Protein fragments ID two new “extremophile” microbes—and may help find alien life

AMERICAN CHEMICAL SOCIETY

 

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PROTEIN FRAGMENTS IDENTIFIED NEW TYPES OF EXTREMOPHILES, WHICH SURVIVE HARSH ENVIRONMENTS ON EARTH, AND COULD SOMEDAY HELP ASTROBIOLOGISTS IDENTIFY ALIEN LIFE.

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CREDIT: ADAPTED FROM JOURNAL OF PROTEOME RESEARCH 2024, DOI: 10.1021/ACS.JPROTEOME.3C00538

Perfectly adapted microorganisms live in extreme environments from deep-sea trenches to mountaintops. Learning more about how these extremophiles survive in hostile conditions could inform scientists about life on Earth and potential life on other planets. In ACS’ Journal of Proteome Research, researchers detail a method for more accurate extremophile identification based on protein fragments instead of genetic material. The study identified two new hardy bacteria from high-altitude lakes in Chile — an environment like early Mars.  

Even though humans tend to avoid settling in extremely hot, cold or high-altitude areas, some microorganisms have adapted to live in such harsh locations. These extremophile microbes are of interest to astrobiologists who are searching for life on other planets. Researchers currently use individual gene sequencing to identify Earth-bound microbes, based on their DNA. However, current methods can’t distinguish closely related species of extremophiles. So, Ralf Moeller and colleagues investigated whether they could identify an extremophile by using its protein signature rather than a gene sequence.

The researchers started their demonstration with water samples from five high-altitude Andean lakes more than 2.3 miles above sea level in the Chilean Altiplano. (For reference, Denver is about one mile above sea level.) From the samples, the researchers cultivated 66 microbes and then determined which of two methods better identified the microorganisms:

• Traditional gene sequencing compared the nucleotides of the 16s rRNA gene (a typical gene for sequence-based microbe analysis) from each sample to a database for identification.
• The newer “proteotyping” technique analyzed protein fragments known as peptides to produce peptide signatures, which the team used to identify microorganisms from proteome databases.

With these methods, the researchers identified 63 of the 66 microorganisms that were cultivated from the high-altitude lake samples. For the three microorganisms that gene sequencing failed to identify because their genetic information wasn’t in the available database, proteotyping identified two potentially new types of extremophile bacteria. These results suggest proteotyping could be a more complete solution for identifying extremophile microorganisms from small biological samples. The team says protein profiling could someday help us search for and identify extraterrestrial life and better explore the biodiversity on our own planet.

The authors acknowledge funding from the Federal Ministry of Education and Research-Association of German Engineers and the Association of Electrical, Electronic and Information Technologies Innovation + Technology grant; German Aerospace Center; German Research Foundation; an Occitania Region grant; and the Volkswagen Foundation.

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The American Chemical Society (ACS) is a nonprofit organization chartered by the U.S. Congress. ACS’ mission is to advance the broader chemistry enterprise and its practitioners for the benefit of Earth and all its people. The Society is a global leader in promoting excellence in science education and providing access to chemistry-related information and research through its multiple research solutions, peer-reviewed journals, scientific conferences, eBooks and weekly news periodical Chemical & Engineering News. ACS journals are among the most cited, most trusted and most read within the scientific literature; however, ACS itself does not conduct chemical research. As a leader in scientific information solutions, its CAS division partners with global innovators to accelerate breakthroughs by curating, connecting and analyzing the world’s scientific knowledge. ACS’ main offices are in Washington, D.C., and Columbus, Ohio.

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JOURNAL

Journal of Proteome Research

DOI

10.1021/acs.jproteome.3c00538 

ARTICLE TITLE

Exploring Andean High-Altitude Lake Extremophiles through Advanced Proteotyping

FUSION-SCI-FI-TEK

Plasma oscillations propel breakthroughs in fusion energy

New insights into plasma oscillations are paving the way for improved particle accelerators and commercial fusion energy

UNIVERSITY OF ROCHESTER

Most people know about solids, liquids, and gases as the main three states of matter, but a fourth state of matter exists as well. Plasma—also known as ionized gas—is the most abundant, observable form of matter in our universe, found in the sun and other celestial bodies.

Creating the hot mix of freely moving electrons and ions that compose a plasma often requires extreme pressures or temperatures. In these extreme conditions, researchers continue to uncover the unexpected ways that plasma can move and evolve. By better understanding the motion of plasma, scientists gain valuable insights into solar physics, astrophysics, and fusion.

In a paper published in Physical Review Letters, researchers from the University of Rochester, along with colleagues at the University of California, San Diego, discovered a new class of plasma oscillations—the back-and-forth, wave-like movement of electrons and ions. The findings have implications for improving the performance of miniature particle accelerators and the reactors used to create fusion energy.

“This new class of plasma oscillations can exhibit extraordinary features that open the door to innovative advancements in particle acceleration and fusion,” says John Palastro, a senior scientist at the Laboratory for Laser Energetics, an assistant professor in the Department of Mechanical Engineering, and an associate professor at the Institute of Optics.

Plasma waves with a mind of their own

One of the properties that characterizes a plasma is its ability to support collective motion, where electrons and ions oscillate—or wave—in unison. These oscillations are like a rhythmic dance. Just as dancers respond to each other’s movements, the charged particles in a plasma interact and oscillate together, creating a coordinated motion.

The properties of these oscillations have traditionally been linked to the properties—such as the temperature, density, or velocity—of the plasma as a whole. However, Palastro and his colleagues determined a theoretical framework for plasma oscillations where the properties of the oscillations are completely independent of the plasma in which they exist.

“Imagine a quick pluck of a guitar string where the impulse propagates along the string at a speed determined by the string’s tension and diameter,” Palastro says. “We’ve found a way to ‘pluck’ a plasma, so that the waves move independently of the analogous tension and diameter.”

Within their theoretical framework, the amplitude of the oscillations could be made to travel faster than the speed of light in a vacuum or come to a complete stop, while the plasma itself travels in an entirely different direction.

The research has a variety of promising applications, most notably in helping to achieve clean-burning, commercial fusion energy.

Coauthor Alexey Arefiev, a professor of mechanical and aerospace engineering at the University of California, San Diego, says, “This new type of oscillation may have implications for fusion reactors, where mitigating plasma oscillations can facilitate the confinement needed for high-efficiency power generation.”

The Office of Fusion Energy Sciences, the Department of Energy National Nuclear Security Administration, and the New York State Energy Research Development Authority supported this research.

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JOURNAL

Physical Review Letters

DOI

10.1103/PhysRevLett.132.095101 

ARTICLE TITLE

Space-Time Structured Plasma Waves

Specialized nursing facility clinicians improve end-of-life care

WEILL CORNELL MEDICINE

Specialized nursing facility clinicians, or SNFists, may decrease the likelihood of nursing home residents experiencing stressful hospitalizations and improve the quality of life in their last days, according to researchers from Weill Cornell Medicine.

The paper, published in JAMA Network Open on Mar. 15, examined how SNFists uniquely impacted the care of nursing home residents in their last 90 days, compared with those cared for by other clinicians. This large-scale study is the first of its kind.

“The literature has described certain features or outcomes that translate into what we think is poor quality at the end of life,” said Dr. Arnab Ghosh, assistant professor of medicine at Weill Cornell Medicine and a hospitalist at NewYork-Presbyterian/Weill Cornell Medical Center. “One example is transferring residents to the hospital and admitting them for conditions like pneumonia or UTIs (urinary tract infections) that may have been managed in the nursing home, or going from nursing home to hospital to another nursing home.”

The physical act of transferring the residents to new environments increases their risk of delirium and discomfort, the researchers said. Transfers also interrupt communication and continuity of care, burdening patients and making them more uncomfortable.

The study defined SNFists as healthcare professionals (physicians, nurse practitioners and physician assistants) who provided at least 80 percent of their patient visits in the nursing home setting. They noted this specialization gives SNFists deeper insight into the clinical conditions facing nursing home residents, which allows for better communication between the residents, their families and other staff members.

The study of 2,091,954 nursing home residents aged 65 and older, during a period from January 2012 to December 2019, found that SNFists managed about 46 percent of this group. The researchers determined that care from an SNFist decreased risk up to 6 percent for hospitalizations due to any reason including pneumonia, urinary tract infection, dehydration or sepsis.

The need for SNFists will only grow as the U.S. population ages and more people develop dementia—two-thirds of all deaths related to Alzheimer’s disease occur in nursing homes. Other professions may also need to step up. “We need more research comparing the quality of care from different nursing home clinicians including medical doctors, nurse practitioners and physician assistants, but we clearly see fewer MDs working in nursing homes while NPs and PAs are increasing,” said Dr. Hye-Young Jung, associate professor of Population Health Sciences at Weill Cornell Medicine.

The researchers suggest that medical schools and residency programs may need to offer more nursing home care experiences to increase the number of physicians in this field. They also emphasize the need for designating an official specialization, as with other areas of medicine like hospitalists, which would provide certification of the unique knowledge and skills needed in the nursing home setting.

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JOURNAL

JAMA Network Open

Opening new doors in the VR world, literally

TOHOKU UNIVERSITY

 

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REDIRECTEDDOORS+ IN ACTION.

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CREDIT: KAZUYUKI FUJITA ET AL

Room-scale virtual reality (VR) is one where users explore a VR environment by physically walking through it. The technology provides many benefits given its highly immersive experience. Yet the drawbacks are that it requires large physical spaces. It can also lack the haptic feedback when touching objects.

Take for example opening a door. Implementing this seemingly menial task in the virtual world means recreating the haptics of grasping a doorknob whilst simultaneously preventing users from walking into actual walls in their surrounding areas.

Now, a research group has developed a new system to overcome this problem: RedirectedDoors+.

The group was led by Kazuyuki Fujita, Kazuki Takashima, and Yoshifumi Kitamura from Tohoku University and Morten Fjeld from Chalmers University of Technology and the University of Bergen.

"Our system, which built upon an existing visuo-haptic door-opening redirection technique, allows participants to subtly manipulate the walking direction while opening doors in VR, guiding them away from real walls," points out Professor Fujita, who is based at Tohoku University's Research Institute of Electrical Communication (RIEC). "At the same time, our system reproduces the realistic haptics of touching a doorknob, enhancing the quality of the experience."

To provide users with that experience, RedirectedDoors+ employs a small number of 'door robots.' The robots have a doorknob-shaped attachment and can move in any direction, giving immediate touch feedback when the user interacts with the doorknob. In addition, the VR environment rotates in sync with the door movement, ensuring the user stays within the physical space limits.

A simulation study conducted to evaluate the performance of the system demonstrated the physical space size could be significantly reduced in six different VR environments. A validation study with 12 users walking with the system likewise demonstrated that this system works safely in real-world environments.

"RedirectDoors+ has redefined the boundaries of VR exploration, offering unprecedented freedom and realism in virtual environments," adds Fujita. "It has a wide range of applicability, such as in VR vocational training, architectural design, and urban planning."

Details of the research were reported in the journal IEEE Transactions on Visualization and Computer Graphics on March 11, 2024.

A system overview of RedirectedDoors+. 
 

CREDIT

Kazuyuki Fujita et al

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JOURNAL

IEEE Transactions on Visualization and Computer Graphics

DOI

10.1109/TVCG.2024.3372105 

ARTICLE TITLE

RedirectedDoors+: Door-Opening Redirection with Dynamic Haptics in Room-Scale VR

ARTICLE PUBLICATION DATE

11-Mar-2024

 

Zircons reveal the history of fluctuations in oxidation state of crustal magmatism and supercontinent cycle

SCIENCE CHINA PRESS

 

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ZIRCONS, A MINERAL NEARLY AS OLD AS EARTH ITSELF, IS A TIME KEEPER, AND ALSO PROVIDES A CHEMICAL WINDOW INTO MANY GEOLOGICAL PHENOMENA, SUCH AS OXIDATION STATE. BY DETERMINING THE OXIDATION LEVELS OF THE MAGMAS THAT FORMED THESE DETRITAL ZIRCONS, SCIENTISTS ARE ABLE TO DEDUCE THE ONSET OF CRUST TO MANTLE RECYCLING, WEATHERING, AND THE SUPERCONTINENT CYCLE.

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CREDIT: ©SCIENCE CHINA PRESS

This study is led by Dr. Rui Wang and his PhD student Shao-chen Wu (Institute of Earth Sciences, China University of Geosciences, Beijing), Dr. Roberto Weinberg and Dr. Peter Cawood (Monash University), and Dr. William Collins (Curtin University).

Zircons, a mineral nearly as old as Earth itself, crystalize when magmas (molten rocks) cool and can be found in trace quantities in magmatic rocks. The formation of magmas constitutes the mountains in the Earth. Through interactions with water and atmosphere, the mountains break down into sediments. Zircons are so durable and resistant to weathering and erosion that they rarely go away, and therefore this mineral in sediments (so call “detrital zircons”) holds the greatest insight into the history of the Earth. Zircon enriches with U (U-Pb dating) is a time keeper, and also provides a chemical window into many geological phenomena, such as oxidation state.

The team uses a new method of Loucks et al (2020) for determining the oxidation state of granitic magmas that uses ratios of Ce, U, and Ti in zircon to track oxidation state change of crustal magmas through Earth history. The calculation does not require ionic charge to be known, nor is determination of crystallization temperature, pressure, or parental melt composition required.

“Previous methods include Ce/Ce* and Eu/Eu* oxybarometers, but each has limitations related to temperature, pressure, host rock chemical compositional variations, or precision of REE elements needed to measure the Ce/Ce* and Eu/Eu* anomalies.” Bob Loucks from Western Australia says.  

This improved oxybarometer allows a more confident evaluation of the variation in oxidation state, which can now be interpreted in terms of global tectonic changes with time. By determining the oxidation levels of the magmas that formed these detrital zircons, scientists are able to deduce the onset of crust to mantle recycling, weathering, and the supercontinent cycle.

The key point is that rocks that lay at the Earth's surface can be carried back down to deep in the Earth's mantle (hundreds to thousands of km below the surface. Our data shows that not only has this happening today but could have been going on for billions of years. Looking at zircons from the early Earth, 3-billion-year-old zircons, to those formed today we have found that the redox state of the magmas in which they formed. The oxidation state (expressed as ΔFMQ) of the detrital zircons rise at ~3.5 billion years followed by a consistent average ΔFMQ > 0 over the last 3 billion years, suggesting recycling of oceanic lithosphere back into the mantle in what eventually became established as subduction zones. It shows that the lower limit of redox state dropped dramatically at 2.6 billion years ago, marking the formation of well-defined continents and the burial of oceanic rocks back into the deep mantle of the Earth. Further to that we found a cyclicity of the redox patterns: every 600 million years or so, continents come together to form supercontinents, like Gondwana, Rodinia, Nura, and Superia.

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JOURNAL

Science Bulletin

DOI

10.1016/j.scib.2023.10.034 

Zircon age histogram and redox variations with the supercontinent amalgamation intervals. 

Moving average of ΔFMQ of the igneous-derived and the sediment-derived zircon (proportion below than 10% is not shown) with the supercontinent amalgamation intervals. The more reduced magmas associated with sedimentary sources with a ca. 600 Ma cyclicity, became established at 2.6 billion years.

CREDIT

©Science China Press

Formation of a new subduction zone with hot or cold incipient channel

SCIENCE CHINA PRESS

 

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COMPARISONS OF DEFINITIONS, FAVORABLE CONDITIONS AND NATURAL CASES BETWEEN HOT AND COLD SUBDUCTION INITIATION

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CREDIT: ©SCIENCE CHINA PRESS

This study is led by Prof. Zhong-Hai Li (University of Chinese Academy of Sciences). The present solid Earth is actually active, with new plates generating in the mid-ocean ridges and some old plates sinking back into the interior through subduction zones. Subduction is thus a key process of the tectonics and geodynamics of the Earth. However, the formation mechanism of a new subduction zone, i.e. subduction initiation (SI), is widely debated. “Comparing to the long-term mature subduction, its initiation is more like an “instantaneous” process with limited geological records. Furthermore, these records experience erosion and modification by the later subduction. Consequently, the remnant geological records are rare, which plays as a major barrier for the better understanding of subduction initiation process.” Li says.

Geologists tried to decipher the SI process through analyzing the characteristic rock records. The most widely studied, characteristic magmatic record is the forearc rock sequence (forearc basalt – boninite – arc tholeiites) in the Izu-Bonin-Mariana (IBM) subduction zone. In addition, the SSZ-type (Supra-Subduction-Zone) ophiolites, e.g. in the Troodos (Cyprus) and Semail (Oman), have comparable petrological and geochemical characteristics with the IBM forearc sequence. Thus, it is further proposed that the SSZ-ophiolite could be generated during subduction initiation. Another type of geological record for SI is the metamorphic sole, which normally emplaces accompanying with the SSZ-ophiolite. All these magmatic and metamorphic records point to a high temperature and low pressure condition for SI. Then, “the question is whether the occurrence of all the subduction initiation in nature requires such a critical condition with rather high temperature at shallow depths.” Li says.

In the present-day ocean, there are several early-stage subduction zones with differential geological records, for example, the Puysegur subduction zone to the south of New Zealand. This SI process lacks the typical magmatic and metamorphic records. Instead, the geological records include the responses of structural deformation and sedimentary evolution. Similarly, there are a series of young oceanic subduction zones in the western Pacific, e.g. the Negro subduction zone in the Sulu Sea, the north Sulawesi and Cotabato subduction zones in the Celebes Sea. The thermal conditions in these incipient subduction channels should be colder, at least lower than the required temperature for the generation of ophiolite and metamorphic sole.

“It thus indicates that the extremely high temperature condition at shallow depths, for the generation of naturally observed ophiolite and metamorphic sole, only represents the high temperature end-member of subduction initiation, but cannot be used as the diagnostics for all the SI.” Li says and he further proposes two contrasting regimes for subduction initiation, i.e. the hot versus cold end-members, as shown in Figure 1. The hot SI regime is more “traditional”, with the geological records of magmatic and metamorphic rocks which have been regarded as the typical responses of SI and even as the diagnostics for deciphering paleo-SI cases in the orogens. In contrast, the cold SI regime lacks such kind of magmatic and metamorphic records, and thus attracts less attention in observational studies, but does occur for many subduction zones.

“Consequently, the SSZ-ophiolite and metamorphic sole are only the typical records of hot SI, but are not necessarily generated in the cold SI regime. Thus, we cannot use such specific rock records to judge the occurrence of SI or not; instead, multiple geological responses should be combined together to get a full view of this puzzling issue.” Li says.

 

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See the article:

Hot versus cold subduction initiation

https://doi.org/10.1093/nsr/nwae012

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JOURNAL

National Science Review

DOI

10.1093/nsr/nwae012 

 

Pre-Cryogenian stratigraphy, palaeontology, and paleogeography of the Tibetan Plateau and environs

SCIENCE CHINA PRESS

 

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IN THE FIGURE CAN BE SEEN THE POSSIBLE PALEOGEOGRAPHIC LOCATIONS OF THE TERRANES IN THE TIBETAN PLATEAU AND ENVIRONS. IND=INDIA; AU=AUSTRALIA; ANT=ANTARCTIC; KAL=KALAHARI; SF=SAN FRANCISCO; CON=CONGO; LAU=LAURENTIA; RIO=RIO DE LA PLATA; AMZ=AMAZONIA; BAL=BALTICA; W.AF=WEST AFRICA; SIB=SIBERIA; ANS=ARABIAN-NUBIAN SHIELD; SC=SOUTH CHINA; AFB=ALBANY-FRASER OROGEN; EGB=EASTERN GHATS OROGEN; KB-IB=KIBARAN AND IRUMIDE OROGENS; G=GREENVILLE OROGEN.

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CREDIT: ©SCIENCE CHINA PRESS

This study is led by Dr. Pei-yuan Hu and Qing-guo Zhai (Institute of Geology, Chinese Academy of Geological Sciences). In this study, the characteristics of pre-Cryogenian sedimentation, paleontology, magmatism, and metamorphism in the Tibetan Plateau and its surrounding areas are systematically summarized. Based on existing data, the records of pre-Cryogenian sedimentation and paleontology are mainly concentrated in the Meso-Neoproterozoic, with relatively few records from the Paleoproterozoic or earlier. The oldest geological record is the Hadean detrital zircons in the metamorphosed sedimentary rocks of the Himalaya and Qamdo areas (ca. 4.0 Ga). The Tibetan Plateau and surrounding areas preserve records related to the formation and evolution of the Kenor supercraton, and the Columbia, Rodinia, and Gondwana supercontinents. Pre-Cryogenian basements can be divided into three types: Tarim-, Yangtze-, and Lhasa-type.

The Tarim-type basement includes the southern Tarim terrane and the northern edge of the Indian continent, which are characterized by (1) magmatic-metamorphic records of the Columbian assembly and detrital zircon age peaks at ca. 2.0-1.8 Ga; (2) the absence of magmatic-metamorphic records and detrital zircon age peaks related to the Rodinia assembly (ca. 1.3-0.9 Ga); and, (3) the development of Cryogenian diamictite, prior to which no large-scale volcanic activity has been observed.

The Yangtze-type basement terranes include the western Yangtze terrane and the western Qinling-Qilian-Kunlun terrane, which are characterized by: (1) widespread development of Cryogenian diamictite, beneath which large-scale volcanic activity related to the global climate cooling can be observed; (2) magmatic-metamorphic records related to Rodinia assembly (ca. 1.1-1.0 Ga) and arc-related magmatism during ca. 1000-750 Ma; and, (3) abundant Meso-Neoproterozoic stromatolite and micropaleoflora fossils.

The Lhasa terrane is located at the core of the Tibetan Plateau and has distinct differences in its pre-Cryogenian basement compared to other terranes in the plateau and adjacent areas. These differences are mainly reflected in: (1) the development of early Neoproterozoic continental rift sedimentary records (ca. 900 Ma); and (2) the presence of a strong 1.2-1.1 Ga detrital zircon age peak in Precambrian to Paleozoic sedimentary strata, accompanied by contemporaneous magmatic-metamorphic records.

The above-mentioned results suggest that the pre-Cryogenian material in the Tibetan Plateau and its surrounding areas have played an important role in studying the formation and evolution of early supercontinents on Earth. Integrating previous studies with this contribution, the Tarim- and Yangtze-type basement terranes are interpreted as having a paleogeographic affinity with the northern margins of the Australian and Indian continents and the Lhasa-type basement possibly came from the African continent.

 

See the article:

Pre-Cryogenian stratigraphy, palaeontology, and paleogeography of the Tibetan Plateau and environs

https://doi.org/10.1007/s11430-022-1127-8

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JOURNAL

Science China Earth Sciences

DOI

10.1007/s11430-022-1127-8 

GOOD AI

Straightening teeth? AI can help

A new tool being developed by the University of Copenhagen and 3Shape will help orthodontists correctly fit braces onto teeth. Using artificial intelligence and virtual patients, the tool predicts how teeth will move, so as to ensure that braces are neither

UNIVERSITY OF COPENHAGEN - FACULTY OF SCIENCE

 

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A DIGITAL TWIN OF A PATIENT'S JAW CREATED THROUGH THE INTEGRATION OF AI SOLUTIONS AND COMPUTATIONAL MODELING, ENABLING PRECISE SIMULATION OF ANTICIPATED TEETH MOVEMENTS UNDER SPECIFIC CONDITIONS. THE COLOR MAP VISUALLY REPRESENTS THE EXTENT AND DIRECTION OF TEETH MOVEMENT, WITH WARMER COLORS INDICATING HIGHER TEETH MOVEMENTS.

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CREDIT: DEPARTMENT OF COMPUTER SCIENCE, UNIVERSITY OF COPENHAGEN.

A new tool being developed by the University of Copenhagen and 3Shape will help orthodontists correctly fit braces onto teeth. Using artificial intelligence and virtual patients, the tool predicts how teeth will move, so as to ensure that braces are neither too loose nor too tight. 

Many of us remember the feeling of having our braces regularly adjusted and retightened at the orthodontist’s office. And every year, about 30 percent of Danish youth up to the age of 15 wear braces to align crooked teeth. Orthodontists use the knowledge gained from their educations and experience to perform their jobs, but without the possibilities that a computer can provide for predicting final results.

A new tool, developed in a collaboration between the University of Copenhagen’s Department of Computer Science and the company 3Shape, makes it possible to simulate how braces should fit to give the best result without too many unnecessary inconveniences.

The tool has been developed with the help of scanned imagery of teeth and bone structures from human jaws, which artificial intelligence then uses to predict how sets of braces should be designed to best straighten a patient’s teeth.

"Our simulation is able to let an orthodontist know where braces should and shouldn’t exert pressure to straighten teeth. Currently, these interventions are based entirely upon the discretion of orthodontists and involve a great deal of trial and error. This can lead to many adjustments and visits to the orthodontist’s office, which our simulation can help reduce in the long run," says Professor Kenny Erleben, who heads IMAGE (Image Analysis, Computational Modelling and Geometry), a research section at UCPH’s Department of Computer Science.

Helps predict tooth movement

It's no wonder that it can be difficult to predict exactly how braces will move teeth, because teeth continue shifting slightly throughout a person’s life.  And, these movements are very different from mouth to mouth.

"The fact that tooth movements vary from one patient to another makes it even more challenging to accurately predict how teeth will move for different people. Which is why we’ve developed a new tool and a dataset of different models to help overcome these challenges," explains Torkan Gholamalizadeh, from 3Shape and a PhD from the Department of Computer Science.

As an alternative to the classic bracket and braces, a new generation of clear braces, known as aligners, has gained ground. Aligners are designed as a transparent plastic cast of the teeth that patients fit over their teeth.

Patients must wear aligners for at least 22 hours a day and they need to be swapped for new and tighter sets every two weeks. Because aligners are made of plastic, a person’s teeth also change the contours of the aligner itself, something that the new tool also takes into account.

"As transparent aligners are softer than metal braces, calculating how much force it takes to move the teeth becomes even more complicated. But it’s a factor that we’ve taught our model to take into account, so that one can predict tooth movements when using aligners as well," says Torkan Gholamalizadeh.

Digital twins can improve treatment 

Researchers created a computer model that creates accurate 3D simulations of an individual patient's jaw, and which dentists and technicians can use to plan the best possible treatment.

To create these simulations, researchers mapped sets of human teeth using detailed CT scans of teeth and of the small, fine structures between the jawbone and the teeth known as peridontal ligaments – a kind of fiber-rich connective tissue that holds teeth firmly in the jaw.

This type of precise digital imitation is referred to as a digital twin – and in this context, the researchers built up a database of 'digital dental patients'.

But they didn’t stop there. The researchers' database also contains other digital patient types that could one day be of use elsewhere in the healthcare sector:

"Right now, we have a database of digital patients that, besides simulating aligner designs, can be used for hip implants, among other things. In the long run, this could make life easier for patients and save resources for society," says Kenny Erleben.

The area of research that makes use of digital twins is relatively new and, for the time being, Professor Erleben's database of virtual patients is a world leader. However, the database will need to get even bigger if digital twins are to really take root and have benefit the healthcare sector and society.

"More data will allow us to simulate treatments and adapt medical devices so as to more precisely target patients across entire populations," says Professor Erleben.

Furthermore, the tool must clear various regulatory hurdles before it is rolled out for orthodontists. This is something that the researchers hope to see in the foreseeable future.

Box: Digital twins

A digital twin is a virtual model that lives in the cloud, and is designed to accurately mirror a human being, physical object, system, or real-world process.

"The virtual model can answer what's happening in the real world, and do so instantly. For example, one can ask what would happen if you pushed on one tooth and get answers with regards to where it would move and how it would affect other teeth. This can be done quickly, so that you know what's happening. Today, weeks must pass before finding out whether a desired effect has been achieved," says Professor Kenny Erleben.

Digital twins can be used to plan, design and optimize – and can therefore be used to operate companies, robots, factories and used much more in the energy, healthcare and other sectors.

One of the goals of working with digital twins at the Department of Computer Science is to be able to create simulations of populations, for example, in the healthcare sector. If working with a medical product, virtual people must be exposed to and tested for their reactions in various situations. A simulation provides a picture of what would happen to an individual – and finally, to an entire population.

Box: About the study

In their study, the researchers developed a simulation tool using CT scans of teeth, which can predict how a dental brace should best be designed and attached.

The research is described in the studies: “Deep-learning-based segmentation of individual tooth and bone with periodontal ligament interface details for simulation purposes” and “Open-Full-Jaw: An open-access dataset and pipeline for finite element models of human jaw”.

The research is part of the EU research project Rainbow, which conducts research into computer-simulated medicine across seven European universities in collaboration with government agencies and industry.

The research was conducted in collaboration with the company 3Shape, which manufactures intraoral scanners and provides medical software for digital dentistry purposes.

 

JOURNAL

IEEE Access

DOI

10.1109/ACCESS.2023.3317512 

ARTICLE TITLE

Deep-Learning-Based Segmentation of Individual Tooth and Bone With Periodontal Ligament Interface Details for Simulation Purposes