Computers Math

A new “image analysis pipeline” is giving scientists rapid new insight into how disease or injury have changed the body, down to the individual cell.
It’s called TDAExplore, which takes the detailed imaging provided by microscopy, pairs it with a hot area of mathematics called topology, which provides insight on how things are arranged, and the analytical power of artificial intelligence to give, for example, a new perspective on changes in a cell resulting from ALS and where in the cell they happen, says Dr. Eric Vitriol, cell biologist and neuroscientist at the Medical College of Georgia.
It is an “accessible, powerful option” for using a personal computer to generate quantitative — measurable and consequently objective — information from microscopic images that likely could be applied as well to other standard imaging techniques like X-rays and PET scans, they report in the journal Patterns.
“We think this is exciting progress into using computers to give us new information about how image sets are different from each other,” Vitriol says. “What are the actual biological changes that are happening, including ones that I might not be able to see, because they are too minute, or because I have some kind of bias about where I should be looking.”
At least in the analyzing data department, computers have our brains beat, the neuroscientist says, not just in their objectivity but in the amount of data they can assess. Computer vision, which enables computers to pull information from digital images, is a type of machine learning that has been around for decades, so he and his colleague and fellow corresponding author Dr. Peter Bubenik, a mathematician at the University of Florida and an expert on topological data analysis, decided to partner the detail of microscopy with the science of topology and the analytical might of AI. Topology and Bubenik were key, Vitriol says.
Topology is “perfect” for image analysis because images consist of patterns, of objects arranged in space, he says, and topological data analysis (the TDA in TDAExplore) helps the computer also recognize the lay of the land, in this case where actin — a protein and essential building block of the fibers, or filaments, that help give cells shape and movement — has moved or changed density. It’s an efficient system, that instead of taking literally hundreds of images to train the computer how to recognize and classify them, it can learn on 20 to 25 images. More

The ancient arts of origami, the art of paper-folding, and kirigami, the art of paper-cutting, have gained popularity in recent years among researchers building mechanical metamaterials. Folding and cutting 2D thin-film materials transforms them into complex 3D structures and shapes with unique and programmable mechanical properties.
In Applied Physics Reviews, by AIP Publishing, researchers in the United States and China categorize origami- and kirigami-based mechanical metamaterials, artificially engineered materials with unusual mechanical properties, into six groups based on two different criteria.
“Origami and kirigami are, by nature, mechanical metamaterials, because their properties are mainly determined by how the crease patterns and/or cuts are made and just slightly depend on the material that folds the origami or kiragami,” said author Hanqing Jiang.
The researchers divided the mechanical metamaterials into three categories that include origami-based metamaterials (folding only), kirigami-based metamaterials (cutting only), and hybrid origami-kirigami metamaterials (both folding and cutting). The hybrid origami-kirigami metamaterials, in particular, offer great potential in shape morphing.
Each group was subdivided into a rigid or deformable category based on the elastic energy landscape. Metamaterials were classified as rigid if energy was stored in the creases or linkages only. Metamaterials were put in the deformable category if energy was stored in both creases or linkages and panels.
The researchers want to discover new origami and kirigami designs, especially curved origami designs, hybrid origami-kirigami designs, modular designs, and hierarchical designs.
They plan to focus on the selection of new materials for origami- and kirigami-based mechanical metamaterials. Traditionally paper is used to prototype metamaterials but there are limits based on the fragility and plasticity of paper. To design for real-world applications, it will be helpful to explore materials with different properties such as thin or thick, soft or hard, and elastic or plastic.
They want to use the energy landscape and energy distribution as two powerful tools to analyze mechanical performances of origami and kirigami and will seek to carefully design the actuation method of origami- and kirigami-based mechanical metamaterials.
“Origami- and kiragami-based mechanical metamaterials can be applied in many fields, including flexible electronics, medical devices, robotics, civil engineering and aerospace engineering,” said Jiang.
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Materials provided by American Institute of Physics. Note: Content may be edited for style and length. More

Mathematicians have analysed global COVID-19 data to identify two constants which can drastically change a country’s rate of infection.
An international team of researchers led by Professor Alexander Gorban from the University of Leicester used available data from 13 countries to determine the rate of stress response, or ‘mobilisation’ and the rate of spontaneous exhaustion, or ‘demobilisation’.
Their findings, published in Scientific Reports, show that social stress — which varied broadly across the countries studied — drives the multi-wave dynamics of COVID-19 outbreaks.
The study analysed data from China, the USA, UK, Germany, Colombia, Italy, Spain, Israel, Russia, France, Brazil, India, and Iran — and contributed to the research team’s proposed new system of models, which combine the dynamics of the established concept of social stress with classical epidemic models.
Alexander Gorban is a Professor of Applied Mathematics at the University of Leicester, and Director of the Centre for Artificial Intelligence, Data Analysis and Modelling. Professor Gorban said:
“We tried to use the pandemic for research and quantify the social and cultural differences between countries. We measured how variable countries are in two processes: mobilisation of people for rational protective behaviour and exhaustion of this mobilisation with destroying of rational behaviour. More

Science has the technology to measure the activity of every gene within a single individual cell, and just one experiment can generate thousands of cells worth of data. Researchers at Lund University in Sweden have now revolutionised the way this data is analysed — by using 3D video gaming technology. The study is published in the journal iScience.
Advanced techniques in DNA and RNA sequencing have opened up the possibility of studying individual cells in tissue in a more comprehensive way than was previously possible. The big challenge with these sequencing techniques is that they lead to large amounts of data.
“When you want to distinguish cancer cells from normal cells, for example, you need to examine thousands of cells to get a proper understanding, which translates into enormous amounts of numerical data,” says Shamit Soneji, researcher in computational biology at Lund University.
To make this data comprehensible, each cell is mathematically positioned in three-dimensional space to form a “roadmap” of the cells, and how they relate to each other. However, these maps can be difficult to navigate using a regular desktop computer.
“To be able to walk around your own data and manipulate it intuitively and efficiently gives it a whole new understanding. I would actually go so far as to say that one thinks differently in VR, thanks to the technique’s ability to involve your body in the analysis process,” explains Mattias Wallergård. researcher in interaction design and virtual reality at Lund University.
The Lund University team have developed the software CellexalVR; a virtual reality environment that enables researchers to use intuitive tools to explore all their data in one place. 3D maps of cells that have been calculated from gene activity and other information captured from individual cells can be displayed, and the researcher can clearly see which genes are active when certain cell types are formed.
Using a VR headset, the user has a complete universe of cell populations in front of them, and can more accurately determine how cells relate to one another. Using two hand controllers, they can select cells of interest for further analysis with simple hand gestures as if they were physical objects.
Since space is not an issue, it is possible to have several cellular maps in the same “room” and compare them side by side, something that is difficult on a traditional computer screen. Researchers can also meet in this VR world to analyze data together, despite being in different places geographically.
“Even if you are not familiar with computer programming, this type of analysis is open to everyone. A virtual world is a fast developing area of research that has enormous potential for scientists that need to access and process big-data in a more interactive and collaborative way,” concludes Shamit Soneji.
The software can be downloaded for free at https://www.cellexalvr.med.lu.se/
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Materials provided by Lund University. Note: Content may be edited for style and length. More

The perception that boys are more interested than girls in computer science and engineering starts as young as age six, according to a new study published in Proceedings of the National Academy of Sciences. That may be one reason why girls and women are underrepresented in these STEM career fields, reports study co-author Allison Master, assistant professor at the University of Houston College of Education.
“Gender-interest stereotypes that say ‘STEM is for boys’ begin in grade school, and by the time they reach high school, many girls have made their decision not to pursue degrees in computer science and engineering because they feel they don’t belong,” said Master.
Researchers at UH and the University of Washington surveyed nearly 2,500 students in firstthrough12th grade from diverse racial and socioeconomic backgrounds. The results of those studies were combined with laboratory experiments to provide important insights into how stereotypes impact children’s motivation.
More children believed girls had less interest than boys in key STEM fields. Specifically, 63% of the students believed girls were less interested in engineering than boys were, while 9% believed girls were more interested in the subject. Regarding computer science, 51% thought girls had less interest while 14% thought girls had more interest than boys.
These interest patterns play out in the job market. According to United States Census Bureau statistics, while women make up nearly half of the workforce, they account for only 25% of computer scientists and 15% of engineers.
Researchers say educators, parents and policymakers can help close these gender gaps by introducing girls to high quality computer science and engineering activities in elementary school before stereotype endorsements take root. They also suggest educators who wish to promote girls’ interest and engagement in STEM should consider using inclusive programs designed to encourage girls’ sense of belonging in STEM.
The laboratory experiments gave children a choice between computer science activities. Fewer girls (only 35%) chose a computer science activity they believed boys were more interested in, compared to the 65% of girls who chose an activity for which they believed boys and girls were equally interested.
“It’s time for all stakeholders to be united in sending the message that girls can enjoy STEM just as much as boys do, which will help draw them into STEM activities,” added Master, who directs UH’s Identity and Academic Motivation (I AM) Lab.
Co-authors on the study are Andrew N. Meltzoff of the University of Washington, Seattle’s Institute for Learning & Brain Sciences; and Sapna Cheryan, University of Washington, Seattle’s Department of Psychology.
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Materials provided by University of Houston. Original written by Sara Tubbs. Note: Content may be edited for style and length. More

Every day, cytologists around the world use optical microscopes to analyze and classify samples of bone marrow cells thousands of times. This method to diagnose blood diseases was established more than 150 years ago, but it suffers from being very complex. Looking for rare but diagnostically important cells is both a laborious and time-consuming task. Artificial intelligence has the potential to boost this method — however it needs a large amount of high-quality data to train an AI algorithm.
Largest open-source database for bone marrow cell images
The Helmholtz Munich researchers developed the largest open access database on microscopic images of bone marrow cells to date. The database consists of more than 170,000 single-cell images from over 900 patients with various blood diseases. It is the result of a collaboration from Helmholtz Munich with the LMU University Hospital Munich, the MLL Munich Leukemia Lab (one of the largest diagnostic providers in this field worldwide) and Fraunhofer Institute for Integrated Circuits.
Using the database to boost artificial intelligence
“On top of our database, we have developed a neural network that outperforms previous machine learning algorithms for cell classification in terms of accuracy, but also in terms of generalizability,” says Christian Matek, lead author of the new study. The deep neural network is a machine learning concept specifically designed to process images. “The analysis of bone marrow cells has not yet been performed with such advanced neural networks,” Christian Matek explains, “which is also due to the fact that high-quality, public datasets have not been available until now.”
The researchers aim to further expand their bone marrow cell database to capture a broader range of findings and to prospectively validate their model. “The database and the model are freely available for research and training purposes — to educate professionals or as a reference for further AI-based approaches e.g. in blood cancer diagnostics,” says study leader Carsten Marr.
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Materials provided by Helmholtz Zentrum München – German Research Center for Environmental Health. Note: Content may be edited for style and length. More

A research team at the University of Washington has developed a wearable device to detect and reverse an opioid overdose. The device, worn on the stomach like an insulin pump, senses when a person stops breathing and moving, and injects naloxone, a lifesaving antidote that can restore respiration.
The results demonstrate the proof-of-concept of a wearable naloxone injector system, according to the paper published Nov. 22 in Scientific Reports.
“The opioid epidemic has become worse during the pandemic and has continued to be a major public health crisis,” said lead author Justin Chan, a UW doctoral student in the Paul G. Allen School of Computer Science & Engineering. “We have created algorithms that run on a wearable injector to detect when the wearer stops breathing and automatically inject naloxone.”
Co-author Jacob Sunshine, an associate professor of anesthesiology and pain medicine at the UW School of Medicine, said one of the unique aspects of opioid overdoses is that naloxone, a benign drug, is highly effective and can save lives if it can be administered in a timely fashion.
The UW team is looking to make these devices widely available, which would first require approval by the U.S. Food and Drug Administration. The FDA is currently working to accelerate efforts to address this critical public health problem and has recently published special guidance on emergency-use injectors.
In a multiyear collaboration, the UW investigators worked on the prototype with West Pharmaceutical Services of Exton, Penn, which developed a wearable subcutaneous injector that safely administers medications. More

A team of University of Arizona researchers has developed an ultra-thin wireless device that grows to the surface of bone and could someday help physicians monitor bone health and healing over long periods. The devices, called osseosurface electronics, are described in a paper published Thursday in Nature Communications.
“As a surgeon, I am most excited about using measurements collected with osseosurface electronics to someday provide my patients with individualized orthopedic care — with the goal of accelerating rehabilitation and maximizing function after traumatic injuries,” said study co-senior author Dr. David Margolis, an assistant professor of orthopedic surgery in the UArizona College of Medicine — Tucson and orthopedic surgeon at Banner — University Medical Center Tucson.
Fragility fractures associated with conditions like osteoporosis account for more days spent in the hospital than heart attacks, breast cancer or prostate cancer. Although not yet tested or approved for use in humans, the wireless bone devices could one day be used not only to monitor health, but to improve it, said study co-senior author Philipp Gutruf, an assistant professor of biomedical engineering and Craig M. Berge faculty fellow in the College of Engineering.
“Being able to monitor the health of the musculoskeletal system is super important,” said Gutruf, who is also a member of the university’s BIO5 Institute. “With this interface, you basically have a computer on the bone. This technology platform allows us to create investigative tools for scientists to discover how the musculoskeletal system works and to use the information gathered to benefit recovery and therapy.”
Because muscles are so close to bones and move so frequently, it is important that the device be thin enough to avoid irritating surrounding tissue or becoming dislodged, Gutruf explained.
“The device’s thin structure, roughly as thick as a sheet of paper, means it can conform to the curvature of the bone, forming a tight interface,” said Alex Burton, a doctoral student in biomedical engineering and co-first author of the study. “They also do not need a battery. This is possible using a power casting and communication method called near-field communication, or NFC, which is also used in smartphones for contactless pay.”
Ceramic Adhesive Grows to Bone
The outer layers of bones shed and renew just like the outer layers of skin. So, if a traditional adhesive was used to attach something to the bone, it would fall off after just a few months. To address this challenge, study co-author and BIO5 Institute member John Szivek — a professor of orthopedic surgery and biomedical engineering — developed an adhesive that contains calcium particles with an atomic structure similar to bone cells, which is used as to secure osseosurface electronics to the bone.
“The bone basically thinks the device is part of it, and grows to the sensor itself,” Gutruf said. “This allows it to form a permanent bond to the bone and take measurements over long periods of time.”
For instance, a doctor could attach the device to a broken or fractured bone to monitor the healing process. This could be particularly helpful in patients with conditions such as osteoporosis, since they frequently suffer refractures. Knowing how quickly and how well the bone is healing could also inform clinical treatment decisions, such as when to remove temporary hardware like plates, rods or screws.
Some patients are prescribed drugs designed to speed up bone healing or improve bone density, but these prescriptions can have side effects. Close bone monitoring would allow physicians to make more informed decisions about drug dosage levels.
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Materials provided by University of Arizona College of Engineering. Original written by Emily Dieckman. Note: Content may be edited for style and length. More