Emily Deschanel on final ‘Bones’ show

It was around 5 a.m. on a day back in December when Emily Deschanel closed the door on a 12-year chapter in her life and finally hung up her lab coat as Dr. Temperance Brennan on Fox’s “Bones.”

The previous night was a lot more than a typical day in the lab, however.

The cast and crew of “Bones” were on location filming the climax of their series finale episode — an intense scene where Brennan and Booth (David Boreanaz) take on vengeful killer Mark Kovac (Gerard Celasco).

Boreanaz was at the helm, serving as director on the action-filled night, full of shoot outs, running, falling, and, eventually, a lot of tears.

Deschanel had planned to come back the next night for a few more scenes, but a half hour before they were set to depart set, Boreanaz told her that he could get everything he needed that evening.

“It was a little bit of a shock,” Deschanel said. “It was emotional. I burst into tears and choked up and said goodbye to people. It was really strange — and then it took two hours to drive home.”

How to say goodbye

It was a bit of a long goodbye for “Bones.”

Fox announced in February 2016 that the show was renewed for what would be a 12th and final season — “a good run,” Deschanel calls it.

The show’s final episode aired Tuesday.

Showrunners had time to plan one final arc and a proper farewell for loyal fans, who’d followed the show to 23 different time slots over the years.

Executive producer Jonathan Collier, who’s been with the show for six seasons, wanted to bring character stories full circle with something impactful. So he and fellow showrunner Michael Peterson looked to the past to find the show’s future.

In a Season 1 episode written by longtime executive producer Stephen Nathan they found their answer — a storyline that recalled Booth’s time as a sniper and a particular instance where he killed a boy’s warlord father during his son’s birthday party.

“We thought this would be a great way to show an emotional journey for Booth for the show,” Collier told CNN. “He finds healing and redemption.”

Kovac was killed in the series finale.

“[Booth] reached a place with Brennan where he’s no longer in pain,” Collier said of the finale. “Or he at least has the tools to deal with his pain.”

Emily Deschanel and David Boreanaz in the series finale episode of "Bones."

Emily Deschanel and David Boreanaz in the series finale episode of "Bones."

Emily Deschanel and David Boreanaz in the series finale episode of “Bones.”

For Brennan, the episode contained another twist. Following a lab explosion in the penultimate episode, she lost the scientific, crime-solving abilities for which she’s become famous. Doing this allowed the writers to show how much she’s grown, Collier said.

Though the character identified herself purely by her abilities in the early seasons, the last 12 years have proven to Brennan that she’s so much more than that.

“She defines herself by her abilities, by this enormous ability she has and this brilliance and this capability, and what happens when you strip that away?” he said. “Maybe something even more important remains….We wanted to have that emotional wholeness at the end.”

Deschanel was fascinated by the concept and encouraged the writers to explore the idea to its deepest depths.

The finale has an especially emotional scene where Booth and Brennan share a sweet conversation in the office about how much Brennan — with her abilities or not — means to Booth.

“I thought they did a great job coming up with a story that really kind of wraps up a lot of storylines and characters,” she said. “It’s dramatic but also satisfying in many ways. I thought they did an amazing job.”

Is this REALLY the end?

The finale also set up all of the show’s favorites for the future.

Camille (Tamara Taylor) and Arastoo (Pej Vahdat) adopted three children. She took a six month leave to help her children settle in.

In her absence, Hodgins (T. J. Thyne) was appointed temporary director — or “king of the lab,” one of the show’s running jokes.

Aubrey (John Boyd) got a promotion that would keep him in D.C. instead of moving across the country. And Angela (Michaela Conlin) wrote a children’s book.

The writers solved a long-time mystery, as well — the meaning of “447,” a number that has popped up repeatedly on the series and has been the subject of fan speculation.

In the closing scene of the final episode, a scene between Brennan and Booth reveals the number is essentially a metaphor for perseverance.

“Oh, that was [decided] up until the end,” Collier said, laughing. “We were trying to figure it out. We all had different ideas for what it should be. All of us weighed in and it was going on for a long time.”

The goal was to leave viewers with a sense of peace and hopefulness, Collier said.

“The characters are okay; they’re well and good,” he said. “The big thing, too, is I really hope it’s a positive message that adversity can be overcome. Everyone has problems in their lives. These people have a problem every week, and a huge problem at the end. But they’re together and they overcome it.”

But is this really the end for “Bones?”

The cast and producers have been open about the fact that the decision to end the show was prompted by the network — but there’s no hard feelings. And no reason to close the door on a possible return of some kind in the future, said Deschanel.

“I would not rule it out,” she said.

Trump puts China in charge of the future

Saying that it would “start a new era of production and job creation,” Trump signed a sweeping executive order Tuesday scrapping much of Barack Obama’s climate legacy.

Some analysts have expressed concern this could enable Beijing — the world’s leading emitter of greenhouse gases — to water down its own commitments, but others say it is more likely China will step into a leading role in the vacuum left by Washington.

“China now finds itself in the unenviable position of being world leader on climate change, thanks to Trump’s willfully blind irresponsibility,” Mark Lynas, a fellow at the Alliance for Science at Cornell University, wrote for CNN Opinion.

Speaking Wednesday, Chinese Ministry of Foreign Affairs spokesman Lu Kang said the country will “continue to work with relevant parties for enhanced dialog and cooperation, hand-in-hand to manage climate change, to promote efforts to put the global economy on a green and low carbon path, in order to pass on a better future to the generations to come.”

New order

While Trump’s actions may force Beijing into a leadership role, it will not be one for which it is unprepared.

“There has been an embracing of environmental issues generally in China over the last few years,” said Matthew Evans, dean of science at the University of Hong Kong (HKU).

“China is increasingly taking its position on the world stage (as) an economic superpower in its own right.”

Speaking in New York last week, China’s ambassador to the UN Liu Jeyi said “whatever the vicissitudes of the international situation… China remains steadfast in its ambition to reinforce actions in responding to climate change.”

Liu said China is committed to “reducing carbon intensity by 40-45% in 2020 compared with 2005 and reaching the peak of carbon emissions by 2030 or even earlier.”

Carbon intensity levels are measured by a country’s emissions relative to economic output. According to the US Environmental Protection Bureau, China and the US were the biggest emitters of carbon dioxide in 2011, the most recent year for which statistics are available.

“(China and the US) are moving in opposite directions on this issue,” said Alex Lo, an expert on climate politics at the University of Hong Kong.

“The Chinese government has made a lot of commitment officially … those policies and initiatives are not going to stop.”

Push and pull

The events of the past few days mark a dramatic turnaround from 2014, when, under rare blue skies in Beijing, Presidents Barack Obama and Xi Jinping announced plans for a cut in greenhouse emissions by close to a third over the next two decades.

It was a dramatic statement of intent by the world’s largest carbon polluters, and a major win for the Obama administration in bringing China on board as an equal partner in the fight against climate change.

In September 2016, the pair underlined that partnership, ratifying the Paris climate agreement alongside each other in Hangzhou.

Following the election of Donald Trump however, Beijing looks to be standing alone.

Solutions

China is already a world leader is renewable energy.

The country’s National Energy Administration said in January that China will spend more than $360 billion through 2020 on renewable technologies such as solar and wind.
China invested more than $88 billion in clean energy in 2016, according to Bloomberg New Energy Finance, down from an all time high of almost $120 billion in 2015, but still significantly more than the $58.8 billion invested by the US last year.

Lo also predicted that China will take major action to introduce an emissions trading scheme this year, a means of controlling pollution via economic incentives.

“China might be able to take leadership in terms of motivating other partners, particularly those countries in the Asia Pacific region to follow suit,” he said.

China is highly vulnerable to climate change, with 145 million people living in areas at risk of flooding due to rising sea levels, and rampant desertification already occurring in much of the country’s northwest.

Risks

China will not stand alone in terms of tackling climate change. The EU is another major player, albeit one hampered by political divisions over issues such as Brexit and the refugee crisis.
A report by the NGO Carbon Market Watch this week claimed that only three EU countries were currently pursuing their goals under the Paris agreement: Sweden, Germany and France.
US states such as California are also taking action, with Governor Jerry Brown vowing to forge ahead on climate policies regardless of Washington.

“If China and the EU choose to act together then I think between them they can manage a lot of this,” said HKU’s Evans.

“But if the US tears up as many of their climate policies as it’s suggesting they’re going to, that will be a loss.”

“The atmosphere is a global good. You can’t constrain greenhouse gases released in the US to stay in the US, we’re all going to suffer from them,” he added.

Another major risk posed by the Trump administration’s action, according to Evans, is that it may encourage countries to move forward on their own on matters such as geoengineering.
Efforts to hack the planet in order to slow or reverse climate change have been put forward, but critics warn they could have unforeseen runaway effects that leave the world in a worse position than before.

“At the moment there’s a moratorium on any country doing that unilaterally,” Evans said.

But for nations most at risk from climate change, “you have to wonder how much of their country they’re willing to see go underwater before they take action unilaterally to modify the climate.”

Clinton makes political remarks

“There is no place I’d rather be than here with you,” Clinton said, before adding: “Other than the White House.”

During her keynote address at the annual conference hosted by the Professional BusinessWomen of California, Clinton spoke largely about women’s equality and peppered in criticism of President Donald Trump and the Republican Party.

“Obviously the outcome of the election wasn’t the one I hoped for, worked for, but I will never stop speaking out for common sense benefits that will allow moms and dads to stay on the job,” Clinton said.

Besides a few comments in public gatherings and tweets from her personal account, Clinton has largely laid low since the election. She was spotted after the election in the woods near her New York home and, along with her husband former President Bill Clinton, she attended Trump’s inauguration.

She called Republicans’ attempted replacement for the Affordable Care Act “a disastrous bill,” adding that the Trump administration has been “met with a wave of resistance” that indicates the protests against Trump’s policies are just getting started.

“People who had never been active in politics told their stories at town hall meetings.” Clinton said. “They were people who had something to say and were determined to be heard.”

During the question and answer portion of her appearance, she grew incredulous at the GOP health care debate.

“Really? Take away maternity care?” Clinton said. “Who do these people talk to?”

Clinton also focused on issues like inclusivity and diversity of women in the workplace and the need for the private sector to make better efforts to bring more women to the table.

“Advancing the rights and opportunities of women and girls is the great unfinished business of the 21st century,” she said, while noting that women’s representation in Washington is “the lowest it’s been in a generation.”

‘A lifetime of practice’

The former secretary of state also responded to racially charged incidents directed at two prominent black women today.

In one, White House press Secretary Sean Spicer told April Ryan, a longtime White House correspondent and one of the few black women journalists in the press briefing room, to “stop shaking your head” and accused her of being “hell-bent on trying to make sure that whatever image you want to tell about this White House stays.”

In another, Fox News host Bill O’Reilly came under fire for racist comments mocking Rep. Maxine Waters’ hair, saying her hair looked like a “James Brown wig.”

O’Reilly later apologized, but not after a slew of controversy. Tuesday, Clinton said Waters had been “taunted by a racist joke about her hair.”

Women of color, said Clinton, have “a lifetime of practice taking precisely these kinds of indignities in stride.”

‘Resist, insist’

On the policy front, Clinton criticized the US for still not having a national paid family leave policy and said those who do benefit from such policies are often among the highest income workers. Clinton called on the private sector to do more to help.

“You’re the people who figured out how to fit computers in the palms of our hands,” she said. “You have the power.”

But overall, Clinton offered an optimistic tone in the face of Trump’s victory.

“Where some see a dark vision of carnage, I see a light shining on creativity and opportunity,” she said, referencing the inaugural address.

She offered the audience her new mantra: “Resist, insist, persist, enlist.”

She encouraged the audience to “resist actions that go against our values as Americans,” insist on “putting people first,” “persist” like Sen. Elizabeth Warren did when she was prevented from reading a letter written by Coretta Scott King about Sen. Jeff Sessions, and “enlist” others by running for office or opening a business.

“I’ll be right there with you every step of the way,” she said.

How paralyzed man regained hand movements

The early stage research has been tested in a lab with just one patient so far, yet someday it may change the lives of many with spinal cord injuries, said lead author Abidemi Bolu Ajiboye, an assistant professor at Case Western Reserve University.

Even though the system would not become immediately available to patients, Ajiboye believes that all the technical hurdles can be overcome within five to 10 years. “We actually have a handle on everything that we need. There are no significant novel discoveries we need to make for the system,” he said.

Ajiboye said that what makes this achievement unique is not the technology, but the patient. Unlike any previous experiments, a man who is nearly completely paralyzed — or tetraplegic — regained his ability to reach and grasp by virtue of a neuroprosthetic.

Cycling accident

Bill Kochevar, a resident of Cleveland, injured his spinal cord in 2006 prior to enrolling in the study.

“It was a bicycling accident,” said Ajiboye, who explained that Kochevar, 53, was doing a 150-mile bicycle ride on a rainy day. “He was following a mail truck and the mail truck stopped and he ended up running into the back of the truck,” said Ajiboye. As a result, Kochevar has paralysis below the shoulders.

“So he can’t walk, he can’t move his arms, he can’t move his hands,” said Ajiboye.

While the American Spinal Injury Association classifies him at the most disabled level of paralysis, Kochevar is capable of both speaking and moving his head. Prior to enrolling in the study, he often used head tracking software technology that relied on him moving his head to move a cursor on a screen. “But he had no ability to do any sort of functional activities,” said Ajiboye.

Kochevar underwent two surgeries fitting him with the neuroprosthetic. The first operation on December 1, 2014, implanted the brain computer interface, or BCI, in the region of Kochevar brain that is responsible for hand movement, called the motor cortex.

The BCI is an electrode array which penetrates the brain between one to one and a half millimeters, said Ajiboye.

Next, Kochevar underwent a second surgery to implant 36 muscle stimulating electrodes into his upper and lower arm. Known as functional electrical stimulation or FES, these electrodes are key to restoring movement in his finger and thumb, wrist, elbow and shoulders.

The Cleveland Functional Electrical Stimulation Center, of which Ajiboye is a part, first developed electrical stimulation technology for reanimating paralyzed function nearly 30 years ago. As Ajiboye explained, the technology is similar to a pacemaker in that it applies electrical stimulation to the muscles in order to stir movement.

After the separate technologies were implanted, the researchers connected Kochevar’s brain-computer interface to the electrical stimulators in his arm. At this point, Kochevar began learning how to use his neuroprosthetic and that process started with a virtual arm.

“We had him watch the virtual arm move, he attempted to move his arm in the same way, and that elicited some patterns of cortical activity — some patterns of electrical neural activity,” said Ajiboye.

This electrical activity was recorded and based on this recording, Ajiboye and his colleagues created a “neural decoder” — an algorithm specific to Kochevar — that could translate the patterns of Kochevar’s recorded brain signals into commands for the electrodes in his arm.

“Then we had him use our algorithm to control the virtual arm on the screen just using his brain signals,” said Ajiboye. “Very early on he could hit the target with 95 to 100% accuracy.” This ‘virtual’ step in the process helped Ajiboye and his colleagues refine the algorithm.

“Then, finally, we basically do the same thing with his actual arm. We manually move his arm, and we have him imagine he’s doing it,” said Ajiboye. Kochevar is then able to move his arm on his own by thinking the command (and so generating once again the same brain pattern when he imagined moving his arm) and this is then actuated through electrical stimulation.

Essentially, the technology circumvents the spinal injury feeding the electrical stimulation of his brain through wires to the electrodes in his arm.

After mastering simple movements, Kochevar was tested on day-to-day tasks, including drinking a cup of coffee and feeding himself. In all of these, Kochevar was successful.

“There were no significant adverse events, the system is safe, so as far as the clinical trial endpoint goes, he has met those,” said Ajiboye.

“Now he has opted voluntarily to continue working as a participant in our study for at least another five years,” said Ajiboye. Kochevar hopes to experience the benefits of the technology for himself while also seeing it advance to the point of becoming available for other people with spinal cord injuries, according to Ajiboye.

CNN attempted to contact Kochevar for comment.

‘Encouraging’ results

A previous unrelated study showed paraplegic people with spinal cord injuries using brain-machine interfaces to gain control of their brain activity and stimulate movement in their legs. A separate study used a brain-spine interface to communicate nerve signals and helped paralyzed monkeys to regain movement.
According to Andrew Schwartz, a professor of neurobiology at the University of Pittsburgh, the new study “shows the potential that [a brain-machine interface] can be used to reanimate a limb.” Schwartz was uninvolved with the current study.

While the “generated movements were somewhat rudimentary” with a rather limited range of action, “the attempt to use multiple degrees of freedom was encouraging,” said Schwartz.

“I liked the idea that movements were decoded first and then transformed to muscle activations,” he added. “For real movements in the real world, this transformation will be very difficult to calculate and that is where real science will be needed.”

In an editorial published alongside the study, Steve I. Perlmutter, an associate professor at University of Washington in Seattle, said the research is “groundbreaking as the first report of a person executing functional, multijoint movements of a paralysed limb with a motor neuroprosthetic. However, this treatment is not nearly ready for use outside the lab.”

Similar to Schwartz, Perlmutter noted that Kochevar’s movements were “rough and slow” and had limited range due to the necessary motorized device.

“Stimulation of nerves or the spinal cord, rather than muscles, and more sophisticated stimulation technology may provide substantial improvements,” wrote Perlmutter.

“The algorithms for this type of brain computer interface are very important, but there are many other factors that are also critical, including the ability to measure brain signals reliably for long periods of time,” Perlmutter said in an email. He added another critical issue is execution of movement.

Hurdles that all motor neuroprostheses must overcome have yet to be addressed, noted Perlmutter, including “development of devices that are small enough, robust enough, and cheap enough to be fully mobile and widely available.”

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Ajiboye acknowledges the need for smaller technologies. Still, he said, his new study differs from previous work done in the field. Although other labs have worked with non-human primates or partially paralyzed participants, his study helped someone who is completely paralyzed.

“This is an exponentially harder problem,” said Ajiboye. “Our study is the first in the world, to my knowledge, to take someone paralyzed and give him the ability to both reach and grasp objects… so that he can regain the ability to perform functional activities of daily living.”

One other way the new study differs from previous research is Ajiboye and his colleagues built their neuroprosthetic from separate technologies, each of which had already been proven viable. This translates to the entire system, when refined, more easily gaining approval and becoming available to patients.

“The goal is to do much more than a cool science experiment,” said Ajiboye.

What caused deadly outbreak at these hospitals

UPMC informed the Allegheny County Health Department, Pennsylvania Department of Health, and U.S. Centers for Disease Control and Prevention that its independent testing led UPMC officials to believe the linens were the likely source of the outbreak, according to the emails.

The new emails reveal additional testing seeking to pinpoint the source of the outbreak.

An email sent May 5, 2016, by Jeff Miller, a field epidemiologist for the CDC, said that environmental samples were taken on February 21, 22 and April 21, 2016, at UPMC Presbyterian and Montefiore hospitals and Paris Co. laundry facilities. The testing was requested by UPMC and conducted by an independent contractor.

A whole genome sequencing report by an independent laboratory based on these specimens “[suggests] that fungi from Paris have been brought into the [Presbyterian University Hospital] laundry,” according to the report provided in the email.

“It is looking more likely than ever, that the linen vendor is the more likely potential source of mucor as you can see by the reports,” said an email sent by Allegheny County Health Department Chief Epidemiologist LuAnn Brink on June 21, 2016, in which she shared “notes from UPMC.” It is unknown who from UPMC sent Brink the notes. Mucor is a species of mucormycosis, which are fungal spores commonly found outdoors. However, they can cause a rare and sometimes fatal fungal infection in patients who are immunocompromised, according to the CDC.

A whole genome sequencing report compares environmental samples from which the DNA has been extracted and sequenced to show the fingerprint of the sample at a high resolution, according to Dr. Barun Mathema, an assistant professor of epidemiology at Columbia’s Mailman School of Public Health who CNN contacted independently on Monday.

“Nobody is a 100% sure, if you read carefully, there will always be a bit of a wiggle room caveat,” said Mathema, who was not involved in testing the samples from Pittsburgh. In general, it is rare that epidemiological testing comes to an absolutely conclusive result because of variables that come into play when epidemiologists attempt to replicate the exact environment in which the case occurred.

Additional testing

This isn’t the first report to link the mold outbreak to hospital linens. In a separate, UPMC-contracted internal report, testing conducted on February 1, 2016 by hospital environmental specialists Andrew Streifel and Michael Buck found a heavy buildup of lint and mold near the Paris Co. linen facility vent through which unfiltered air dried the linens.

When Streifel and Buck went to the hospitals and tested linen from Paris Co., a cart of wet sheets delivered to the Montefiore laundry storage area bore “heavy fungal growth of Mucor and rhizopus,” according to their report, which was not made public until early 2017.

“Our hospitals are safe, and our ongoing monitoring and testing show no evidence of a mold outbreak. We and the nation’s top health regulators have found no definitive or unifying cause of the previous infections, which are known to occur on occasion at most major medical centers,” UPMC spokeswoman Allison Hydzik said in a statement to CNN when asked to respond to the contents of these emails.

UPMC “will address specific allegations in court and not in the media,” Hydzik said.

The Allegheny County Health Department provided CNN with the emails, which were incorrectly redacted to reveal more information than intended. The emails were provided in response to an open records request under the state’s Right to Know Law. The county records department withheld several other emails on the grounds of privacy for patients’ information.

“While we were made aware of all steps that UPMC was taking to identify potential sources, including looking at linens, there was no identification of the linens as the source of the outbreak. Similarly, as has already been stated by the department, ACHD was an observer in this process, not the regulatory agency looking into this,” Allegheny County Health Department spokeswoman Melissa Wade said in a statement to CNN when asked about the emails.

“Our products are safe. We have nothing to hide. We have followed and continue to follow protocols of the Healthcare Laundry Accreditation Council by providing hygienically clean linens to our customers,” Paris Co. CEO Dave Stern said in a statement to CNN when asked about the content of the emails.

CDC and state officials respond

In a phone interview this week, Sharon Watkins, director of the bureau of epidemiology for the Pennsylvania Department of Health said the mold investigation is continuing. At no time has the state or the CDC determined that linens were the most likely cause of the UPMC mold outbreak, she said.

“I don’t know why anyone would say that,” Watkins said, referring to the email that said “the linen vendor is the more likely potential source of mucor.”

UPMC is required to provide the Pennsylvania Department of Health with regular updates concerning the investigation, Pennsylvania Department of Health spokeswoman April Hutcheson said.

Since May 2016, the Pennsylvania health department has been “in constant consultation with the CDC on this issue, including epidemiological evaluation of new information, a site visit, and current review of system-wide UPMC data,” Hutcheson told CNN in a statement when asked about the emails.

“There is no evidence to indicate an ongoing outbreak at this time; however, the state health department is in the process of reviewing additional information as part of the ongoing investigation.”

The UPMC hospital system mold outbreak began in October 2014. By September 2015, four patients had died of fungal infections at UPMC Presbyterian and Montefiore hospitals. By that time, the transplant ICU at Presbyterian had temporarily closed.

In September 2015, while the Presbyterian transplant ICU was closed, the CDC investigated possible sources of the mold outbreak. The results of the investigation were published in the May 2016 Morbidity and Mortality Weekly Report. Investigators said that the fatal infections were not attributed to the mold-covered linens, but rather to ventilation that may have allowed dust and mold spores to enter the hospital rooms.

The CDC maintains that conclusion despite what the newly uncovered emails say, Skinner said. The CDC findings were not addressed in the recently released emails.

In May 2016, Pennsylvania Governor Tom Wolf again requested the CDC consult with the state health department and UPMC because a fifth fungal infection recipient had been identified in the Presbyterian ICU, CDC spokesperson Tom Skinner told CNN when asked about the content of the emails. Wolf’s press secretary, J.J. Abbott, confirmed the request in an email to CNN.

That additional patient was Daniel Krieg, a kidney transplant patient who died in July 2016. UPMC medical reports show Krieg had fungal pneumonia and that fungal-infected sections of his left lung were removed. A CDC representative returned to UPMC on June 22, 2016, with officials from the state and county departments of health to discuss the outbreak and Krieg’s case, Skinner told CNN on Monday.

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An agenda in the newly revealed emails said health officials were to discuss laundry processes at Presbyterian, Montefiore, and Shadyside hospitals at the June 22, 2016 CDC visit.

The day before that visit, an June 21, 2016, email sent by Brink also said that UPMC was working with the linen vendor to “improve their product.” The email also said the hospital system was “aggressively pursuing” an alternative linen solution for all transplant patients in the ICU at Presbyterian hospital.

UPMC said in a January 2016 statement that high-risk transplant patients would receive linens with a lower bacterial count going forward. Hospital linens are required to be “hygienically clean,” according to the Healthcare Laundry Accreditation Council. (PDF) That means linens are not sterile, but in a clean state, free of pathogens in sufficient numbers to minimize risk of infection, and the clean textiles are not inadvertently contaminated before use, according to the CDC.

“Despite the lack of a definitive source, UPMC still went above and beyond state and federal recommendations in order to implement changes to protect our patients. One of the many changes includes the provision of specially treated bioburden-reduced linens to our highest risk transplant patients,” UPMC spokeswoman Hydzik told CNN previously.

Gorsuch path unclear; filibuster, nuclear option loom

But the exact math behind breaking a filibuster or changing the Senate rules did not yet appear to add up as of Tuesday evening.

Senior Democrats predicted their caucus will ban together to block Gorsuch on a key procedural vote expected next Thursday. And they held out hope that not all Republicans would back McConnell’s use of the nuclear option, a controversial rule change that would lower the threshold for overcoming a filibuster for Supreme Court nominees from 60 to 51 and allow them to confirm Gorsuch on a partly line vote.

“I don’t want to change the rules of the Senate, and I hope we’re not confronted with that choice,” said Sen. Susan Collins of Maine, one of several GOP moderates Democrats think might vote against the nuclear option. In an interview with CNN, Collins stopped short of saying whether she would vote for the rule change.

But Sen. John Cornyn of Texas, the GOP whip, predicted enough Republicans would vote together to approve the nuclear option.

“I hope it doesn’t come to that but if the Democrats force our hand, then we’ll be prepared to do what we need to do to confirm the judge,” Cornyn said.

Senate Minority Leader Chuck Schumer, who actively whipped members of his caucus on the issue, said Gorsuch didn’t “impress” Democrats during his confirmation hearings and faces “an uphill climb” to get to 60 votes. Only a handful of Democrats appeared to be even contemplating advancing Gorsuch, although some Democrats thought the number might climb as the vote nears.

“I’m going to base my decision on him, input from Montanans, and what his opinions are,” said Sen. Jon Tester, D-Montana, who is under immense pressure from fellow lawmakers and outside interest groups. The second-term senator is running for re-election in a state President Donald Trump easily won in November.

Tester said he hoped the Republicans would not use the nuclear option because it would make the Senate more like the House — where majority party can rule without much input from the minority party — but insisted that issue would not weigh into his decision.

The status of the Democratic filibuster

Republicans are struggling to come up with the eight Democrats needed to join them in breaking the filibuster.

Only two Democrats — Sen. Joe Manchin of West Virginia and Sen. Heidi Heitkamp of North Dakota — have signaled they would oppose the filibuster, but even those two senators have hesitated to be definitive about it.

The Republican National Committee targeted 12 Democrats from mostly states that Trump won, urging them through paid ad campaigns to support an up-or-down vote on Gorsuch — code for opposing the filibuster.

However, several of those senators, like Tammy Baldwin of Wisconsin and Bob Casey of Pennsylvania, have said they’ll join the filibuster and won’t support Gorsuch.

Republicans are still waiting to hear from some of the targeted Democrats, like Tester, Sen. Claire McCaskill of Missouri, and Sen. Joe Donnelly of Indiana, all of who have been mum this week on where they’re leaning.

Sen. Michael Bennet of Colorado has also stayed silent. He introduced Gorsuch, who’s from his home state, at his hearing last week but said he was doing so out of tradition and wasn’t necessarily telegraphing his support.

Democratic Sen. Chris Coons of Delaware, who also hasn’t announced his decision, said Monday on MSNBC that he doesn’t think Gorsuch will get the 60 votes he needs to end the filibuster.

While unlikely, Democrats are hoping their filibuster will result in Republicans deciding against using the nuclear option and instead put forth a different nominee.

“If the nominee cannot earn the support of 60 Senators, the answer is not to break precedent by fundamentally and permanently changing the rules and traditions of the Senate, the answer is to change the nominee,” Schumer said Tuesday on the Senate floor.

According to CNN’s latest whip count, 26 Democrats are on the record planning to join the filibuster. That’s a little more than half of the Democratic caucus. More are expected to announce their decision in the coming days.

But the real number to focus on is eight — the number of Democrats needed to vote against the filibuster.

And so far there are only two maybes, and its not immediately clear whom the remaining six would be.

Republicans threaten controversial nuclear option

While Republicans can win at the end of the day using the nuclear option, it’s not a choice they’re particularly thrilled to make.

It was a controversial move when Harry Reid lowered the filibuster threshold in 2013 for cabinet nominees, and it would be just as controversial for Republicans do so now.

Sen. Mike Rounds of South Dakota said they don’t “have a choice.”

“It’s very unfortunate. I think it turns our stomach,” the first term Republican told reporters Tuesday, adding that he’s uneasy with the idea of setting a new precedent. “Once it’s been used once, it’s going to be used time and time again.”

Rounds expressed concern that it could ultimately be used to impact legislation, in addition to presidential nominees, and he thinks Democrats are privately wanting the rules change so that Republicans can shoulder some of the drama that Democrats stirred up in 2013.

“I think it hurt the Democrats when they did it, and I think they’d like to share that with Republicans in the future,” he argued.

When asked whether he’d support the nuclear option, Sen. Pat Roberts, R-Kansas, said he hopes it doesn’t get to that point and questioned “whether long term it makes any sense at all.”

“If we keep doing that, you eventually end up being very much like the House and historically that’s not a good thing for the Senate according to what the Founding Fathers wanted,” he added.

Sen. Tim Scott, R-South Carolina, said he was playing it “straight and narrow right now” on whether he was leaning in favor of the nuclear option or against it. But he added: “I think his confirmation is an absolutely necessity.”

What happens next

The Senate Judiciary Committee will meet next Monday to vote on Gorsuch and send him to the full Senate with a final confirmation vote expected Friday evening, according to a GOP leadership aide who explained the anticipated schedule for next week.

On Tuesday, McConnell would move to end floor debate on Gorsuch. This would set up the key procedural vote Thursday morning when the chamber’s 52 Republicans hope to get at least eight Democrats to join them in defeating a filibuster of the judge.

If the filibuster is not defeated, McConnell would then move immediately on the nuclear option, which would need a simple majority of those present and voting to succeed. Vice President Mike Pence is expected to be in the chamber if he is needed to break a tie.

If Republicans hold together and the nuclear option passes, the Senate would vote again to break the filibuster of Gorsuch, this time needing just 51 votes to do so.

After that, Senate rules allow for up to 30 hours of what’s called “post-cloture” debate time. That would set up a final confirmation vote for Gorsuch sometime Friday evening. He would only need a simple majority on that final vote.

Emily Deschanel on final ‘Bones’ show

It was around 5 a.m. on a day back in December when Emily Deschanel closed the door on a 12-year chapter in her life and finally hung up her lab coat as Dr. Temperance Brennan on Fox’s “Bones.”

The previous night was a lot more than a typical day in the lab, however.

The cast and crew of “Bones” were on location filming the climax of their series finale episode — an intense scene where Brennan and Booth (David Boreanaz) take on vengeful killer Mark Kovac (Gerard Celasco).

Boreanaz was at the helm, serving as director on the action-filled night, full of shoot outs, running, falling, and, eventually, a lot of tears.

Deschanel had planned to come back the next night for a few more scenes, but a half hour before they were set to depart set, Boreanaz told her that he could get everything he needed that evening.

“It was a little bit of a shock,” Deschanel said. “It was emotional. I burst into tears and choked up and said goodbye to people. It was really strange — and then it took two hours to drive home.”

How to say goodbye

It was a bit of a long goodbye for “Bones.”

Fox announced in February 2016 that the show was renewed for what would be a 12th and final season — “a good run,” Deschanel calls it.

The show’s final episode aired Tuesday.

Showrunners had time to plan one final arc and a proper farewell for loyal fans, who’d followed the show to 23 different time slots over the years.

Executive producer Jonathan Collier, who’s been with the show for six seasons, wanted to bring character stories full circle with something impactful. So he and fellow showrunner Michael Peterson looked to the past to find the show’s future.

In a Season 1 episode written by longtime executive producer Stephen Nathan they found their answer — a storyline that recalled Booth’s time as a sniper and a particular instance where he killed a boy’s warlord father during his son’s birthday party.

“We thought this would be a great way to show an emotional journey for Booth for the show,” Collier told CNN. “He finds healing and redemption.”

Kovac was killed in the series finale.

“[Booth] reached a place with Brennan where he’s no longer in pain,” Collier said of the finale. “Or he at least has the tools to deal with his pain.”

Emily Deschanel and David Boreanaz in the series finale episode of "Bones."

For Brennan, the episode contained another twist. Following a lab explosion in the penultimate episode, she lost the scientific, crime-solving abilities for which she’s become famous. Doing this allowed the writers to show how much she’s grown, Collier said.

Though the character identified herself purely by her abilities in the early seasons, the last 12 years have proven to Brennan that she’s so much more than that.

“She defines herself by her abilities, by this enormous ability she has and this brilliance and this capability, and what happens when you strip that away?” he said. “Maybe something even more important remains….We wanted to have that emotional wholeness at the end.”

Deschanel was fascinated by the concept and encouraged the writers to explore the idea to its deepest depths.

The finale has an especially emotional scene where Booth and Brennan share a sweet conversation in the office about how much Brennan — with her abilities or not — means to Booth.

“I thought they did a great job coming up with a story that really kind of wraps up a lot of storylines and characters,” she said. “It’s dramatic but also satisfying in many ways. I thought they did an amazing job.”

Is this REALLY the end?

The finale also set up all of the show’s favorites for the future.

Camille (Tamara Taylor) and Arastoo (Pej Vahdat) adopted three children. She took a six month leave to help her children settle in.

In her absence, Hodgins (T. J. Thyne) was appointed temporary director — or “king of the lab,” one of the show’s running jokes.

Aubrey (John Boyd) got a promotion that would keep him in D.C. instead of moving across the country. And Angela (Michaela Conlin) wrote a children’s book.

The writers solved a long-time mystery, as well — the meaning of “447,” a number that has popped up repeatedly on the series and has been the subject of fan speculation.

In the closing scene of the final episode, a scene between Brennan and Booth reveals the number is essentially a metaphor for perseverance.

“Oh, that was [decided] up until the end,” Collier said, laughing. “We were trying to figure it out. We all had different ideas for what it should be. All of us weighed in and it was going on for a long time.”

The goal was to leave viewers with a sense of peace and hopefulness, Collier said.

“The characters are okay; they’re well and good,” he said. “The big thing, too, is I really hope it’s a positive message that adversity can be overcome. Everyone has problems in their lives. These people have a problem every week, and a huge problem at the end. But they’re together and they overcome it.”

But is this really the end for “Bones?”

The cast and producers have been open about the fact that the decision to end the show was prompted by the network — but there’s no hard feelings. And no reason to close the door on a possible return of some kind in the future, said Deschanel.

“I would not rule it out,” she said.

April Ryan: The press is ‘under attack by this administration’

Story highlights

  • “I happen to be a black woman, but I’m part of the press,” Ryan said
  • Spicer told Ryan to “stop shaking your head” at a White House briefing

“We are — the press is — under attack. We are under attack by this administration,” American Urban Radio Networks correspondent April Ryan said on CNN’s “New Day.” “It’s about discrediting credible media.”

Spicer told Ryan at Tuesday’s briefing to “stop shaking your head” and accused her of being “hell-bent on trying to make sure that whatever image you want to tell about this White House stays,” after she asked him about the investigation into contacts between Trump campaign associates and Russian officials.

Ryan, one of the few black female journalists in the press briefing room, declined to say if she thought Spicer treated women journalists differently but did highlight another recent incident involving Spicer and another female journalist.

“I happen to be a black woman, but I’m part of the press,” she said. “But this is part of a series of two women this week who have been in the news over something with the press secretary.”

“I just see from the weekend that reporter from Politico who he called an idiot and then this situation, it’s showing a pattern,” Ryan added.

Ryan was referring to a Saturday tweet from Politico’s Tara Palmeri that said President Donald Trump is considering removing White House Chief of Staff Reince Priebus. Spicer denied her report.
“She is an idiot with no real sources,” Spicer told Breitbart News in an email.

Spicer and Ryan had a much more positive exchange at Wednesday’s briefing when Ryan was the first journalist the press secretary called on. The two exchanged pleasantries while smiling and laughing as others in the room laughed.

Ryan previously had a tense exchange in February with Trump over his desire to meet with black lawmakers.

When questioned on whether he planned to meet with the Congressional Black Caucus, a group of African-American lawmakers on Capitol Hill, Trump asked Ryan if she could organize it herself.

“No,” Ryan replied, adding that she was “just a reporter.”

Clinton makes political remarks

“There is no place I’d rather be than here with you,” Clinton said, before adding: “Other than the White House.”

During her keynote address at the annual conference hosted by the Professional BusinessWomen of California, Clinton spoke largely about women’s equality and peppered in criticism of President Donald Trump and the Republican Party.

“Obviously the outcome of the election wasn’t the one I hoped for, worked for, but I will never stop speaking out for common sense benefits that will allow moms and dads to stay on the job,” Clinton said.

Besides a few comments in public gatherings and tweets from her personal account, Clinton has largely laid low since the election. She was spotted after the election in the woods near her New York home and, along with her husband former President Bill Clinton, she attended Trump’s inauguration.

She called Republicans’ attempted replacement for the Affordable Care Act “a disastrous bill,” adding that the Trump administration has been “met with a wave of resistance” that indicates the protests against Trump’s policies are just getting started.

“People who had never been active in politics told their stories at town hall meetings.” Clinton said. “They were people who had something to say and were determined to be heard.”

During the question and answer portion of her appearance, she grew incredulous at the GOP health care debate.

“Really? Take away maternity care?” Clinton said. “Who do these people talk to?”

Clinton also focused on issues like inclusivity and diversity of women in the workplace and the need for the private sector to make better efforts to bring more women to the table.

“Advancing the rights and opportunities of women and girls is the great unfinished business of the 21st century,” she said, while noting that women’s representation in Washington is “the lowest it’s been in a generation.”

‘A lifetime of practice’

The former secretary of state also responded to racially charged incidents directed at two prominent black women today.

In one, White House press Secretary Sean Spicer told April Ryan, a longtime White House correspondent and one of the few black women journalists in the press briefing room, to “stop shaking your head” and accused her of being “hell-bent on trying to make sure that whatever image you want to tell about this White House stays.”

In another, Fox News host Bill O’Reilly came under fire for racist comments mocking Rep. Maxine Waters’ hair, saying her hair looked like a “James Brown wig.”

O’Reilly later apologized, but not after a slew of controversy. Tuesday, Clinton said Waters had been “taunted by a racist joke about her hair.”

Women of color, said Clinton, have “a lifetime of practice taking precisely these kinds of indignities in stride.”

‘Resist, insist’

On the policy front, Clinton criticized the US for still not having a national paid family leave policy and said those who do benefit from such policies are often among the highest income workers. Clinton called on the private sector to do more to help.

“You’re the people who figured out how to fit computers in the palms of our hands,” she said. “You have the power.”

But overall, Clinton offered an optimistic tone in the face of Trump’s victory.

“Where some see a dark vision of carnage, I see a light shining on creativity and opportunity,” she said, referencing the inaugural address.

She offered the audience her new mantra: “Resist, insist, persist, enlist.”

She encouraged the audience to “resist actions that go against our values as Americans,” insist on “putting people first,” “persist” like Sen. Elizabeth Warren did when she was prevented from reading a letter written by Coretta Scott King about Sen. Jeff Sessions, and “enlist” others by running for office or opening a business.

“I’ll be right there with you every step of the way,” she said.

What caused deadly outbreak at these hospitals

UPMC informed the Allegheny County Health Department, Pennsylvania Department of Health, and U.S. Centers for Disease Control and Prevention that its independent testing led UPMC officials to believe the linens were the likely source of the outbreak, according to the emails.

The new emails reveal additional testing seeking to pinpoint the source of the outbreak.

An email sent May 5, 2016, by Jeff Miller, a field epidemiologist for the CDC, said that environmental samples were taken on February 21, 22 and April 21, 2016, at UPMC Presbyterian and Montefiore hospitals and Paris Co. laundry facilities. The testing was requested by UPMC and conducted by an independent contractor.

A whole genome sequencing report by an independent laboratory based on these specimens “[suggests] that fungi from Paris have been brought into the [Presbyterian University Hospital] laundry,” according to the report provided in the email.

“It is looking more likely than ever, that the linen vendor is the more likely potential source of mucor as you can see by the reports,” said an email sent by Allegheny County Health Department Chief Epidemiologist LuAnn Brink on June 21, 2016, in which she shared “notes from UPMC.” It is unknown who from UPMC sent Brink the notes. Mucor is a species of mucormycosis, which are fungal spores commonly found outdoors. However, they can cause a rare and sometimes fatal fungal infection in patients who are immunocompromised, according to the CDC.

A whole genome sequencing report compares environmental samples from which the DNA has been extracted and sequenced to show the fingerprint of the sample at a high resolution, according to Dr. Barun Mathema, an assistant professor of epidemiology at Columbia’s Mailman School of Public Health who CNN contacted independently on Monday.

“Nobody is a 100% sure, if you read carefully, there will always be a bit of a wiggle room caveat,” said Mathema, who was not involved in testing the samples from Pittsburgh. In general, it is rare that epidemiological testing comes to an absolutely conclusive result because of variables that come into play when epidemiologists attempt to replicate the exact environment in which the case occurred.

Additional testing

This isn’t the first report to link the mold outbreak to hospital linens. In a separate, UPMC-contracted internal report, testing conducted on February 1, 2016 by hospital environmental specialists Andrew Streifel and Michael Buck found a heavy buildup of lint and mold near the Paris Co. linen facility vent through which unfiltered air dried the linens.

When Streifel and Buck went to the hospitals and tested linen from Paris Co., a cart of wet sheets delivered to the Montefiore laundry storage area bore “heavy fungal growth of Mucor and rhizopus,” according to their report, which was not made public until early 2017.

“Our hospitals are safe, and our ongoing monitoring and testing show no evidence of a mold outbreak. We and the nation’s top health regulators have found no definitive or unifying cause of the previous infections, which are known to occur on occasion at most major medical centers,” UPMC spokeswoman Allison Hydzik said in a statement to CNN when asked to respond to the contents of these emails.

UPMC “will address specific allegations in court and not in the media,” Hydzik said.

The Allegheny County Health Department provided CNN with the emails, which were incorrectly redacted to reveal more information than intended. The emails were provided in response to an open records request under the state’s Right to Know Law. The county records department withheld several other emails on the grounds of privacy for patients’ information.

“While we were made aware of all steps that UPMC was taking to identify potential sources, including looking at linens, there was no identification of the linens as the source of the outbreak. Similarly, as has already been stated by the department, ACHD was an observer in this process, not the regulatory agency looking into this,” Allegheny County Health Department spokeswoman Melissa Wade said in a statement to CNN when asked about the emails.

“Our products are safe. We have nothing to hide. We have followed and continue to follow protocols of the Healthcare Laundry Accreditation Council by providing hygienically clean linens to our customers,” Paris Co. CEO Dave Stern said in a statement to CNN when asked about the content of the emails.

CDC and state officials respond

In a phone interview this week, Sharon Watkins, director of the bureau of epidemiology for the Pennsylvania Department of Health said the mold investigation is continuing. At no time has the state or the CDC determined that linens were the most likely cause of the UPMC mold outbreak, she said.

“I don’t know why anyone would say that,” Watkins said, referring to the email that said “the linen vendor is the more likely potential source of mucor.”

UPMC is required to provide the Pennsylvania Department of Health with regular updates concerning the investigation, Pennsylvania Department of Health spokeswoman April Hutcheson said.

Since May 2016, the Pennsylvania health department has been “in constant consultation with the CDC on this issue, including epidemiological evaluation of new information, a site visit, and current review of system-wide UPMC data,” Hutcheson told CNN in a statement when asked about the emails.

“There is no evidence to indicate an ongoing outbreak at this time; however, the state health department is in the process of reviewing additional information as part of the ongoing investigation.”

The UPMC hospital system mold outbreak began in October 2014. By September 2015, four patients had died of fungal infections at UPMC Presbyterian and Montefiore hospitals. By that time, the transplant ICU at Presbyterian had temporarily closed.

In September 2015, while the Presbyterian transplant ICU was closed, the CDC investigated possible sources of the mold outbreak. The results of the investigation were published in the May 2016 Morbidity and Mortality Weekly Report. Investigators said that the fatal infections were not attributed to the mold-covered linens, but rather to ventilation that may have allowed dust and mold spores to enter the hospital rooms.

The CDC maintains that conclusion despite what the newly uncovered emails say, Skinner said. The CDC findings were not addressed in the recently released emails.

In May 2016, Pennsylvania Governor Tom Wolf again requested the CDC consult with the state health department and UPMC because a fifth fungal infection recipient had been identified in the Presbyterian ICU, CDC spokesperson Tom Skinner told CNN when asked about the content of the emails. Wolf’s press secretary, J.J. Abbott, confirmed the request in an email to CNN.

That additional patient was Daniel Krieg, a kidney transplant patient who died in July 2016. UPMC medical reports show Krieg had fungal pneumonia and that fungal-infected sections of his left lung were removed. A CDC representative returned to UPMC on June 22, 2016, with officials from the state and county departments of health to discuss the outbreak and Krieg’s case, Skinner told CNN on Monday.

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An agenda in the newly revealed emails said health officials were to discuss laundry processes at Presbyterian, Montefiore, and Shadyside hospitals at the June 22, 2016 CDC visit.

The day before that visit, an June 21, 2016, email sent by Brink also said that UPMC was working with the linen vendor to “improve their product.” The email also said the hospital system was “aggressively pursuing” an alternative linen solution for all transplant patients in the ICU at Presbyterian hospital.

UPMC said in a January 2016 statement that high-risk transplant patients would receive linens with a lower bacterial count going forward. Hospital linens are required to be “hygienically clean,” according to the Healthcare Laundry Accreditation Council. (PDF) That means linens are not sterile, but in a clean state, free of pathogens in sufficient numbers to minimize risk of infection, and the clean textiles are not inadvertently contaminated before use, according to the CDC.

“Despite the lack of a definitive source, UPMC still went above and beyond state and federal recommendations in order to implement changes to protect our patients. One of the many changes includes the provision of specially treated bioburden-reduced linens to our highest risk transplant patients,” UPMC spokeswoman Hydzik told CNN previously.

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