This story is part of CT Mirror Explains, an ongoing effort to distill our wide-ranging reporting into a "what you need to know" format and provide practical information to our readers.

This story has been updated.

Though judges temporarily blocked a directive from President Donald Trump’s administration to pause trillions of dollars in federal financial assistance, many agencies, nonprofits and municipal governments are still dealing with the fallout.

In Connecticut, that has included research universities, municipalities and the state’s 17 community health centers.

Here’s a look at what the uncertainty surrounding federal aid has meant, and could mean, for Connecticut.

UConn and Yale could see significant research funding cuts.

A slash in funding provided to research institutions through the National Institutes of Health means Connecticut’s major research institutions, like UConn and Yale, could see significant cuts.

Last week, NIH announced that the funding it provides to grantees for “indirect costs,” like lab, utility and administrative personnel costs, would be limited to 15% of the grant award. Currently, the average indirect cost rate is between 27% and 28%, though some organizations have rates that are much higher, according to the agency.

On Monday, less than a day after the states filed suit, a federal judge granted a temporary restraining order prohibiting the implementation of the funding cuts. The order went into effect immediately and will remain in place “until further order” of the court, according to a court filing.

The plan would eliminate $35 million in funding for the University of Connecticut and the University of Connecticut Health Center for research into issues like cancer, Alzheimer’s disease and depression, according to a statement from Connecticut Attorney General William Tong. The institutions together received a total of over $620 million in NIH funding this year, he added.

In federal fiscal year 2023, Yale School of Medicine ranked fourth in the nation for total NIH funding provided to medical schools, receiving a total of $571 million, with an indirect cost rate of roughly 29%.

Community health centers are navigating uncertainty and funding delays.

The uncertainty surrounding federal funding, coupled with potential changes to Medicaid, have left federally qualified health centers — which largely serve patients who are on HUSKY, the state’s Medicaid system, or are uninsured — feeling uneasy about their futures. 

CEOs and medical providers from half a dozen clinics across Connecticut said some staff are wondering if they should consider finding other jobs, and some patients are choosing not to come in due to fear stemming from various executive orders.

They said there are weeklong delays for some funding requests that normally have a 24-hour turnaround.

While funding was supposed to keep flowing amid the court’s temporary halt on Trump’s freeze, several clinics were unable to draw down their funds through the Health Resources & Services Administration’s payment management system.

In other parts of the country, some facilities have shuttered, laid off staff or ceased certain services. But for now in Connecticut, community health centers have been able to keep the lights on and generally keep up services amid the fallout from the funding freeze.

But there has been a common thread in their experiences across the state: they are operating in uncharted territory, and any future changes to Medicaid or federal funding could further threaten their ability to provide care.

In New Haven, environmental projects have been delayed.

New Haven officials can’t access a federal Treasury account containing the money needed to continue work on a geothermal project underneath Union Station.

The initial planning phases of the $16.5 million project had just gotten underway when officials discovered on Feb. 3 that they no longer had access to the account, which held nearly 60% of the dedicated funds for the project.

The lockout continued until Feb. 7, when city leaders said their access was restored without any immediate explanation from federal officials. But last week, the program reverted to “suspended” once again.

“Our staff has spent so much time trying to navigate this situation that was created by a piece of paper,” Mayor Justin Elicker said in an interview a day before the funding was initially restored. “Our staff should be busy doing the work to provide services to our residents, rather than flailing to respond to some ridiculous executive order that doesn’t, in the end, have any clarity of purpose.”

Other programs in New Haven have been affected as well — like a $20 million Community Change grant the city won that was fully “obligated” by the Biden administration on Jan. 17 but that city officials have been unable to access. That fund’s status changed to “suspended” on Feb. 10.

Connecticut has joined a lawsuit to stop the cuts.

Connecticut and 21 other states jointly sued to stop the federal funding freeze. Their lawsuit was filed on Jan. 28, the day the freeze was supposed to take effect.

In a statement that day, Tong called it a “full assault on Connecticut families” and “an unprecedented and blatantly lawless and unconstitutional attack on every corner and level of our government and economy.”

The lawsuit is among several Connecticut has joined since Trump took office. The stated has sued over the health research funding cuts and efforts to deny birthright citizenship. New Haven also joined a coalition of cities suing over Trump’s executive order limiting federal funds for cities with “sanctuary” protections for immigrants.

A previous version of this story incorrectly stated that a project to supply geothermal heating to an area near Union Station in New Haven has resumed after funding was “suspended.” That program’s status has been reverted to “suspended” again.