Category Archives: Transhuman News

Geneticists are expected to shed light on whether or not Richard III had a dark side

Art Images / Getty Images

History, it is often said, is written by the victors. Such has been the case of the much maligned King Richard III, the last of the Plantagenet line, who has been remembered rather unfavourably as the murderer of his two nephews, 'the Princes in the tower' and characterised as a villainous hunchback by Shakespeare, following his defeat at the Battle of Bosworth by Henry Tudor, the father of the dynasty of the same name and future King Henry VII.

Now, geneticists are hoping to discover just how true these allegations against Richard III might be through advanced genome science that might be able to reveal his personality, and whether he was pre-disposed to conditions such as narcissism or psychopathy.

The move comes after scientists at Leicester University - the same who managed to prove that bones excavated in a carpark in 2013 belonged to the 15th century monarch - have sequenced his complete genome, the first time that this has been done for a historical figure.

Professor Turi King

David Wong / South China Morning Post via Getty Images

Professor Turi King, of the university's department of genetics and genome biology, told The Times: 'Its really interesting and runs the gamut from his blood type to was he lactose intolerant to was he genetically predisposed to baldness or heart disease.'

As well as his health, including discovering the origins of his scoliosis, which gave him the curved spine he is remembered for in Shakespeare, it is also believed that scientists will be able to learn more about what Richard looked like. Following the 2013 excavation, they were able to work out that he was blond-haired and blue-eyed.

The next stage after that could see links being made between certain genes and personality traits, such as violent aggression, psychopathy and narcissism. However, it is important to caveat that discovery of any of these predispositions does not 'prove' either reading of Richard as crook or hero misjudged by history, with his environment also having an impact on his personality, as the endless debate over nature vs. nurture would point out.

Professor King will appear on BBC 2's new series DNA Family Secrets weekly from tomorrow at 9pm.

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Will new DNA technology dispel the myth that Richard III was one of history's villains? - Tatler

Do you like to take a nap during the day? (Getty)

If youre the sort of person who enjoys a little nap in the afternoon, you might not be able to help it because it could be in your DNA.

Researchers from Massachusetts General Hospital (MGH) have found several gene regions that appear to be related to the tendency to take naps during the day,

They used data from the UK Biobank, which includes genetic information from 452,633 people for the study, published in Nature.

The researchers say some people who wake up early may "catch up" with a nap, while others need a nap because of disturbed sleep and others may simply need more sleep.

Watch: How to improve your sleep

Read more: Drinking Oolong tea could help you burn fat in your sleep

Hassan Saeed Dashti of Harvard Medical School said napping is "somewhat controversial", and that its difficult to disentangle napping from the culture around it, such as in Spain where it used to be part of the culture but is now discouraged.

"It was important to try to disentangle the biological pathways that contribute to why we nap, he wrote.

Participants wore fitness-band-style acceleratometers to monitor their activity and filled in quizzes on whether they napped "rarely", "sometimes", or "usually".

Read more: There might once have been life on the moon

The researchers performed a genome-wide association study (GWAS), which involves rapid scanning of complete sets of DNA, or genomes, of a large number of people.

A large number of the genes near or at regions identified by the GWAS are already known to play a role in sleep, such as KSR2, which has previously been found to play a part in sleep regulation.

Several gene variants linked to napping were already associated with a neuropeptide called orexin, which plays a role in wakefulness.

Iyas Daghlas, a medical student at Harvard Medical School, said: "This pathway is known to be involved in rare sleep disorders like narcolepsy, but our findings show that smaller perturbations in the pathway can explain why some people nap more than others.

Story continues

Read more: New theory on where space rock which killed dinosaurs came from

Dashti said: "This tells us that daytime napping is biologically driven and not just an environmental or behavioral choice.

"Future work may help to develop personalised recommendations for siesta.

Watch: Simple steps to a healthier life

Read more:
If you like to nap, the reason could be in your DNA - Yahoo Sports

SAN JOSE, Calif.--(BUSINESS WIRE)--OmniTier announced today that its CompStor family now supports mitochondrial analysis in both its secondary and tertiary analysis appliances.

Accurate identification of the mitochondrial genome and its translocations into the nuclear genome are key requirements for researchers and clinicians seeking to improve their understanding of mitochondrial dysfunction.

CompStor Novos now generates small-variant identification that is compatible with GATKs best-practices for mitochondrial variants. Variant calling on the mitochondrial genome must overcome additional challenges that are not present in standard nuclear genome analysis. Because mitochondrial DNA is circular, standard linear analysis produces errors at the ostensible extremities of the mitochondrial sequence. In addition, the number of types of mitochondrial DNA that may be present in a single sample is not simply bounded. CompStor Novos handles these challenges optimally, producing accurate identification of multi-plasmic variants even at the reference extremities.

Uniquely, CompStor Novos also identifies structural variants (SVs) in the nuclear genome which have been copied at some point in time from the mitochondrial genome. These nuclear mitochondrial SVs (NuMTs) may modulate the action of mitochondrial genes and therefore can play an important part of any modern mitochondrial study. CompStor Novos typically identifies 10-30 NuMTs in a sample; the vast majority of these NuMTs (> 80%) are not detected by any alternative, generally available SV pipeline.

CompStor Insight, OmniTiers tertiary analysis appliance, has been expanded to include annotation and interpretation of known mitochondrial variants which are associated with various levels of plasmy and population frequency, according to several industry-standard databases. Exclusive mitochondrial DNA visualization technology within CompStor Insight gives researchers a complete summary of small-variant plasmy and population frequency at a single glance.

About Mitochondrial DNA analysis

Circular mitochondrial DNA (mtDNA) chromosomes, inherited maternally, nominally contain 16,569 base pairs. mtDNA interests researchers and clinical scientists not only for tracing matrilineal phylogeny, but because it exhibits a higher mutation rate than nuclear DNA. mtDNA mutations have been associated with diverse forms of human disease and aging and may predispose individuals to Alzheimer's disease and Parkinson's disease.

Availability

Mitochondrial variant identification, annotation and interpretation will be included at no additional charge for new CompStor customers, and for those customers on support and maintenance.

About CompStor Novos

CompStor Novos is a high throughput, low cost, integrated, easy to use, genomics secondary analysis appliance supporting Illumina, PacBio and BGI sequencers. Delivering complete, end-to-end, WGS and WES secondary analysis pipelines, CompStor Novos includes both alignment and de novo assembly for genome reconstruction.

About CompStor Insight

CompStor Insight is the first tertiary analysis appliance on the market and enables faster time-to-results, and low variant interpretation per-subject cost. With an easy set up and straightforward web browser interface, scientific teams can collaborate and take advantage of push-button workflows for annotation, filtering, visualization and querying of variant data.

About OmniTier

OmniTier develops AI and multiomics appliances and software for bioinformaticians and clinical researchers that deliver affordable analysis solutions. Its integrated appliance solutions accelerate data-intensive genomic workflows and analysis utilizing machine learning and AI. Founded in February 2015, the company has R&D operations in Milpitas, CA and Rochester, MN.

CompStor appliances are for research purposes only. CompStor Novos, CompStor Insight and CompStor are trademarks of OmniTier, Inc.

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Mitochondrial DNA Analysis Is Added to OmniTier's CompStor Family of Genomics Secondary and Tertiary Analysis Appliances - Business Wire

STONY BROOK, N.Y.--(BUSINESS WIRE)--Applied DNA Sciences, Inc. (NASDAQ: APDN) (Applied DNA or the Company) a leader in Polymerase Chain Reaction (PCR)-based DNA manufacturing, announced today that it has received United States Patent No. 10,920,274 entitled Nucleic Acid Coated Submicron Particles for Authentication from the United States Patent and Trademark Office. The newly issued patent strengthens the Companys intellectual property position which includes 92 issued patents and 40 pending patent applications.

The claims of the issued patent cover methods of authenticating an object through the attachment and later authentication of submicron particles coated with a nucleic acid taggant. Claimed exemplary submicron particles include metal oxides, which encompass titanium dioxide and silicon dioxide that are commonly used as pharmaceutical and nutraceutical excipients for solid oral dosage forms and powdered formulations. In addition, submicron metal oxide particles are commonly used in the cosmetic industry.

We are excited by our recent patent issuance, which we believe helps protect our CertainT platform and its Signature DNA molecular taggants as physical-chemical identifiers (PCID) for solid oral dosage forms and powders utilized in the pharmaceutical and nutraceutical markets, said Dr. James Hayward, President and CEO, Applied DNA. While much of our recent focus has been on the biotherapeutic applications of our LinearDNATM platform, the global problem of counterfeit or adulterated pharmaceuticals and nutraceuticals has not gone away with the onset of the COVID-19 pandemic. We continue to pursue the implementation of the CertainT platform in the pharmaceutical and nutraceutical markets as an important business vertical with our industry partners.

About Applied DNA Sciences, Inc.

Applied DNA is commercializing LinearDNA, its proprietary, large-scale polymerase chain reaction (PCR)-based manufacturing platform that allows for the large-scale production of specific DNA sequences.

The LinearDNA platform has utility in the nucleic acid-based in vitro diagnostics and preclinical nucleic acid-based drug development and manufacturing market. The platform is used to manufacture DNA for customers as components of in vitro diagnostic tests and for preclinical nucleic acid-based drug development in the fields of adoptive cell therapies (CAR T and TCR therapies), DNA vaccines (anti-viral and cancer), RNA therapies, clustered regularly interspaced short palindromic repeats (CRISPR) based therapies, and gene therapies. Applied DNA has also established a COVID-19 diagnostic and testing offering that is in the early stages of commercialization and is grounded in the Companys deep expertise in DNA.

The LinearDNA platform also has non-biologic applications, such as supply chain security, anti-counterfeiting and anti-theft technology. Key end-markets include, textiles, pharmaceuticals and nutraceuticals, and cannabis, among others.

Visit adnas.com for more information. Follow us on Twitter and LinkedIn. Join our mailing list.

The Companys common stock is listed on NASDAQ under ticker symbol APDN, and its publicly traded warrants are listed on OTC under ticker symbol APPDW.

Applied DNA is a member of the Russell Microcap Index.

Forward-Looking Statements

The statements made by Applied DNA in this press release may be forward-looking in nature within the meaning of Section 27A of the Securities Act of 1933, Section 21E of the Securities Exchange Act of 1934 and the Private Securities Litigation Reform Act of 1995. Forward-looking statements describe Applied DNAs future plans, projections, strategies and expectations, and are based on assumptions and involve a number of risks and uncertainties, many of which are beyond the control of Applied DNA. Actual results could differ materially from those projected due to its history of net losses, limited financial resources, limited market acceptance, the uncertainties inherent in research and development, the risk of not obtaining necessary regulatory approval from U.S. FDA or equivalent foreign regulatory agencies and various other factors detailed from time to time in Applied DNAs SEC reports and filings, including our Annual Report on Form 10-K filed on December 17, 2020 and our subsequent quarterly report on Form 10-Q filed on February 11, 2021, and other reports we file with the SEC, which are available at http://www.sec.gov. Applied DNA undertakes no obligation to update publicly any forward-looking statements to reflect new information, events or circumstances after the date hereof or to reflect the occurrence of unanticipated events, unless otherwise required by law.

Continued here:
Applied DNA Granted U.S. Patent Covering Methods of Utilizing DNA Tagged Submicron Particles for Authentication - Business Wire

The appeal of Susan Neill-Fraser has moved to closing arguments ahead of schedule, following a volatile two days which saw the convicted murderer's lawyers abandon their key witness.

Neill-Fraser is serving a 23-year sentence for the murder of her partner Bob Chappell.

Mr Chappell disappeared from his yacht, which was moored in Hobart's River Derwent, on Australia Day 2009.

There was no body or murder weapon and the court today heard that the original trial relied entirely on "circumstantial evidence".

In 2019, Neill-Fraser was granted leave to appeal after a Supreme Court judge found she had fresh and compelling evidence.

Neill-Fraser's team has now begun closing arguments.

On Monday, the court heard that Meghan Vass whose DNA was found on the yacht was the key witness and her oral evidence would be "fresh and compelling".

"She's our case," said Robert Richter QC, lead counsel for Sue Neill-Fraser.

On day one, Ms Vass gave evidence that she had been aboard the yacht with three men when they encountered Mr Chappell.

She told the court one of the men started "flipping out" and the fight turned violent.

ABC News: Luke Bowden

But during cross-examination on day two of the appeal, Ms Vass began to recant all of her evidence.

She said there had been just two men on the yacht, then one and then said she had never been on the boat.

"You can't remember being on that boat, can you?" asked Director of Public Prosecutions Daryl Coates.

"No," Ms Vass said.

Mr Richter later told the court he wanted to relieve Ms Vass and abandon her evidence, with the exception of the DNA that was found on the yacht.

"We are in a situation which we concede cannot support the notion of fresh and compelling evidence leading to miscarriage of justice," he said.

Facebook: Susan Neill-Fraser is Innocent

On Wednesday morning, the court had expected to hear from a DNA expert witness, but the prosecution did not proceed with the evidence.

Chris Carr SC began closing submissions for Neill-Fraser's case.

Mr Carr said the evidence Ms Vass had given over two days was "not of any relevance to this court's task".

He took the court through the original trial in order to "identify issues".

"The real issue at trial was whether the prosecution excluded any evidence of a hypothesis consistent with innocence," he said.

He pointed to an account from the original trial of a grey dinghy that was not the Four Wind's tender tied up alongside the yacht late on the afternoon of 26th January, 2009.

He also told the court there had been no rational explanation for how Ms Vass's DNA had gotten on the Four Winds.

ABC News

"At some stage Meghan Vass was on the Four Winds," he said.

"[It's an] equally plausible hypothesis that she went there with the grey dinghy with some friends.

"[It was] hardly likely that she'd admit that to police she can't account for where she was on the 26th of January.

Twelve years ago, Bob Chappell disappeared from his yacht, never to be seen again. Now, the woman convicted of his murder has a fresh chance to prove her innocence. Learn how the original case unfolded and what the appeal is based around.

"The way the prosecution dealt with this reasonable hypothesis and demolished it as unreasonable hypothesis at trial was untenable or at least sufficiently impugned."

Mr Carr also cited evidence from another DNA expert, Maxwell Jones, who wrote reports for the appeal hearing.

He is challenging the idea, put forward by the Crown at trial, that Ms Vass's DNA could have arrived on the boat through a secondary transfer, such as someone walking it on.

"Mr Jones articulates what would in fact be required for the transference to have led to the deposit of the DNA that was actually found on the Four Winds," he said.

"That explanation is entirely inconsistent with the way the matter was put to the jury on this critical issue by the learned prosecution at trial."

Mr Carr told the court that had the original jury been offered the opinion of Mr Jones, and taken into account the report of the "grey dinghy", they would have been left with a reasonable doubt.

"There was a substantial miscarriage of justice and the appeal should be allowed and a retrial ordered," said Mr Carr.

Crown Prosecutor Daryl Coates SC has addressed how the DNA came to be on the boat.

"The Four Winds was found sinking on the morning of the 27th January [2009]," he said.

"It was not treated as a crime scene [and] it was [eventually] transferred to Cleanlift in Goodwood that does boat repairs."

The court heard on Monday that Ms Vass's partner at the time lived in Goodwood and she spent time in that area.

Mr Coates told the court the swab that had the DNA sample from Ms Vass was not taken until the 30th of January.

"At least 21 people apart from scientists got on the boat, prior to the swab being taken," he said.

"They included people like the person who towed the boat, insurance assessors, other civilians, police officers, accused and her family."

ABC News

He said the Crown maintained its position that Ms Vass was never on the boat, however he did point to a second theory.

"If the jury rejected that [it was a secondary transfer], they could've still concluded that she got on the boat afterwards," he said.

He also said a significant part of Mr Jones's evidence was "more favourable to the Crown".

"He gave evidence that given the quantity of the DNA, and the fact there was no degradation, he thought the most likely [scenario] was the sample had only been there one or two days," he said.

"It strongly supports that it was transferred or Ms Vass being there after sinking."

In his response, Mr Carr challenged the Crown's claims that the DNA evidence supported the case against Neill-Fraser.

He told the court Mr Jones had said the DNA could have stayed on a textured surface, like the deck of the yacht, for a long time.

In summing up he said there was a "significant possibility that the jury would have delivered a different verdict if the evidence of Jones had been before it".

"The Prosecution's removal of that pillar of the defence case, namely Ms Vass's DNA indicated her presence on the yacht, and as a result there has been a substantial miscarriage of justice."

The judges have reserved their decision.

Original post:
Susan Neill-Fraser murder appeal moves to closing arguments after DNA expert witness dropped by prosecutor - ABC News

SAGINAW, MI The Saginaw Police Department has partnered with an independent DNA laboratory in hopes of learning the name of a homicide victim whose identity has remained a mystery for more than 30 years.

Newly working with the department is Othram Inc., based in The Woodlands, Texas. Founded in 2018, Othram is self-described as the worlds first private DNA laboratory built specifically to apply the power of modern parallel sequencing to forensic evidence.

The case dates to October 1988, when police responded to a report of a body inside a house in the 400 block of Carroll Street. Officers arrived to find the body of a young Black man who had died a few hours prior from a shotgun wound to his face.

The slain man had brown eyes and black hair, with a slightly raised mohawk and fade on the sides. He stood 5 feet 7 inches tall, weighed about 165 pounds, and is believed to have been 15 or 16 when he died, said Detective Sgt. Matthew Gerow.

The victim also had a very light mustache and was wearing a green and yellow T-shirt, black jeans, white Nike Air tennis shoes, and two gold chains. He bore some birthmarks on his abdomen and several keloid scars overgrowths of scar tissue on his knees and right shoulder.

The decedent matched no missing person cases in the area and no one has come forward with information related to his or the killers identity, police said. Gerow said there is reason to believe the decedent may have hailed from the Detroit area.

Investigators have revisited the case several times over the years, with artists from the Michigan State Police and National Center for Missing and Exploited Children having created multiple forensic images of the man.

Police now hope that with Othram, advanced DNA testing and forensic genealogy will provide them with the deceased mans name, or lead them to a relative.

The companys scientists work with the military, law enforcement, private investigators, historians, and academic researchers to extract the most value from human DNA samples when other investigative approaches have failed.

Anyone with information about the decedent is encouraged to contact the Saginaw Police Department at 989-759-1235. An online fundraising effort has been established to cover the costs of the testing for this case. Those interested in donating can do so at http://www.dnasolves.com/articles/saginaw_john_doe/

Read more:

After 43 years, DNA test provides new information in 1978 Jackson County cold case homicide

After 35 years, body found in Jackson still unidentified, public asked to help identify unknown female

Family in Bay City cold case seeks Justice for Jan

Read more from the original source:
Saginaw police partner with Texas DNA lab to ID teen killed in 1988 - MLive.com

(via Fotolia.com)

Why was Dr. John Snow designated the "Father of Epidemiology?" His painstaking investigations of the outbreaks of deadly cholera in London in the 1850s led him to conclude that the disease was caused by contaminated water. His meticulous data gathering pinpointed the source at a single water pump.

Not only had no one ever mapped the incidence of death before, but even the concept of the "germ theory" was still discredited. It took almost twenty years for the scientific and medical profession to accept his premise, but since the water pump was disabled, the cholera epidemic ceased. (See map at end of the piece).

Why did a commercial NLP company, John Snow Labs, choose this name? Though not exclusively producing models for healthcare and life sciences, that is a significant part of their business. I've had the chance to speak with them on several occasions, and they are a remarkable organization, in many ways, which I'll explain. But first, let's review how at least some aspects of NLP work.

By now, everyone is familiar with conversational NLP like Siri. For augmented analytics, the conversation may be, "Download the latest pricing analysis to my phone." The critical thing to remember is that the computer does not understand what you are saying, nor does it understand what it is saying. It can process it and answer, but make no mistake; it's all done with math.

Organizations that offer NLP capabilities do not start from scratch. There are open source libraries that can slot in and wrap their software around it, such as Spark NLP from John Snow Labs, for example. Or other open-source Python libraries such as spaCy, textacy, or nltk. Just to be clear, here are the steps an NLP goes through to satisfy your question. It isn't one model - "Parse my sentence." Each step is a different model. I'm oversimplifying here, but to give you a sense of how part of this works, here are the steps to "understand" a sentence:

Consider that John Snow Labs offers a community version (free) of its Spark NLP that supports an astounding 375 languages, some of which have fewer than 10,000 native speakers. The first question is how and the second question is why. The how is pretty complicated, and I'll save that for another article. But it involves training using deep learning techniques, but the why is pretty compelling.

John Snow Labs is a commercial company focused on Life Sciences, Genomics, and Healthcare. Unlike IBM's proclamation ten years ago that Watson would cure cancer (and failed), John Snow Labs set out to use NLP technology to assist practitioners in assembling credible medical records that are, to this day, scattered, siloed, and inconsistent.

Particularly with oncology, this is crucial because cancer treatment is still very complicated, and practitioners need all the data they can get. hen data is cloistered in multiple EMRs, John Snow Labs frees it. But why 375 languages? As David Talby, the company's founder and CTO said to me recently, accuracy in B2C transactions is useful, but it's not a matter of statistics in oncology. Everyone single person is important, whether they're at Mount Sinai Hospital or a Doctors Without Borders camp.

You may wonder, if these models aren't "smart" in any human intelligence fashion, how can you trust them? Alter all, human language is very complex, often ambiguous if not nonsensical. The answer is that a few years ago, the accuracy of NLP models hovered around 50%. Today, Spark NLP achieves better than 95% accuracy in academic peer-reviewed results.

We have lots of problems with "AI" companies, especially those with venture funding, expected to exhibit the growth their investors demand. As a result, ethical considerations about the products they produce take a severe hit. John Snow Labs is not in that category:

Why is it so crucial for John Snow Labs to have these policies and enforce them? The AI industry is riddled with ethical problems. Many companies engage in a sinister practice, "Ethics washing,"fabricating or exaggerating their commitment to equitable AI. It'sinauthentic and distracts from whether or not actual steps are being taken toward building a world where professional standards demand AI that works just as good for women, people of color, or young people as it does for the white men who make up themajority of people making AI systems.

Training in ethics has not been very effective, at least partly because it's been aimed at AI developers and researchers who make important determinations that can harm people. In contrast, they need to know when the technology benefits and harms. It is clear that better testing and engineering practices, grounded in concern for AI's implications, are urgently needed.

However, focusing on engineers without accounting for the broader political economy within which AI is produced and deployed runs the risk of placing responsibility on individual actors within a much larger system, erasing very real power asymmetries. Those at the top of corporate hierarchies have much more power to set direction and shape ethical decision-making than individual researchers and developers. Racism and misogyny are treated as "invisible" symptoms latent in individuals, not as structural problems that manifest in material inequities. These formulations ignore that engineers are often not at the center of the decisions that lead to harm and may not even know about them. For example, some engineers working on Google's Project Maven weren't aware that they were building a military drone surveillance system. Indeed, such obscurity is often by design, with sensitive projects being split into sections, making it impossible for anyone developer or team to understand the ultimate shape of what they are building and where it might be applied.

In January 2021, John Snow Labs released NLU 1.1, which integrates 720+ new models from the latestSpark-NLP 2.7 release. Including state-of-the-art results with Sequence2Sequence transformers on problems like text summarization, question answering, translation between 192+ languages, and extracted Named Entity in various Right to Left written languages like Arabic, Persian, Urdu, Hebrew, and languages that require segmentation like Korean, Japanese, Chinese, and many more in 1 line of code. These new features are possible because of integratingGoogle's T5 models andMicrosoft's Marian models.

NLU 1.1 has over 1,000 pertained models. In addition to this, NLU 1.1 comes with nine new notebooks showcasing training classifiers for various review and sentiment datasets and seven notebooks for the new features and models. You can browse the complete list of models in this release.

I'll sum it up this way. Facebook is the world's largest deliberate purveyor of disinformation. A company with, in my estimation, no soul. John Snow Labs is a small commercial NLP company of roughly 75 employees that provides an open source library with hundreds of pre-trained models, including tools, in contrast to Facebook, for detecting disinformation.

John Snow's original cholera data points map.

More here:
For John Snow Labs, doing good with NLP is in their DNA (and yours) - Diginomica