycopene. By decreasing the strength of the ribosomal binding sites on the crtEBI genes, we enabled full repression of lycopene
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pubs.acs.org pubs.acs.org
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the paper-based device has the potential to be used as a small, portable device to detect SARS-CoV-2 in wastewater on site
Zhugen Yang's Sensors lab seems to be making these devices for CoV2 - https://www.cranfield.ac.uk/press/news-2020/wastewater-test-could-provide-early-warning-of-covid-19
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pubs-acs-org.ezproxy.rice.edu pubs-acs-org.ezproxy.rice.edu
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Although infective SARS-CoV-2 has not yet been confirmed in stool samples, the SARS-CoV-2 RNA shedding pattern suggests viruses are replicating in the GI tract
Four SARS-CoV-2 positive fecal specimens with high copy numbers were cultured
Source: Wang, Wenling, et al. "Detection of SARS-CoV-2 in different types of clinical specimens." Jama (2020).
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Viruses have a direct connection to wastewater and drinking water purification when they are excreted in feces or urine
How does this compare with spit and nasal secretions which also connect to the wastewater? Is this a bigger source of viral particles in the case of a respiratory virus?
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www.nature.com www.nature.com
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colonization by this strain does not require pre-administration of antibiotics
This has only been demonstrated in the immune compromised IL-/- and 129X1/SvJ strains right?
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Detection of tetrathionate in the presence of fluctuating and low-level inflammation that remained below histological detection further demonstrates the ability of PAS638 to detect a subclinical inflammatory environment.
This is a poorly backed statement. How did you assume that it is detecting tetrationate?
If you don't understand why there is inflammation in this mouse model and you have not not been able to locate inflammation by histology, you should have measured the tetrathionate by other methods as in fig 2C.
Otherwise this statement sounds like a circular logic to support the use of this new tool while trying to verify its function.
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this concentration is on the order of the in vitro EC50 of our sensor
Which might not be desirable if the goal is to detect with high sensitivity right?
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ability to turn off memory under repeated streaking
Why is memory turning off?
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E. coli strain NGF-1
Isolated from BALB/c mice. Colonizes gut atleast 6 months even post modification
Source: Escherichia coli NGF-1, a Genetically Tractable, Efficiently Colonizing Murine Gut Isolate, 2018
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slatestarcodex.com slatestarcodex.com
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A few points to summarize and comment on part one
- Community relationships vs arms-length transactions
The benefits of reliance on community relationships with lesser emphasis on finances are clear when there is a close knit group. When applied to large communities with disparate groups, it translates to the creation of castes/subcategories, disparate advantages to the socially powerful creating a powerful feedback loop to sustain power, nepotism and other evils. There are successful examples showing the benefits of banking on the community such as Grameen bank's microfinance business model by Mohammad Yunus
- Direct payments by insurance creating a disconnect between the patient and the cost
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watermark.silverchair.com watermark.silverchair.com
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According to a 2013 report by the American Academy of Microbiology (AAM), How Microbes Can Help Feed the World,
https://people.unil.ch/iansanders/files/2013/10/FeedTheWorld.pdf
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www.nature.com www.nature.com
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More than a dozen research groups worldwide have started analysing wastewater for the new coronavirus as a way to estimate the total number of infections in a community
This article lacks references :(
- Netherlands - Presence of SARS-Coronavirus-2 in sewage - medRxiv
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de Roda Husman’s group detected traces of SARS-CoV-2 in wastewater at Schiphol Airport in Tilburg only four days after the Netherlands confirmed its first case of COVID-19 using clinical testing
Source: Lancet30087-X/fulltext) correspondence, April 1, 2020 - SARS-CoV-2 in wastewater: potential health risk, but also data source
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pubs-acs-org.ezproxy.rice.edu pubs-acs-org.ezproxy.rice.edu
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ultrafiltration method resulted in mean recoveries (±SD) of 25.1% (±3.6%) and 18.2% (±9.5%) for the enveloped MHV and ϕ6, respectively
The efficiency here is measured by the functional viral particles (using plaque assays).
- It is not relevant if the internal standard is solely for PCR based viral measurements
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Local file Local file
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The SARS outbreak was fueled by bioaerosol generation during the collection and transport of sewage that allowed for distant disease transmission (Roy and Milton, 2004; Yu et al., 2014)
movement of SARS-contaminated sewage through the floor drains generated high concentrations of aerosolized virus that remained virulent and of sufficient dose to cause infection after airborne travel a considerable distance from the original source
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wastewater treatment disease transmission studies from that time did not usually consider respiratory pathogens.
During the 1980s, there were few pathogens that were both known to initiate infection in the lungs and frequently occur in wastewater (U.S. Environmental Protection Agency, 1980). It was viewed as an anomaly if an enteric pathogen was “uniquely infectious by the aerosol route”, with the noted exception of the respiratory bacterium Mycobacterium tuberculosis
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science.sciencemag.org science.sciencemag.org
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To collect, process, and act on information, cells must be able to accurately record signals.
This premise needs more substantiation. Why do we need to study memory devices
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www.chem.uiuc.edu www.chem.uiuc.edu
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the number of ionized water molecules is so low (1.0 X 10-7 mol in 1000 mL water)
Ss this value derived, measured or is it a covention?
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www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
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dA-tailing to add an “A” base to the 3′ end of the fragment
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Sequencing begins at the single-stranded 5′ end of the Y adapter, followed by the “template” strand
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www.nature.com www.nature.com
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In an attempt to mitigate the problem of DNA from inactive cells influencing microbial analysis, molecular techniques have been developed to remove or bind the extracellular DNA prior to cell lysis
Are inactive cells considered to be dead and lysed such that they release their DNA extracellularly?
- Is there a possibility of intact but inactive cells?
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www.nature.com www.nature.com
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It is unlikely that colistin pressure in the environment and animals, especially in water environment, may be the only cause of the existence of such an ubiquitous presence of these enzymes that could be mobilized within bacteria.
Is it possible that the gene exists in the population by being neutral - imposing no burden and causing no benefit?
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Our innovative approach, i.e. massive genome analysis, appears to be a powerful tool and a new concept that opens a new field of big data analysis and research
Is this massive genome search a new concept? I feel that it is too simple to have not been done before. Also innovative does not sound like the right adjective for this work
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www-sciencedirect-com.ezproxy.rice.edu www-sciencedirect-com.ezproxy.rice.edu
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By administering hydroxychloroquine combined with azithromycin, we were able to observe an improvement in all cases
Improvement compared to what?
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www.nature.com www.nature.com
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HFHS
high fat high sugar diet
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low-fat (LFPP) diet
low fat high plant polysaccharide diet
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www.nature.com www.nature.com
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in bacterial communities where prior evolution led to greater persistence of conjugative plasmids encoding resistance to different antibiotics, we expect the likelihood of hosts acquiring multiple distinct plasmids to be higher, thereby priming the emergence of MDR.
The plasmid persistence enhancing mutations discussed here are either specific to the plasmid system (conjugation, post segregation killing) or the specific antibiotic resistance mechanism (cost alleviating mutations in the genome).
Does this mean that evolving for persistence of 1 plasmid does not necessarily enhance the persistence of a different plasmid
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www-sciencedirect-com.ezproxy.rice.edu www-sciencedirect-com.ezproxy.rice.edu
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Conclusion
The contribution of the microbial characterization to this conclusion seems very meager. Was it really worth performing?
Considering that the two main takeaways from this study have already been established in literature cited in this paper, what exactly is this paper adding to the body of scientific knowledge and understanding?
- Higher denitfication rates in I. pseudacorus could be explained by higher root exudate release
- Higher nitrification rates in P. australis can be explained by higher oxygen release from roots
- The microbial diversity between both the plants is different but there is no explanation as to how it is linked to the nitrification-denitrification rates
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The assays detected IgG antibody to HIV-1
What is the antigenic epitope of these antibodies that were detected?
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pubs.acs.org pubs.acs.org
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pharmacological studies indicate that essential oil of garlic is an exceptional source of organosulfur compounds, possessing strong antioxidant, antibacterial, antifungal, anticancer, and antimicrobial properties
Citations?
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As mentioned above, the high organosulfur compounds in garlic essential oil are expected to have strong interactions with the amino acids of the ACE2 protein
Why are organosulfur compounds expected to interact strongly with ACE2?
I did not find any previous reference to this as mentioned in here
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The fact is that the study of HIV-1 resistance to reverse transcriptase inhibitors was reported by Tarasova et al
how does this fit into this paragraph? I did not understand the context
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www.biostathandbook.com www.biostathandbook.com
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One option is to treat it as a nominal variable with five (or seven, or however many) items
Why is it not a ranked variable instead?
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rdgao.github.io rdgao.github.io
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if you depend heavily on Google Doc for writing, or read primarily on a synced mobile device, then unfortunately it will be difficult to use.
Zotero has google docs support now and it works decently as far as I have seen. I haven't tested it in large documents with many citations but I have heard there might be difficulties
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www.frontiersin.org www.frontiersin.org
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Would the ingestion of probiotic cultures, which may act as donors or recipients, therefore increase the antibiotic resistance gene pool in the enteric ecosystem?
How would the resistance gene pool increase if ingested cultures act as recipients?
- Most of the ingested microbes do not colonize the enteric ecosystem right?
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msystems.asm.org msystems.asm.org
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(4, 11, 12, 20, 21)
exploratory culture from environments
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advances.sciencemag.org advances.sciencemag.org
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Variability in the components of complex samples such as blood can affect the readouts
Especially difficult to account for, when the components of the matrix vary between tests. Does blood components vary from person to person enough to complicate measurements?
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a parallelized calibration scheme that uses the patient sample to generate custom reference curves
This great idea for on site calibration is what is converting a qualitative colour output into a quantitative output!
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advances-sciencemag-org.ezproxy.rice.edu advances-sciencemag-org.ezproxy.rice.edu
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DOC causes a significant decrease in the signal when evaluating flavonoids having three (naringenin) and four (luteolin) hydroxyl groups, but not with a flavonoid having five hydroxyl groups (quercetin)
Mechanism?
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various flavonoids have distinct chemical properties and functional groups, these mechanisms have the potential to differentially affect flavonoid movement through the soil matrix
Why were flavinoids chosen? There are other below ground communication molecules as well that can be chosen like strigolactones
the interaction between plant roots and mycorrhizal fungi depends on diverse secondary metabolites, including strigolactones and terpene lactone carotenoid derivatives. source: Ref 6
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few studies have considered the influence of abiotic environmental parameters on the efficiency of signal transmission through soils.
Maybe because they are likely to be non-specific?
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signaling repression occurs between dissolved OC and flavonoids
What is the mechanism?
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link.springer.com link.springer.com
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In the biosensor, the promoter regions of lasI, rhlI, pqsA, and ambB (QS genes) controlled the fluorescent reporter genes of Turbo YFP, mTag BFP2, mNEON Green, and E2-Orange
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www.frontiersin.org www.frontiersin.org
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however, their presence in cosmopolitan thermophilic phototrophic mats remains largely unknown
That is not a satisfactory reason for studying them
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evolutionnews.org evolutionnews.org
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intelligent
Claiming a certain thing as 'intelligent' is in itself not falsifiable.
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All cities are designed, in that they are the product of human minds
This is a pedantic argument. The author means that there is no central top-down design in many cities. Those cities come up by actions of small agents, which is design by human agents but decentralized.
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The falsification of intelligent design is Darwinism. The falsification of Darwinism is intelligent design.
This is a fallacy. Falsification of darwinism is by no means supporting intelligent design. This two are not mutually exclusive.
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royalsocietypublishing-org.ezproxy.rice.edu royalsocietypublishing-org.ezproxy.rice.edu
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Soil moisture content, if determined by rainfall, will vary temporally at scales from minutes to months, and changes in community composition will only occur for those organisms that react at the same time scales.
Important idea of time-lag of cause and effect relationships
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Most are descriptive, do not address scientific aims or questions and are not designed to increase understanding or test hypotheses.
Wow, that is a bold statement!
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In this review, the most common traditional techniques, such as cyclic voltammetry, chronoamperometry, chronopotentiometry, impedance spectroscopy, and various field-effect transistor based methods are presented along with selected promising novel approaches, such as nanowire or magnetic nanoparticle-based biosensing
Good comprehensive review
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jb.asm.org jb.asm.org
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Promoter, terminator, and operator sites should be indicated as described by Bachmann and Low
For operon abcDEF, in which abcD is the first gene transcribed, the naming would be abcDo (operator), abcDp (promoter), abcDe(leader), abcDa (attenuator), andabcDi (initiator) Linkage map of E.coli K12 - Edition 6
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www.medrxiv.org www.medrxiv.org
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a significant proportion of cases
Should mention the actual number and the proportion
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www.bloomberg.com www.bloomberg.com
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Do the studies, make the vaccines, but allow doctors to have what they feel is working now.
Bad suggestion. Doctors gut feeling is no substitute for clinical trials
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www.sciencedaily.com www.sciencedaily.com
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Better monitoring of coronaviruses in biofilms might be necessary to prevent outbreaks.
What do bacterial biofilms have to do with human coronaviruses? Is it expected to stick by hydrophobic interactions?
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home.iitk.ac.in home.iitk.ac.in
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While, whathappened in Gujarat was vile and reprehensible, how does it make sense to help othercountries declare sanctions on India? Who does it hurt most?
If certain actions cause severe punishments, is that a valid argument to hide the truth? Who does it hurt is not the right question, but who benefits from this testimony?
Your claim is that international forces benefit, to Indian state's loss.
Maybe in an ideal world, this works as a deterrent in the future. But it is true that the personal standing or fame of the person might have been the motive. It is a debatable decision but certainly not objectively wrong
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Then what do we say about those who might plot against the obscenity that blights theirland, as Stauffenberg did, who fight to free India of it? Are they patriots? If so, what ifthey welcomed a force from abroad that toppled this hypothetical regime, as many Iraqisdid? Are they still patriots?
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www.jstor.org www.jstor.org
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ions. The stationary continuance of the functioning of certain social institutions is easily regarded as desirable when those institutions are "explained" in terms of the-possibly vital-functions they are performing in the existing s
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www.vox.com www.vox.com
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parents are being asked to somehow work and entertain housebound children
How big of a problem is taking care of really young children vs entertaining children > 10 y age?
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en.wikipedia.org en.wikipedia.org
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then it takes on any given value between f(a) and f(b) at some point within the interval
What is the definition of 'any' given value. Is it any value in the co-domain or the range?
I'm wondering in the context of a function that is defined on rational numbers -> real numbers. Where certain values of real numbers are not possible because the domain is restricted.
Specific example of \(x^2 - 2\), not taking 0 because domain is restricted to rational numbers discussed here
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scroll.in scroll.in
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Using the median, the case fatality rate for India drops to 0.4 deaths per 100 patients, nearly ten times.
It is unclear what the median is for. Is it statewide data within india or data for different countries?
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- Mar 2020
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www.biorxiv.org www.biorxiv.org
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Cool ideas as extensions to this paper Can this be done in vivo - in the sand filter? - Zach Has anyone analysed cells with plasmid vs cell expressing the genes? - Zach Analyzing a mobilizable vs a conjugative plasmid simultaneously (or even independently) in the same community
- The two plasmids should be identical except for the removal of self mobilizing features (that will be present on a helper plasmid or integrated into the donor)Does permissivity change if in a biofilm - assuming sand filters are housing biofilms?
What are the goals of spreading a catabolic gene inside a native community?
1. Long term residence in the community 2. Target to organisms capable of high expression or function 3. Residence in high abundance and highly active community membersTo maximize all these goals, we can develop a blanket strategy that combines best aspects of all Create a combinatorial library of all plasmid origins, all host organisms, transposons with your payload in it This will enable the widest possible dissemination of the desired function in the community at the expense of understanding
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Instead of letting the faucet run while you’re shaving so you can clean off the razor, fill up your sink with some water
It us better to have a small container filled with water than filling up a whole sink
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inkscape.org inkscape.org
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watch out for those nonstandard Affinity SVGs. Their viewbox/scale is broken (and more)
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www.physiciansweekly.com www.physiciansweekly.com
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we must abide by the voluntary quarantine rules verbatim
Why is this quarantine voluntary? What purpose does this achieve compared to a legally enforced quarantine?
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Turkey’s government says it is not disclosing the location of cases to prevent the risk of increasing transmission rates by encouraging people to move from areas with high rates to places where there are no or few cases.
I'm amused as to how many possible reasons governments come up with to not disclose data.
I do not understand how likely people are to move between areas, do people have more than 1 housing options?
There is an obvious conflict of interest in a government hiding information that is bound to invite questions or make their performance look poor in contrast to other countries etc.
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www.biorxiv.org www.biorxiv.org
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demonstrate that adapting a strain to the intended growth condition increases fitness and in turn improves the stability of the engineered function over hundreds of generations
Does this imply that an organism taken from a native environment, modified with a plasmid and re-introduced is likely to be stable?
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selected after transformation and used to inoculate liquid cultures
Would the variability be the same if the colonies were picked from a streaked plate (from glycerol stock) instead of a transformation plate?
I would expect the glycerol stock method to have more variability, but it would be good to test
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While encoding the function did not measurably affect host fitness
Could the fitness difference be finite but undetectable? In which case we can think of a multi-day competition experiment to enhance the fitness differences.
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www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
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assay based on engineered selectable CRISPR-spacer integration reporter plasmids
CRISPR on a plasmid
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pubs.acs.org pubs.acs.org
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There is no discussion about the presence or titres of SARS-CoV-2 in wastewater and the sensitivity of detection of the assays.
- Considering that it is a respiratory pathogen, which rarely enters the enteric system and feaces, how much of the viral load do we expect to find in the wastewater?
- What is the detection limit of the paper based assays in the presence of other matter from wastewater?
Given the lack of this critical points, the article does very little to answer the question raised in the title except educate us about paper based diagnostics
Can a Paper-Based Device Trace COVID-19 Sources with Wastewater-Based Epidemiology?
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betterposters.blogspot.com betterposters.blogspot.com
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but the nature of that relationship remains unstated)
This is where icons come in handy
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Sentences can express many more relationships
The assumption is that the readers have enough time to read everything
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www-sciencedirect-com.ezproxy.rice.edu www-sciencedirect-com.ezproxy.rice.edu
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the start-up (achieving 70% TN removal) was shortened from 21 days to 5 days when Anammox sludge concentration increased from 0.02 g VSS L−1 to 0.2 g VSS L−1 with 2 g VSS L−1 AS as inoculum
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link.springer.com link.springer.com
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Hydrazine addition resulted in much higher anammox biomass enrichment observed as higher nitrogen removal rate [0.512 kgN (m3 d)−1 with hydrazine versus 0.256 kgN (m3 d)−1 without reagent]
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www.sciencedirect.com www.sciencedirect.com
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less than the most commonly used
sentence is incomplete
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matrix effect, assessed based on the use of an internal standard, was associated with an underestimation that ranged 0.1–0.9 log gene copy number mL−1 of sample
Who reports differences in terms of fold logs? It is very confusing what this means
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esajournals.onlinelibrary.wiley.com esajournals.onlinelibrary.wiley.com
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neutral theory contends that high diversity is because all species within the same functional group are equivalent in their competitive ability
What is functional group?
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Nannochloropsis started to decline
What is the explanation for this decline, cell death?
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highly artificial environments
Should point out the exact differences between the artificial environment and the North sea
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one multispecies competition experiment and two pairwise competition experiments
Do the multispecies experiments run parallel to the pairwise experiments?
Is it possible that presence of other species affect the growth rates and R* values of the two species in the pairwise study by unknown interactions (symbiosis?) with other species in the mixed community? .
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Moreover, even though the P‐limited competition experiments started from very different initial species abundances, they ultimately led to the same equilibrium outcome
They don't seem the same. The nanochloropsis differs by ~10 fold it looks like from figure 4
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neutral theory assumes that species abundances change by chance
Implies that species composition upon nutrient fluctuation is not predictable
- Does this theory also imply that there is no steady state in time?
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rviews.rstudio.com rviews.rstudio.com
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Thanks to ggforce, you can enhance almost any ggplot by highlighting data groupings, and focusing attention on interesting features of the plot
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www.sciencedirect.com www.sciencedirect.com
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has shown that the mean duration of viral shedding in patients suffering from COVID-19 in China was 20 days
should definitely include the sample size of this study here.
There were 191 patients in total
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www.nature.com www.nature.com
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Vero E6 cells were infected with 2019-nCoV
Interesting to know that the virus has a tropism that extends beyond the lung epithelial cells into kidney epithelial cells
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www-sciencemag-org.ezproxy.rice.edu www-sciencemag-org.ezproxy.rice.edu
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draconian manner
This report hints at this point multiple times without elaborating how the measures were draconian. This is unfair to the subject and takes away from neutrality of reporting
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infected people rarely spread the virus to anyone but members of their own household
How did an infected household get groceries?
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journals.plos.org journals.plos.org
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provided by a plasmid lacking a functional oriT
Does the mobilized plasmid need to have a Mob relaxase along with the OriT?
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www-ncbi-nlm-nih-gov.ezproxy.rice.edu www-ncbi-nlm-nih-gov.ezproxy.rice.edu
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oriT mimic, minimally contains a 126-bp region encompassing three overlapping inverted-repeat sequences (IR1-3), at least one copy of an accessory repeat (AR) and a defined relaxase core region
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recently documented “relaxase-in trans” mechanism of conjugative mobilization facilitated by conjugative plasmids
in Staphylococcus aureus
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mmbr.asm.org mmbr.asm.org
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Mobilizable plasmids carry only the relaxosomal components oriT, a relaxase gene, and one or more nicking auxiliary proteins
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www.nerdwallet.com www.nerdwallet.com
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Rental Cover
24$ per day (on 20 March 2020)
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www.jstage.jst.go.jp www.jstage.jst.go.jp
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Although several studies have been made onthe isolation of bacteria with conjugative plasmids fromenvironmental samples, few have compared the distri-bution and characteristics of plasmid mobilizers in vari-ous environments
Is there any reason to assume all conjugative plasmids are not mobilizers?
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acsess-onlinelibrary-wiley-com.ezproxy.rice.edu acsess-onlinelibrary-wiley-com.ezproxy.rice.edu
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IncP plasmids are considered mobilizing plasmids and may transfer other nonconjugative plasmids into new hosts
Aren't all conjugative plasmids capable of mobilizing? According to the paper -
IncP, IncN, and IncW are conjugative plasmids that transfer and can be maintained in a diverse array of bacterial hosts
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academic.oup.com academic.oup.com
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IncP-1beta plasmids
Is a minimal origin for IncP-1beta plasmids known?
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pubs-acs-org.ezproxy.rice.edu pubs-acs-org.ezproxy.rice.edu
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bacterium proved to be an efficient nitrogen-fixing biofertilizer in itself by increasing the root mass storage of radishes by up to 1440%
Why would anybody represent such a high number as a %? increases by 14 fold is a much better way to represent this
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pediatrics.aappublications.org pediatrics.aappublications.org
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children often experience respiratory infections (e.g., respiratory syncytial virus (RSV)) in winter, and may have higher levels of antibody against virus than adults
Is it known that antibodies against a virus are able to protect against infection from a different family of virus?
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www.biorxiv.org www.biorxiv.org
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therefore does not secrete glucose
Is the glucose secretion low or zero? Does it secrete galactose?
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www.nytimes.com www.nytimes.com
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Establishment Democrats are desperately hoping to avoid a reprise of 2016, when Mr. Sanders battled to the bitter end against Hillary Clinton; his posture enraged some in the party who later blamed him for stoking division among Democrats that led to her loss to Mr. Trump.
Wow! It is the height of foolishness from the establishment democrats if they can still not understand that their moderate-centrist policies are unable to connect with the bulk of the populace, increasingly disillusioned with status quo.
Unfortunately Bernie wasn't able to do much to broaden the party base as he was tasked to do since 2016. But there was no doubt of his intentions to unite the party when he endorsed Hillary after losing the primary as he said he would this time too. It is just plain undemocratic for the establishment to continue this attitude and blaming any outsiders bringing in new ideas, trying to connect with people (think Ralph Nader) when it is increasingly clear that they are no longer representing priorities important to the electorate.
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it is only after the other side has had a chance to put testimony to the test, through cross-examination, that it can be given the status of “evidence”
Similar to peer review process in science? (probably applicable more so to post-publication review)
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www.wired.com www.wired.com
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The app, which was developed in partnership with a contractor, will run on iPhone 8 devices provided by the bureau
Why not invest in an android app as well? I would assume it would lead to more widespread use on personal devices
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www.investopedia.com www.investopedia.com
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essential functions
Essentially might not be easily and universally agreed upon
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basic infrastructure
Each and every word of this can be debated upon.
What comes under basic infrastructure?
I presume everyone thinks about high investment hard infrastructure like roads, rail networks, fibre optic and electric lines, airports etc.
Are public schools and colleges included?
- Are medicare and social safety nets counted as basic infrastructure?
- Is defining criteria of intellectual property and granting patents counted?
- What about public transportation?
- Funding early scientific research?
Or do we expect all of these to be funded through charity?
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openwetware.org openwetware.org
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4200 rpm in Beckman J-4.2
3635 x g (calculated with rotor radius of 184 mm)
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www.whitehouse.gov www.whitehouse.gov
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physically present within the Schengen Area during the 14-day period preceding their entry or attempted entry into the United States.
Does this include transit through airports on the EU of aliens originating travel from nom-EU locations?
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www-nature-com.ezproxy.rice.edu www-nature-com.ezproxy.rice.edu
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PAM-independent loci were targeted using degenerate codons, thereby making it possible to modify any site in the genome
From the paper -
we identified a PAM site in the closest proximity (within the 70 bp coverage of the MAGE oligo) and we introduced a secondary silent mutation that disrupts the nearby PAM sequence while coding for the same amino acid
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www-sciencedirect-com.ezproxy.rice.edu www-sciencedirect-com.ezproxy.rice.edu
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due to resource constraints, community-level tradeoffs exist between growth yield and resource acquisition, and that nutrient limitation affects community metabolism and reduces growth yield.
Why should the community come into picture? Individual cell metabolism can also explain reduced growth yield right?
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cals.arizona.edu cals.arizona.edu
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Subsurface drip irrigation provides the ultimate in water use efficiency for open-field agriculture, often resulting in water savings of 25-50% compared to flood irrigation
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www.sciencedirect.com www.sciencedirect.com
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trace contaminants such as heavy metals in the upper horizons may be accumulated, which may eventually lead to deterioration of soil and groundwater quality and affect the sustainability of land-based disposal of effluent
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www.sciencedirect.com www.sciencedirect.com
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Eggplant yield under treated effluent was twice the average eggplant production under fresh water irrigation using conventional fertiliser application in Jordan
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journals.asm.org journals.asm.org
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included bacteria belonging to the Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria classes of proteobacteria
Does the proteobacterial specificity arise from the RP4 or from the donor being Psuedomonas?
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zygotically inducible
Indicates that expression will occur after conjugation. This term comes from developmental biology field for genes expressed in the zygote - https://en.wikipedia.org/wiki/Maternal_to_zygotic_transition
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www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
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After purification, more than 30% of the bacterial cells in the primary soil were extracted
That is quite low
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www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
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In situ probes using fluorescence and infrared spectroscopy are also available on the market and have been extensively studied
Good references for bio-monitoring in situ
- Purely analytical methods, not biosensors
Other points from the same paper
- capable of monitoring the chemical properties of fermentation broths such as biomass, glucose, and protein concentration.
- infrared spectroscopy can have problems with sensitivity, for low abundance products such as protein products or substrates such as glycerol or glucose.
- fermentation broths are extremely complex and hence there might be interference?
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pacific-mathforindustry.springeropen.com pacific-mathforindustry.springeropen.com
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it is assumed that the decay modifies the growth multiplicatively as a function of the time
1st order decay
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www-nature-com.ezproxy.rice.edu www-nature-com.ezproxy.rice.edu
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Typically, double terminators are used to stop transcription. Because these parts can be up to ∼168 bp of DNA, this use of double terminators can lead to homologous recombination when used at multiple locations in a design
double terminators
Did you test the double terminator strength against your library?
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In E. coli, homologous recombination occurs most frequently when there is a contiguous stretch of sequence >25 bp
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www.biorxiv.org www.biorxiv.org
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Exposure to short chain-length AHLs resulted in a decrease in the abundance of different taxa than exposure to higher molecular weight AHLs
Is there any discussion on how these AHLs are affecting gram positive vs gram negative bacteria?
- AHLs are linked more often to gram negative bacteria in both production and response, so do they find these connections as well?
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- Feb 2020
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www.indiatoday.in www.indiatoday.in
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cognizable offence
What is the definition of a 'cognizable' offense? Are the police allowed to interpret the definition of this term and refuse to file an FIR as we hear in the news on multiple occasions?
I found a definition and some useful information here - https://www.humanrightsinitiative.org/publications/police/fir.pdf
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www.npr.org www.npr.org
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Don't see the graphic above? Click here.
What is the connection of these countries to China?
- Travel?
- Trade?
Or is it just a case of random chance?
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www.nature.com www.nature.com
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the leakiness and inducibility of the ligand-inducible LacI repressor mutants have been quantified and classified
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newrepublic.com newrepublic.com
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One return New York-to-London transatlantic flight delivers roughly the same exposure (0.16 mSv) as a nuclear power worker receives in a year (0.18 mSv)
This is a very interesting fact. Anyone know different sources for this fact?
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www.forbes.com www.forbes.com
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only
Only is a strong word, we do not know alternate scenarios
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hydro-electric dams are one of the cheapest ways that poor nations can gain access to reliable electricity
Cheapest way might not be the best or long lasting way
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opponents of hydro-electric dams and flood control claim those technologies
There are lot of shortcomings of large dams - most importantly mass migration of people
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not the first time those who are most alarmist about an environmental problem have been most opposed to solving it.
Maybe the specific olutions you are talking about are being opposed for a reason. This statement is wrong.
A problem does not have unique solution and opposing bad solutions is as important as finding good solutions or adapting the bad ones to be better
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large dams,
These have a whole slew of problems - especially on overpopulated areas. Look at Narmada river in India
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nuclear weapons have contributed to the Long Peace since World War II,
This is a contentious link between weapons of mass restrictions and peace. Is there wide agreement about this?
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aem-asm-org.ezproxy.rice.edu aem-asm-org.ezproxy.rice.edu
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produced from abiotic photochemical reduction of Fe(III)-OM, thus closing a cryptic iron cycle under photic conditions
Is this a significant pathway in a possible cycle in the environment? The photochemical reduction seems quite slow compared to the oxidation, there may be a much faster biotic reduction in the actual envirnoment right. Comments?
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Fe(II) concentrations and cell abundances in R. ferrooxidans SW2 growth experiments
Is this really a cycle? The timescales seem very different
Fe(2) -> Fe(3) complete in 8 days and growth almost stalls after 14 days. Maybe 8-14 days growth requires the Fe(3) -> Fe(2) step and that's why its a cycle?
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Abiotic photochemical reduction of Fe(III).
Timescales of this reduction are very slow compared to bacterial oxidation
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Fe(II) concentrations were determined anoxically using the ferrozine assay
Can Fe(3) also be determined easily? Would have been good supplementary information to prove that Fe(2) is being converted to Fe(3)
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were placed horizontally under a 40-W incandescent light bulb
Why do you need light for the bacteria to oxidize Fe(2)?
- Isn't there simultaneous photochemical reduction of Fe(3) happening in this experiment?
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2 mM FeCl2
Why is this higher than the previous experiment?
- Previous one was 0.1 mM, this is 2 mM of Fe ions
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Oxidation of Fe(II) by R. ferrooxidans SW2
Does it make sense to fit enzyme kinetics curves to these reactions rather than join the data points?
- Might be complicated since there are multiple steps involved - Substrate import into cells, Enzymatic degratation
Also dotted lines are distracting
- Why didn't you measure Fe(3) concentrations?
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guarantees that cells are actively metabolizing but no cell growth is possible, and that therefore, changing cell numbers does not influence the quantification of metabolic rates.
This will miss any Fe compound induced gene activation a which might give higher rates to the redox reactions.
- Gene transcription and translation is not as efficient in stationary phase for most growth associated genes
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aem-asm-org.ezproxy.rice.edu aem-asm-org.ezproxy.rice.edu
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there was no Fe(II) oxidation in the abiotic controls
This should have been reported for 54 h like the Fe(3) reduction experiment in Fig.2
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en.wikipedia.org en.wikipedia.org
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right-wing paramilitaries
?
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www.marxists.org www.marxists.org
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Commerce follows theland and sea routes of the earth, going to whatever country hasany thing to exchange, be it a monarchy or a republic. Let us bein union with the whole world and not with just a part of it, notwith one part against another.
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www.biorxiv.org www.biorxiv.org
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After many generations in the lab, mice from the desert consumed significantly less water than mice from other localities, indicating that this difference has a genetic basis.
This could also be explained by epigenetic inheritance. Basically something hereditary - either genetic or epigenetic
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www.nytimes.com www.nytimes.com
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all the polling evidence says that America is basically a center-left nation
But unfortunately Democratic party is dead centre, and does not represent the people as much as it could
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is someone who plays right into that strategy, by declaring that he is indeed a socialist.
Bernie Sanders is championing the causes of the working class and had has always been consistent in his track record. It is justified to fear the ill effects of general perception of 'socialism' but it is high time the americans stop vilifying 'isms' and looking at policies for what they are, the details.
This column does a very bad job at recognizing working class issues, the same issues that got the republicans into power and Bernie Sanders had the exact mandate to really connect the democratic party with the masses, which I unfortunately think has not been successfully done
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www.nytimes.com www.nytimes.com
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But were big banks really at the heart of the financial crisis, and would breaking them up protect us from future crises?
Yes, keeping investment banking and consumer banking separate is a good idea. Glass Stegall act is a good regulation to do so.
I heard economists argue on both sides of the spectrum but the main question is why is this article so motivated to paint the Sanders campaign as bad?
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www.conradbastable.com www.conradbastable.com
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same workers in Spain are less equipped to compete for Manufacturing jobs
But a few highly skilled among them have the possibility of emigrating to Germany?
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you might as well get the most productive workers for your “buck”, right?
I am curious as to why German workers are more productive? Can the other EU nations implement any policies to improve their human resources likewise?
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Don’t hate corporations for playing to win — they don’t make the rules, you do.
Well articulated!
That reference to computer games is awesome but the problem comes down the the fact that winners of the corporate game are influencing the rules - the corporate tax law, regulations etc.
Now this is also another problem with how the rulemakers are chosen or how the rules are made. So maybe the solution is to rectify the few rules that influence many other rules being made!
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you can’t ever stop because one correction will undo all your spending
"It is like riding a white tiger" - Byrraju Ramalingaraju. Former chairman of Satyam, convicted of corporate account fudging (a similar game of artificially upholding the value of an entity - except, in this case it was illegal) Source: outlook India
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www.sirlin.net www.sirlin.net
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wouldn't you be a fool for not using that move?
Maybe the game is not exciting anymore if everyone always 'had' to play that move
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www.nature.com www.nature.com
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The researchers from the earlier, statistically significant, study
Citation?
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aem.asm.org aem.asm.org
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The host range for three of the plasmids (pBF1, pB7, and pB9) was further investigated by the GFP method described above
Does the host range of transfer go wider than the population where GFP is observed?
This is my idea of distinctive overlapping categories of host range as venn diagrams.

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Consequently, the plasmid donor cells do not express gfp
Does the leaky expression not hinder the detecting and quantification of transconjugants in epifluorescence microscopy?
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support.office.com support.office.com
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you can take a screen clipping to create an image that combines and keeps items together
This makes the objects no longer editable
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VLPs were discriminated from bacteria or detritus based on pixel dimensions: the pixel area of the smallest known bacterium was established as a maximum cutoff; all objects smaller than this were counted as VLPs.
Viruses are in size range of 100-500 nm. This is very close to the diffraction limit of light. How is the assumption that anything smaller than bacteria is a virus like particle justified and quantitatively accurate in this regard?
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www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
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is similar
What is the % similarity? How can an abstract be so vague?
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www.nature.com www.nature.com
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Modeled trends of soil bacterial carrying capacity and diversity are compared to empirical observations
Isn't this circular logic? The testing empirical data is the same as the data used to build the model
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soil becomes sufficiently dry, almost all aqueous habitats are physically isolated and might contain only a few species
Why is this?
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www.the-scientist.com www.the-scientist.com
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David Robert Grimes, an Irish science writer who has published research showing homeopathy to be ineffective
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www.the-scientist.com www.the-scientist.com
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In biology there’s rarely things that happen for no reason
That is a teleological statement.
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bitesizebio.com bitesizebio.com
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teach science to a general audience
Aren't most comics based on cultural references like hollywood that are not universal across different cultures and languages. What is a good way to relate to wider general audience?
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www.journalofhospitalinfection.com www.journalofhospitalinfection.com
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persist on inanimate surfaces like metal, glass or plastic for up to 9 days
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www-nature-com.ezproxy.rice.edu www-nature-com.ezproxy.rice.edu
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For n < 5 we recommend showing the individual data points.
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www.biorxiv.org www.biorxiv.org
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hypothesized that any single quorum-sensing signal should only induce prophages within a small subset of closely related host bacteria
This seems like the new thing here compared to Ref 22
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fivethirtyeight.com fivethirtyeight.com
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scientific laboratories create an amazing amount of plastic waste, consume large amounts of water, create risks from hazardous chemicals and use significantly more energy
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plated out on warm agar plates
It is unclear if the plates contain V2 salts or not
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electroporation buffer (680 mM sucrose, 7 mM K2HPO4, pH 7)
Why not 10% glycerol?
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sfamjournals.onlinelibrary.wiley.com sfamjournals.onlinelibrary.wiley.com
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idyllic conditions
:) funny!
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politics.stackexchange.com politics.stackexchange.com
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in a pure socialist world everything would be needed to be controlled by the government
Is this true? I don't know if there is a precise and widely accepted definition of socialism but I would think that socialism is about community ownership of means of production. (I see a complex definition of socialism and capitalism here - https://plato.stanford.edu/entries/socialism/)
Community can mean the elected government, but in a local sense, it could also be adapted to mean the community that owns, operates, works-in and is frequently served by a given industry. I can think of a simple example of a coffee shop or restaurant in a small town.
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plato.stanford.edu plato.stanford.edu
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Most socialists, however, tend to find the profit motive problematic.
Is it worthwhile to envision a society where people's motives are pre-anticipated or controllable?
I think social systems should be robust enough to account for stable functioning of society, independent of the motives and only depending on actions.
Only actions can be observed, and hence only actions can be regulated in any form of organized society and highly so in capitalism.
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www.nytimes.com www.nytimes.com
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socialists do not support capitalism, meaning they want workers to control the means of production
Workers controlling the means of production sounds like co-operative industries. This paradigm is not antithetical to 'capitalism' in the sense that there is still private ownership of the means of production. I disagree with the statement that democratic socialists do not support capitalism.
A good debate on this topic here - https://politics.stackexchange.com/questions/323/are-worker-cooperatives-socialist-capitalist-or-their-own-category
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jcheminf.biomedcentral.com jcheminf.biomedcentral.com
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The main priorities of different ELN features
A ranked order in the plot would have been more insighful
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www-nature-com.ezproxy.rice.edu www-nature-com.ezproxy.rice.edu
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whether shared systems of signalling synthesis and degradation
Do you mean the same organism able to simultaneously perform or switch between the two functions of synthesis and degradation? Or does this mean sharing within the community?
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www.nature.com www.nature.com
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a single-tube, single-step PCR, performed in <2 hours from setup to transformation
How does the efficiency compare with Gibson assembly and other in vitro methods? Specifically
- # of colonies
- Fraction of successful assemblies among the colonies
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login.ezproxy.rice.edu login.ezproxy.rice.edu
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Rice alumni with accounts on the Alumni Portal are automatically allowed to access a few of the university's licensed electronic resources through the EZproxy server
Which resources?
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www-nature-com.ezproxy.rice.edu www-nature-com.ezproxy.rice.edu
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Bloom filter
Good guide here - https://llimllib.github.io/bloomfilter-tutorial/
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if applied to raw sequence data they would only find matches completely contained within a single read.
How does the BIGSI method address this concern?
- Do the k-mers span between reads or
- Do you make k smaller if there is partial match at the edges of reads?
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