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By Hannah Rappleye, Eric Salzman and Kate Snow

CLARINDA, Iowa — Mahoghany Chambers thought Clarinda Academy would be a fresh start.

The residential treatment facility, a cluster of brick buildings planted between corn fields, is a home of last resort for at-risk teens from Iowa and nearly two dozen other states.

Chambers, 20, was sexually assaulted twice as a young girl. Her anger grew as the years wore on. She started getting into trouble with the police, sometimes because she fought with her mother.

"I was mad at the world," Chambers said.

In 2015, at the urging of her mother and her probation officer, the then-17-year-old flew to Iowa from her home state of Texas. She joined some of the nation's most vulnerable children, including foster children, and kids who had been placed there by courts as an alternative to juvenile detention. Chambers believed Clarinda would help her.

"They told me it was going to be a good place," she said.

Then one night, a male counselor raped her outside her bedroom.

The man, Antonio Aranda, worked overnight, supervising girls in her dorm. When she gathered enough courage to report the assault to a teacher, Chambers said she initially wasn't believed.

"Girls go there to get help," she said. "Not to get hurt all over again."

Mahoghany Chambers, 20, was sexually assaulted by a youth counselor at Clarinda Academy. "Girls go there to get help," she said. "Not to get hurt all over again."NBC News

In 2016, as part of a plea deal, Aranda pleaded guilty to sexual misconduct with a juvenile, an aggravated misdemeanor. Chambers is now suing the former counselor and Clarinda, which is owned by a for-profit company called Sequel Youth and Family Services that runs 43 other behavioral healthcare programs across the country.

Her allegations, which include charges of negligence and a failure to supervise male staff who had access to troubled girls, are among the latest in a growing chorus of complaints about the facility.

The suit contends that Clarinda Academy acted negligently by hiring Aranda, because he had been previously convicted of a felony. Sequel told NBC News that Aranda had disclosed a conviction for felony petty theft in California — a misdemeanor in Iowa — on his employment application, and that the conviction occurred nearly 15 years before he applied to work at the facility.

An NBC News review of documents, including state inspections, along with interviews with attorneys, former employees, students and parents, raises additional questions about the welfare of children placed at Clarinda Academy.

Former students told NBC News that some staff improperly used physical restraints to control children, sometimes to the point of injury. Those injuries, according to interviews and documents obtained from state agencies, include broken bones, bruises, and loss of consciousness. One student alleged that a male staff member sexually abused her during a physical restraint.

Some students said they felt forgotten by the caseworkers and courts that were charged with monitoring their well-being after being placed at Clarinda.

"Everybody forgot about me there," said Jesus Lopez, 21, a former foster child from Washington state who was placed at Clarinda in 2015.

Sequel declined to make a representative available for an interview with NBC News, but did respond to written questions.

In a statement, CEO John Stupak said the company has "internal quality control and rigorous training to ensure that the care and support we provide our students is consistent with all best practices and reaches our own high standards of respect for our students' dignity. We continually adjust our practices to ensure that we are providing the best care possible for our students."

Sequel "fully cooperated" with authorities in the arrest and conviction of Aranda, Stupak added.

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"His actions were egregious and totally unacceptable," he said. "As soon as we became aware of the situation, we immediately contacted the authorities, suspended him and then terminated him for violating multiple policies."

Stupak also said that over the past 12 months, state regulatory agencies conducted 28 different on-site assessments of Clarinda Academy, including many that were unannounced. An audit completed by Iowa's Department of Human Services last fall, he said, "noted no deficiencies and renewed our full licensure status."

Days after receiving inquiries from NBC News, Sequel announced that it will be implementing the Ukeru Behavior Management Program, a trauma-informed approach to crisis management that minimizes the use of restraint, at all of its facilities across the country — beginning with a pilot program at Clarinda.

'It's hard for workers to adapt'

Clarinda Academy opened in 1992, as a residential foster care facility for boys, on the same grounds as a medium security prison. Today, the facility is licensed to treat 242 girls and boys between the ages of 12 and 18. According to Sequel, there has never been an incident involving juveniles having contact with inmates since the facility's opening.

Children are placed there by courts and child welfare agencies across the country, from Oregon to Ohio. Out of state residents make up a large proportion of Clarinda's student body — about 68 percent of the facility's population, according to figures collected by Iowa's DHS in February.

On March 1, according to the agency, California had 21 children placed at Clarinda, more than any other state. South Dakota had 17 children placed, the second-highest. Public records requested by NBC News show that states and counties outside Iowa can pay up to twice as much per day to place children there. In Chambers' case, her county's juvenile probation department paid $162 a day for her treatment at Clarinda. Depending on a child's needs, Iowa's DHS pays Clarinda $88 or $119 per day.

Clarinda Academy shares grounds with a correctional facility. According to Sequel Youth and Family Services, there has never been an incident involving juveniles having contact with inmates.NBC News

No matter where they come from, students at Clarinda Academy cope with a variety of emotional and behavioral issues, such as post-traumatic stress disorder and oppositional defiance disorder. Many of its residents have histories of abuse and neglect.

Members of the Clarinda staff, which includes counselors, teachers and social workers, work in an often unpredictable, and sometimes violent, environment.

Former students said that fights often broke out between teens. Documents obtained from state agencies in Iowa and California detail escape attempts and physical altercations between residents and staff. Police reports dating back to 2010 reveal instances of staff being punched and kicked by students.

In February, representatives of Iowa's DHS interviewed five children at Clarinda. According to notes provided to NBC News by the agency, all children interviewed reported feeling unsafe.

"They all reported a recent increase in youth-to-youth physical assaults," the notes state. "They felt the staff was ill-equipped to manage the assaults and there was an increase in restraints in response."

Sandy Santana, executive director of Children's Rights, a national advocacy organization for abused and neglected children, believes that private companies that rely on shift workers, who aren't properly trained to work with children with serious behavioral challenges, are more likely to resort to using physical restraint.

"When kids act out with behavior that is symptomatic of their mental health issues, it's hard for workers to adapt, and very hard for them to access techniques that a well-trained person would access immediately," Santana said. "So they rely on restraints."

The use of physical restraints to control children, especially children with disabilities, is controversial. Restraints can lead to injuries and in some cases, even death. No Clarinda Academy students have died from restraints. Many states, including Iowa, have regulations that govern the use of physical restraint in schools.

Clarinda staff must follow a seven step de-escalation process before resorting to physical restraints, and then only as an emergency safety intervention. But documents reviewed by NBC News raise questions as to whether that policy is always followed.

Reports compiled by California's Department of Social Services reveal instances, dating to 2012, in which students were injured during physical restraints.

In 2012 a resident's collarbone was broken by an "unapproved physical restraint technique." Staff involved in the incident were found to have participated in a "'cover up' of any wrongdoing." Two staff were fired.

In 2013 a youth "passed out" the day after a restraint "due to possible head trauma." The child required emergency hospitalization. The staffer who performed the restraint was placed on Iowa's Central Abuse Registry for "founded" allegations of physical abuse.

'They just kept dropping me'

Some former students said that staff often did not follow protocol, and instead put children in painful physical restraints, sometimes for long periods of time, in cases where nonphysical interventions may have been sufficient.

Jesus Lopez, 21, is one.

He entered Washington's foster care system when he was just 3 years old. By 17, after churning through more than two dozen placements, he was close to aging out of the system, a particularly stressful time for a foster child. Like many other states, Washington was struggling with a shortage of placement options for children like him.

Child welfare experts say that while vulnerable children are best served near their communities, tight budgets, a shortage of foster homes and therapeutic facilities, along with a reluctance to invest in services have meant that states continue to risk sending them to institutions far from home.

"Our states have not developed the infrastructure to take care of these kids in their homes," said Santana. "This is emblematic of a broken child welfare system throughout the country."

When his caseworker said he could get vocational training at Clarinda Academy, Lopez jumped at the chance.

"I packed clothes, packed everything up," Lopez said. "I was excited and everyone was excited for me."

After arriving at Clarinda in the fall of 2015, his excitement quickly faded.

He couldn't leave campus. He felt alone and intimidated by the other kids. He felt, he said, like he was in juvenile detention. Although he had no home to go to, he decided to leave.

After running downstairs in an attempt to escape, staff grabbed his wrists and ankles and carried him into a closet, according to Lopez and records of a subsequent investigation performed by Iowa's DHS. They pulled his arms back and held his legs down. Lopez, who was frightened and in pain, resisted.

An aerial view of Clarinda Academy's campus. The facility houses and treats some of the nation's most vulnerable children.NBC News

Staff then brought him into his bedroom.

"Jesus said every time they asked him if he was ready to go to bed and he answered, 'no,' staff would come behind him, put their arms beneath his arms and pull him back and then the staff would throw him to the ground," according to DHS records. "Jesus said this occurred about 10 times with different staff taking turns."

"They were dropping me over and over again," Lopez said. "They just kept dropping me and they kept asking me if I was ready to comply. They seemed angry."

His head hit the floor several times, he said, before he fell unconscious. According to DHS records, he suffered severe bruising on his forehead, as well as bruising on his arms, legs and back.

At least two male staff members involved in the restraint told investigators they had been working "lots of hours," including a shift from 7 a.m. to 11 p.m. that day. One had a prior history of using improper restraints. Another staff member interviewed said that "too many staff are working double shifts and their [sic] tired and frustrated."

Lopez's caseworker was not informed of the incident until nearly two months later, according to the report.

Debra Johnson, a spokesperson for Washington's Department of Children, Youth and Families, said the agency could not comment on individual cases. In a statement, she said that in-state resources must be "exhausted" before placing foster children, like Lopez, out of state.

Last fall, Disability Rights Washington, a state chapter of the national advocacy organization for individuals with disabilities, released a report detailing allegations by three foster children at Clarinda of verbal abuse and improper restraints. The report also found that some 80 other foster children had been sent to about a dozen other states, including to other Sequel-owned facilities.

Washington, which had been paying Clarinda about $274 per day for the care of its foster children, removed all of its youth from the program after the report. The agency also dispatched staff to visit every Washington youth placed at an out-of-state facility, and tightened oversight requirements to include quarterly in-person visits.

"On occasion, the level of care required by a youth is not available in the state of Washington, either because there is no sufficient capacity in current programs or because the needed service does not yet exist in the state," Johnson said. She added that over the past year the agency has reduced out-of-state placements by 32 percent. "DCYF recognizes the need to develop additional in-state resources."

Nebraska's Department of Health and Human Services also pulled children from Clarinda after the report, according to a spokesperson with the agency.

In a statement, Stupak, Sequel's CEO, disputed the report's findings.

"The report is based on the views of three out of the 188 young men and women at Clarinda Academy in February 2018," Stupak said.

"We work very hard to help young people who are the most troubled and in-need lead healthy, independent and fulfilling lives," he added. "The report by Disability Rights Washington is filled with false statements, is an attack on our integrity and grossly misrepresents how we operate. … Unfortunately DRW's agenda here was simply to instigate media agitation to further its legislative agenda and to pressure the state of Washington to move all care for at-risk youth in-state."

The report also prompted investigation by Iowa's DHS and Department of Inspections and Appeals.

According to agency documents, an audit completed last November "revealed no current concerns regarding physical restraints of children." Several children interviewed by investigators reported feeling safe, and said that physical restraints were used for "safety reasons." Staff interviewed reported they had been trained in proper restraint procedure.

The audit "concluded that our use of restraints as an emergency safety intervention were all appropriate and were consistently utilized for the safety of students and people around them," Stupak said. "Clarinda students receive regular, required child welfare checks from their case workers/foster care agencies and families, who meet with students directly."

However, in February, four youth interviewed by Iowa's DHS said they had not had any contact with their guardians ad litem, who are appointed by a court to advocate for the best interests of a child. None reported having any visits from family. Staff noted that, between October and February, only four guardians ad litem visited Clarinda.

In a statement to NBC News, Jerry R. Foxhoven, director of Iowa's DHS, said that the February review "identified concerns related to treatment plans, lack of outside contact or visitors, medication management and safety."

Foxhoven said DHS has increased monitoring of youths in custody, and is reviewing Clarinda Academy's contract, as well as the contract of Woodward Academy, a second Sequel-owned facility in the state.

Now back in Washington, Lopez is rebuilding his life. He regularly volunteers to speak to foster and at-risk children about his experiences. But the memory of what happened at Clarinda hasn't left him.

"I can remember the room," he said. "I can remember the staff. I can remember their faces. It's a memory I'll never forget."

'They weren't careful'

Like Chambers, Clara Sanchez was 17 when she was placed at Clarinda Academy in 2013 by her probation officer in Texas. She started getting into trouble at 13, experimenting with drugs and skipping school.

Sanchez had spent time in a secure facility for juveniles in Texas, and had been restrained before for acting out.

But at Clarinda, she said, it felt like "staff were angry with you."

"They weren't careful," she said.

Sanchez, now 23, said she was restrained several times by Clarinda staff, sometimes because she fought with other girls, other times for nonviolent misbehavior.

One day, when she saw her best friend being restrained with what she called "excessive force," Sanchez tried to intervene. A male staffer grabbed her arms and pulled her to the floor.

"I had my legs straight out in front of me and he put all his weight on my back, and had my nose touching, right in between my legs," Sanchez said. "Just excruciating pain. I started hyperventilating. I was breathing really, really hard and really fast."

As she gasped for breath, she said, the man put her in what she described as a "chokehold."

Then, she said, she felt the man rub his erect penis against her buttocks.

"He did it in a motion where you know it's intentional," Sanchez said. "That's when I started feeling like I wanted to throw up."

Sanchez said she then fell unconscious. She did not report her allegation of sexual abuse to Clarinda Academy or the police.

Clara Sanchez, 23 was a student at Clarinda Academy in 2013. She said she was sexually abused during a physical restraint. "You're just causing more damage to kids who already experienced a lot," she said.NBC News

An attorney for Sequel said the company was prohibited by law from commenting on individual allegations, but in response to questions about specific accusations, described them as baseless and unverified.

One youth did report an allegation of sexual abuse.

In 2016, a female teacher was charged with felony exploitation for allegedly touching the genitals of a male student.

The charge was dismissed before it could go to trial. The alleged victim — who was from California — stopped participating, according to Carl Sonksen, the Page County Attorney.

In Mahoghany Chambers' case, her perpetrator received 10 years of probation and was required to register as a sex offender for the duration of his supervision. He did not receive any prison time.

Chambers said representatives from Clarinda had assured her mother that male staff would not be supervising female dorms. That was not the case.

There were no cameras to capture the assault, either. Sequel said in a statement that it has begun to install surveillance cameras at Clarinda Academy, as well as at its other residential campuses.

"They allowed students to get hurt," Chambers said. "Don't bring them inside of a residential home or whatever it is, foster care, just to hurt them all over again. Because you just came from somewhere that you were hurting from, and you're trying to find peace, and a way to deal with it."

She still carries the memory of what happened to her. She fights depression and anxiety. It's hard for her to make eye contact with people.

But, she said, she has hope.

"I'm trying to break out of that feeling that I have," Chambers said. "I'm telling my story so other girls can open up and tell their story too. Because I know I'm not the only one to have a story."