@LancetGH looks at data collection on deaths from the war in #Syria

Thursday, December 14, 2017

The January 2018 issue of Lancet Global Health features an article (and associated commentary) on an analysis of civilian and combatant deaths using data from the Violations Documentation Center (VDC, which until now I didn't even know existed).
This study makes use of the systematic recording of violent deaths from the Syrian civil war by the Violation Documentation Center over 6 years of conflict to provide a systematic analysis of civilian and opposition combatant violent deaths, their demographic characteristics, the causative method or weapon, and spatial and temporal patterns of direct deaths during the conflict. We relate patterns and causes of death to possible violations of international humanitarian law.
The authors don't mince words - they are explicit in their conclusion that the results of the analysis indicate possible war crimes. Of course, pretty much everyone who still cares about Syria already knows that, but additional evidence never hurts - even if it will never make the UN move. What is particularly horrifying is the effect that the increasing use of aerial bombardment in general, and barrel bombs in particular, on civilian deaths - over a quarter of which were children.

Unfortunately, the VDC data only contains deaths that occurred in areas outside of government control (as “information on victims in government-controlled areas can be difficult to obtain”), so the analysis is geographically incomplete and does not include any deaths among Syrian government forces. But the data that is available is incredibly detailed and valuable:
Documentation of the health impact of war and conflict is one of the most difficult yet important public health challenges....Yet, the health and population impact of conflicts is dramatic and their effects long lasting. Any attempt to understand these events requires careful data collection and contemporaneous analysis to capture data that would otherwise be lost. Only through collection efforts such as those mounted by the VDC and analyses like the one presented by Guha-Sapir and colleagues can propel researchers and policymakers into recognising the true costs of current wars and the need to mitigate such consequences in the future.

Last week in @CDCMMWR: #GuineaWorm eradication

Tuesday, December 12, 2017

Dracunculiasis (commonly known as Guinea worm) is by far the most likely candidate for the second disease mankind will succeed in eradicating from the earth. (The first, and only, one so far is smallpox.) Last week's edition of MMWR featured a progress report on eradicating Guinea worm, describing progress in the last 18 months after some setbacks in 2016:
The number of human dracunculiasis cases reported worldwide during 2016 increased to 25 cases in three countries in 2016 from 22 cases in four countries in 2015. However, during January–June 2017, the number of cases reported decreased from 10 cases in three countries during the same period in 2016, to eight, all in Chad. The number of infected domestic dogs doubled from 503 in 2015 to 1,011 in 2016, but declined to 537 during January–June 2017 compared with 653 during the same period of 2016.
Aside from infected dogs, the most significant barriers to eradication are "civil unrest and insecurity in Mali and South Sudan." Somebody please get them to quit fighting over there so I am no longer subjected to images of a Guinea worm coming out of some poor bastard's lower leg in my e-mails from MMWR.

#HIV Round-up: webinars, @AMJPublicHealth articles, and a special issue of @HHRJournal

Monday, December 11, 2017

World AIDS Day is December 1 - which means, first and foremost and most importantly, that we are still fighting HIV and that the work is not done. The silver lining (for epi nerds like me) is that December produces a steady stream of great research and learning material on the full cascade (har) of HIV-related issues in all parts of the world. Below is a sampling of some of the content that caught my eye last week.

  • Biomedical Advances in HIV Prevention: PrEP, PEP, Microbicides and U=U,” collaboratively hosted by Regional Resource Network Program (RRNP), the U.S. Department of Health and Human Services, and the Office of the Assistant Secretary for Health, Region II. The provided description was minimal and basically rehashed the title, so I won't include it here, but I will note that "U=U" stands for "undetectable=untransmittable," shorthand for the finding that PLHIV who maintain viral suppression have effectively zero risk of transmitting the virus to their sexual partners. Run time: 1 hour, 33 minutes.
  • "What is the Future of HIV Funding?" by the Kaiser Family Foundation and Funders Concerned About AIDS. True to form (because they are fabulous), KFF has made the slides available in PDF format as well. Run time: 1 hour, 4 minutes.
    As we recognized World AIDS Day this year, the outlook for funding to address the global and domestic HIV/AIDS epidemics remained uncertain. What is the status of U.S. government funding for domestic and global HIV efforts? What about other donor governments and multilateral efforts? What role does private philanthropy play in fighting the epidemic? What is at stake looking ahead? On Friday, December 8, the Kaiser Family Foundation (KFF) and Funders Concerned About AIDS (FCAA) hosted a web briefing to look at the latest data on funding for HIV, trends over time, and what we might expect going forward. The briefing included time for audience Q&A.
  • "Increasing Virologic Suppression: Promising Practices from HIV Health Improvement Affinity Group States" by the National Academy for State Health Policy. (Bonus: NASHP has its own YouTube channel!) Run time: 1 hour, 22 minutes.
    Increasing rates of virologic suppression among people living with HIV is critically important to improving their quality of life and decreasing the risk of further HIV transmission. For the last 12 months, the HIV Health Improvement Affinity Group has worked with state health departments and Medicaid agencies from 19 states to develop and implement performance improvement projects aimed at improving rates of sustained virologic suppression among Medicaid beneficiaries living with HIV. This webinar will feature leaders from the Office of HIV/AIDS and Infectious Disease Policy in the US Department of Health & Human Services, the Centers for Medicare & Medicaid Services, the Health Resources and Services Administration, and the Centers for Disease Control and Prevention. It will also feature Affinity Group states, Alaska and North Carolina, that will share lessons learned and best practices from their performance improvement projects.

Articles from the American Journal of Public Health:
While AJPH did not run a special December issue on HIV, it has put out a call for papers on "Monitoring Disparities in Prevention and Treatment of HIV, Viral Hepatitis, STDs, and TB" (submissions due January 31, 2018). The January 2018 issue featured several pieces that either directly addressed HIV or are relevant to HIV:

Special edition of Health and Human Rights Journal:
Harvard's HHR Journal does two editions per year, one in June and one in December. Fittingly, the December 2017 edition contained a special section on HIV and Human Rights, done in collaboration with UNAIDS. It features pieces by heavyweights such as Michel Sidibé (current UNAIDS executive director) and Peter Piot (first and former UNAIDS executive director)...and me, in my first publication as sole author! I got a kick out of seeing my paper criticizing South Korea's misrepresentation of itself as having no HIV-related travel restrictions alongside pieces by UNAIDS officials, who recognize South Korea as a restriction-free country despite mountains of evidence to the contrary. I suppose it is a moot point, as UNAIDS has mostly scrubbed its website clean of its initiative to eliminate HIV-related travel restrictions. The link to the issue on its human rights page goes nowhere. Ah, well.

@KHNews calls out @JohnsHopkins and @UMMC for ignoring asthma in Baltimore

Thursday, December 7, 2017

Kaiser Health News published a hard-hitting piece on asthma in low-income housing in Baltimore yesterday, essentially calling out Johns Hopkins and the University of Maryland Medical Center for profiting from the poor in the city's worst asthma hot spot. The article asserts that the two medical centers receive tax benefits and research dollars for "serving the community" while also reaping profits from Medicaid clients who are repeatedly hospitalized with severe asthma attacks, because they do next to no community-based work with the clients themselves - in effect, by not serving the community.
The supreme irony of the localized epidemic is that Keyonta’s neighborhood in southwest Baltimore is in the shadow of prestigious medical centers [Johns Hopkins and UMMC]...Both receive massive tax breaks in return for providing “community benefit,” a poorly defined federal requirement that they serve their neighborhoods.
But like hospitals across the country, the institutions have done little to address the root causes of asthma. The perverse incentives of the health care payment system have long made it far more lucrative to treat severe, dangerous asthma attacks than to prevent them.
The authors conducted interviews with asthma patients and their family members in zip code 21223 and visited homes to report on environmental conditions. They also analyzed three years of de-identified hospital admissions data for the state of Maryland. (The methodology is detailed in a box at the bottom of the article.) The analysis is eye-popping, but sadly familiar to those of us who have worked with Medicaid or similar data:
For each emergency room visit to treat Baltimore residents for asthma, according to the data, hospitals were paid $871, on average. For each inpatient case, the average revenue was $8,698. In one recent three-year period, hospitals collected $6.1 million for treating just 50 inpatients, the ones most frequently ill with asthma, each of whom visited the hospital at least 10 times.
They then go on to depict officials from Hopkins passing the buck:
Hopkins’ own research shows that shifting dollars from hospitals to Lemmon Street and other asthma hot spots could more than pay for itself. Half the cost of one admission — a few thousand dollars — could buy air purifiers, pest control, visits by community health workers and other measures proven to slash asthma attacks and hospital visits by frequent users.

“We love” these ideas, and “we think it’s the right thing to do,” said Patricia Brown, a senior vice president at Hopkins in charge of managed care and population health. “We know who these people are...This is doable, and somebody should do it.”
The subtext, of course, is that "somebody other than us should do it," a subtext made all the more obvious with the article's direct contrast to the Children's National Health System in DC, which sends asthma patients to a clinic that provides education to families on how to manage their medications and remove environmental asthma triggers in the home.

The piece highlights the health consequences of low-income housing in a powerful way. I imagine the average middle-class American has no idea that there are people in this country who live in houses with dirt-floor basements or neighborhoods with no trash pickup to speak of, or that there are moms who resort to "[wielding] a BB gun to keep rats from her asthmatic child." I also like the way it draws attention to the divide between the ivory tower and the real world, so to speak - well-paid researchers who receive millions in grants to run studies on asthma public health interventions and publish papers in high-profile journals, but then who have no connection to, or interest in, community programs that could actually scale up those interventions for the benefit of people living in their own backyards.

At the same time, I can see how it could be frustrating for administrators at these hospitals to be villainized in a piece like this when they are also held to account for the other 982 public health crises in a community like Baltimore, which all have their roots in a fragmented, overpriced health care system. The authors mention off-hand that "[e]xecutives...acknowledge that they should do more about asthma in the community but note that there are many competing problems: diabetes, drug overdoses, infant mortality and mental illness among the homeless." Arguably, those executives are absolutely right, and I would argue that it does make more sense for them to prioritize things like drug overdose and infant (and maternal) mortality, particularly when the asthma triggers in low-income housing should be addressed by agencies like HUD. The article interviews Ben Carson and paints him in a positive, almost sage-like light, when it could justifiably throw an equal share of the blame at his feet. It is HUD and similar agencies, not hospitals, that should be providing assistance like holding landlords accountable for shitty housing conditions and interfacing with municipal governments to clean up crack houses and ensure a trash pick-up schedule that respects human dignity.

Overall, though, this is an important piece that draws attention to an issue that does not get enough of it.

@CDCMMWR Vital Signs report: The impacts of undiagnosed and delayed diagnosis of #HIV

Friday, December 1, 2017

An MMWR "Vital Signs" early release on undiagnosed HIV infection and its impact on the epidemiology of the epidemic has been making the rounds this week. The report uses data from the National HIV Surveillance System through 2015 to calculate an estimate for the annual number of HIV infections, both diagnosed and undiagnosed:
The first CD4 test after HIV diagnosis and a CD4 depletion model indicating disease progression were used to estimate year of infection and the distribution of time from HIV infection to diagnosis among persons with diagnosed infection. The distribution of diagnosis delay was used to estimate the annual number of HIV infections, which includes persons with diagnosed infection and persons with undiagnosed infection.
The number of persons with undiagnosed HIV infection was estimated by subtracting the number of reported cumulative diagnoses from the number of estimated cumulative infections. The percentage of undiagnosed infections was determined by dividing the number of undiagnosed infections by the total HIV prevalence.
I found the bit about the "CD4 depletion model" to be particularly interesting. This refers to calculating the length of an individual's infection based on their CD4 level at diagnosis by using biomedical data on how quickly HIV kills off CD4 cells. (Most HIV surveillance data comes from lab reports, so surveillance programs receive CD4 and viral load information automatically when the lab report is received.) They can then "backtrack" and compare those estimates with the number of cases that were actually reported for a given year, which allows them to estimate the overall prevalence of HIV and the percentage of those cases that are undiagnosed. The math is relatively simple, but it underscores the importance of supporting disease surveillance systems, as the data they collect can clarify so much of the picture of the overall epidemic.

The article also looks at data on groups at high risk for HIV infection from the National HIV Behavioral Surveillance System, a survey program which collects data from MSM, PWID, and heterosexuals at high risk. Those numbers show that testing has increased among all three groups, but that there were missed opportunities that could be addressed through more widespread routine screening in healthcare settings:
Among persons interviewed through NHBS, the percentage reporting an HIV test in the 12 months preceding the interview increased over time among MSM (from 63% in 2008 to 71% in 2014), persons who inject drugs (from 50% in 2009 to 58% in 2015), and heterosexual persons at increased risk for infection (from 34% in 2010 to 41% in 2016).
In each risk group, at least two thirds of persons who did not have an HIV test had seen a health care provider in the past year (Table 2). Among those who had not tested in the past year and had visited a health care provider, approximately three quarters reported not having been offered an HIV test at any of their health care visits.
Unfortunately, it's tough for me to get excited about progress like this because this kind of national data is always two years delayed. The Obama administration made it a priority to reduce the number of HIV infections, so the importance of HIV prevention programs was taken as a given. It remains to be seen whether this progress will be sustained under the current political climate, particularly in the light of the raging opioid epidemic. Unfortunately, we won't know for another two years.

I am now caught up on #opendata highlights - with infectious diseases and genetics!

Thursday, November 30, 2017

Because I've had a gap in blogging over the last few months, I thought I would ease back into things by highlighting public health-related data sets going back through Data is Plural, one edition at a time.

This is the last one - I'm finally caught up!

The June 28 edition of Data is Plural features two health-related data sets - one on infectious diseases in Europe and another that contains people's self-published results of commercial genetics tests:
Infectious diseases in Europe. The European Centre for Disease Prevention and Control’s Surveillance Atlas of Infectious Diseases lets you browse, map, and download data on the historical incidence of several dozen diseases — from anthrax to Zika — in each of the European Economic Area’s countries. Related: Keila Guimarães’s recent investigation into penicillin shortages, which uses the Centre’s data on syphilis cases.

People’s genes. OpenSNP is a website that lets people publish the results of their genetic tests (such as those sold by 23andMe, deCODEme, FamilyTreeDNA), “find others with similar genetic variations, [get] the latest primary literature on their variations, and help scientists find new associations.” Since 2012, users have uploaded more than 3,000 sets of genetic variants, which you can download individually or in bulk or access via OpenSNP’s API. Users can also list various personal traits, such as eye color, height, coffee consumption, and lactose intolerance. Useful primer: SNP stands for “single nucleotide polymorphism,” the NIH explains. They’re “the most common type of genetic variation”; each one “represents a difference in a single DNA building block, called a nucleotide.”

More #opendata highlights: Brain scans

Wednesday, November 29, 2017

Because I've had a gap in blogging over the last few months, I thought I would ease back into things by highlighting public health-related data sets going back through Data is Plural, one edition at a time.

The August 16 edition of Data is Plural contains a data set with two collections of MRI brain scans:
Brain scans. The Open Access Series of Imaging Studies (OASIS) project is “aimed at making MRI data sets of the brain freely available to the scientific community,” with the goal of “[facilitating] future discoveries in basic and clinical neuroscience.” So far, the project has published two collections: a cross-sectional dataset of scans from 416 people, ages 18 to 96; and a longitudinal dataset, based on 150 people aged 60 to 96, each of whom were scanned at least two different times. [h/t Andrew Beam]

Last week in @CDCMMWR: #Smoking policies in airports

Monday, November 27, 2017

Last week's edition of MMWR featured an article on the smoking policies in the world's 50 busiest airports. Not surprisingly (to those of us who have traveled in Asia, at least), very few of the airports on the list in Asia have smoke-free policies. However, I was surprised to discover that three large US airports (Las Vegas, Atlanta, and Denver) still have indoor smoking rooms. The other North American airport on the list with indoor smoking still allowed is Mexico City.
There is no risk-free level of exposure to secondhand smoke. Eliminating smoking in indoor spaces fully protects nonsmokers from exposure to secondhand smoke. An overwhelming majority of large-hub airports in the United States prohibit smoking indoors.
Among the 50 busiest airports worldwide, 23 airports (46%), including five of the 10 busiest airports, prohibit smoking in all indoor areas. While smoke-free airports among the 50 busiest are common in North America (14 of 18), few airports in Asia (4 of 22) have implemented smoke-free polices.
This issue also features an article on the status of polio eradication in Pakistan.

More #opendata highlights: #malaria mosquitoes

Wednesday, November 22, 2017

Because I've had a gap in blogging over the last few months, I thought I would ease back into things by highlighting public health-related data sets going back through Data is Plural, one edition at a time.

The August 23 edition of Data is Plural (there were no data sets directly related to health in any of the September editions) features geospatial data on Anopheles mosquitoes, which is the type that carries malaria:
A century of malarial mosquitoes. A team of researchers has compiled “the largest ever geo-coded database of anophelines in Africa.” [...] The database covers 1898 to 2016 and includes more than 13,400 observations of mosquitoes in specific locations. For each observation, the dataset lists the country, administrative region(s), and latitude/longitude, as well as the time period, the species identified, the sampling method, and the source of the information. [h/t Michael Chew]

All kinds of good stuff in @LancetGH's December issue: injection drug use, maternal mortality data, and antimicrobial resistance

Tuesday, November 21, 2017

The December issue of Lancet Global Health features articles and commentary on several hot-button issues in global health. I was quite pleased to see two systematic reviews related to injection drug use: one on the prevalence of IDU worldwide and the rates of HIV, HBV, and HCV among IDU, and another on interventions to address HIV and HCV risk among PWID (including syringe exchange programs). The accompanying commentary is a great read:
However, the coverage of NSP [needle and syringe programs], OST [opioid substitution therapy], and HIV services for PWID...is very limited. Of the countries and territories with evidence of IDU, only 52% reported the presence of NSP and 48% reported the presence of OST. The situation is even worse for the uptake of comprehensive harm reduction programmes: the authors estimate that, globally, less than 1% of PWID live in countries with a high coverage of both NSP and OST. It is important to note that many countries in the most affected regions criminalise drug use (with some still having death penalties for drug offences), do not allow access to harm reduction services, or both.
Although the two systematic reviews show that some progress has been made in the estimation of IDU and infection prevalence, they also brutally underscore the absence of significant improvement in the scaling-up of increasingly well documented, evidence-based interventions to prevent new infections among PWID in countries and regions with expanding epidemics.
The headlining editorial looks at the effort to combat antimicrobial resistance, and the issue also features a piece on missing the forest for the trees when trying to classify maternal mortality data. And if you're into vision loss, cerebral palsy, or malnutrition, there's something for you, too.

Last week in @CDCMMWR: Global routine #vaccination coverage, rubella, and #opioid reports

Monday, November 20, 2017

Last week's edition of MMWR featured two global health-focused articles. The one that caught my eye was an update on coverage of routine vaccinations for children around the world. While progress has been substantial since the WHO launched the Expanded Program on Immunization in 1974, it appears to have stalled in the last few years:
Since then, global coverage with vaccines to prevent tuberculosis, diphtheria, tetanus, pertussis, poliomyelitis, and measles has increased from less than 5% to 85% or greater and additional vaccines against hepatitis B, Haemophilus influenzae type B, Streptococcus pneumoniae, rotavirus, and rubella have been included in vaccine recommendations introduced in multiple countries.
Global coverage with the third dose of diphtheria and tetanus toxoids and pertussis–containing vaccine, the third dose of polio vaccine, and first dose of measles- containing vaccine coverage has remained unchanged at 84%–86% since 2010. Among new or underused vaccines, global coverage increased during 2010–2016 for completed vaccine series against rotavirus (8% to 25%), Streptococcus pneumoniae (11% to 42%), rubella (35% to 47%), Haemophilus influenzae type B (42% to 70%) and hepatitis B vaccine (74% to 84%).
There is also an article on the progress of rubella elimination worldwide. As of December 2016, " Elimination of rubella and congenital rubella syndrome was verified in the WHO Region of the Americas in 2015, and 33 (62%) of 53 countries in the European Region have now eliminated endemic rubella and congenital rubella syndrome."

Bonus: The journal has compiled a list of all articles and reports on opioids published since 2000.

More #opendata highlights: X-rays and air quality

Monday, November 13, 2017

Because I've had a gap in blogging over the last few months, I thought I would ease back into things by highlighting public health-related data sets going back through Data is Plural, one edition at a time.

The October 4 edition of Data is Plural featured air quality data and chest X-rays from the EPA and the NIH, respectively:
Four decades of U.S. air quality. The Environmental Protection Agency collects air quality samples from thousands of monitoring stations across the country. The resulting datasets, which go back to the 1980s, are available as daily files, annual files, and via an API. The monitored pollutants include ozone, carbon monoxide, sulfur dioxide, nitrogen dioxide, particulate matter, volatile organic compounds, and more. You can also download daily Air Quality Index ratings and information about each monitoring station. Previously: Global air pollution datasets from Berkeley Earth (DIP 2017.03.22) and from the World Health Organization (DIP 2016.06.15). [h/t Swier Heeres]

Chest x-rays. Last week, the National Institutes of Health released a datasetcontaining more than 100,000 anonymized chest x-rays, from 30,000 patients, “including many with advanced lung disease.” For each image, the associated metadata includes the patient’s age, gender, and diagnosis labels. (The dataset’s authors used natural language processing to extract those labels from radiological reports; they estimate that fewer than 10% of the labels are incorrect.) Related:Andrew L. Beam’s list of medical datasets for machine learning. [h/t Chris Hamby]

This week in @CDCMMWR: Assessing Kenya's and Ghana's immunization information systems

Saturday, November 11, 2017

I'm trying to get back into blogging regularly by doing some regular, manageable features. Since I read CDC's MMWR every week and it often contains articles relevant to global health and/or data quality, I am going to try to feature articles of interest here.

This week's MMWR has an article on a recently revamped data quality assessment tool that is intended to measure immunization information systems in low- and middle-income countries. The WHO partnered with the CDC to develop updated assessment guidelines in 2014, as the original guidelines developed in 2001 were missing the mark. The article presents the results of using the updated assessment tool in Kenya in 2015 and in Ghana in 2016:
The availability, quality, and use of immunization data are widely considered to form the foundation of successful national immunization programs. Lower- and middle-income countries have used systematic methods for the assessment of administrative immunization data quality since 2001, when the World Health Organization (WHO) developed the Data Quality Audit methodology. WHO adapted this methodology for use by national programs as a self-assessment tool, the Data Quality Self-Assessment. This methodology was further refined by WHO and CDC in 2014 as an immunization information system assessment (IISA).
The experience gained from implementing assessments using updated IISA guidance in Kenya and Ghana provides an opportunity to inform other countries interested in best practices for assessing their data quality and creating actionable data quality improvement plans. Data quality improvement is important to provide the most accurate and actionable evidence base for future decision-making and investments in immunization programs. This review provides best practice experiences and recommendations for countries to use an IISA to assess data quality from national administrative structure down to the facility level. This methodology also meets the requirements for use by Gavi, the Vaccine Alliance, for monitoring national immunization data quality at a minimum interval of every 5 years in conjunction with funding decisions.
The issue also has articles on tobacco use and waterborne disease outbreaks in the U.S. - including in drinking water (which is scary, since most of us in the states take safe drinking water for granted).

More public data set highlights: Wildfires, vehicle safety, and water quality

Thursday, November 9, 2017

Because I've had a gap in blogging over the last few months, I thought I would ease back into things by highlighting public health-related data sets going back through Data is Plural, one edition at a time.

The October 11 edition of Data is Plural featured data sets on wildfires, vehicle safety, and the water quality of the San Francisco Bay:
Wildfires.Monitoring Trends in Burn Severity (MTBS) is an interagency program whose goal is to consistently map the burn severity and extent of large fires across all lands of the United States”; the most recent release contains more than 20,000 fires from 1984 to 2015. You can explore the data online, or download it in bulk. For more recent data, see GeoMAC, which aims to map all current wildfires; NOAA’s Hazard Mapping System, which uses satellites to detect fire locations and smoke plumes; and NASA’s MODIS and VIIRS datasets, which provide satellite-based detections for the entire globe. Previously: National Fire Incident Reporting System , which also includes structure fires and vehicle fires (DIP 2016.07.20). [h/t Max Joseph ]

Commercial vehicle safety. The Federal Motor Carrier Safety Administration helps to regulate the United States’ large trucks and passenger buses. The datasets available through its Safety Measurement System include a census of all regulated carriers, the results of safety inspections, and reported crashes. The crash files list the number of injuries and fatalities; the weather, light, and road conditions; the involved vehicle’s VIN and license plate number; and more. [h/t Dan Brady]

San Francisco Bay water. The U.S. Geological Survey has been measuring water quality in the San Francisco Bay for nearly 50 years. The agency recently published 210,826 of these measurements, collected from dozens of monitoring stations between April 1969 and December 2015. (It’s “one of the longest records of water-quality measurements in a North American estuary,” according to a recent academic article describing the data.) Each row specifies the measurement’s date, station, depth, temperature, and salinity; many rows include levels of chlorophyll, oxygen, nitrate, ammonium, and other matter.

More public data set highlights: Puerto Rico's disaster recovery

Saturday, November 4, 2017

Because I've had a gap in blogging over the last few months, I thought I would ease back into things by highlighting public health-related data sets going back through Data is Plural, one edition at a time.

The October 18 edition of Data is Plural featured a data set with different metrics related to Puerto Rico's disaster recovery efforts:
Puerto Rico’s recovery. Since shortly after Hurricane Maria hit Puerto Rico, the territory’s government has been publishing a dashboard of recovery statistics. The website tracks a couple dozen metrics, including the percent of homes with electricity, number of people in shelters, and the number of open hospitals. For several of the main metrics, researcher Michael A. Johansson has been scraping daily figures from the dashboard and publishing them as a CSV file. Related: The Washington Post has been charting the recovery, and published a deep dive into the island’s ongoing power outages.

Public data set highlights: Deepwater Horizon and cardiovascular epidemiology

Friday, November 3, 2017

This week's Data is Plural newsletter features two health-related datasets: one with NOAA data on the effects of the Deepwater Horizon explosion and one on cardiovascular mortality from IHME at the University of Washington. Hooray epidemiology!
Deepwater Horizon’s effects. For years, the National Oceanic & Atmospheric Administration has been working to assess the damage done to natural resources by the April 2010 Deepwater Horizon explosion and oil spill. As part of that effort, they’ve collected and compiled several dozen related datasets, including toxicity studies, plankton samples, necropsies of stranded turtles, dolphin health assessments, and a “backyard boater” survey. [h/t Sebastian Kraus]

County-level cardiovascular deaths. Researchers at the University of Washington’s Institute for Health Metrics and Evaluation to estimated cardiovascular mortality rates for each U.S. county, for every year between 1980 and 2014. The findings, based on 32 million de-identified death records, population data from the Census, and other sources, are also broken down by particular disease (e.g., aortic aneurysm, ischemic stroke, etc.) and gender. Related: The researchers’ JAMA article describing their methodology and findings. Previously: The Global Burden of Disease dataset, published by the same institute (DIP 2016.07.27). [h/t Michael A. Rice, a teacher at Ingraham High School in Seattle]
Bonus: The newsletter also has a public data set on all the sexual assault allegations for recent high-profile cases, including Cosby, Weinstein, and Trump.

Public dataset highlights: Antibiotic resistance

Friday, June 16, 2017

This is a big one and has been getting a lot more attention ever since the UN met last September to wring their hands over it. This week's Data is Plural features a publicly available dataset on antibiotic resistance genes:
Antibiotic resistance. ResistoMap is an interactive visualization of antibiotic drug resistance, based on more than 1,500 bacteria genome samples from people’s intestinal tracts. The data behind the visualization is available to download. It’s partly based on two prior datasets: McMaster University’s Comprehensive Antibiotic Resistance Database (“a bioinformatic database of resistance genes, their products and associated phenotypes”) and the University of Gothenburg’s BacMet (“an easy-to-use bioinformatics resource of antibacterial biocide- and metal-resistance genes”).

Public dataset highlights: Migrating scientists, workplace injuries, and beach bacteria

Wednesday, June 7, 2017

This week's Data is Plural features three datasets of public health and scientific interest - including one that includes yours truly! I have an ORCID, which means my research profile is included in the first dataset.
Millions of scientists, and their migrations. ORCID is a nonprofit organization that provides unique identifiers for researchers — mostly scientists so far — to make it easier to distinguish between them. It has issued more than 3 million IDs so far, and provides annual bulk downloads of all researchers’ public profiles . In many cases, the researchers have supplied their education and employment histories. That enabled Science magazine to analyze the migrations of more than 110,000 researchers who’ve listed multiple countries in these public CVs. (The data and code underlying the analysis are also available to download .)

Severe workplace injuries. Beginning in January 2015, the Occupational Safety and Health Administration began requiring U.S. employers to report “all severe work-related injuries, defined as an amputation, in-patient hospitalization, or loss of an eye.” You can download a spreadsheet of these injuries — some 20,000 in 2015 and 2016 combined. It contains the injury dates, descriptions, and outcomes, as well as the employers’ names and locations. Previously: OSHA’s more detailed (but slightly more cumbersome) inspection data and API (DIP 2016.07.13).

E. coli at Ocean Beach. The San Francisco Public Utilities Commission’s Beach Water Quality Monitoring Program measures bacteria levels at fifteen locations on the city’s shoreline. You can download the measurements by clicking the “raw data” link below this map . The data powers the (unsurprisingly) unofficial @BeachPooBot account on Twitter.

Things I loved this week: #LegalEpidemiology, @HepVu, and @CDCgov's Healthy Behavior Data Challenge

Friday, May 19, 2017

Part of why I love my new gig at Cadence Group is that, in my responsibility to be informed and up-to-date on all things public health, I am constantly nerding out on new and exciting topics in my favorite fields. I had the chance to watch a webinar on one of those emerging areas - legal epidemiology - earlier this week. It's basically exactly what it sounds like: "the scientific study of law as a factor in the cause, distribution, and prevention of disease in a population." Despite its potential as a complex and fruitful area of study, there isn't much literature out there on the topic, though CDC's Public Health Law Program appears to be the best place to start). Lucky for me (and anyone else who is curious), the National Environmental Health Association is hosting a three-part webinar series on the topic this summer. The first webinar was held last week, with the recording and slides posted. The second installment is on June 14th, and the third on August 16th.

Data visualizations are one of my favorite things, a perfect marriage between my love of data and my experience leading the Communications Committee for APHA's International Health Section. Naturally this meant I got super excited when AIDSVu launched, happened just before I began working as an epidemiologist with the Texas HIV prevention program. Today I discovered that the initiative has launched a similar site, HepVu, which (as the name implies) makes hepatitis surveillance data available via interactive maps and data visualizations.

Finally, I stumbled across the Healthy Behavior Data Challenge, a call by CDC "for new ways to address the challenges and limitations of self-reported health surveillance information and tap into the potential of innovative data sources and alternative methodologies for public health surveillance":
The Healthy Behavior Data (HBD) Challenge will support the development and implementation of prototypes to use these novel methodologies and data sources (e.g., wearable devices, mobile applications, and/or social media) to enhance traditional healthy behaviors surveillance systems in the areas of nutrition, physical activity, sedentary behaviors, and/or sleep among the adult population aged 18 years and older in the US and US territories.

The collection of health data through traditional surveillance modes including telephone and in-person interviewing, however, is becoming increasingly challenging and costly with declines in participation and changes in personal communications. In addition, the self-reported nature of responses particularly in the areas of nutrition, physical activity, sedentary behaviors, and sleep has been a major limitation in these surveillance systems, since self-reported data are subject to under/over reporting and recall bias. Meanwhile, the advent of new technologies and data sources including wearable devices ( such as: smart watches, activity trackers, sleep monitors, etc.), mobile health applications on smartphones or tablets, and data from social media represents an opportunity to enhance the ability to monitor health-related information and potentially adjust for methodological limitations in traditional self-reported data.

The Healthy Behavior Data (HBD) Challenge will be conducted concurrently with a similar challenge proposed by the Public Health Agency of Canada. This will enable the two countries to learn from their respective challenges and leverage information. We expect increased efficiency with a dual challenge.
It struck me as pretty reminiscent of the Data for Climate Action challenge by UN Global Pulse.

Happy Friday!

Public dataset highlights: The cost of food

Wednesday, May 17, 2017

This week's Data is Plural features a dataset on global food prices:
Global food prices. The UN World Food Programme’s vulnerability analysis group collects and publishes food price data for more than 1,000 towns and cities in more than 70 countries. The dataset, which goes back more than a decade, covers basic staples, such as wheat, rice, milk, oil, and more. It’s updated monthly and feeds into (among other things) the UNWFP’s price-spike indicators. Related: The Humanitarian Data Exchange, which hosts the dataset for the UN. Also: The Economist’s Big Mac Index. [h/t Andrew McCartney]

Spatial epidemiology on @NPR @MorningEdition: #Malaria and gold mining

Thursday, May 11, 2017

I've unexpectedly found myself in hog heaven since moving to the Maryland side of DC for a new position at the beginning of this month. I'm staying with a friend while I look for my own place and, while I have a much longer commute than I am used to, I am enjoying all 40 minutes of it because I am spending all of them listening to WAMU, the DC-area NPR station out of American University. I've always liked NPR, not only because they provide (I feel) balanced coverage of major news items, but also because they feature so many interesting stories that wouldn't normally get much press, including engaging pieces on public health and human rights.

Case in point: Yesterday's Morning Edition featured a story on how illegal gold mining has been linked to malaria in Colombia. The segment featured an interview with Sandra Rozo, an economist with USC's Marshall School of Business, whose recent work has focused on providing an evidence base for qualitative data suggesting a link between alluvial gold mining and higher incidence of malaria:
As illegal gold mining is mainly performed in open sky mines that are commonly located inside or close to water surfaces where large pits are dug, it is plausible to conceive that these pits are later filled with water, which would make them ideal breed sites for Anopheles mosquito larva. Because these mines do not follow any protocols or rules and are not registered with local authorities, it is likely that illegal miners have limited knowledge of the need for or methods of malaria prevention. They are likely to leave the pits open and do not take any measures to protect themselves against malaria. Finally, illegal gold miners are also a population that sustains high migration rates, which could also help to propagate the parasite incidence to other areas. Due to data limitations, however, at present, the existing evidence has been concentrated on qualitative studies or on documenting correlations between malaria incidence and gold exploitation.
As she points out in her paper, however, there are a number of other factors that could contribute to the correlation without the relationship being causal per se - hence the value of supporting quantitative epidemiological analysis. Rozo is not the first to explore this from an epidemiological perspective, either. This paper by Castellanos et al finds a strong correlation between gold production rates and malaria cases using malaria surveillance data and government data on legal mining activities. One major limitation, though, was that they could examine correlations to legal mining activities - that is, mining operations that are registered with, and regulated by, the government. The paper also notes that between the two types of mining (traditional alluvial vs. the more modern "open sky"), the "open sky" technique is less regulated and more likely to be performed illegally.

Rozo's analysis is interesting for a couple of reasons. She combines satellite data identifying mining operations with geographic data on geochemical anomalies of gold and matches that to malaria surveillance data to determine the relationship between gold mining activity and malaria incidence. She also controls for several potential confounders, including poverty levels, presence of government and health institutions, climactic factors, and chronic disease.

This is the type of analytical application that makes spatial epidemiology so exciting and demonstrates how epidemiology can be used to build or strengthen the case for policy change to benefit public health. It also spotlights why political and economic forces that we don't typically think of as explicitly health related are still very much relevant to public health researchers and policy makers. Less than a month before Rozo's paper was posted, the New York Times ran a story on how malaria has come back with a vengeance in Venezuela since the economic crisis. As many professionals had turned to gold mining to survive, they were repeatedly getting sick with malaria - and taking it back to the cities with them.

Public dataset highlights: Groceries and PhDs

Wednesday, May 10, 2017

This week's Data is Plural edition features two health-related datasets that caught my eye: one on grocery shopping from Instacart and one from the National Science Foundation on doctoral degree holders in the science, engineering, and health fields.
Three million grocery orders. Groceries-on-demand startup Instacart has released a dataset containing 3 million orders from 200,000 (anonymized) users. “For each user, we provide between 4 and 100 of their orders, with the sequence of products purchased in each order,” the company’s head of data science writes. “We also provide the week and hour of day the order was placed, and a relative measure of time between orders.” Here’s the data dictionary.

What do you do with a PhD in science?The National Science Foundation’sSurvey of Doctorate Recipients “is a longitudinal biennial survey conducted since 1973 that provides demographic and career history information about individuals with a research doctoral degree in a science, engineering, or health (SEH) field from a U.S. academic institution.” You can download aggregated data and detailed survey responses going back to 1993. The next release is scheduled for this month. Related: The NSF has published an interactive graphic of the data. [h/t Peter Aldhous]

Progress toward #polio eradication is a much-needed reminder that global health is still winning

Monday, May 8, 2017

Note: This was cross-posted to the IH Blog.

I always love spotlighting polio eradication. Along with Guinea worm, it is one of the few candidates to follow smallpox to the eternal (or so we all hope) halls of eradicated diseases. While the eradication effort has suffered its setbacks in recent years, public health workers have persisted, steadily marching onward. And frankly, there has been so much hand-wringing in global health in recent weeks that it is important to occasionally remember that there are still wins we can, and should, celebrate.

What makes this success possible in addition to trackable is the global network of polio surveillance systems, which was featured in CDC's MMWR at the beginning of April:
The primary means of detecting poliovirus transmission is surveillance for acute flaccid paralysis (AFP) among children aged [less than] 15 years, combined with collection and testing of stool specimens from persons with AFP for detection of WPV and vaccine-derived polioviruses (VDPVs)...in WHO-accredited laboratories within the Global Polio Laboratory Network. AFP surveillance is supplemented by environmental surveillance for polioviruses in sewage from selected locations. Genomic sequencing of the VP1-coding region of isolated polioviruses enables mapping transmission by time and place, assessment of potential gaps in surveillance, and identification of the emergence of VDPVs. For public health nerds like me, all of MMWR's polio reports can be found here.
Basically, a combination of syndromic and environmental surveillance allows public health systems to track polio where it pops up, and genetic sequencing helps to trace how the virus got to where it did to shed light on transmission patterns and find gaps in surveillance.

The WHO followed with two YouTube videos featuring the global polio surveillance system and polio vaccination, which is what will make eradication possible:

This is all pretty straightforward stuff - we all know generally that surveillance systems do, in fact, work when their infrastructure is properly supported and that children should be vaccinated against polio. But it's important to not lose focus on our successes and global health progress, even when it is simple, straightforward, and sometimes slow.

Public data set highlights: Women's empowerment and family planning

Saturday, April 29, 2017

This week's Data is Plural features two datasets of public health interest: one on women's empowerment metrics from India's National Family Health Survey and one on metrics related to family growth and family planning in the US.
Women’s empowerment in India. For each of India’s 36 states and Union Territories, the country’s latest National Family Health Survey includes 114 metrics, such as the percentages of “households using iodized salt” and “men who have comprehensive knowledge of HIV/AIDS.” Unfortunately, the government publishes the reports only as PDFs. But the Hindustan Times has extracted the data for the survey’s eight “women’s empowerment and gender based violence” metrics, including the percentages of “ever-married women who have ever experienced spousal violence” and “women having a bank or savings account that they themselves use.” They’ve published that data as a spreadsheet and used it to construct an interactive Women Empowerment Index. [h/t Gurman Bhatia]

Marriage and divorce, pregnancy and infertility in the U.S. The CDC has been running its National Survey of Family Growth since 1973. For the first three decades, it surveyed only women ages 15-44. Starting in 2002, it began also surveying men. The latest surveywas conducted in 2013-15, when it collected data from 10,205 residents about sexual activity and contraception, pregnancy and infertility, marriage and divorce, adoption, parenting, and more. [h/t Allen B. Downey]

Policy on #HIV related travel restrictions adopted by @WFPHA_FMASP at #WCPH2017 now posted

Friday, April 21, 2017

Note: This was cross-posted to the IH Blog.

After APHA adopted its permanent policy statement on HIV-related immigration restrictions at last year's Annual Meeting, I worked with my colleagues in the International Health Section to submit a corresponding policy proposal on behalf of APHA to the World Federation of Public Health Associations, which held its 15th World Congress on Public Health this month in Melbourne, Australia. The proposal was accepted and passed by the WFPHA Policy Committee at the meeting, and has now been posted the website (PDF). The text of the policy (excluding references) is below.
Scientific evidence and treatment needed to combat the spread of HIV - not ineffective travel bans

Submitted by the American Public Health Association
(Contact person D. Walker)

HIV-related restrictions against entry, stay, and residence remain common around the world. Various countries have policies that mandate HIV testing of all or certain groups of foreign nationals as a condition of obtaining a visa for employment. These policies have no basis in science and violate migrant workers’ human rights to confidentiality and informed consent to testing, exposing them to exploitation by their employers. According to UNAIDS, 35 countries currently have official HIV-related travel restrictions. Furthermore, HIV-related travel restrictions against foreign nationals have been shown by international treaty bodies, international legal scholars, and human rights organizations to constitute discrimination based on race, ethnicity, and/or country of origin.

Scope and Purpose
Restrictions on travel, immigration, or residence related to HIV status are a violation of the principles of nondiscrimination and equal treatment in all international human rights laws, treaties, and agreements. The International Covenant on Civil and Political Rights guarantees the right to equal protection under the law, free from discrimination based on race, color, sex, language, religion, political or other opinion, national or social origin, property, birth, or other status, and the UN Commission on Human Rights has determined that this includes discrimination based on health status, including HIV infection. According to the Siracusa Principles on the Limitation and Derogation Provisions in the International Covenant on Civil and Political Rights, while international human rights law allows governments to restrict rights in cases of emergency or serious public concern, the restrictions must be the minimum necessary to effectively address the concern - and HIV-related travel restrictions have been overwhelmingly ruled as both overly intrusive and ineffective public health policy. Within such restrictions, compulsory HIV testing is a serious violation of numerous human rights principles, including the right to bodily integrity and dignity. The accompanying deportation and/or loss of employment and residency status of HIV-infected migrants that frequently accompanies such testing violates the rights of PLWHA to privacy, work, and appropriate medical care. The International Labour Organization (ILO) has specifically stated that neither HIV tests nor private HIV-related personal information should be required of employees or job applicants.

Despite this robust evidence base, according to UNAIDS, 35 countries currently have official HIV-related travel restrictions openly acknowledged and enforced by the government. These restrictions vary from outright entry bans, which bar PLWHA from entering the country, to restrictions on stays longer than a specified period of time or to obtain employment visas or residency status. Others have inconsistent policies and/or intentionally misrepresent their policies with HIV-related restrictions. Such policies and practices, and the number of migrants impacted by them, are difficult to track because of differing or ambiguous definitions and a lack of data. Some of the most restrictive policies subject immigrants to mandatory HIV testing, either when applying for residency or for an employment visa, which is frequently required by states for legal residency.

The two primary justifications provided by governments for mandatory HIV tests for migrant workers and other HIV-related travel restrictions are to protect public health and reduce the cost burden on the country’s healthcare system imposed by providing HIV care services to foreign nationals. While countries have the right to employ measures to protect their populations from communicable diseases of public health concern, HIV is not transmitted by casual contact, meaning there is no scientific basis for attempting to control its spread via immigration policies. Furthermore, countries that do not have HIV-related travel restrictions have not reported any negative public health consequences compared to those that do, and recent analysis suggests that even migration from countries with generalized HIV epidemics does not pose a public health risk to destination countries.

In fact, immigration policies banning or restricting entry or employment based on HIV status often have the opposite effect of their protective intention, causing direct harm to the health of both of immigrants and citizens. They marginalize PLWHA, regularly discourage people from accessing HIV testing and treatment, and reinforce stereotypes and discriminatory attitudes against PLWHA in the general population. Regulations requiring HIV tests of immigrants can promote the idea that foreigners are dangerous to the national population and a public health risk, as well as creating a false sense of security by reinforcing the notion that only migrants are at risk for infection. Additionally, such attitudes can adversely impact the host country’s own HIV epidemic, as citizens who are unaware of their HIV-positive status, underestimating their own HIV risk and avoiding testing due to stigmatization, are more likely to transmit the virus to others, driving up infection rates.

State-enforced HIV screening of migrants costs far more than it saves in treatment costs. Screening travelers and migrants for HIV is impractical and expensive.[5][13][19] Labor migrants (both regular and undocumented) bring significant economic benefits to their host countries, in addition to themselves, and this cost-benefit balance remains even when migrants are HIV-positive and rely on the host country’s health care system for treatment and support.

Fields of Application:
  • National public health associations and their members
  • Human rights and HIV advocacy groups
  • The World Federation of Public Health Associations
Action Steps:
The WFPHA joins with UNAIDS, the World Health Assembly, and other HIV and human rights organizations (e.g., Amnesty International, Human Rights Watch, ILO) to call on all countries that still maintain and/or enforce HIV-related restrictions on entry, stay, or residence to eliminate such restrictions, ensuring that all HIV testing is confidential and voluntary and that counseling and medical care be available to all PLWHA within its borders, including migrants and foreign nationals.

The WFPHA affirms the following principles:
  • All people have the right to confidential and voluntary HIV testing and counseling.
  • Persons living with HIV/AIDS (PLWHA) have the right to privacy, to work, and to appropriate medical care.
  • All HIV-related travel and immigration restrictions currently in place should be removed.
  • Agencies and businesses who employ foreign nationals should not use HIV tests as a means to discriminate against potential employees.
  • Governments should provide HIV prevention and treatment services that are equally accessible to citizens and foreign nationals.
  • Migrant workers should have access to culturally appropriate HIV prevention and care programs in languages that they can understand.
The WFPHA recommends that:
  1. Public health associations in every country should:
    1. Develop policies opposing HIV-related travel restrictions;
    2. Document and/or support human rights and HIV advocacy groups in documenting immigration policies that explicitly discriminate, or allow employers to discriminate, against migrants based on HIV status;
    3. Document and/or support human rights and HIV advocacy groups in documenting any HIV testing practices that are not voluntary or confidential;
    4. Inform their members and the public that HIV-related travel restrictions and compulsory HIV testing of foreign nationals is a violation of human rights and does not protect public health or reduce health care costs; and
    5. Advocate for the removal of any and all HIV-related travel restrictions enforced or condoned by their country governments.
  2. UNAIDS should take steps to ensure that its protocols to research and investigate countries’ HIV-related travel restrictions are sufficiently thorough by monitoring and documenting any reported instances of HIV-related discrimination targeting immigrants, particularly when presented with evidence demonstrating that recognition of a country’s removal of HIV-related travel restrictions is unwarranted, in order to ensure that governments are not able to misrepresent their policies in order to gain undeserved recognition for supporting human rights with regard to HIV/AIDS.

WFPHA supports the removal of all HIV-related travel restrictions and travel related mandatory testing.

Public data set highlights: Prescription data and vaccination rates

Wednesday, April 19, 2017

This week's Data is Plural features several datasets of public health interest. The first item highlights monthly prescription drug data in England made available by the UK's National Health Service, US Medicare prescription drug data, and Australian prescription drug data. The second features vaccination rates by US state.
UK, US, Rx.The UK’s National Health Service publishes monthly data on drugs prescribed in England through the country’s single-payer health care system. (Drugs prescribed in Scotland, Wales, or Northern Ireland aren’t included.) For each prescriber-and-drug combination, the dataset includes the quantity and cost of prescriptions for each month since August 2010. The US publishes similar data about prescriptions issued through Medicare, but only on an annual basis and currently only covering 2013 and 2014. Related:ProPublica’s Prescriber Checkup, which uses the Medicare data to examine doctors’ prescribing patterns. Previously: A decade-plus of Australian prescription data (DIP 2016.08.24). [h/t Adam Crahen]

Vaccination rates by state.The CDC’s National Center for Immunization and Respiratory Diseases collects and publishes state-by-state vaccination rates for infants, kindergartners, teens, and adults — plus, flu vaccination rates for several age groups. Each dataset includes several years’ worth of data, with many going back to 2008 or 2009. Related: California Shows The Rest Of The Country How To Boost Kindergarten Vaccination Rates,” by my colleague Peter Aldhous, with additional county-level data from the Golden State. Previously: International vaccination rates and policies (DIP 2016.08.03).

Public data set highlights: Pirated peer-reviewed research and MCH aid

Thursday, April 13, 2017

This week's Data is Plural highlights one dataset of interest to global health professionals (particularly maternal and child health specialists) and one that is potentially contentious within the scientific community at large. Posted without comment or value judgment re: research piracy.
Pirated papers. Sci-Hub, which describes itself as “the first pirate website in the world to provide mass and public access to tens of millions of research papers,” recently released a list of the 62,835,101 academic papers it has collected. That dataset identifies each paper only by its DOI — a short, unique ID. Helpfully, graduate student Bastian Greshake has extracted the journal name, publisher, and publication ear from those DOIs. Greshake has also combined that data with six months of Sci-Hub download data (previously featured in DIP 2016.05.04), and analyzed the datasets together. Among his findings: Both are “largely made up of recently published articles, with users disproportionately favoring newer articles and 35% of downloaded articles being published after 2013.”

International aid for maternal and child health. Researchers at the World Health Organization have assembled a dataset of international aid — both from official government assistance and private grants — devoted to reproductive, maternal, newborn, and child health from 2003 to 2013. The dataset, which the researchers described in a recent academic article, draws on 2.1 million records, and is based largely on the OECD’s Creditor Reporting System. Related: Earlier this month, the U.S. State Department cut all its funding for the UN's family planning agency; it was the agency’s third-largest donor.
Note: You can see all of the public health relevant open datasets I've featured to date here. At this point, most of them come from Vine's Data is Plural, but I'm hoping to branch out and find more. Then again, he seems to be pretty good at spotlighting the best ones, so maybe I won't reinvent the wheel for the time being.

#D4CA Challenge: UN Global Pulse calls for research proposals to analyze business data to combat #climatechange

Friday, April 7, 2017

One of my colleagues from APHA's International Health Section sent me information about the Data for Climate Action challenge, which I thought I would share in an attempt to wake up this slumbering blog. It's an initiative by the UN's Global Pulse to recruit researchers and data scientists to "leverage private big data to identify revolutionary new approaches to climate mitigation and adaptation" - that is, use corporate datasets, which have been de-identified and made available by participating companies, for projects or analyses that "generate innovative climate solutions." According to the press release:
Data for Climate Action will target three areas relevant to the United Nation’s Sustainable Development Goal on climate action (SDG 13): climate mitigation, climate adaptation, and the linkages between climate change and the broader 2030 Agenda.

The challenge aims to generate original research papers and tools that demonstrate how data-driven innovation can inform on-the-ground solutions and transform efforts to fight climate change. It builds upon the model of data science competitions pioneered by organizations like Kaggle, and company-specific initiatives to share big data for the public good, such as the “Data for Development” challenges hosted by Orange.

Researchers who are selected to participate in Data for Climate Action will have four months to conduct their research. A diverse panel of experts in climate change and data science will evaluate final submissions based on their methodology, relevance, and potential impact. Winners will be announced in November of 2017.
The data being offered includes retail transaction data, social media posts, meteorological and air quality data, and user-generated data on road conditions. Data sets can be combined with each other or with other publicly available datasets like those featured on Data is Plural. Individuals or teams can submit proposals, and the only apparent requirement is that all participants be at least 18 years old.

They've apparently extended the deadline from April 10th to the 17th, so any analysts or programmers who aspire to code for the public good still have ten days to get their applications together and apply.

APHA Component letter to @UNAIDS: South Korea’s #HIV immigration restrictions

Tuesday, April 4, 2017

Note: This was cross-posted to the IH Blog.

After two years, two APHA policy statements (one interim and one permanent), dozens of e-mails (and perhaps just as many drops of blood, sweat, and tears), and a few phone calls, we have finally sent a letter to UNAIDS urging it to revoke its recognition of South Korea's status as a country without any HIV restrictions - until it actually produces and enforces policies that actually reflect that status.

Heartfelt thanks to Dr. Laura Altobelli, our Section Chair; Mona Bormet, our Advocacy/Policy Committee's policy coordinator; and all of the Components who signed on to this hard-won letter (and the policy proposals that led up to it):
If there is one thing I have learned through this odyssey, it is that the work of advocacy is exhausting. It takes the old adage of "marathon not sprint" to a whole new level. The patience required to work within the boundaries, and according to the rules, of whatever framework you are trying to leverage to produce change can be maddening at times, but I suppose that is the inevitable price we pay to work with others. The larger your advocacy "vehicle" is, the more likely it is to be effective, but the more restrictions you have to work within. Or around, as the case may be.

On a more positive note, we also got a corresponding policy approved for adoption by the World Federation of Public Health Associations at their assembly (which kicked off today!). It will be posted here as soon as it is published, with potentially more letters to follow. Stay tuned.

The full text of the letter, followed by an embedded PDF, is below.
Dear Executive Director Dr. Michel Sidibé:

On behalf of the International Health Section of the American Public Health Association (APHA), we write to notify you of a new APHA policy statement, “Opposition to Immigration Policies Requiring HIV Tests as a Condition of Employment for Foreign Nationals,” which was adopted at the Association's 2016 Annual Meeting.1 As you may know, APHA was founded in 1872 and is the oldest organization of public health professionals in the world. It has a long-standing commitment to promoting global health and protecting human rights, recognizing that these two go hand-in-hand.

HIV-related travel restrictions are recognized as a violation of human rights and have been well-established as ineffective at reducing the spread of HIV. Such policies further marginalize people living with HIV/AIDS (PLWHA), discourage people from accessing HIV testing and treatment, and reinforce stereotypes and discriminatory attitudes against PLWHA in the general population. According to APHA's policy statement, “[immigration] policies that mandate HIV testing of [foreign nationals] as a condition of obtaining a visa for employment...have no basis in science and violate migrant workers’ human rights to confidentiality and informed consent to testing, exposing them to exploitation by their employers.”

Increasing awareness of the harms of mandatory testing and accompanying pressure from multilateral institutions and human rights advocates has begun to prompt countries to lift travel bans and change their immigration policies. We recognize that UNAIDS has been instrumental in this effort and laud the organization both in its leadership on this initiative and the progress that it has made. APHA's policy statement specifically cites the work of the UNAIDS International Task Team on HIV-related Travel Restrictions and notes that “[a]dvocacy efforts using [the Task Team's findings] have resulted in several countries loosening these restrictions or, in some cases, dropping them entirely: the number was reduced from 59 to 45 countries in 2011 and, as of September 2015, to 35.” APHA's policy statement calls on UNAIDS and others to “continue to call on all countries that still maintain and/or enforce HIV-related restrictions on entry, stay, or residence to eliminate such restrictions, ensuring that all HIV testing is confidential and voluntary and that counseling and medical care be available to all PLWHA within its borders.” We urge UNAIDS to continue this work to make further progress in the remaining countries that enforce HIV travel restrictions.

The policy statement also recommends that “UNAIDS take steps to ensure that its protocols to research and investigate countries’ HIV-related travel restrictions are sufficiently thorough by monitoring and documenting any reported instances of HIV-related discrimination targeting immigrants, particularly when presented with evidence demonstrating that recognition of a country’s removal of HIV-related travel restrictions is unwarranted, in order to ensure that governments are not able to misrepresent their policies in order to gain undeserved recognition for supporting human rights with regard to HIV/AIDS.”

One such example of misrepresentation of HIV-related immigration policy can be found with the Republic of Korea (ROK), which subjects foreign nationals applying for visas to work or study under several visa categories to mandatory HIV testing.2,3 Recent decisions by the UN Committee on the Elimination of Racial Discrimination4 and the National Human Rights Commission of Korea5 both confirm the ongoing existence and enforcement of mandatory testing for E-2 visa applicants and recommend that they be struck down. Unfortunately, despite this discriminatory requirement, ROK representatives declared at the 2012 International AIDS Conference that their government had removed all HIV-related travel restrictions and, as a result, the country was granted “green” (restriction-free) status by UNAIDS6, while other states with HIV-related restrictions similar to those enforced by ROK7 are still classified as “yellow” on this map. This inconsistency in the application of UNAIDS' assessment criteria could threaten the progress made on reducing HIV-related travel restrictions. We strongly urge UNAIDS to revoke ROK's status as a country with no HIV-related travel restrictions until it eliminates all mandatory HIV testing policies.

Finally, we express our continued commitment to the UNAIDS goals of reducing HIV transmission, fortifying the rights of all who live with HIV/AIDS, and eliminating stigma and discrimination.


Laura C. Altobelli, DrPH, MPH
Chair, International Health Section

Willi Horner-Johnson, PhD
Chair, Disability Section

Randolph D. Hubach, PhD, MPH
Chair, HIV/AIDS Section

Lea Dooley, MPH, MCHES
Chair, Population, Reproductive, and Sexual Health Section

Gabriel M. Garcia, PhD, MA, MPH
Chair, Asian Pacific Islander Caucus

Titilayo A. Okoror, PhD
Chair, Caucus on Refugee and Immigrant Health

Gabriel Galindo, DrPH, MPH, CHES
Chair, LGBT Caucus of Public Health Professionals

Benjamin Mason Meier, JD, LLM, PhD
Chair, Human Rights Forum