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Posts Tagged ‘epidemiology

“Not with a bang, but with a whimper”*…

 

death

Death Table from Tuberculosis in the United States, prepared for the International Congress on Tuberculosis, September 21 to October 12, 1908. Image: U.S. National Library of Medicine

 

Recent history tells us a lot about how epidemics unfold, how outbreaks spread, and how they are controlled. We also know a good deal about beginnings—those first cases of pneumonia in Guangdong marking the SARS outbreak of 2002–3, the earliest instances of influenza in Veracruz leading to the H1N1 influenza pandemic of 2009–10, the outbreak of hemorrhagic fever in Guinea sparking the Ebola pandemic of 2014–16. But these stories of rising action and a dramatic denouement only get us so far in coming to terms with the global crisis of COVID-19. The coronavirus pandemic has blown past many efforts at containment, snapped the reins of case detection and surveillance across the world, and saturated all inhabited continents. To understand possible endings for this epidemic, we must look elsewhere than the neat pattern of beginning and end—and reconsider what we mean by the talk of “ending” epidemics to begin with…

Contrary to hopes for a tidy conclusion to the COVID-19 pandemic, history shows that outbreaks of infectious disease often have much murkier outcomes—including simply being forgotten about, or dismissed as someone else’s problem: “How Epidemics End.”

* T. S. Eliot, “The Hollow Men”

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As we contemplate the end, we might send insightful birthday greetings to Nettie Maria Stevens; she was born on this date in 1861.  A geneticist– and one of the first American women to achieve recognition for her contributions to scientific research– she built on the rediscovery of Mendel‘s paper on genetics (in 1900) with work that identified the mechanism of sexual selection: its determination by the single difference between two classes of sperm—the presence or absence of (what we now call) an X chromosome.

220px-Nettie_Stevens source

 

“Law; an ordinance of reason for the common good, made by him who has care of the community”*…

 

vaccination

 

In the fall of 1713, measles struck the city of Boston, where Cotton Mather, a Puritan theologian and pastor, lived with his pregnant wife and numerous children. Within a month, his wife, their twin newborn babies, another child, and their maidservant had all died. On November 12, Mather wrote in his journal, “The epidemical Malady began upon this Town, is like to pass thro’ the Countrey. . . . it [might] be a service unto the public, to insert in the News-paper, a brief Direction for the managing of the sick. I will advise with a Physician or two.” On November 21, he wrote, “Lord I am oppressed; undertake for me!” On November 23, he wrote, “My poor Family is now left without any Infant in it, or any under seven Years of Age.”

Eight years later, when an explosive smallpox epidemic threatened Boston’s population of eleven thousand, Mather became an outspoken advocate for a new prophylactic against the virus: inoculation. Dr. William Douglass, one of the few doctors in town with a medical degree, rallied others to oppose Mather, claiming that the method was untested (which was true, at least in the new colony) and that it jeopardized the lives of all those who received it. In young Boston, the fight over inoculation tore at epidemic-addled nerves. In November 1721, a bomb was thrown through Mather’s window. A letter attached to it read, “Cotton Mather, you dog, dam you! I’ll inoculate you with this; with a pox to you.”

Douglass won out, quashing Mather’s plans for a systematic inoculation of the town’s population. Eight hundred and forty-four people died of the virus, accounting for 75 percent of all deaths in Boston that year. The unexploded bomb on Mather’s floorboards disabuses those of us living in 2019 of the impression—generated over the past two years by endless news stories about the current global measles outbreak—that inoculation controversies are a novel feature of our present hyper-mediated, hyper-politicized time.

Measles was considered to be eliminated in the United States in 2000. Still, the virus has regained extraordinary ground—and claimed an increasing number of lives—in recent years. Seven hundred and four cases were reported in the United States in the first four months of 2019, according to the Centers for Disease Control and Prevention. The count reached 1,077 by mid-June, occurring in twenty-eight states. More than six hundred cases have occurred in New York City alone since September of 2018.

In June, the CDC issued a warning to travelers planning to leave the country, by which point outbreaks were occurring in all the places you’d expect, countries beset by depressed economies, poor public health management, war, or extreme poverty, including Ethiopia, Madagascar, Kyrgyzstan, the Democratic Republic of Congo, the Philippines, Sudan, and Georgia (not the U.S. state, although cases have been reported there as well). But also, cases were appearing in countries where entrenched vaccination systems existed and where measles had been thought largely a disease of the past: Belgium, France, Germany, and Italy.

The grand cause for these infections—and for the 300 percent growth of reported measles cases around the world in the first quarter of the year over the same quarter the previous year—is precisely the absence of what Cotton Mather proposed for 1721-era Boston: systematic vaccination of the population. The more interesting question, beyond simple international vaccination logistics, is: What ideological and historical shifts have allowed the reemergence of a disease once believed to be under controlled decline?…

A history of the debates over vaccination that asks, can the social contract be protected from a measles outbreak?: “Herd Immunity.”

* Thomas Aquinas

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As we pull up our sleeves, we might send healing birthday greetings to Giovanni Maria Lancisi; he was born on this date in 1654.  A doctor (he was personal physician to three popes), epidemiologist (he made the correlation between mosquitoes and malaria), and anatomist (his study of the heart resulted in the eponymous Lancisi’s sign), he is considered the first modern hygienist.

He carried out extensive anatomical and physiological studies, also epidemiology studies on malaria, influenza and cattle plague.  Contrary to the then-traditional conception of “mal’ aria ” – literally, “bad air” – Lancisi observed that the lethal fever, malaria, disappeared when the swamps near to the city were cleared.  He concluded that injurious substances transmitted from flies and mosquitoes were the origin of the disease.

250px-Giovanni_Maria_Lancisi source

 

 

Written by LW

October 26, 2019 at 1:01 am

“Extreme remedies are very appropriate for extreme diseases”*…

 

frog

The Toad Mountain harlequin frog is endangered and at risk from the Bd fungus

 

A century ago, a strain of pandemic flu killed up to 100 million people—5 percent of the world’s population. In 2013, a new mystery illness swept the western coast of North America, causing starfish to disintegrate. In 2015, a big-nosed Asian antelope known as the saiga lost two-thirds of its population—some 200,000 individuals—to what now looks to be a bacterial infection. But none of these devastating infections comes close to the destructive power of Bd—a singularly apocalyptic fungus that’s unrivaled in its ability not only to kill animals, but to delete entire species from existence.

Bd—Batrachochytrium dendrobatidis in full—kills frogs and other amphibians by eating away at their skin and triggering fatal heart attacks. It’s often said that the fungus has caused the decline or extinction of 200 amphibian species, but that figure is almost two decades out-of-date. New figures, compiled by a team led by Ben Scheele from the Australian National University, are much worse.

Scheele’s team estimates that the fungus has caused the decline of 501 amphibian species—about 6.5 percent of the known total. Of these, 90 have been wiped out entirely. Another 124 have fallen by more than 90 percent, and their odds of recovery are slim. Never in recorded history has a single disease burned down so much of the tree of life. “It rewrote our understanding of what disease could do to wildlife,” Scheele says…

The story of an unprecedented pathogen: “The Worst Disease Ever Recorded.” (Lest one rest too easily because this threat seems to target not humans but animals at some distance on the tree of life, see here.)

* Hippocrates

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As we do our best to stave off extinctions, we might recall that on this date in 1981, Nature set the world’s record for “Longest Scientific Name” when it published the systematic name for the deoxyribonucleic acid (DNA) of the human mitochondria; it contains 16,569 nucleotide residues and is thus about 207,000 letters long.

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The 16,569 bp long human mitochondrial genome with the protein-coding, ribosomal RNA, and transfer RNA genes

source

 

Written by LW

April 9, 2019 at 1:01 am

“Without data, you’re just another person with an opinion”*…

 

It used to be that we’d see a poorly made graph or a data design goof, laugh it up a bit, and then carry on. At some point though — during this past year especially — it grew more difficult to distinguish a visualization snafu from bias and deliberate misinformation.

Of course, lying with statistics has been a thing for a long time, but charts tend to spread far and wide these days. There’s a lot of them. Some don’t tell the truth. Maybe you glance at it and that’s it, but a simple message sticks and builds. Before you know it, Leonardo DiCaprio spins a top on a table and no one cares if it falls or continues to rotate.

So it’s all the more important now to quickly decide if a graph is telling the truth…

Nathan Yau (Flowing Data) provides a very helpful (and very amusing) guide: “How to Spot Visualization Lies.”

* W. Edwards Deming

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As we key our eyes open, we might send healthy birthday greetings to John Snow; he was born on this date in 1813.  A physician and a leader in the adoption of anaesthesia and medical hygiene, he is considered the father of modern epidemiology, in large measure because of his work in tracing the source of a cholera outbreak in Soho, London, in 1854.  His On the Mode of Communication of Cholera (1849) suggested that cholera was a contagious disease easily transmitted by contaminated water. But the widely-held theory was that diseases are caused by bad air led to his idea being ignored.  Then, in London’s 1854 cholera emergency, he painstakingly correlated individual cholera casualties to the water supply they had used in each case.  He then communicated his results with a map that underlined his point, and ended the deadly epidemic by removing the pump handle of the community water pump that he found to be the culprit.

Snow’s map of cholera cases

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His findings inspired fundamental changes in the water and waste systems of London, which led to similar changes in other cities, and a significant improvement in general public health around the world.  His mode of communicating them contributed to the rise of data visualization.

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Written by LW

March 15, 2017 at 1:01 am

“Eventually, all things merge into one, and a river runs through it”*…

 

Cartographer Daniel Huffman has created a series of maps in which American river systems are visualized as subway maps (specifically, in the manner of Harry Beck’s 1930s London Tube maps), with nodes representing connections between streams and tributaries.

Huffman strikes a particular chord in the map-lover’s heart. On an Internet brimming with sleek, sharp geo-visualizations, Huffman’s maps offer a sweetly idiosyncratic view of the world. The signatures of historic figures turn into street vectors. Oregon’s wine country gets the ‘90s computer-game treatment. A simple bike path becomes a work of calligraphy.

“What it really probably comes down to is a desire to do things differently than others,” he says in an email. “I crave variety, and so it often leads me to thinking of weird ideas and saying, ‘I wonder if I can do X[.]’”

Lately, a trend has emerged out of Huffman’s impulses towards novelty—an idea he calls “Modern Naturalism,” in which his maps present natural features in the type of “highly-abstracted, geometrically precise visual language that we often apply to the constructed world on maps,” according to his website

More on Huffman and his marvelous maps at “When Rivers Look Like Subway Systems.”

* Norman Maclean, A River Runs Through It and Other Stories

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As we hop onto our rafts, we might send healing birthday greetings to Florence Nightingale, born on this date in 1820. Famed for her work as a nurse in the Crimean War, she went on to found training facilities and nursing homes– pioneering both medical training for women and what is now known as Social Entrepreneuring.  Less well-known are Nightingale’s contributions to epidemiology, statistics, and the visual communication of data in the field of public health.  Always good at math, she pioneered the use of the polar area chart (the equivalent to a modern circular histogram or rose diagram) and popularized the pie chart (which had been developed in 1801 by William Playfair).  Nightingale was elected the first female member of the Royal Statistical Society, and later became an honorary member of the American Statistical Association.

“Diagram of the causes of mortality in the army in the East” by Florence Nightingale, an example of the the polar area diagram (AKA, the Nightingale rose diagram)

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Written by LW

May 12, 2015 at 1:01 am

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