Science, Stalled

According to the Nature News blog, federal websites containing widely used scientific data are expected to be back up and running soon.

October 11, 2013

Food-borne illness strikes

With the government shutdown essentially shuttering the federal agencies responsible for monitoring the nation’s food supply, including the Centers for Disease Control and Prevention (CDC), the US Food and Drug Administration (FDA), and the US Department of Agriculture (USDA), a salmonella outbreak that has already sickened nearly 280 people across 18 states continues largely unabated. State health departments have been monitoring the outbreak, which appears to have emanated from three plants operated by California-based poultry processor Foster Farms, and on Wednesday (October 9) the CDC recalled 30 furloughed workers to help with the investigation, according to The Christian Science Monitor. But the nationwide coordination of efforts to study and control the outbreak have largely been absent with the hobbling of the federal agencies.

Apparently, Foster Farms was cited 12 times between January 1 and September 27 for having poultry carcasses tainted with feces in its facilities, according to the CDC. Especially worrying is that the salmonella at the center of the outbreak is of the Heidelberg strain, which is virulent and resistant to antibiotics. Earlier this week, the USDA sent a letter to Foster Farms explaining that the three suspect facilities would be shut down if the company couldn’t provide viable plans to correct the problems at each by the end of yesterday (October 10), but stopped short of issuing a recall of the company’s products.

“Antibiotic-resistant Salmonella is simply too hot to handle in [consumers’] kitchens,” food safety expert Caroline Smith DeWaal told NPR. “The USDA should direct Foster Farms to recall all potentially contaminated chicken from the market.”

Thursday evening (October 10), the USDA announced that it would not be closing the facilities at the center of the outbreak. “Foster Farms has submitted and implemented immediate substantive changes to their slaughter and processing to allow for continued operations,” USDA spokesman Aaron Lavallee told the Detroit Free Press.

National labs to close?

The Department of Energy’s (DOE) system of national laboratories is preparing to power down as the government shutdown approaches the two-week point. The labs, including Los Alamos, Sandia, Pacific Northwest, and Oak Ridge, stayed open through the shutdown thus far thanks to the fact that they are technically operated by subcontractors. But the DOE facilities have been tapering off their activities as the agency’s money runs low, according to Nature. Los Alamos could close as early as October 18, while other labs, such as Pacific Northwest and Oak Ridge could stay open through November.

NIH patients get in

When the National Institutes of Health (NIH) was forced to furlough thousands of workers as a result of the government shutdown, the federal agency said that the change would affect enrollment in clinical trials being conducted at the NIH hospital on its Bethesda, MD, campus. But NIH spokesperson Renate Myles revealed this week that from the start of the shutdown on October 1 through Tuesday (October 8), the NIH hospital has been able to accept 12 critically ill patients, most of whom have cancer.

Tania Santillan’s 5-year-old daughter was one of those patients. Doctors had told Santillan, of Beloit, WI, that an experimental treatment was her daughter’s best option after a bone marrow transplant to treat an aggressive form of leukemia failed. The shutdown meant that the trial was essentially stopped. “They were afraid they were turning down kids with cancer,” Santillan told the AP, recounting the efforts of her daughter’s oncologists to implore colleagues at the NIH to accept the girl. “They said they will accept her, because she needs it.”

October 8, 2013

Picking up slack

As the government shutdown stretches into its  eighth day, academia appears to be taking up at least some of the scientific services left undone by shuttered federal agencies. Researchers at the University of Minnesota, Iowa State University, Kansas State University, and South Dakota State University, for example, are continuing to collect data on Porcine Epidemic Diarrhea virus, or PEDv, which is sweeping through US pig populations, as the Department of Agriculture’s National Animal Health Laboratory Network (NAHLN) slumbers. Workers at the USDA’s Animal and Plant Health Inspection Service, which had been tracking the spread of the deadly pathogen, were furloughed along with hundreds of thousands of federal employees, and the agency was forced to cease posting its weekly updates and testing results on the spread of PEDv to the NAHLN.

"It’s important to monitor the numbers, from the standpoint of having the information, and whether there are any large increases or decreases coming through” in positive PEDv cases, Tom Burkgren, executive direction of the American Association of Swine Veterinarians, told Reuters. PEDv, which kills 75 to 100 percent of the young pigs it infects, has cropped up in 17 states so far, with most outbreaks occurring in Iowa and Oklahoma.

Missed meetings

Furloughed government researchers are not only barred from their labs during the shutdown, they also cannot travel to key scientific meetings. According to Nature, one group of National Institutes of Health researchers attending a meeting in San Francisco as the government ground to a halt last week (October 1) was summoned back to Bethesda and told that if they delivered their planned presentations after the shutdown went into effect, their talks would be considered federal crimes. Anthony Fauci, director of the National Institute of Allergy and Infectious Disease (NIAID), was not able to deliver the keynote address at an international AIDS conference in Barcelona as he was scheduled to yesterday. He did however, phone in to the meeting’s opening press conference.

Fieldwork fumbled

The shutdown is also throwing a wrench in the collection of some field data that was being collected by government researchers. Brian Davis, a graduate student at the University of Maryland (UMD), told The Scientist that his project, a collaboration between UMD and the USDA’s Agricultural Research Service to study greenhouse gas emissions and sustainable agriculture, has been essentially put on hold by the shutdown.

“All of our lab space, field sites, and samples are on federal property; nothing can be accessed,” Davis wrote in an e-mail. “Our technicians are not working, and so anything that I relied on staff to do I have to make sure gets done myself. Admittedly, there's not much I can do without access to the lab, samples, and the field site. I am technically an employee of the university, so I had assumed that I would be able to continue working during the shutdown, but all of my research is housed in a facility that’s completely locked and barred.”

As is the case with most projects with a fieldwork component, throwing off the timing of data collection can set projects back months if not years. “This is an especially critical time for agricultural research,” Davis said. “Crops need to be harvested, and winter cover needs to be planted. Environmental monitoring, like mine, relies on regular access to construct annual estimates of impact. If the shutdown continues for multiple weeks, we could lose major points in our data from this past season, and if the winter cover fails due to weather or wildlife, we will lose next year entirely. I'm used to worrying about the rain and pests, but this is a whole new level of concern.”

Meanwhile researchers in Antarctica are in danger of losing an entire field season to the shutdown. The National Science Foundation may have to shutter research stations on the frozen continent and cancel field seasons if the shutdown drags on through mid-October, according to Nature. Diana Wall, an ecologist at Colorado State University in Fort Collins who has studied population of soil-dwelling organisms in Antarctica since 1989, told Nature that losing a whole field season would be “hell.”

“If we are not there to capture the demographics this year, our whole data set could be unintelligible,” she said.

October 3, 2013

On Monday (October 1), The Wall Street Journal reported that National Institutes of Health (NIH) Clinical Center would be turning away approximately 200 patients—including around 30 children—from treatment on the agency’s Bethesda, Maryland, campus each week as a result of the government shutdown. In response, House Republicans yesterday introduced a bill to restore NIH funding in the face of the current budgetary lockdown, Majority Leader Eric Cantor (R-VA) told the WSJ. Cantor said the bill would not only restore funds for new patients, but the entirety of the NIH budget. But Democrats rejected the approach, according to the WSJ, instead looking to reach a resolution that would restore government funding across the board.

Meanwhile, problems with PubMed—the NCBI repository for published research —continue, affecting scientists around the globe who rely on the resource for their daily work. “Not getting [a] PubMed update on our work is a minor irritant compared to more serious effect on biomedical scientists that work at NIH,” Yale University School of Medicine’s Vishwa Deep Dixit, a professor of comparative medicine and immunobiology, told The Scientist in an e-mail. A Cell Metabolism paper published this week (October 1) by Dixit and his colleagues was one of likely thousands that was not indexed by PubMed on schedule because of the shutdown.

And concerns about the timely processing of federal grants mount. Applicants and reviewers alike are waiting the shutdown out, wondering whether their grants will be reviewed or their reviews read anytime soon. “NIH asked . . . reviewers to download all the grants and meeting materials before the shutdown, since there is now no access to the system,” Leonid Kruglyak from the University of California, Los Angeles, wrote in an e-mail to The Scientist. “This means, for example, that we can't upload our reviews until it’s back up.” NIH has asked Kruglyak and other reviewers to stay tuned, as the agency plans to cancel study section meetings on a rolling basis, 48 hours before they were scheduled to take place. “I don't think they can communicate further with us during the shutdown,” he said. “If the meetings are cancelled, the grants should still be reviewed eventually, but it will be complicated to get all the reviewers together, since these are typically scheduled many months in advance.”

And in Science, the journal’s editor-in-chief Marcia McNutt suggested how U.S. scientists might make good out of a bad situation. “I sincerely hope that this shutdown is resolved quickly and that the impacts are minor,” McNutt wrote in an October 2 editorial. “But if not, I urge the research community to take stock of  real economic hardships, opportunities lost, and damage done, so as to more effectively argue for congressional action on the federal budget.”

October 2, 2013

Processing grants
Federally-funded researchers have been told that their grant applications will not be processed during the shutdown, potentially creating delays in award assessments and disbursement in the coming weeks and months. NIH has advised applicants not to submit proposals while the agency is being affected by the shutdown. The National Science Foundation (NSF) issued similar guidance this week.

• “We have a grant that is currently awaiting review—the panel is scheduled to meet October 21. . . . So that will likely be delayed.”—Robert Britton, Michigan State University (See “Federally Funded Researchers Fear Shutdown Delays”)
• “Honestly, I am unsure how the shutdown will affect my research group and/or my institution. . . . Fortunately, the NIH is saying, ‘All work and activities performed under currently active NIH grant awards may continue.’"—Timothy Girard, Vanderbilt University School of Medicine (See “Federally Funded Researchers Fear Shutdown Delays”)
• “Reading NIH grants for a study section that may or may not take place . . .”—Leonid Kruglyak, University of California, Los Angeles (Twitter)

Tending to experiments, field work
Some intramural researchers are locked out of their labs, while some extramural investigators supported by federal grants are unable to complete their field work as planned.

• “For me, the ultimate impact is loss of time.”—CDC Research Fellow Cory Gall, Washington State University (describing in an interview with The Scientist how he had to terminate his mosquito colonies because he is no longer able to enter the campus and go to his lab, per CDC furlough rules.)
• “I work in a USDA [U.S. Department of Agriculture] building, and they shut the building and our field sites down entirely. We JUST got next year's trials planted (let's hope for rain!) but this past year's need to be harvested soon. Of course, my environmental monitoring will go . . .  unmonitored. If our new trials fail during the shutdown, then we've lost an entire year of fieldwork. Our interns are technically university employees, so we're trying to keep them busy on borrowed benches so they can make rent.”— slightlyanonusername (Reddit)

Publishing
PubMed is being manned by a minimal staff. Since October 1, the NCBI resource has indexed zero new papers. Journals, too, are feeling the pinch.

• “We are sorry, but we cannot tweet or respond to comments during the government shutdown. We'll be back as soon as possible!”—@PubMedHealth (Twitter)
• “PLOS ONE reviewers and editors employed by or affiliated with the US government may or may not be available to handle manuscripts.”— Michelle Dohm, Public Library of Science (PLOS’s Everyone blog)

Public health
The U.S. Food and Drug Administration (FDA) and the Centers for Disease Control and Prevention (CDC) are both limping along with skeleton crews. As a result, scheduled meetings between FDA and drugmakers may be postponed. While some FDA food inspectors continue to report to work, many researchers from the CDC are forced to stay home. The CDC’s program to track the spread of influenza throughout the US, for example, is postponed. On Tuesday (October 1), CDC Director Tom Frieden issued the following message on Twitter: “CDC had to furlough 8,754 people. They protected you yesterday, can't tomorrow. Microbes/other threats didn't shut down. We are less safe.”

• CDC’s Frieden told CBS News: “I am losing sleep because we don't know that we will be able to find and stop things that might kill people. . . .  We will be less able to determine when it's come, what kind of flu has come or to respond to outbreaks.”

October 1, 2013

It probably wasn’t until logging onto PubMed today that most U.S. scientists experienced the effects of the government shutdown spurred by Congress’s inability to pass a temporary 2014 spending bill. Just after start-of-business this morning, the National Center for Biotechnology Information (NCBI) resource had posted the following message to users:

Due to the lapse in government funding, PubMed is being maintained with minimal staffing. Information will be updated to the extent possible, and the agency will attempt to respond to urgent operational inquiries.

Or maybe it was when they checked Grants.gov, Research.gov, or the National Science Foundation’s FastLane, finding at each some variation of the same message. All three sites have gone semi-operational or altogether dark until further notice.

But employees of federal agencies are feeling the effects first hand, with some 800,000 asked to stay home (with or without pay). And a lack of website updates are far from their only concerns. Some intramural researchers and federally funded investigators took to Reddit and Twitter, among other places, to commiserate—hoping for the best, planning for the worst.

In an American Association for the Advancement of Science (AAAS) statement issued today, Joanne Carney, director of the Office of Government Relations, warned that the nation’s scientific reputation was at stake. “If the Government shutdown continues for a week or more, it is going to make the United States less desirable as an international research collaborator,” Carney said.

While many such ongoing discussions are speculative as the lasting effects of the U.S. government shutdown on research remain to be seen, stay tuned for The Scientist’s continuing coverage to stay abreast of the situation. We’ll be updating this page as new information and stories of the shutdown’s impact come to light.

This story has been corrected to reflect Leonid Kruglyak's affiliation. He was formerly at Princeton University, and is now at the University of California, Los Angeles.

As the government shutdown continues, The Scientist will closely monitor its impacts on science. Follow the evolving #governmentshutdown situation on Facebook and Twitter and stay tuned to www.the-scientist.com for updates and analysis.