Cat and Human Genomes

Welcome back. Do you remember when former President Trump was stricken with COVID-19? One of the treatments to speed recovery was the antiviral drug remdesivir. A few years earlier, researchers with the University of Missouri-Columbia’s College of Veterinary Medicine had learned that remdesivir was effective in curing cats of a coronavirus-induced disease, feline infectious peritonitis. That opened the door for them to consider the drug for treating humans with COVID-19. Why? Because the receptors for the virus are similar between cats and humans.

Lest you think that was an anomalous or lucky connection, It turns out that cats are more genetically similar to humans than nearly any other mammal. And that similarity can potentially facilitate the expansion of genomic medicine for both cat and human healthcare.

The human genome—some 20,000 to 25,000 genes in 23 pairs of chromosomes in each cell (from www.genomicsengland.co.uk/understanding-genomics/what-is-a-genome/).

Before I go any further, it’s probably best to mention that genomics is the branch of molecular biology concerned with the structure, function, evolution and mapping of genomes--the complete set of genes or genetic material, composed of DNA, that’s present in a cell or organism; genome mapping identifies a series of landmarks in a genome; genome sequencing spells out the order of every DNA base in a genome; and as for DNA bases, there are more than 3 billion base pairs of DNA in the mammal genome.

Comparative Geonomics
Despite the progress in sequencing the human genome, advances in precision medicine rely on more than accurate and complete human genome sequences. Comparing sequences in different species and exploring what variations mean for the biology and disease of other species are significant in developing precision therapeutics. High-quality reference genomes, particularly of species where genomes are conserved (essentially unchanged throughout evolution) and follow the same order as that in humans, are essential.

Comparative genomics by National Human Genome Research Institute of the National Institutes of Health (graphic modified from www.genome.gov/about-genomics/fact-sheets/Comparative-Genomics-Fact-Sheet, August 2020).

Although the discovery of single-gene mutations that cause rare conditions progresses well with the human genome, most common diseases are more complex. Since these are common conditions affecting cats as well as humans, research comparing genomes can possibly help identify the genes and mechanisms causing the diseases.

Toward that end, a University of Missouri-led consortium developed a genome reference assembly from the genomes of 54 domestic cats, annotating the feline variations in the context of human genes. The team is continuing to expand that resource to obtain more accurate genome assemblies that might identify novel variations responsible for traits and conditions of importance to animal and human genomic medicine.

“Dark Matter” DNA
One area of special interest is understanding the functions of “dark matter” DNA.

Of the 3 billion-plus base pairs of DNA that form the mammal genome, only 2% is coded into proteins that help our bodies perform natural functions. The other 98% of DNA--the so-called dark matter DNA--is not fully understood but might include regulatory elements that switch our genes on or off.

Finding regulatory sequences in the cat genome and potentially developing therapies to turn those sequences on or off would be a major breakthrough in managing genetic mutations.

Wrap Up
Whether loved or hated, cats are often undervalued by the scientific community. Research in comparative genetics is proceeding rapidly, and the genome match is such that cats could be the optimal species for advancing precision medicine, especially for inherited diseases that affect both cats and humans.

Henry, dreaming about comparing his genome with Noah’s (photo by Noah Philipson).

There is ample justification for the University of Missouri-led consortium to believe that feline genomics holds great potential and promise for advancing human medicine and mammalian biology.

Thanks for stopping by.

P.S.
Genomics:
www.genome.gov/about-genomics/fact-sheets/A-Brief-Guide-to-Genomics
www.genomicsengland.co.uk/understanding-genomics/what-is-a-genome/
en.wikipedia.org/wiki/Genomics
Comparative geonomics:
www.genome.gov/about-genomics/fact-sheets/Comparative-Genomics-Fact-Sheet
en.wikipedia.org/wiki/Comparative_genomics
Review of feline genomic medicine and consortium research in Trends in Genetics journal: www.cell.com/trends/genetics/fulltext/S0168-9525(21)00142-6
Article on review on EurekAlert! website: www.eurekalert.org/news-releases/923830
Review of feline genome assembly in PLOS Genetics journal: journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1008926
Article covering both feline genome reviews on Genetic Engineering & Biotechnology News website: www.genengnews.com/insights/cat-in-the-lab-feline-genomes-fuel-precision-medicine/

Made in USA

American flag made in China (sunwardflag.com/american-flags-should-be-made-in-america/).

Welcome back. Thanks for stopping by. I’ve got some news you may have missed. The Federal Trade Commission finalized a Made in USA Labeling Rule, effective 13 August.

In short, the rule prohibits Made in USA labels on products unless: (1) final assembly or processing of the product occurs in the U.S., (2) all significant processing that goes into the product occurs in the U.S. and (3) all or virtually all ingredients or components of the product are made and sourced in the U.S.

Hat that Warren bought in 2002 during a research study at the Naval Air Weapons Station in China Lake, Calif.

To be clear, the rule does not change the FTC’s requirement that imported products show information regarding the country of origin, and there is no requirement for products made in the U.S. to be labeled. The Made in USA label is solely for marketing purposes. The new rule is to stop deceptive claims.

The marketing Made in USA claim on the Naval Air Weapons Station hat label.

You might ask, “Does country of origin matter?”

“Made in USA” Didn’t Matter
A study presented in 2015 by a researcher with Towson University examined the importance of country of origin in consumers’ decision-making process.

The researcher conducted an internet-based empirical analysis of factors important to nearly 900 U.S. consumers when considering the purchase of a small home appliance. The focus was the consumers’ perception of a Made in USA claim separately and compared to a Made in China claim.

The analysis showed that country of origin was one of the least important factors in a purchase decision. Moreover, at least in 2015, products with a Made in China label were seen more favorably than those with a Made in USA claim.

Wait! “Made in USA” Does Matter
A recently released paper by researchers with the University of Chicago also examined the effect of the Made in USA label on consumer demand.

They studied four brands that had been the subject of FTC investigations for deceptive Made in USA claims. The brands included Gorilla Glue, Loctite Glue, Gorilla Tape and Tramontina cookware.

Comparing sales before and after the label was removed from the products as well as from advertising and websites, they found three of the four brands were affected negatively. Weekly store sales of Tramontina cookware dropped 19.5%, Loctite Glue, 6.1%, and Gorilla Glue,1.9%. The fourth brand, Gorilla Tape, experienced a “trend decline.”

Tramontina, a Brazilian company that makes kitchenware in several countries, including the U.S., was investigated by the FTC for deceptive Made in USA claims (Graphic from Amazon).

Pursuing the analysis further, the researchers conducted over 900 three-day auctions on eBay, selling a single product, screen protectors for handheld devices. They compared consumer demand when the product was advertised with and without the Made in USA claim.

The eBay experiment showed the claim mattered. Auction transaction prices were 28% higher when advertised as Made in USA. While the higher prices may not be enough to justify relocating manufacturing to the U.S., the increase certainly provides incentive to display the claim.

Wrap Up
Two studies aren’t enough to address the importance of country of origin in the global marketplace. Though I scratched the surface with two, it’s a popular topic.

Does a product’s country of origin matter to you? Did your concern arise over the last several years? Is your concern related to trust in product quality, support for American workers or the economy, patriotism or other factors? Is your concern directed only at China?

Once again, many thanks for stopping by. I hope it was worth your time.  

P.S.
FTC’s new Made in USA rule:
www.ftc.gov/news-events/press-releases/2021/07/ftc-issues-rule-deter-rampant-made-usa-fraud
www.federalregister.gov/documents/2021/07/14/2021-14610/made-in-usa-labeling-rule
Towson University study of Made in USA: link.springer.com/chapter/10.1007/978-3-319-18687-0_103
University of Chicago study of Made in USA: papers.ssrn.com/sol3/papers.cfm?abstract_id=3468543
Article on Univ. of Chicago study on EurekAlert! website: www.eurekalert.org/pub_releases/2021-06/ifor-di063021.php

Tapping Twitter’s Potential

Welcome back. In case you were wondering, I don’t have a Twitter account. Yes, I sometimes check friends’ tweets about technical news, and yes, I certainly considered joining the Twitterverse. I even shared my pros and cons in a long-ago blog post, Tweet?.

More important, I want to tell you about a powerful, new tool for curating and analyzing tweets, specifically, about 10% of all the tweets made every day around the globe. I think you’ll find it of interest.

Twitter’s Potential
Paul Lewis, with The Guardian, described Twitter as the digital footprint of things that are happening around the world. And there’s no question that Twitter, founded in 2006, has tremendous promise if one can get by the lies and rumors.

As early as 2009, Jake Coyle, with the Associate Press, wrote: Twitter has in many ways been a boon to the media…Most outlets now have a presence on Twitter with a feed directing readers to their respective sites… But truthfulness remains the biggest problem…False rumors spread daily on Twitter.

An exemplar topic addressed in different research investigations in Twitter’s early years was its use for detecting disease outbreaks. Through the years, Twitter’s value for reporting outbreaks and disasters has been demonstrated repeatedly, though rumors have often interfered (see my post Tweets Misreport Disasters).

All of which brings me to Storywrangler, the tool developed by researchers with the University of Vermont, Charles River Analytics and MassMutual Data Science.

Storywrangler website header (storywrangling.org/).

Storywrangler
Storywrangler provides a natural language processing framework that extracts, ranks and organizes tweets, generating frequencies for words (1-, 2- and 3-word phrases), hashtags, handles, numerals, symbols and emoji.

Capturing time-stamped messages and storylines in more than 150 languages, from Twitter’s inception to the present, Storywrangler makes the datasets available through an interactive time-series viewer and as downloadable time-series and daily distributions.

While Storywrangler could, in principle, be modified to operate on other social media platforms, Twitter offers some advantages. One noteworthy example is Twitter’s social amplification mechanisms--retweets and quote tweets, which enable the explicit encoding of popularity.

Visual Comparison of Phrase Popularity
In their published paper, the researchers presented a sample of Storywrangler’s online viewer visualizations. On one graph, they illustrated how different Twitter features capture three global events from the first half of 2020.

Storywrangler visualizations of three global events from first half of 2020: the death of Iranian general Qasem Soleimani; the beginning of the COVID-19 pandemic (term “coronavirus” as yellow, virus emoji, green); and the Black Lives Matter protests following the murder of George Floyd (from advances.sciencemag.org/content/7/29/eabe6534/tab-article-info).

Storywrangler showed a spike of tweets and retweets of the word "Soleimani" on 3 January, when the U.S. killed the Iranian general Qasem Soleimani with a drone strike.

There was a rise of the word "coronavirus" as well as the virus emoji as COVID-19 spread with the beginning of the pandemic in the spring.

And the hashtag "#BlackLivesMatter" jumped on and after 25 May, the day George Floyd was murdered.

Wrap Up
Storywrangler can be used to follow, trace and explore the serious and the not-so serious--disasters, political matters, vaccines, federal reserve actions, entertainment, fashion, dark matter, the dark web--and monitor discourse by or about the famous and the not-so famous.

But as the Storywrangler website warns, Twitter provides a non-representative subsample of utterances made by a non-representative subsample of Earth’s population; and Storywrangler reflects only a random 10% of those messages.

Though Storywrangler doesn’t resolve the lies and rumors that come with Twitter, the tool provides the opportunity to dig a little deeper. That’s at least a head start. Thanks for stopping by.

P.S.
Twitter:
en.wikipedia.org/wiki/Twitter
twitter.com
Twitter’s potential:
- Jake Coyle: abcnews.go.com/Technology/story?id=7979891&page=1
- Paul Lewis: theconversation.com/how-twitter-has-helped-the-emergence-of-a-new-journalism-19841
Study on development of Storywrangler in Science Advances journal: advances.sciencemag.org/content/7/29/eabe6534/tab-article-info
Article on study on EurekAlert! website: www.eurekalert.org/news-releases/527597
Storywrangler website: storywrangling.org/
 

Emoji

Welcome back. Forgive me. I’m certain most of you didn’t need my reminder, but I neglected to alert you that 17 July was World Emoji Day.

For those who may not recognize the word from Japanese, emoji or emojis (either is plural) are pictograms, logograms or ideograms and smileys used in electronic messages and web pages to add emotional cues to typed conversation.

I’ll bet you’ve seen smiley faces. Well, there are 3,521 approved emoji. In recognition of World Emoji Day, the draft candidates for the next emoji release, Emoji 14.0, were revealed along with the results of Adobe’s 2021 Global Emoji Trend Report.

Examples of candidate emoji for 14.0 release include a melting face, a face holding back tears, new handshake combinations, a gender-neutral person wearing a crown, a pregnant man, a troll with a club and coral (from emojipedia.org/emojipedia/14.0/).

Although I can’t recall adding an emoji to anything I’ve ever written, I appreciate their creativity. I’ll do my best to tell you about emoji, summarize the trend report and highlight a recent study of how the world uses emoji. To squeeze it all in, I’ll tuck ample references under the P.S.

Emoji Admin
The working list of emoji is determined by the California-based Unicode Consortium. The consortium is a non-profit corporation devoted to developing, maintaining and promoting software internationalization standards and data, particularly the Unicode Standard, which specifies the representation of text in software products and standards.

Consortium members include computer corporations, software producers, database vendors, government ministries, research institutions, international agencies and others.

Emojipedia, a member of the Unicode Consortium, is the central bank of all approved emoji. Emojipedia’s reference website documents the meaning and common usage of each emoji character.

The draft emoji announced on World Emoji Day may change prior to final approval in September. Companies such as Apple, Google and Microsoft apply stylized versions of the consortium's designs to their operating systems, vendor designs vary from those released by major vendors, and Emojipedia's draft images may be updated. The emoji will likely be seen on all platforms by June 2022.

Global Emoji Trend Report
Adobe’s Global Emoji Trend Report for 2021 is based on a survey of 7,000 emoji users in Australia, France, Germany, Japan, South Korea, the U.K. and U.S. Though details of how the survey was conducted weren’t available, I was impressed by some of the results.

Global emoji users’ top five favorite emoji (from blog.adobe.com/en/publish/2021/07/15/global-emoji-trend-report-2021.html#gs.656huw).

Global emoji users find emoji make it easier to communicate across language barriers (89% of respondents); can help spark positive conversations about cultural and societal issues (70%); and are an important communication tool for creating unity, respect and understanding (76%).

On the personal side, the users find emoji make it easier to express themselves (90%); are more likely to feel empathetic toward someone if they use an emoji (88%); and are more comfortable expressing emotions through emoji than over the phone (55%) or in-person (51%). They feel that using emoji has positively impacted their mental health (65%).

The most effective work motivating emoji (from blog.adobe.com/en/publish/2021/07/15/global-emoji-trend-report-2021.html#gs.656huw).

In the work environment, global emoji users like it when people use emoji (66%). They feel their use helps share ideas quickly (73%); can improve the efficiency of team decision-making (63%); and positively impacts likeability (71%) and credibility (62%).

How the World Uses Emoji
Researchers with the University of Southern California analyzed tens of millions of tweets, in 30 languages and countries, to evaluate how 1,700 emoji are used on Twitter in different linguistic and national contexts.

Total number of unique emoji (about 600 to 1700) in tweets of 30 different language codes in October 2016 (from www.sciencedirect.com/science/article/pii/S2468696421000318).

Employing rigorous statistical and informational theoretical methodologies, the researchers determined that emoji usage and diversity are strongly dependent upon both language and country, the latter having a more pronounced effect.

The popularity of emojis, globally and within a given language, seems to follow a robust trend that is language-independent. They emerge quickly, over a single day, and remain largely consistent thereafter.

Findings regarding specific emoji usage and countries, though interesting, may be out of date given that the study relied on data collected over one month in 2016.

Wrap Up
The most important study takeaway was that emoji represent the human condition; we are more alike than different. Universal emotions dominate.

To close, I’ll draw from the Global Trend Report to make the case that you and I should use emoji. Global emoji users think people who use emoji are friendlier, funnier and…get this...cooler than those who don’t (67%). Thanks for stopping by.

P.S.
Emoji:
en.wikipedia.org/wiki/Emoji
unicode.org/standard/standard.html
en.wikipedia.org/wiki/Unicode_Consortium
Emojipedia:
emojipedia.org/
en.wikipedia.org/wiki/Emojipedia
World Emoji Day: en.wikipedia.org/wiki/World_Emoji_Day
Emoji 14.0:
blog.emojipedia.org/new-emojis-in-2021-2022/
emojipedia.org/emojipedia/14.0/
www.dailymail.co.uk/sciencetech/article-9794749/Heres-emoji-set-coming-smartphone-2022.html
Adobe’s 2021 Global Emoji Trend Report: blog.adobe.com/en/publish/2021/07/15/global-emoji-trend-report-2021.html#gs.656huw
Study of emoji usage on Twitter in Online Social Networks and Media journal: www.sciencedirect.com/science/article/pii/S2468696421000318
Article on study on EurekAlert! website: www.eurekalert.org/pub_releases/2021-07/uosc-hdt071321.php