So you’re moving to Boston?
Here are some useful maps.
1) Location of the different Universities.
2) Rental costs accross the different neighboorhoods
3) Commute time using the subway system
Very cool video from the Kishony lab @ Harvard. Here we see evolution happening live and point mutation propagating overcoming the antibiotic gradient.
tdl:
OMG — watch bacterial evolution with your eyeballs!
This is a timelapse of an experiment in the Observatory of Mutation and Growth, a unique 4 foot x 2 foot petri dish built by the Kishony Lab.
Here, we have spotted bacteria on the sides of the observatory.
We set the bacteria up for an interesting challenge by putting the antibiotic trimethoprem in the dish in a particular pattern. Each vertical stripe towards the center of the plate has a 10fold higher concentration of trimethoprem (you can imagine it sort of like a hill of concentration).
Only the few lucky bacteria that have made the right errors while copying their DNA make it to the next stripe.
Then we took a video over the next 6 days time, 1 frame every 10 minutes. I’m so proud of it right now.
Time’s magazine 2011 person of the year “The Protester”. Awesome.
Great cover art as well by Shepard Fairey.
Via boingboing
You know you are a biologist when…
You open the toothpaste with one hand.
You wash your hands before and after using the washroom.
For you, media is something which increases your culture.
You have a callus on your thumb.
You use the word “aliquot” in regular sentences.
Sometimes you momentarily vanish from social activities because of a timepoint.
You don’t fear rodents, rodents fear you.
You say “orders of magnitude” in regular sentences.
You flinch when you hear the word “significant”.
Showing up at 10AM and having a coffee is a productive day.
You’re very good at diluting things.
You’re also very good at transferring small amounts of liquid between containers.
You are fed up of people saying alcohol, when they mean ethanol.
You hear the word ‘Molar’ and teeth are the last thing on your mind.
You say “conjugation” instead of “sex”, and “pili” sounds dirty.
SOB is not an insult, it’s what you grow your bugs in.
You say “mills” and “megs”.
Nobody in your family has any idea what you do.
You consider a green laser pointer to be science bling.
A falcon is not a bird.
And you have 5 of them with different types of water.
You own invitrogen t-shirts and actually wear them.
You think that drosophila geneticists have a good sense of humour.
You’d refer to your children as the F1.
You’ve suffered carpal tunnel from the pipetman.
You’ve used kimwipes as kleenex.
A timer clipped to the hip is not only practical, but dead sexy.
You’ve played Battleship using tip boxes.
You think the following is a solid insult: “I’ve seen cells more competent than you!”.
You’ve made dry ice grenades.
And you’ve lost many friends to ice grenades
Tip of the hat to Mojca @ D&A Blog and @babyhaussmann
tdl:
Pilobolus: Ultra-High-Speed Fungus Spore Discharge (by hayleyscomet)
“The fungus Pilobolus fires off its sporangiophore using a water cannon or “squirt gun,” reaching accelerations that are among the fastest in nature.
Here we present a montage of high-speed video clips showing sporangiophore discharge in the fungus Pilobolus kleinii. The videos were obtained at camera frame rates of up to 250,000 fps. Each discharge is completed in less than 0.25 milliseconds; an eye blink takes 100 milliseconds, or 400 times longer! The music is Verdi’s Anvil Chorus.”
Tweets vs. Seismic waves
The East Coast of the US has been struck by an “unusual” earthquake of magnitude 5.9.
“Unusual” because it was centered in Virginia about a 130 km South West of Washington DC. It is one of these mysterious intraplate earthquake - one that doesn’t occur at the boarder of tectonic plates but deep within them. The causes are ususallt unclear, but hypothesis are fairly interesting.
As it turns out those event are rare compared to interplate earthquake but happen relatively frequently on the East Cost of the US, and exemple include 6.3 earthquake in 1755 Boston, 8.1 in 1818 New Madrid or 1888 5.3 earthquake in NYC. The North American Coast line is composed of a number of forgotten and aborted rift systems, the Keweenawan, the Saint Laurence and the Reelfoot rift systems that could have led to the formation of an ocean spanning from the St Laurence to the Gulf of Mexico. These ancient failed rifts present the weakness within the otherwise stable interior of the plate where constrains can more easily be evacuated.
Another geological detail, the US East Coast is mainly composed of old and rigid rock formations with fewer sediments making the travel of seismic wave relatively easy and fast. In fact the earthquake was clearly felt in NYC, in Boston (I can testify) and in part of Ontario.
Tweets vs. Seismic waves
There is this great xkcd comic that has been stuck in my head these last few days comparing the speed of seismic waves versus the speed of tweets. It basically predicts that about 100km out of the epicenter tweets wave will have overtaken the seismic waves thus predicting their arrival.
Did tweets actually overtook seismic waves in the 2011 Virginia Quake?
I found this interesting video that we can analyze:
(Green dots are tweets about earthquakes. Gray dots are tweets about other topics. Each frame is one second - total of 12 minutes).
Based on the above parameters, the Washington DC people - about 130km from the epicenter - wouldn’t have had the time to be warned. We can assume the first green dots appearing in DC are actual tweets of people feeling the quake. Are the first green dots in NYC and Boston tweets (actually feeling the quake) or REtweets (posting about people in DC feeling the quake)?
- NYC and Boston are respectively 330 and 640 km away from DC. Taking the upper speed of 5km/sec, the seismic wave needed about a minute to get from DC to NYC and 2 minutes to get to Boston.
- Based on the above video (made using the Twitter streaming API), the first tweet in NYC appeared about 3 minutes after the first tweet in DC and the first tweet in Boston appears about 9 minutes after the first tweet in DC.
Both in NYC and Boston, the first tweets seems to be appearing after the seismic wave went by. We cannot exclude however that some people did see the DC tweets before feeling the quake, they just did not have the time to retweet - or actually looked for shelter ;)
EDIT1: Seems like there is an official project about actually making a Twitter-based earthquake detector. You can find it here
![tdl:
Some pretty serious plagiarism detected…
Abstract from Colombo et al, 2006, Journal of Clinical Microbiology:
Candidemia studies have documented geographic differences in rates and epidemiology, underscoring the need for surveillance to monitor trends. We conducted prospective candidemia surveillance in Brazil to assess the incidence, species distribution, frequency of antifungal resistance, and risk factors for fluconazole-resistantCandida species. Prospective laboratory-based surveillance was conducted from March 2003 to December 2004 in 11 medical centers located in 9 major Brazilian cities. A case of candidemia was defined as the isolation ofCandida spp. from a blood culture. Incidence rates were calculated per 1,000 admissions and 1,000 patient-days. Antifungal susceptibility tests were performed by using the broth microdilution assay, according to the Clinical and Laboratory Standards Institute guidelines. We detected 712 cases, for an overall incidence of 2.49 cases per 1,000 admissions and 0.37 cases per 1,000 patient-days. The 30-day crude mortality was 54%. C. albicans was the most common species (40.9%), followed by C. tropicalis(20.9%) and C. parapsilosis (20.5%). Overall, decreased susceptibility to fluconazole occurred in 33 (5%) of incident isolates, 6 (1%) of which were resistant. There was a linear correlation between fluconazole and voriconazole MICs (r = 0.54 and P < 0.001 [Spearman’s rho]). This is the largest multicenter candidemia study conducted in Latin America and shows the substantial morbidity and mortality of candidemia in Brazil. Antifungal resistance was rare, but correlation between fluconazole and voriconazole MICs suggests cross-resistance may occur.
Abstract from Cisterna et al, 2011, Same journal, no related authors:
Candidemia studies have documented geographic differences in rates and epidemiology, underscoring the need for surveillance to monitor trends. We conducted prospective candidemia surveillance in Spain to assess the incidence, species distribution, frequency of antifungal resistance, and risk factors for acquiring a Candida infection. Prospective laboratory-based surveillance was conducted from June 2008 to June 2009 in 40 medical centers located around the country. A case of candidemia was defined as the isolation of aCandida species from a blood culture. Incidence rates were calculated per 1,000 admissions. Antifungal susceptibility tests were performed by using broth microdilution assay according to the guidelines of the Clinical and Laboratory Standards Institute. We detected 984 cases, for an overall incidence of 1.09 cases per 1,000 admissions. The crude mortality was 20.20%. Candida albicans was the most common species (49.08%), followed by C. parapsilosis (20.73%), C. glabrata (13.61%), and C. tropicalis (10.77%). Overall, decreased susceptibility to fluconazole occurred in 69 (7.01%) incident isolates. Antifungal resistance was rare, and a moderate linear correlation between fluconazole and voriconazole MICs was observed. This is the largest multicenter candidemia study conducted to date and shows the substantial morbidity and mortality of candidemia in Spain.
The data appears to be different in these cases— likely from the different countries claimed, yet some numbers (e.g. patient age) are identical. Much much much of the paper is exactly or nearly identical. Interestingly, despite different authorship, the first sentence of the Acknowledgements is also exactly the same:
This paper was partially supported by an independent medical grant provided by Pfizer, Inc.
Pfizer should hire some better ghost writers…](http://25.media.tumblr.com/tumblr_lpoeo4aOC81qzti0xo1_r1_500.png)
tdl:
Some pretty serious plagiarism detected…
Abstract from Colombo et al, 2006, Journal of Clinical Microbiology:
Candidemia studies have documented geographic differences in rates and epidemiology, underscoring the need for surveillance to monitor trends. We conducted prospective candidemia surveillance in Brazil to assess the incidence, species distribution, frequency of antifungal resistance, and risk factors for fluconazole-resistantCandida species. Prospective laboratory-based surveillance was conducted from March 2003 to December 2004 in 11 medical centers located in 9 major Brazilian cities. A case of candidemia was defined as the isolation ofCandida spp. from a blood culture. Incidence rates were calculated per 1,000 admissions and 1,000 patient-days. Antifungal susceptibility tests were performed by using the broth microdilution assay, according to the Clinical and Laboratory Standards Institute guidelines. We detected 712 cases, for an overall incidence of 2.49 cases per 1,000 admissions and 0.37 cases per 1,000 patient-days. The 30-day crude mortality was 54%. C. albicans was the most common species (40.9%), followed by C. tropicalis(20.9%) and C. parapsilosis (20.5%). Overall, decreased susceptibility to fluconazole occurred in 33 (5%) of incident isolates, 6 (1%) of which were resistant. There was a linear correlation between fluconazole and voriconazole MICs (r = 0.54 and P < 0.001 [Spearman’s rho]). This is the largest multicenter candidemia study conducted in Latin America and shows the substantial morbidity and mortality of candidemia in Brazil. Antifungal resistance was rare, but correlation between fluconazole and voriconazole MICs suggests cross-resistance may occur.
Abstract from Cisterna et al, 2011, Same journal, no related authors:
Candidemia studies have documented geographic differences in rates and epidemiology, underscoring the need for surveillance to monitor trends. We conducted prospective candidemia surveillance in Spain to assess the incidence, species distribution, frequency of antifungal resistance, and risk factors for acquiring a Candida infection. Prospective laboratory-based surveillance was conducted from June 2008 to June 2009 in 40 medical centers located around the country. A case of candidemia was defined as the isolation of aCandida species from a blood culture. Incidence rates were calculated per 1,000 admissions. Antifungal susceptibility tests were performed by using broth microdilution assay according to the guidelines of the Clinical and Laboratory Standards Institute. We detected 984 cases, for an overall incidence of 1.09 cases per 1,000 admissions. The crude mortality was 20.20%. Candida albicans was the most common species (49.08%), followed by C. parapsilosis (20.73%), C. glabrata (13.61%), and C. tropicalis (10.77%). Overall, decreased susceptibility to fluconazole occurred in 69 (7.01%) incident isolates. Antifungal resistance was rare, and a moderate linear correlation between fluconazole and voriconazole MICs was observed. This is the largest multicenter candidemia study conducted to date and shows the substantial morbidity and mortality of candidemia in Spain.
The data appears to be different in these cases— likely from the different countries claimed, yet some numbers (e.g. patient age) are identical. Much much much of the paper is exactly or nearly identical. Interestingly, despite different authorship, the first sentence of the Acknowledgements is also exactly the same:
This paper was partially supported by an independent medical grant provided by Pfizer, Inc.
Just how do the other countries do at S&P credit rating?
For the first time ever, the United States of America lost its perfect credit rating as Standard & Poor’s reduced its U.S. long-term debt assessment from AAA to AA+ with a negative outlook (August 5, 2011).
But how do the other countries do at S&P credit rating?
via chartsbin.com
Standard & Poor’s Ratings:
- AAA: The best quality borrowers, reliable and stable
- AA: Quality borrowers, a bit higher risk than AAA
- A: Economic situation can affect finance
- BBB: Medium class borrowers, which are satisfactory at the moment
- BB: More prone to changes in the economy
- B: Financial situation varies noticeably
