Hexbyte Glen Cove An online game to crowdsource the science of letter shapes

Hexbyte Glen Cove

Main page of the glyph website. Credit: Max Planck Institute for the Science of Human History, PSL SCRIPTA

A team of cognitive scientists lead by Dr. Yoolim Kim (Korea Institute at Harvard and Max Planck Institute for the Science of Human History) and Dr. Olivier Morin (Max Planck Institute for the Science of Human History and PSL University, Paris) have just launched a free gaming applet. The game, called “glyph”, allows players to compete with each other to sort letter shapes from various writing systems into categories of their own creation. The most original and informative classifications win extra points.

Dr. Kim explains “Science is good at sorting things into classifications. Chemists have the table of elements, biologists have the system of species—there are rules to sort even Pokémon! But there is no such thing for letters. For some writing, yes, but not for all the letters in the world.”

The field of visual psychology, or the study of how things we see affect the ways we think, currently lacks a vocabulary for describing shapes. So far, letters have mostly been studied from the point of view of linguistics, and only a few studies have looked at their shapes and visual properties with reflecting the diversity of the world’s scripts.  The team hopes the glyph applet will lead to the emergence of a common standard that can unify the study of writing system across linguistics and vision science.

The first question they will attempt to answer with this data concerns the distinctiveness of letters: how do letters in a script manage to be different enough from one another without being too difficult to process.

Playing to sort the letters of the Nabatean script: a screen capture from the applet. Credit: Max Planck Institute for the Science of Human History, PSL SCRIPTA

A visual grammar of letter shapes

Crowdsourcing—asking a large number of players to contribute to a project—will allow researchers to obtain a typology of letter shapes with reproducible and transparent classification rules. The research team hopes to build a grammar of letter shapes, achieving for the of writing what linguists have done for the sounds of language.

“A typology for letters will really open the doors into research on writing and writing systems,” says Kim. “But instead of asking specialists to create one, we’re asking the public for help.”

The game works by presenting players with a set of characters from one of the 45 written languages included in glyph. Players tap on the characters to create a group based on their visual similarities and then create rules that describe the similarities of the group. The team will then run machine learning tools on the participants’ contributions to identify the most reliable and informative rules.

More information:
Scientific project description on the Open Science Framework: osf.io/j9zhn/

An online game to crowdsource the science of letter shapes (2022, February 17)
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Hexbyte Glen Cove How superbugs use mirror images to create antibiotic resistance

Hexbyte Glen Cove

A colorized scanning electron micrograph of MRSA. Credit: National Institute of Allergy and Infectious Diseases

Methicillin-resistant Staphylococcus aureus (MRSA) is a bacterial infection that has become resistant to most of the antibiotics used to treat regular staph infections. Duke University computer scientist Bruce Donald and collaborators at the University of Connecticut are working to develop new enzyme inhibitors to fight MRSA. In research published in PLOS Computational Biology, the team discovered how a single small mutation makes a big difference in drug efficacy.

They examined dihydrofolate reductase (DHFR), an enzyme that antibiotics target to fight MRSA. Drugs that inhibit DHFR work a bit like locks and keys; they bind to enzymes in MRSA, which have a specific three-dimensional structure that only allows molecules that fit precisely to attach to them.

A mutation can change the structure of a bacterial enzyme and cause drugs to lose effectiveness. The F98Y mutation is a well-known resistance mutation. A slight change in the 98th amino acid in the DHFR enzyme changes a phenylalanine to a tyrosine. “Those two amino acids are structurally similar,” said Graham Holt, grad student in the Donald lab, “but the mutation has a huge effect on the efficacy of the inhibitors.” In essence, it changes the lock.

Pablo Gainza, Ph.D., former graduate student in the Donald lab, thought he should be able to predict this mutation using OSPREY, a suite of programs for computational structure-based protein design developed in the Donald lab. But he couldn’t. After knocking down hypothesis after hypothesis to figure out why he was unable to predict this mutation, he went back to examine the starting structure.

“We looked at the electron density data from the crystallographer and found something strange,” Donald said. In trying to determine the structure of the F98Y mutant, crystallographers used a computer program that—unbeknownst to them—flipped the chirality, or made a mirror image, of the NADPH cofactor to get a better fit. The “flipped” chemical species they discovered through their analysis exists in experimental conditions in the laboratory and plausibly in vivo.

“Using OSPREY, we discovered this flipped chirality,” Donald said, “which we believe happened because of the F98Y mutation.” As in 2-factor authentication, the single enzyme mutation and the flipped cofactor appear to conspire together to evade the inhibitor.

This “chiral evasion” changes the structural basis for resistance. But now Donald and colleagues know not only how a single small mutation changed the lock, but also the structure they need to make a better key—a better drug inhibitor.

“This is the first example of an that exploits the chirality of its cofactor in order to evade its inhibitors,” Holt said. “Now that we see this happening, that will help inform computational strategies to develop better inhibitors.”

The Donald lab showed that by taking flipped into account, OSPREY’s predictions closely match experimental measurements of inhibitor potency. They worked with collaborators at the University of Connecticut who conducted biochemical experiments to test the theory and provide structural evidence.

“This is only the beginning of the story,” Donald said. “Our discovery of chiral evasion should lead to more resilient : better drug designs.” Right now, most drug design is reactive, waiting for resistance to arise, which it always does. “We hope to make design proactive, by using our algorithms to anticipate resistance,” Donald said.

More information:
Siyu Wang et al, Chiral evasion and stereospecific antifolate resistance in Staphylococcus aureus, PLOS Computational Biology (2022). DOI: 10.1371/journal.pcbi.1009855

How superbugs use mirror images to create antibiotic resistance (2022, February 17)
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Hexbyte Glen Cove Study assesses cooperation networks in the Utah State Legislature

Hexbyte Glen Cove

Politicians whisper during the 2022 Utah Legislative session. From left to right are republican Representatives Karianne Lisonbee, Walt Brooks, and Cory Maloy in the House Chamber of Utah State Legislature in Salt Lake City, Utah. Credit: Connor Davis

Do politicians act like humans? Many jokes suggest otherwise, but the question is real.

Groups of humans follow basic social rules: They build relationships, form alliances and exchange favors to help one another survive. In contrast, the stereotype of a politician is a person motivated by self-interest—the lust for power and re-election will supersede their human tendency towards collaboration. But legislators must cooperate to enact policy and survive in their political environment. So, do they operate under the same as human societies across the globe?

Political scientists have recently utilized tools that anthropologists and sociologists have long used to study human behavior in groups. These “social network analyses” suggest that politicians pay great attention to their social environments. They tend to find friends with similar demographic and cultural traits (known as “homophily”) and build trust by taking turns helping each other (““). However, past studies have focused on competitive, high-stakes political institutions that receive national media attention… somewhere like the U.S. Congress.

For the first time, a University of Utah-led study has assessed cooperation networks in the Utah State Legislature, an institution with a supermajority of legislators by both gender (male) and party affiliation (Republican). The authors asked a new question: Do Democrats and female legislators still choose to work with similar colleagues, even when Republicans and male legislators control the levers of power?

The study finds that despite the supermajorities, Utah legislators overwhelmingly initiate alliances with members from within their own political and gender groups. They also repay their social debts, reciprocating policy favors at high rates.

“There’s a whole swath of literature in biology and anthropology focused on the importance of building trust and relationships in constrained environments. And politically, the Utah State Legislature is one of the most constrained environments,” said lead author Connor Davis, a master’s student in anthropology at the University of Utah. “There’s only 45 days in the session to determine a whole year’s worth of legislation. It’s chaotic. It’s a mess. But we still do it. So, how does that work?”

The study was published on Feb. 17, 2022, in the journal Human Nature.

The Utah State Legislature has special rules for introducing legislation. Each bill can only have a single sponsor; legislators must enlist a colleague (a “floor sponsor”) from the other chamber to champion the bill in their respective chamber.

The researchers examined bill floor sponsorship in the Utah State Legislature from 2005-2008 and analyzed the characteristics that influenced who cooperated with whom. They looked at gender, seniority and party affiliation. They found that politicians were more likely to serve as a floor sponsor for a colleague of the same gender and political affiliation. Seniority in the had no effect.

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Hexbyte Glen Cove Study spearheads the chemical fingerprint of Viking weapons

Hexbyte Glen Cove

Credit: Pixabay/CC0 Public Domain

A new study examining the chemical makeup of iron artifacts from the Viking age aims to uncover new insights into where they came from that could reveal previously unknown information about historic events.

Scientists from the University of Nottingham are leading the study that will examine 90 iron Viking-age artifacts. These are that were used in battles at Fulford in North Yorkshire and Bebington Heath on the Wirral. Other material comes from the Viking camp at Torksey in Lincolnshire, and from the former Viking seaport of Meols.

Fulford was the location for a battle in AD 1066 between Norse invaders and the Anglo-Saxons, immediately before the better-known battle of Stamford Bridge. The archeological material consists of iron weapons found at a number of short-lived iron recycling sites that were abandoned by the Norse victors at Fulford when they were defeated at Stamford Bridge five days later. The iron material from Bebington Heath was recovered from the possible location of the AD 937 battle of Brunanburh, between Norse-Scottish and Anglo-Saxon armies. The material has been typologically assigned to the late Saxon/Viking period and shows parallels with the artifacts from Fulford. Torksey, Lincs, in the lower Trent Valley, was the site of the winter encampment of the Viking Great Army in AD 872-873 and iron working is documented at the site.

Credit: University of Nottingham

The researchers from Nottingham are working with the University of Toulouse (Dr. Jean Milot), the University of York (Professor Dawn Hadley and Professor Julian Richards), Fulford Battlefield Society (Chas Jones) and the Nottinghamshire-based British Geological Survey at Keyworth (Professor Jane Evans) to identify the chemical isotope signature of the iron using , and iron . Lead isotope analysis has proved effective for provenancing ancient metal artifacts of silver and copper, and the team have already conducted a successful pilot study on a smaller sample of artifacts that showed this combination of analyses is effective for provenancing iron artifacts, even when the items are highly corroded.

“In this study we will be testing our hypothesis that it is possible to use isotope analysis with iron to pinpoint more specifically than ever before where the artifact originates from. If successful, it could lead to this method being used with many more historic artifacts, which will help us learn more about historic events and people,” says Professor Stephen Harding, expert in the scientific study of Viking artifacts and research lead.

Professor of Mediterranean Prehistory Mark Pearce adds, “This is an exciting collaboration that will use the latest scientific techniques to reveal the unique isotope composition of these ancient artifacts and how this informs us where they were made. The project will revolutionize our understanding of archeological objects, finally giving us a method accurately to pinpoint their origin.”

Study spearheads the chemical fingerprint of Viking weapons (2022, February 17)
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