Thursday, June 5, 2014


News Clips For The Day


Boy's Mysterious Infection Cured After DNA Sequencing – NBC
BY MAGGIE FOX
First published June 4th 2014

Modern genetic sequencing helped doctors diagnose and cure a teen boy’s mysterious infection, offering a glimpse into hospital techniques of the future.

A report in the New England Journal of Medicine describes how the youngster's case was baffling doctors, who tried treatment after treatment as his brain swelled. Current tests gave no clue as to what was causing it.

Finally, a new sequencing technique that looks at all the genetic material circulating in the boy's spinal fluid gave up the culprit — leptospirosis, a bacterial disease, probably contracted when he went swimming on a trip to Puerto Rico.

While such tests are still beyond the reach of the average doctors, they won’t be for long, experts predict.

“We are hoping we can apply this to any patient who comes into the hospital with any infection,” said Dr. Charles Chiu of the University of California, San Francisco, who led the research team.

“This is the wave of the future, although it will take a little bit of time to iron out the wrinkles,” agreed Dr. William Schaffner, an infectious diseases expert at Vanderbilt University, who was not involved in the research.

The 14-year-old boy, who isn’t identified in the report, had severe combined immunodeficiency or SCID, sometimes known as bubble-boy disease. In this case, his immune system was strong enough for him to live normally and even travel.

“He had gone on a missionary trip to Puerto Rico during the first two weeks of August 2012 where he swam in a river and the ocean,” Chiu’s team wrote.

The boy visited the hospital three times over four months with fever and headache. Eventually his brain swelled up and he had to be put into a medically induced coma.

Frantic doctors ran a battery of tests, but didn’t suspect bacterial meningitis. They thought it might be something a cat gave him — the boy’s family had pets, and the boy’s group had interacted with feral cats in Puerto Rico.

They gave him immune globulin treatment, Rituxan to counter a possible autoimmune reaction and even took a brain biopsy. He got even more immune-boosting treatments — but did not get better.

The boy’s family agreed to enroll him in a clinical trial using next-generation sequencing. This approach uses modern, fast genetic sequencing to look at all the DNA in a sample. It found evidence of leptospirosis infection in his spinal fluid and doctors decided to treat him with penicillin — the cheap, basic antibiotic that best attacks the infection. That did the trick.

The boy got well enough to go home a month later.

Later on, specific testing using polymerase chain reaction (PCR) confirmed it was leptospirosis. “We suspect that the patient most likely contracted leptospirosis during his trip to Puerto Rico,” the researchers wrote. Another teen on the trip was hospitalized with fever and blood in the urine and may have had the same infection.

Infections such a meningitis and pneumonia often stump doctors. The standard way to test is to take some blood or perhaps coughed-up sputum and try to culture, or grow, bacteria. But more than 100 different agents, including bacteria, viruses, mold and fungi, can cause meningitis.

“More than half the cases of meningoencephalitis remain undiagnosed, despite extensive clinical laboratory testing,” Chiu’s team wrote. Leptospires, the bacteria that cause leptospirosis, are hard to detect and they don’t grow well in standard tests that culture bacteria.

“We spend a huge amount of money to work up these cases, and despite the latest generation of tests, we’re still unable to diagnose up to 30 percent of cases of pneumonia in hospitalized patients,” Chiu told NBC News.

“We estimate that the cost of hospitalization for this boy was well over $250,000."

“We’re unable to make a diagnosis, using older methods, like growing out cultures. More recently, other types of tests have become available, such as PCR, which looks for specific sequences — but for only one organism at a time, and you have to have a prior target,” he added.

“Current diagnostic techniques, especially to find viruses, often don’t work well.”

The downside is the gene-sequencing machine — this one’s made by a company called Illumina — costs $100,000 or more. That’s a lot for a hospital to invest in. Chiu estimates a test would cost $2,000 a pop.

But Chiu argues that next-generation sequencing will save money. “We estimate that the cost of hospitalization for this boy was well over $250,000,” he said. “There was probably $30,000 spent on diagnostic tests that turned out negative.”

And that doesn’t include the distress to his family. “If we could have done it on the very first day he came to the hospital, we would have potentially spared him three hospitalizations , an invasive brain biopsy and a stay in the ICU,” Chiu said.

Other experts agreed the case could illustrate what’s coming in a few years.

"This article is about a single case, but I believe it represents a turning point in the use of sequencing to diagnose infections,” said genetics expert Dr. Robert Green of Brigham and Women’s Hospital and Harvard Medical School, who was not involved in the study.

“While I would not expect this to become integrated into care immediately, I would not be surprised if this is sort of genomic characterization of infectious agents is deeply integrated into clinical care within the next five years."




“Genomic characterization of infectious agents” seems like a natural, given the amount of use in general that scientists are making of DNA testing today. “'If we could have done it on the very first day he came to the hospital, we would have potentially spared him three hospitalizations , an invasive brain biopsy and a stay in the ICU,' Chiu said.” Dr. Robert Green says “'This article is about a single case, but I believe it represents a turning point in the use of sequencing to diagnose infections.”

DNA testing used to take longer to process and require larger amounts of the material being tested, but everything has improved in the last ten years. Now it's quicker than growing cultures and can be done on very small quantities. I'm reading a book by an archaeologist on DNA and other molecular testing on human and animal bones, as well as residues of plant materials which have been found in pottery used for food storage and cooking. An archaeologist found that one particular pot had only had members of the cabbage family cooked in it. They went on to identify a large flat piece of pottery as being a drip pan which had been used for roasting pork. Those pots haven't been washed with dish detergent and scrubbed, since there was no such thing in prehistoric times, but just scoured out with sand or rinsed, so they retained chemicals from the contents. What they can do now with a little bit of material is amazing.





Wilson High Principal Pete Cahall Comes Out as Gay During Pride Day – NBC

A Washington, D.C., principal was met with cheers as he came out to his students as gay during a Pride Day event that drew protest threats from Westboro Baptist Church.

"I turned 50. I'm tired of hiding," Principal Pete Cahall said before praising Wilson High School's students for the supportive environment they've created since Westboro Baptist Church made their plans known.

This is the first time Cahall, who has been the principal at Wilson for six years, has come out publicly. D.C. Mayor Vincent Gray was informed of his decision just moments before.

The school held its second annual Pride Day event Wednesday, bringing together over 20 organizations that support the needs of LGBTQ youth.

Westboro, known for its public crusade against gay people at military funerals, announced plans to protest the school's Pride celebration on June 9 and called the school's support of gay and lesbian students a "shame." That protest is just one of 12 the church has planned in the D.C. area over the next few days.

After Westboro made its intentions known, students at Wilson began planning a peaceful counter-protest, The Washington Post reported. Around 1,000 students volunteered to participate in the silent protest.

Cahall's announcement was also met with support from local politicians, like D.C. Councilmember David Catania, who is openly gay. 




Westboro Baptist Church has a number of websites. One is called “Godhatesfags,” and other “sister sites” state that God hates “Islam, the media, the world, Jews killed Jesus, Beast Obama, and finally, Priests Rape Boys. They are one of those churches that have gone so far into the political culture wars that they don't seem to emphasize the Sermon on the Mount and love thy neighbor as thyself anymore. They are everything that religion shouldn't be, as far as I'm concerned. There's no peaceful meditation, openhearted thinking, crusading for justice, or other helpful interaction with the world. In fact, they say they hate “the world.” That really says it all!

Principal Pete Cahall praised his students for their “supportive environment” since Westboro's planned protests. “The school held its second annual Pride Day event Wednesday, bringing together over 20 organizations that support the needs of LGBTQ youth.” Around 1,000 students are expected to turn out for a silent protest against the church group. That is appropriate, and reminds me of Gandhi's massive protests against British rule. I'm glad to see high school age kids doing something other than competing over expensive clothing or joining gangs. They are already concerned about the world and issues.





Corpse Rides Hundreds of Miles After Driver Refuses to Stop – NBC
— Gil Aegerter
First published June 4th 2014

A man drove most of the way from Phoenix to the Detroit area this week with a corpse for company, authorities say.

Ray Tomlinson told NBC station WDIV that he picked up a 31-year-old woman after she checked out of a mental health facility in Phoenix, near where he and his 92-year-old mother spend winters. On Sunday, the three of them set out in his van for Warren, Mich., 1,900 miles away.

Tomlinson, 62, said that they were in New Mexico on Monday when he couldn’t wake the younger woman, described as his girlfriend, who was sitting in the front passenger seat.

He nudged her. "I just said, you know, you want something? And at this point in time she was stiff," Tomlinson told WDIV. "There wasn't jerking or moans or groans, or cries for help, she just fell asleep."

But he said he checked the internet on his phone and found he had 48 hours to get her to a morgue.

"I can just take her to the Macomb County morgue, because that was my plan," he said.

Then someone at the mental health facility called the woman’s phone to check on her. Tomlinson told them she was dead.

"I just drove and drove, and I knew I'd be in some kind of trouble," Tomlinson told WDIV.

He was. The facility called the police and they met Tomlinson on Tuesday in Warren.
So why didn’t he just stop? Tomlinson told WDIV that he wanted to get his mother home and was worried that police might impound his van.

“There is no crime. It’s not illegal for carrying a body across the country,” he said.
Still, Tomlinson’s mother was taken into protective custody and prosecutors are considering whether he should face a misdemeanor charge of failure to produce a body, WDIV said.

The woman had substance abuse problems and may have taken oxycodone during a bathroom stop in Flagstaff, Ariz., Warren Police Commissioner Jere Green told The Associated Press.

"We're guessing she might have overdosed," Green said.

The county medical examiner’s office is waiting on toxicology tests to determine what killed her.

"It's strange to think someone could drive 26 hours with a dead person sitting next to them,” Green told WDIV.




Ray Tomlinson “picked up a 31-year-old woman after she checked out of a mental health facility in Phoenix,” and failed to notice that the woman – his girlfriend – had died until later, at which point she “was stiff,” which means that a number of hours had passed. He feared that the police would impound his vehicle, so he continued on to his destination rather than taking her to a morgue along the way. Police are considering a charge of “failure to produce a body,” and his mother, who was in the car the whole time, has been taken into protective custody. This story is grisly, but police say that merely transporting a body is not against the law. It is bizarre, however, and probably a sign of unclear thinking. I think the instinctive reaction of the ordinary person who finds a dead body is to call the police immediately.





G-7 Summit: Obama Meets Key European Allies on Ukraine – NBC
Alastair Jamieson
First published June 5th 2014

President Barack Obama met key European allies Thursday – with the Ukraine crisis top of the agenda – as G-7 leaders sat down to their first meeting without Russia in 17 years.

The president was expected to have one-to-one talks with British Prime Minister David Cameron on the sidelines of the Brussels summit.

Later, he will fly to Paris - ahead of events commemorating the 70th anniversary of the Allied invasion of Normandy – where he will have dinner with French President Francois Hollande.

There were smiles early Thursday as the leaders met in front of the cameras and posed for the traditional group photographs. Obama was flanked by Canadian Prime Minister Stephen Harper and Herman Van Rompuy, president of the European Council.

Thursday’s summit was originally supposed to have taken place in Sochi, Russia, but those plans were canceled when Russia annexed the Crimean Peninsula.

It is the first time since 1997 that the summit has taken place without Russia.

"Our free nations will stand united so that further Russian provocations will only mean more isolation and costs for Russia," Obama said late Wednesday.

Obama foreign policy adviser Ben Rhodes said G-7 leaders would discuss the future approach on sanctions during their meetings. "We'll have to evaluate going forward, what are the triggers for different types of sanctions," Rhodes told The Associated Press. "That would be reviewing whether or not Russia is continuing to destabilize Eastern Ukraine and whether or not Russia is continuing to support separatist groups."

Also on the summit agenda are the global economic outlook, climate change and development issues.




“G-7 leaders sat down to their first meeting without Russia in 17 years.... 'Our free nations will stand united so that further Russian provocations will only mean more isolation and costs for Russia,' Obama said late Wednesday.” The representatives of European nations will discuss Russia's apparent current position in regard to Ukraine and the separatists, and whether or not to increase sanctions.





Ireland Investigates Alleged Discovery of 800 Babies in Sewer Tank – NBC
BY ALEXANDER SMITH
First published June 5th 2014

Grim reports that nearly 800 dead babies were discovered in the septic tank of a home run by nuns has set off a round of soul-searching in Ireland and sparked calls for accountability from government and Catholic Church officials.

Fresh research suggests that some 796 children were secretly buried in the sewage tank of the home in Tuam, County Galway, where unmarried pregnant women were sent to give birth in an attempt to preserve the country's devout Catholic image.

Officials said they were "horrified" at the discovery and said it revealed "a darker past in Ireland," a country often haunted by its history of abuse within powerful church institutions.

The home was run by nuns from the Bon Secours Sisters congregation between 1925 and 1961. It was one of the "mother and baby" homes across Ireland, similar to the Sean Ross Abbey, in Tipperary, where Philomena Lee gave her child up for adoption in a story that was this year made into the eponymous Oscar-nominated film "Philomena."

People who lived near the home said they have known about the unmarked mass grave for decades, but a fresh investigation was sparked this week after research by local historian Catherine Corless purportedly showed that of the hundreds of children who died at the home, only one was buried at a cemetery.

Speaking to the Irish Mail, which first reported her research,she also said that health board records from the 1940s said conditions at the home were dire, with children suffering malnutrition and neglect and dying at a rate four times higher than in the rest of Ireland.

Charlie Flanagan, minister for children and youth affairs, said Wednesday night that there was a "cross-departmental initiative underway" to determine how to react to allegations.

"Many of the revelations are deeply disturbing and a shocking reminder of a darker past in Ireland when our children were not cherished as they should have been," Flanagan said.

Ireland's Roman Catholic Church told the order of nuns who ran the former home that it must co-operate with any inquiry into the discovery, according to the Reuters news agency.

Tuam's Archbishop Michael Neary said Wednesday that the diocese had no part in running the home but urged the Bon Secours Sisters to "act upon their responsibilities in the interests of the common good."

"I am horrified and saddened to hear of the large number of deceased children involved and this points to a time of great suffering and pain for the little ones and their mothers," he said.

The Bon Secours congregation did not respond to NBC News' request for comment.

The claims came to light after Corless obtained death records for the home and cross checked them with local cemetery records.

Two local boys reportedly unearthed the concrete-covered tank used by the home while playing in 1975 and found hundreds of children's bones inside. The tank has now been surrounded by a housing estate, but an officer from Ireland's Gardai police force said remains had recently been found after a police survey at the site.

"We do not know what we’re dealing with here yet, it could go back much further," the officer told NBC News on condition of anonymity. "This is a historical investigation going back to the 1950s.

"We are investigating this matter, the grounds have been surveyed and there is what appears to be human remains discovered. But [the remains] could go back as far as famine times, which is 160 years, we just don't know yet."

Police could not confirm if a full excavation of the site was planned.

Ireland's once-powerful Catholic Church has been rocked by a series of scandals over the abuse and neglect of children in recent years. The Church operated as a quasi social service in the 20th century and the mother and baby homes were run in a similar fashion to the Magdalene Laundries, where single women who became pregnant were sent away.

"Children went in there so the families could conceal their shame"

While government and church officials were quick to express their shock at reports of Tuam's high infant mortality rate and allegations of mass burial, the traits were not uncommon for such institutions in Ireland, according to Eoin O'Sullivan, associate professor at Trinity College Dublin.

"Tuam was a former workhouse and conditions were pretty bleak," said O'Sullivan, co-author of the 2001 book "Suffer the Little Children: The inside Story of Ireland's Industrial Schools."

"Ireland's first mother and baby home, at Bessborough, in Cork, had an even worse infant mortality rate of around 82 percent: In the year ending March 31, 1944, 124 children were born or admitted there, and 102 died."

O'Sullivan added that the practice of mass burial, often with just one headstone marking the site, was not uncommon in many mother and baby homes and psychiatric hospitals at the time.

"Remember that the children went in there so the families could conceal their shame, and the kids were often adopted," he said. "The nuns were not going around grabbing pregnant women; the women were taken there by their families who knew what conditions were like.

"Why have politicians and the Church reacted with such shock? I'm not sure. I suppose they have to every time something like this comes out connected with religious institutions."





“Fresh research suggests that some 796 children were secretly buried in the sewage tank of the home in Tuam, County Galway, where unmarried pregnant women were sent to give birth in an attempt to preserve the country's devout Catholic image.” The Catholic Church has done many good things, but this is one of several situations that I call “abuse of power,” which happens in strict religions, within many local police departments, among wealthy families in small towns and in other cases where anyone is given a status of absolute trust. That includes our federal government in the case of NSA, CIA and FBI. These institutions fulfill a needed role in society, but there does need to be some “watchdog” overseeing them and watching for abuses.

In this case, that would be the Vatican. I think this current pope is aware of severe problems within the church and is trying to examine the situations, especially the sexual molestation of children and women by priests. I did watch the movie Philomena recently, and it is very powerful. I suggest that anyone who hasn't seen it should take two hours off work and watch it.

Further information on this particular home comes from the article. “People who lived near the home said they have known about the unmarked mass grave for decades, but a fresh investigation was sparked this week after research by local historian Catherine Corless purportedly showed that of the hundreds of children who died at the home, only one was buried at a cemetery.” “'Ireland's first mother and baby home, at Bessborough, in Cork, had an even worse infant mortality rate of around 82 percent:'” The Irish church, according to this article, was fulfilling a “quasi-social service,” apparently in the absence of help from the government. One conservative US politician within the last few years stated that helping the poor should be done by charities and not the government. I think this story shows the problems with that.

Local historian Catherine Corless reported that living conditions were terrible at the home, and the babies died at a rate “four times higher than in the rest of Ireland.” Charlie Flanagan, minister for children and youth affairs, calls it “'a shocking reminder of a darker past in Ireland when our children were not cherished as they should have been.'” “Tuam's Archbishop Michael Neary said Wednesday that the diocese had no part in running the home.” The police investigatin the site said, “'But [the remains] could go back as far as famine times, which is 160 years, we just don't know yet.'"

“The practice of mass burial, often with just one headstone marking the site, was not uncommon in many mother and baby homes and psychiatric hospitals at the time, according to Eoin O'Sullivan of Trinity College in Dublin. The article says, “'Children went in there so the families could conceal their shame,'” so the lack of oversight is probably not surprising. Whenever societal pressure, such as social shame, overcomes individual conscience there is trouble. O'Sullivan's book from 2001 book called "Suffer the Little Children: The inside Story of Ireland's Industrial Schools" about the “work houses” is a book I would like to read. Maybe the public library will have it or be able to order it through an interlibrary loan.





Facebook Post Blamed for Fatal Beating of Young Indian – NBC
Alastair Jamieson and Wajahat S. Khan
First published June 5th 2014

A young Muslim IT manager in India was fatally beaten by suspects linked to Hindu fundamentalism amid sectarian tensions sparked by a Facebook post, police told local media.

Mohsin Sadiq Shaikh, a 24-year-old from the Solapur district of the city of Pune, was attacked with sticks and stones on his way home from prayers on Monday night by men who had been publicly protesting the circulation of offensive images desecrating two historic Hindu figures.

"A gang of youths blocked his way near the lane just behind his house and started hitting him with sticks,” the victim’s cousin told The Times of India, adding that the attackers also bludgeoned Shaikh with stones before fleeing. “He was lying covered in blood for about 15 minutes. His brother rushed there and took him to a nearby hospital where he died during treatment.”

Seven men, aged between 19 and 24, were arrested, police told the newspaper. A further six were later detained, the Indian Express reported.

The victim’s friend alleged that the victim was targeted because he was wearing a skull cap and had a beard.

“I ran from the spot and called his brother Mobin for help. However, by the time Mobin came, Mohsin was badly beaten up and the assailants were about to leave,” the friend told The Indian Express.

The attack came amid anger over a Facebook post that lampooned two Hindu folk heroes: Bal Thakeray, a right-wing politician who wanted Indian Muslims to convert back to Hinduism, and Shivaji, an 17th century Hindu king hailed as a hero of the Hindu right for his campaigns against the Muslim Moghul Empire.

Police took steps to block the post, preventing its circulation, according to local media, but that did little to dampen public protests including one that led to a local bakery being set on fire, the Hindustan Times reported.

Police told The Times of India that all of the first seven suspects arrested were associated with Hindu Rashtra Sena, a fundamentalist Hindu outfit led by Dhananjay Desai.

However Desai, who was separately arrested for distributing inflammatory pamphlets earlier this year, told the Indian Express that his organization was not involved in the killing.

“We understand that circulating derogatory pictures is a cyber crime but the problem cannot be solved by killing innocent persons,” he told the newspaper. “We did condemn the uploading of derogatory pictures, but we did not plan attacks on innocent persons.”




Mohsin Sadiq Shaikh, a young Islamic man, “was attacked with sticks and stones on his way home from prayers on Monday night by men who had been publicly protesting the circulation of offensive images desecrating two historic Hindu figures.... The victim’s friend alleged that the victim was targeted because he was wearing a skull cap and had a beard.” The event is linked to unrest over two Facebook posts that made fun of Hindu “folk heroes.” The attackers are members of a fundamentalist Hindu organization. The leader of the group, Dhananjay Desai, said, “'We did condemn the uploading of derogatory pictures, but we did not plan attacks on innocent persons.'”

Fundamentalist religion is on the rise across the world, and leads to violence and hatred. I wish people would back away from their doctrinaire viewpoints and consider how to get along with others. That includes fundamentalist Christians. A case in point is the Westboro Baptist Church from the earlier article today. They have killed anyone yet – that I know about – but they have half a dozen hate sites on the Internet. People are just getting too hostile and hidebound in their “beliefs,” including some politicians. To me that sort of thing is not religion at all, but a kind of war. I don't choose to “believe” things that are not rational or kind in the name of personal improvement. As Jesus said of some rival faiths, you have to look at the fruit of a tree to see if it is good. Too few people follow that rule.