Tag Archive for Plasmodium

Fun with twitteR

There has been talking about using social media for epidemiological purposes. For example, in areas where there is an increase of key-words such as “malaria” in social media, an increase in malaria prevalence is to be expected. I don’t think social media can be applied for epidemiological purposes. There are to many biases. Still, it doesn’t mean that there aren’t any nice scientific applications using social media as tool.

To start from the beginning, how do you extract keywords from social media? For example, what are the latest associated words around the subject #plasmodium? Here I will be using an R- Application Programming Interface (API) to search through the Twitter data.

To set up your API for twitter, follow the explanation on the Decision stats website.

Before you set-up connection with twitteR, load the libraries for R that you’re going to use:

library(twitteR)
library(tm)
library(wordcloud)
library(RColorBrewer)
library(XML)
library(igraph)

Setting up connection with twitteR can sometimes be a pain. When you use R-Studio, you need to type-over the web address containing the long token key. After you shook hands with Twitter, search through their database for a subject and convert the data to a dataframe:

## Plasmodium twitter cloud 
a <- searchTwitter("#plasmodium", n=1000)
tweets_df = twListToDF(a) #Convert to Dataframe

Next, clean up the dataframe.

b=Corpus(VectorSource(tweets_df$text), readerControl = list(language = "eng"))
 b <- tm_map(b, tolower) #Changes case to lower case
 b <- tm_map(b, stripWhitespace) #Strips White Space
 b <- tm_map(b, removePunctuation) #Removes Punctuation
 b <- tm_map(b, removeWords, stopwords("english")) #Removes English stopwords like 'the'
 b <- tm_map(b, removeNumbers) #Removes numbers
 inspect(b)
 tdm <- TermDocumentMatrix(b)
 m1 <- as.matrix(tdm)
 v1 <- sort(rowSums(m1),decreasing=TRUE)
 d4 <- data.frame(word = names(v1),freq=v1)

And plot the wordcloud:

wordcloud(d4$word,d4$freq, random.order=FALSE, colors=brewer.pal(8, "Dark2"))

You get a twitter wordcloud around #plasmodium:

plasmodium

 

This is just one example. Data can be presented the way you like. On the website ‘mining in Twitter with R‘, you can find some more nice examples.

This twitter data mining tool is a goldmine for marketing. How to use it for more scientific purposes? Well, for example, you can search for the associative words or subjects between  ‘#malaria’ and ‘@billgatesfoundation’. What are the trends? Maybe useful when you are writing a grand-proposal!

Cryopreserved malaria sporozoites

Injections may take the bite out of malaria studies
From: Bridget M. Kuehn, MSJ. JAMA. 2012;308(22):2325. doi:10.1001/jama.2012.105690.

Studies of experimental malaria interventions have long relied on a tried-and-true method of causing malaria infections in healthy volunteers by subjecting them to bites from mosquitos infected with Plasmodium falciparum parasites. But results from a preliminary study presented at the American Society of Tropical Medicine and Hygiene in November suggest that injections of purified cryopreserved P. falciparum sporozoites may also do the trick.
Malaria lifecycle
Added by Robert ten Hove:

The P. falciparum lifecycle continues when sporozoites enter the bloodstream and infect livercells. Obtaining these sporozoites, Anopheles mosquitos need to be grown in a strictly controlled cultivation chamber. The mosquitoes are exposed to infected blood, before they are fed on the study-participants. Using cryopreserved sporozoites, these cultivation procedures are something of the past. Whats more, study-participants can be exposed to well defined number of sporozoites.

Locally acquired Malaria in Europe

A patient with falciparum malaria locally acquired in the south of France

From: J.E. Arends & J.J. Oosterheert. Nederlands Tijdschrift voor Medische Microbiologie. December 2012, nr. 4.

Malaria caused by Plasmodium falciparum is not endemic in Europe. Reported cases are almost exclusively from imported cases from travelers to endemic areas. Here we describe one patient who had not been in malaria epidemic areas for years, but acquired falciparum malaria locally in the south of France.

A 34-year old woman originating from Sierra Leone was recently seen at the out patients department complaining of periodic  spiking fever lasting pain in her abdomen and athralgia for 2 weeks. Her last visit to malaria-endemic country (Sierra Leone) was in 2003. Before presentation she stayed in France (Bourgogne area) with her family in an apartment. Several people recently returning from Africa to the apartment block, came down with malaria. On physical examination, small wounds of insect bites were seen around the ankles. In her blood results the most striking was the anemia with a haemoglobin of 7.1 mmol/L, a thrombosytopenia of 80x10E9/L and a leukocytopenia of 3.7x10E9/L with a normal differentiation. Further investigation with microscopy of a thick smear and malaria antigen test (Binax Now) were postive for Plasmodium falciparum with a parasitaemia of 0.18%. She was started on a 3-day course of Malarone (atovaquon/proguanil) 4 times daily and returned home. She fully recovered and at follow-up visits in the out patients department no malaria parasites were seen on thick smear. Vectors for Plasmodium falciparum are observed throughout Europe. Together with more immigration, local transmission of malaria could become a problem in Europe in the future.

Note from Robert ten Hove

Another possible source of infection of malaria that has been proposed in literature are Anopheles mosquitoes infected with Plasmodium spp transported by airplanes from endemic area.

Second, the authors’ prospect of P. falciparum  becoming an increasing problem in Europe due to local vectors, immigration and local transmission is something very unlikely. Life cycle of P. falciparum are very much depended on higher temperature throughout the year. Also, in order for the transmission cycle to be closed, a large group of malaria patients is necessary from which the vector can pick up the parasite.

However, if there is one thing that parasites have tough us, adaptability is their key to survival.

Video of malaria parasite lifecycle

Amazing video showing the life cycle of the malaria parasite.

With support from the Howard Hughes Medical Institute