Latest Article Alert from BMC Infectious Diseases

The following new articles have just been published in BMC Infectious Diseases

Case report
Quantification of the antibody response to Propionibacterium acnes in a patient with prosthetic valve endocarditis: – a case report
Herren T, Middendorp M, Zbinden R
BMC Infectious Diseases 2016, 16:185 (29 April 2016)
Abstract http://www.biomedcentral.com/1471-2334/

Latest Article Alert from BMC Cardiovascular Disorders

The following new article has just been published in BMC Cardiovascular Disorders

Case report
Inverted stress- induced cardiomyopathy as a unusual variant of acute heart failure after cesarean delivery- a case report
Ledakowicz-Polak A, Bartodziej J, Majos A, Zielińska M
BMC Cardiovascular Disorders 2016, 16:76 (29 April 2016)
Abstract http://

Open Policy Network

The mission of the Open Policy Network is to foster the creation, adoption and implementation of open policies and practices that advance the public good by supporting open policy advocates, organizations and policy makers, connecting open policy opportunities with assistance, and sharing open policy information….”

Tummy bug 2: The scientific literature teaches us about Isospora

In the previous post we showed how ContentMine could give immediate knowledge about a scientific topic – we analysed “Isospora”, which is a nasty tummy bug. Let’s just read Wikipedia to get some idea of the language we’ll need

 

Life Cycle

PHIL 3398 lores

  • An oocyst with one sporoblast is released in stool of infected person
  • After the oocyst has been released, the sporoblast matures further and divides into two
  • After the sporoblasts divide they create a cyst wall and become sporocysts
  • The sporocysts each divide twice, resulting in four sporozoites
  • Transmission occurs when these mature oocysts are ingested
  • The sporocysts excyst in the small intestine where sporozoites are released
  • The sporozoites then invade epithelial cells and schizogony is initiated
  • When the schizonts rupture, mereozoites are released and continue to invade more epithelial cells
  • Trophozoites develop into schizonts, containing many mereozoites
  • After about one week, development of male and female gametocytes begin in the mereozoites
  • Fertilization results in the development of oocysts, which are released in the stool [1][6]

The sporulation time of this parasite’s egg is usually 1–4 days, and the entire life cycle takes about 9–10 days.[7]

 

Wow! That’s complicated! But that’s because Life is complicated! These parasites have complex life cycles. You have to learn the terms – but it’s no harder than learning the terms in a new game, or a law case, or soccer strategy. You just need to want to do it! And Wikipedia will help. Wikipedia is always there. These parasites are all Apicomplexans and here’s their language https://en.wikipedia.org/wiki/Apicomplexan_life_cycle#oocyst

 

So if you are interested in more than just Isospora, use ContentMine to search for “Apicomplexan”.

 

Most of the papers have well defined messages. The first was about opportunistic infections in HIV patients. Read the word cloudlet for each paper here and see if you can guess the subject of papers 2,3,4,5,6. If you know the species behind the latin names that helps. If you don’t use your friend Wikipedia.

 

Here’s my thinking:

  1. Already done
  2. “Caninum, Parasitology, Vets – probably about Dogs. Toxoplasma I’ve heard of – it’s a parasite and https://en.wikipedia.org/wiki/Toxoplasma_gondii confirms it. Never heard of Neospora or Hammondia but I wouldn’t eat them. Check – https://en.wikipedia.org/wiki/Neospora , https://en.wikipedia.org/wiki/Hammondia_hammondi yes they are both Apicomplexa, the latter of cats. Did we get it right?

Canine faecal contamination and parasitic risk in the city of Naples (southern Italy).

  1. Seems to be about ferrets , and mink (Mustela) getting influenza.  Ferrets develop fatal influenza after inhaling small particle aerosols of highly pathogenic avian influenza virus A/Vietnam/1203/2004 (H5N1).

It is. But why are people worried about ferrets getting sick?? Because influenza uses non-human hosts such as birds and ferrets so we might get it from them. And when I was in the pharma industry they used ferrets as a model of human disease.
Where’s the Isospora?
The animals lacked signs of epizootic catarrhal enteritis, and were negative by microscopy for enteric protozoans such as Eimeria and Isospora species using fecasol, a sodium nitrate fecal flotation solution (EVSCO Pharmaceuticals, Buena, NJ).

 

Translation: we made sure the test animals didn’t have other infections that could distort our research (and we told you how we did it).

  1. I know Gallus is a hen. And we’re going to add an icon and a mouseover on the table so you don’t need to look it up. Eimeria is an apicomplexan, and because it occurs 6 times in the paper it’s pretty important. I’m guessing it’s about parasites of hens. But what’s the rest? There are lots of genes and my guess is that they being used for c omparative genetics or possibly modes of action.
    I don’t know what “QTL”. I probably should, but why bother when we have Wikipedia?

 

A quantitative trait locus (QTL) is a section of DNA (the locus) that correlates with variation in a phenotype (the quantitative trait).[1] The QTL typically is linked to, or contains, the genes that control that phenotype.

 

Rough Translation: The phenotype is what we feel, touch, smell, observe in an organism. and the QTL is that part of the genes that affects it.
So the paper is probably about genomic studies on parasites and chickens. Let’s look: QTL detection for coccidiosis (Eimeria tenella) resistance in a Fayoumi?×?Leghorn F? cross, using a medium-density SNP panel.

Rough translation: analysing the genome of chickens for regions that confer resistance the the most serious parasite. Eimeria is an apicompelxan, so I expect the paper mentions a range of them, including Isospora. (Yes: “Coccidia are sub-classified into several genera, including Eimeria, Isospora, Cryptosporidium, Toxoplasma and Sarcocystis. ) So we’re becoming experts on Apicomplexan names!

  1. Turdus, Coccothraustes … Thrushes and Hawfinch. Also cloudlet show “birds” and “iron”. “Deadly Outbreak of Iron Storage Disease (ISD) in Italian Birds of the Family Turdidae” . This is the paper where they examines the birdshit for parasites…

 

So that seems a lot of work – and we are only 5 papers through. But some of those are relevant to Natalie and some aren’t – her false positives. So can we get ContentMine to select just the ones she needs?
We hope so. If the paper has a lot about apicomplexans it’s probably relevant. If it’s about other diseases such as HIV or flu it’s probably not. So we could remove those automatically.

And that would save a lot of time. And hopefully help us learn bioscience in an efficient manner.

 

   

How ContentMine can help you! Our example looks for “tummy bug” for Natalie

Yesterday Tom, Natalie and I had coffee together. Natalie’s a Vet student – at Royal Veterinary College – and we got talking about her project – 8 weeks doing practical research on Isospora. I’ve never heard of it. No idea what it is.

But ContentMine will know, so we’ll ask it…

We’ll be showing you in later posts how it all works, but just accept that we type:

getpapers -q isospora -x

Wait a minute for ca 207 open access papers to be downloaded , and then

cmine isospora

And wait another minute for ami to crunch through the data. Ami has already created summary files and we’ll look at full.dataTables.html which gives an overall view of all the “plugins” we have used (species, genes, words, etc.). Here’s the first few papers:

Screen Shot 2016-04-29 at 14.04.19

No need to squint – We’ll describe them in larger detail. (Note: some of the links are broken and there are a few false positives, both are being cleaned up).

 

The first column results gives links to the papers (PMC2758902 is a PubMedCentral id and clicking it will link to the EuropePubMedCentral repository of full text papers). Yes, YOU can read them. 200 free papers. If your are interested in Isospora, they are all yours! So here’s the first paper of the 200..

PMC2758902 local

 

We still don’t know what Isospora is, so let’s click on Isospora belli . It’s linked to Wikipedia which says:

Cystoisospora belli, previously known as Isospora belli, is a parasite that causes an intestinal disease known as cystoisosporiasis.[1] This protozoan parasite is opportunistic in immune suppressed human hosts.[2] It primarily exists in the epithelial cells of the small intestine, and develops in the cell cytoplasm.[2] The distribution of this coccidian parasite is cosmopolitan, but is mainly found in tropical and subtropical areas of the world such as the Caribbean, Central and S. America, India, Africa, & S.E. Asia. In the U.S., it is usually associated with HIV infection and institutional living.[3]

So, to paraphrase,

“Isospora is the old name of a nasty tummy bug, found mainly, but not exclusively, in the sub/tropical world that can infect HIV-sufferers”

Biological science is often hard to read for newcomers, but with practice you learn how to translate. Here’s a sentence from one paper:

Coprological examination of fresh stool specimens revealed coccidian oocysts of the genus Isospora in 36% of the birds

Translated:

We examined birdshit and found parasite eggs in 36%.

The long words are useful – they aren’t there just to put you off or be pompous. They help translate between human languages, and they increase precision. If we search for “parasite eggs in birds” we might end up with bird eggs, whereas “oocytes” is more precise. ContentMine loves precise words because it reduces false positives (results that aren’t relevant to what you want).

Column “words” is a list of the commonest word tokens. In this case it’s just “patients”. That confirms that the paper is probably about human infection (though Natalie and other Vets call animals “patients”). So were we right? Click on PMC2758902 and we’ll see:

Screen Shot 2016-04-29 at 14.49.41

So it’s about HIV, and drug treatment. Where’s the Isospora? Search down the full text and we find:

The reasons for hospitalization were: disseminated tuberculosis (month 5), reactivation of oropharyngeal Kaposi’s sarcoma (month 3), and Isospora belli diarrhea with severe dehydration

So if you are interested in finding all papers where Isospora has infected HIV papers, ContentMine can immediately help you.

Nataliie’s main interest is veterinary, so we’ll look at the next few papers. But that shows how much there is in just ONE paper. And why we need machines to help us. Natalie probably mainly wants papers about animals and we can address that as well…

 

… in the next blog post!

 

Latest Article Alert from Archives of Public Health

The following new article has just been published in Archives of Public Health

Research
Sustainable employability for older workers: an explorative survey of belgian companies
Verbrugghe M, Kuipers Y, Vriesacker B, Peeters I, Mortelmans K
Archives of Public Health 2016, 74:15 (28 April 2016)
Abstract http://www.archpublichealth.com/content/74/1/15/abstract
Full

Latest Article Alert from Acta Neuropathologica Communications

The following new articles have just been published in Acta Neuropathologica Communications

Research
Differential roles of hypoxia and innate immunity in juvenile and adult dermatomyositis
Preuße C, Allenbach Y, Hoffmann O, Goebel H, Pehl D, Radke J, Doeser A, Schneider U, Alten R, Kallinich T, Benveniste O, von Moers A, Schoser B, Schara U, Stenzel W
Acta

Latest Article Alert from Environmental Health

The following new articles have just been published in Environmental Health

Research
Neighbourhood walkability, road density and socio-economic status in Sydney, Australia
Cowie C, Ding D, Rolfe M, Mayne D, Jalaludin B, Bauman A, Morgan G
Environmental Health 2016, 15:58 (27 April 2016)
Abstract http://www.ehjournal.net/content/15/1/58/abstract
Full text

Latest Article Alert from Annals of Clinical Microbiology and Antimicrobials

The following new article has just been published in Annals of Clinical Microbiology and Antimicrobials

Research
Comparison of molecular detection methods for pertussis in children during a state-wide outbreak
Qin X, Zerr D, Kronman M, Adler A, Berry J, Rich S, Buccat A, Xu M, Englund J
Annals of Clinical Microbiology and Antimicrobials 2016, 15:28 (27 April 2016)
Abstract

Latest Article Alert from Breast Cancer Research

The following new article has just been published in Breast Cancer Research

Research article
Immune response in breast cancer brain metastases and their microenvironment: the role of the PD-1/PD-L axis
Duchnowska R, Pęksa R, Radecka B, Mandat T, Trojanowski T, Jarosz B, Czartoryska-Arłukowicz B, Olszewski W, Och W, Kalinka-Warzocha E, Kozłowski W, Kowalczyk