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A few years ago, I started looking online to fill in chapters of my family history that no one had ever spoken of.
Phillip Trotter's insight:
Maryn McKenna has consistenly written about the threat of increasing antibiotic resistance for some time and her articles in Wired and other media are worth finding and reading. This is her long form essay on medium, it covers some of the same ground as her other articles it is still very much but its worth reading and reflecting on. 
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"Superbug" bacterial infections that are resistant to common antibiotics are increasing at an alarming rate. But traditional antibiotics aren't the only way to battle dangerous germs. Biomedical scientists are investigating new additions to their arsenal.
Phillip Trotter's insight:
Given the WHO announcement that antibacterial resistance is now a global threat - article on popular mechanic outlines some of the alternate treatments to antibiotics.
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When it comes to our immune response, genetics takes a back seat to pathogens.
Phillip Trotter's insight:
Our adaptive immune system, the one that responds to specific pathogens, relies on T cells and B cells. These cells make proteins that have a key job: distinguish between the harmless proteins in all of our cells and foreign proteins that may be harmful. In T cells, these molecules are creatively called T cell receptors (TCRs), and in B cells they are antibodies.
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Evidence from skulls in east London shows plague had to have been airborne to spread so quickly
Phillip Trotter's insight:
With the exhumation of 25 skeletons, originally buried in the mid 14th Century scientists in London are discovering new clues which indicate the black death was an pulmonary airborne disease. Good article in the Guardian on the initial findings.
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Trophic cascade effects occur when a food web is disrupted by loss or significant reduction of one or more of its members. In East African Rift Valley lakes, the Lesser Flamingo is on top of a short food chain. At irregular intervals, the dominance of their most important food source, the cyanobacterium Arthrospira fusiformis, is interrupted. Bacteriophages are known as potentially controlling photoautotrophic bacterioplankton. In Lake Nakuru (Kenya), we found the highest abundance of suspended viruses ever recorded in a natural aquatic system. We document that cyanophage infection and the related breakdown of A. fusiformis biomass led to a dramatic reduction in flamingo abundance. This documents that virus infection at the very base of a food chain can affect, in a bottom-up cascade, the distribution of end consumers. We anticipate this as an important example for virus-mediated cascading effects, potentially occurring also in various other aquatic food webs. Via Ed Rybicki
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The global spread of epidemics, rumors, opinions, and innovations are complex, network-driven dynamic processes. The combined multiscale nature and intrinsic heterogeneity of the underlying networks make it difficult to develop an intuitive understanding of these processes, to distinguish relevant from peripheral factors, to predict their time course, and to locate their origin. However, we show that complex spatiotemporal patterns can be reduced to surprisingly simple, homogeneous wave propagation patterns, if conventional geographic distance is replaced by a probabilistically motivated effective distance. In the context of global, air-traffic–mediated epidemics, we show that effective distance reliably predicts disease arrival times. Even if epidemiological parameters are unknown, the method can still deliver relative arrival times. The approach can also identify the spatial origin of spreading processes and successfully be applied to data of the worldwide 2009 H1N1 influenza pandemic and 2003 SARS epidemic.
The Hidden Geometry of Complex, Network-Driven Contagion Phenomena Science 13 December 2013: Via Complexity Digest
Phillip Trotter's insight:
This is an awesome insight that needs tested across other datasets to find out how universal it is. Good paper.
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A few years ago, I started looking online to fill in chapters of my family history that no one had ever spoken of.
Phillip Trotter's insight:
Maryn McKenna has been writing a number of articulate well informed and frankly terrifying articles in Wired on the rise of drug resistant antibiotics and their societal implications. This 4000 word essay on medium is certainly worth reading and explains her personal interest in the subject.
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This report, Antibiotic resistance threats in the United States, 2013gives a first-ever snapshot of the burden and threats posed by the antibiotic-resistant germs having the most impact on human health. Each year in the United States, at least 2 million people become infected with bacteria that are resistant to antibiotics and at least 23,000 people die each year as a direct result of these infections. Many more people die from other conditions that were complicated by an antibiotic-resistant infection.
Phillip Trotter's insight:
For those tracking public healthcare issues or modeling disease the new Antibiotic Resistance Threats in the United States from CDC makes chilling reading. The CDC report is the first time the agency has provided hard numbers for the incidence, deaths and cost of all the major antibiotic resistant organisms. The report is also the first time the CDC has ranked resistant organisms by how imminent a threat they pose, using seven criteria: health impact, economic impact, how common the infection is, how easily it spreads, how much further it might spread in the next 10 years, whether there are antibiotics that still work against it, and whether things other than administering antibiotics can be done to curb its spread. For each organism, the report explains why it is a public health threat, where the trends are headed, what actions the CDC is taking, and what it is important for health care institutions, patients and their families, and states and local authorities to do to help. It also makes explicit where the trend of increasing and more common resistance is taking the country, outlining the risks to people taking chemotherapy for cancer, undergoing surgery, taking dialysis, receiving transplants, and undergoing treatment for rheumatoid arthritis.
Michael Totten's comment,
September 23, 2013 12:29 AM
One thing we all should be doing is avoid using any of the anti-microbial soaps that now found around every faucet. The triclosan in the soap kills off all the benign bacterial, creating a vacuum for the more virulent bacteria to thrive. It's a commercial gimmick that should be resisted and reversed. See the medical advice posted at Alliance for Prudent use of Antibiotics, http://www.tufts.edu/med/apua/ and particularly the White Paper on Triclosan, http://www.tufts.edu/med/apua/consumers/personal_home_21_4240495089.pdf
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Researchers have reported the first case of human-to-human transmission of the new bird flu that has emerged in China.
Phillip Trotter's insight:
First recorded case of human to human transmission of H7N9 is being reported by BBC following publication of research findings and an editorial in the British Medical Journal. However the case does not mean the virus can easily spread between humans and according to DrJames Rudge of the London School of Hygiene and Triopical Medicine the occurance is is not suprising since limited transmission has been seen in other bird flu viruses such as H5N1.
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Google Inc launched an open data platform yesterday to share information on natural disasters in Taiwan such as typhoons and floods, with the aim of building the country into a model area for the cloud computing-based system.
Phillip Trotter's insight:
Google has been responding to natural disasters since Hurricane Katrina in 2005 by making information such as storm paths, shelter locations, emergency numbers, and donation opportunities easily accessible. Its great to see them extending these services.
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Since February 2013, China experienced an outbreak of the novel H7N9 avian flu, causing 131 cases of infection, and a death toll of 39. his particular H7N9 strain is considered to be one of the most worrisome pathogens since the H5N1 pandemic in 1997; a reputation based on the virus’ ability to spread easily across species and to infect humans
Phillip Trotter's insight:
With any emergent strain of flu - there is always concern. H7N9 is making headlines because unlike the H5N1 breakout in 1997, where birds died from infection and dead birds indicated presense of H5N1, H7N9 does not appear to harm the host but can infect humans. H7N9 has been shown to infect the upper respiratory tract of pigs and ferrets follow contact with infected birds. This las led to the conclusion so far that human cases exist as a result of direct contact with infected birds. What is unclear at this point if H7N9 (or some future evolution of it) will efficiently transfer from human to human. Until this is demonstrated talk of potential future pandemic needs to be carefully measured. Scientists are now examining how the immmune systems of ducks respond to avian influenza might point the way to new antiviral drugs against H5N1, H7N9, and other avian flu outbreaks in humans.
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A man has died of the novel coronavirus (NCoV) in Tunisia, in what is believed to be the first such case in Africa.
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Networks are commonly used to define underlying interaction structures where infections, information, or other quantities may spread. Although the standard approach has been to aggregate all links into a static structure, some studies have shown that the time order in which the links are established may alter the dynamics of spreading. In this paper, we study the impact of the time ordering in the limits of flow on various empirical temporal networks. By using a random walk dynamics, we estimate the flow on links and convert the original undirected network (temporal and static) into a directed flow network. We then introduce the concept of flow motifs and quantify the divergence in the representativity of motifs when using the temporal and static frameworks. We find that the regularity of contacts and persistence of vertices (common in email communication and face-to-face interactions) result on little differences in the limits of flow for both frameworks. On the other hand, in the case of communication within a dating site and of a sexual network, the flow between vertices changes significantly in the temporal framework such that the static approximation poorly represents the structure of contacts. We have also observed that cliques with 3 and 4 vertices containing only low-flow links are more represented than the same cliques with all high-flow links. The representativity of these low-flow cliques is higher in the temporal framework. Our results suggest that the flow between vertices connected in cliques depend on the topological context in which they are placed and in the time sequence in which the links are established. The structure of the clique alone does not completely characterize the potential of flow between the vertices.
Flow motifs reveal limitations of the static framework to represent human interactions Luis E. C. Rocha and Vincent D. Blondel Phys. Rev. E 87, 042814 (2013) http://dx.doi.org/10.1103/PhysRevE.87.042814 Via Complexity Digest
Phillip Trotter's insight:
In our own research temporality of relationships or interactions between agents is a common property of various systems (think infection, traffic, economic exchange). Maybe its coming from a computer graphics background but their use of Flow motifs reminds me a lot of flow fields and glyph representations in scientific visualizations.
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New WHO report provides the most comprehensive picture of antibiotic resistance to date, with data from 114 countries
Phillip Trotter's insight:
Resistance to antibiotics poses a "major global threat" to public health, says a new report by the World Health Organization (WHO). The WHO team analysed data from 114 countries and said resistance was happening now "in every region of the world". The report describes a "post-antibiotic era", where people die from simple infections that have been treatable for decades.
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In Western Tanzania tribes of wandering foragers called Hadza eat a diet of roots, berries, and game. According to a new study, their guts are home to a microbial community unlike anything that's been seen before in a modern human population -- providing, perhaps, a snapshot of what the human gut microbiome looked like before our ancestors figured out how to farm about 12,000 years ago.
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Digital volunteers are racing to map regions in West Africa where the Ebola virus, which has a 90 percent fatality rate, continues to spread
Phillip Trotter's insight:
The use of OpenStreetMap (OSM) as an unifying geodata system is increasing in humanitarian aid. The current Ebola outbreak in West Africa is a challenge at multiple levels for teams trying to coordinate a response. Due to years of war there are few up to date maps in the region and multiple boundaries mean different groups are collecting data. Digital volunteers creating new OSM entries will be a key asset in enabling health officials to manage the outbreak and hopefully bring things under control.
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A food poisoning bacterium may be implicated in MS, say US researchers.
Phillip Trotter's insight:
Lab tests in mice by the team from Weill Cornell Medical College revealed a toxin made by a rare strain of Clostridium perfringens caused MS-like damage in the brain. And earlier work by the same team, published in PLoS ONE, identified the toxin-producing strain of C. perfringens in a young woman with MS. However experts urge caution, saying more work is needed to explore the link. Click on title or image to go the story.
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A painful mosquito-borne disease is spotted in the Western Hemisphere for first time, boosting U.S. risk. Given a choice between dengue fever or another mosquito-borne disease called chikungunya fever, choose dengue every time. Neither has an available vaccine or treatment, but chikungunya (pronounced chik-un-GUHN-ya) is far more severe – it literally means “that which bends up” because patients are often stooped over from debilitating joint pain. If you’re a resident of the Caribbean island of St. Martin (or lucky enough to be traveling there for the holidays) you are now at risk of both. The island, roughly the size of Manhattan and located some 300 kilometers east of Puerto Rico, has the first confirmed outbreak of chikungunya in the Western Hemisphere. Via Ed Rybicki
Ed Rybicki's curator insight,
December 28, 2013 1:15 PM
I hate to say it, but why is something only severe when it threatens the US? As it is, global warming has now brought chikungunya (which comes from near where I grew up) to near the US - and it will almost certainly join West Nile as being endemic fairly soon. Which means we may get a vaccine....
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The dynamics of economies and infectious disease are inexorably linked: economic well-being influences health (sanitation, nutrition, treatment capacity, etc.) and health influences economic well-being (labor productivity lost to sickness and disease). Often societies are locked into ``poverty traps'' of poor health and poor economy. Here, using a simplified coupled disease-economic model with endogenous capital growth we demonstrate the formation of poverty traps, as well as ways to escape them. We suggest two possible mechanisms of escape both motivated by empirical data: one, through an influx of capital (development aid), and another through changing the percentage of GDP spent on healthcare. We find that a large influx of capital is successful in escaping the poverty trap, but increasing health spending alone is not. Our results demonstrate that escape from a poverty trap may be possible, and carry important policy implications in the world-wide distribution of aid and within-country healthcare spending.
Escaping the poverty trap: modeling the interplay between economic growth and the ecology of infectious disease http://arxiv.org/abs/1311.4079 Via Complexity Digest, Eugene Ch'ng
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Key features of Alzheimer's, which affects about 5 million Americans, are wholesale loss of synapses -- contact points via which nerve cells relay signals to one another -- and a parallel deterioration in brain function, notably in the ability to remember. Now research by Carla Shatz, PhD, professor of neurobiology and of biology and senior author of a study that will be published Sept. 20 in Science,, suggests that Alzheimer's disease starts to manifest long before plaque formation becomes evident
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A malaria vaccine has shown promising results in early stage clinical trials, according to researchers.
Phillip Trotter's insight:
Researchers found the vaccine, which is being developed in the US, protected 12 out of 15 patients from the disease, when given in high doses. The method is unusual because it involves injecting live but weakened malaria-causing parasites directly into patients to trigger immunity.
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The new Mers virus, which has killed half of those infected, is "unlikely" to reach the same scale as Sars, ministers in Saudi Arabia say.
Phillip Trotter's insight:
The source of the Mers virus is still unknown. Given that Mers is from the same group of viruses as Sars and Common Cold - understanding the genotype and phenotype differences and how they relate to pathogenic and vector pathways in its related family could help to better understand both Mers and related groups and perhaps indicate a source. Viral evolution is something we still know relatively little about - and understanding of how they coevolve and relate to microbial habitat are becoming increasingly important to health planning and treatments.
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Phillip Trotter's insight:
StanMed is always worth reading and the Standford Medicine Summer 2013 Special Report is an awesome collection of articles. Crossing Paths with disease bearing pests is a great article on disease mapping and modeling using malaria as an illustrative example for guiding effective health policy. However with articles on debugging dhaka's water, citezin scientists and neighbourhood health, learning lessons from Hurrican Sandy, interview with matt Damon and Gary White about their Water.org work the rest of the issue is worth looking at too.
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There have been 131 cases of infection confirmed cases of H7N9 in mainland China with 39 deaths. A lack of information about the virus and its mode of transmission led to public concerns that H7N9 could be a pandemic waiting to happen.A map of avian influenza (H7N9) risk is now available. The map is comprised of bird migration patterns, and adding in estimations of poultry production and consumption, which are used to infer future risk and to advise on ways to prevent infection.
Phillip Trotter's insight:
Professor Jiming Liu who led the study explained, "By basing our model on wild bird migration and distribution of potentially infected poultry we are able to produce a time line of the estimated risk of human infection with H7N9. The preliminary results of our study made a prediction of bird flu risk which could explain the pattern of the most recent cases. By extending the model we will be able to predict future infection risks across central and western China, which will aid in surveillance and control of H7N9 infections. Since the effect of poultry-to-poultry infection is not really understood it may become necessary to regulate the activity of poultry markets. To learn more click on the image or title.
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BackgroundOn March 30, 2013, a novel avian influenza A H7N9 virus that infects human beings was identified. This virus had been detected in six provinces and municipal cities in China as of April 18, 2013. We correlated genomic sequences from avian influenza viruses with ecological information and did phylogenetic and coalescent analyses to extrapolate the potential origins of the virus and possible routes of reassortment events.MethodsWe downloaded H7N9 virus genome sequences from the Global Initiative on Sharing Avian Influenza Data (GISAID) database and public sequences used from the Influenza Virus Resource. We constructed phylogenetic trees and did 1000 bootstrap replicates for each tree. Two rounds of phylogenetic analyses were done. We used at least 100 closely related sequences for each gene to infer the overall topology, removed suspicious sequences from the trees, and focused on the closest clades to the novel H7N9 viruses. We compared our tree topologies with those from a bayesian evolutionary analysis by sampling trees (BEAST) analysis. We used the bayesian Markov chain Monte Carlo method to jointly estimate phylogenies, divergence times, and other evolutionary parameters for all eight gene fragments. We used sequence alignment and homology-modelling methods to study specific mutations regarding phenotypes, specifically addressing the human receptor binding properties.FindingsThe novel avian influenza A H7N9 virus originated from multiple reassortment events. The HA gene might have originated from avian influenza viruses of duck origin, and the NA gene might have transferred from migratory birds infected with avian influenza viruses along the east Asian flyway. The six internal genes of this virus probably originated from two different groups of H9N2 avian influenza viruses, which were isolated from chickens. Detailed analyses also showed that ducks and chickens probably acted as the intermediate hosts leading to the emergence of this virulent H7N9 virus. Genotypic and potential phenotypic differences imply that the isolates causing this outbreak form two separate subclades.InterpretationThe novel avian influenza A H7N9 virus might have evolved from at least four origins. Diversity among isolates implies that the H7N9 virus has evolved into at least two different lineages. Unknown intermediate hosts involved might be implicated, extensive global surveillance is needed, and domestic-poultry-to-person transmission should be closely watched in the future.FundingChina Ministry of Science and Technology Project 973, National Natural Science Foundation of China, China Health and Family Planning Commission, Chinese Academy of Sciences.
Phillip Trotter's insight:
Firstly sidestepping the important findings for H7N9 virus, this paper illustrates the importance of rgorous methodology and key research methods for understanding disease evolution and contagence pathways. the paper details correlated genomic sequences and ecological information using phylogenetic and coalescent analyses to extrapolate the potential originsand possible routes of reassortment events in H7N9 virus. As for the findings - novel avian influenza viruses are a major concern for world wide public health - the research work in this paper raises the need for understanding intermediate hosts, viral evolution pathways and domestic poultry wild animation contact on a global scale for future health policy. Worth reading.
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It seems that we are about to get closer to death, as our antibiotics, pesticides, herbicides and all other methods of cheating death, disease and crop failure fail.
This is before we get into conversations about the looming international and intranational conflicts that are simmering beneath the surface. At least these can be dealt with with sensible policy changes and changes in attitude, perspective and disposition, if not out right content in our leadership cadres.
But alas, I don't see that happening in the foreseeable future.
Time is ticking away.
And we too will go through an indiscriminate die off phase where friends and family will die off, along with enemies and pestilential people as well.
I'd like to think that we'd come off better than before.
But, that's the thing about these indiscriminate methods of killing large swaths of the population. It very rarely yields anything other than what was already present.
At least wages should be better, due to the new shortage of laborers (assuming that robots haven't taken over our labor force in the meantime).
I'd like to think that our lot is constantly improving, even during these negative phases.
But, I know that it's not going to be easy, especially for most of our Western and American population who don't have experience handling these kinds of things.
Ah well.
Think about it.