Revive the map: 4D Building Reconstruction with Machine Learning (Engineering)

Research team from Skoltech and FBK (Italy) presented a methodology to derive 4D building models using historical maps and machine learning. The implemented method relies on geometric, neighbourhood, and categorical attributes in order to predict building heights. The method is useful for understanding urban phenomena and changes that contributed to defining our cities’ actual shape.  The results were published in the MDPI Applied Sciences journal.

Historical maps are the most powerful source used to analyze changes in urban development. Nevertheless, maps represent the 3D world in the 2D space which describes the main features of the urban environment but fails to incorporate other spatial information, such as building heights. In 3D/4D city modelling applications based on historical data, the lack of building heights is a major obstacle for accurate space representation, analysis, visualization or simulations.

Scientists from Skoltech and 3DOM research unit of FBK Trento explored machine learning solutions for inferring building heights from historical maps.

Their method tested on four historical maps of Trento (years 1851, 1887, 1908, and 1936) and Bologna (years 1884 and 1945) reflecting the biggest  changes in the urban structures over the last centuries helped to reconstruct multi-temporal (4D) versions of these cities.

“The implemented learning and predictive procedure tested on historical data has proved to be effective and promising for many other applications. Based on few attributes for the prediction, it will soon be expanded to diverse real-life contexts with missing elevation data. The resulting  models will be a great help in bridging the geospatial knowledge gap in past or remote situations” Emre Ozdemir, a Skoltech and FBK Trento PhD student, explains.

Images credit: The Revive maps © Farella E.M, et al./ MDPI Applied Sciences


Reference: Farella, Elisa M.; Özdemir, Emre; Remondino, Fabio. 2021. “4D Building Reconstruction with Machine Learning and Historical Maps” Appl. Sci. 11, no. 4: 1445. https://www.mdpi.com/2076-3417/11/4/1445/htm https://doi.org/10.3390/app11041445


Provided by Skoltech

Scientists Describe Earliest Primate Fossils (Paleontology)

A new study published Feb. 24 in the journal Royal Society Open Science documents the earliest-known fossil evidence of primates.

A team of 10 researchers from across the U.S. analyzed several fossils of Purgatorius, the oldest genus in a group of the earliest-known primates called plesiadapiforms. These ancient mammals were small-bodied and ate specialized diets of insects and fruits that varied by species. These newly described specimens are central to understanding primate ancestry and paint a picture of how life on land recovered after the Cretaceous-Paleogene extinction event 66 million years ago that wiped out all dinosaurs — except for birds — and led to the rise of mammals.

Gregory Wilson Mantilla, a University of Washington professor of biology and curator of vertebrate paleontology at the UW’s Burke Museum of Natural History & Culture, co-led the study with Stephen Chester of Brooklyn College and the City University of New York. The team analyzed fossilized teeth found in the Hell Creek area of northeastern Montana. The fossils, which are now part of the collections at the University of California Museum of Paleontology, are estimated to be 65.9 million years old, about 105,000 to 139,000 years after the mass extinction event. Based on the age of the fossils, the team estimates that the ancestor of all primates —including plesiadapiforms and today’s primates such as lemurs, monkeys and apes — likely emerged by the Late Cretaceous and lived alongside large dinosaurs.

“It’s mind blowing to think of our earliest archaic primate ancestors,” said Wilson Mantilla. “They were some of the first mammals to diversify in this new post-mass extinction world, taking advantage of the fruits and insects up in the forest canopy.”

The fossils include two species of PurgatoriusPurgatorius janisae and a new species described by the team named Purgatorius mckeeveri. Three of the teeth found have distinct features compared to any previously known Purgatorius species and led to the description of the new species.

High resolution CT scans of an assortment of fossilized teeth and jaw bones of Purgatorius.Gregory Wilson Mantilla/Stephen Chester

Purgatorius mckeeveri is named after Frank McKeever, who was among the first residents of the area where the fossils were discovered, and also the family of John and Cathy McKeever, who have since supported the field work where the oldest specimen of this new species was discovered.

“This was a really cool study to be a part of, particularly because it provides further evidence that the earliest primates originated before the extinction of non-avian dinosaurs,” said co-author Brody Hovatter, a UW graduate student in Earth and space sciences. “They became highly abundant within a million years after that extinction.”

“This discovery is exciting because it represents the oldest dated occurrence of archaic primates in the fossil record,” said Chester. “It adds to our understanding of how the earliest primates separated themselves from their competitors following the demise of the dinosaurs.”

Co-author on the study was the late William Clemens who was a professor emeritus at the University of California, Berkeley and former director of the UC Museum of Paleontology. Additional co-authors are Jason Moore and Wade Mans of the University of New Mexico; Courtney Sprain of the University of Florida; William Mitchell of Minnesota IT Services; Roland Mundil of the Berkeley Geochronology Center; and Paul Renne of UC Berkeley and the Berkeley Geochronology Center. The research was funded by the National Science Foundation, the UC Museum of Paleontology, the Myhrvold and Havranek Charitable Family Fund, the UW, the CUNY and the Leakey Foundation.

Featured image: Shortly after the extinction of the dinosaurs, the earliest known archaic primates, such as the newly described species Purgatorius mckeeveri shown in the foreground, quickly set themselves apart from their competition — like the archaic ungulate mammal on the forest floor — by specializing in an omnivorous diet including fruit found up in the trees. © Andrey Atuchin


Reference: Gregory P. Wilson Mantilla, Stephen G. B. Chester, “Earliest Palaeocene purgatoriids and the initial radiation of stem primates”, ROYAL Society Publishing B, 2021. https://royalsocietypublishing.org/doi/10.1098/rsos.210050


Provided by University of Washington

New Technique Shows Promise in Preventing Recurrent Stroke (Medicine)

Research From Cedars-Sinai Leads to Planning for a Multicenter National Study

A surgical procedure advanced and studied by vascular neurosurgeons at Cedars-Sinai dramatically reduced the rate of recurrent strokes among patients with atherosclerotic disease, a new study shows.

Atherosclerotic disease, also known as hardening of the arteries, is a buildup of plaque that narrows the arteries leading to the brain. The condition is known to increase patients’ risk of having a series of strokes.

Exciting new results from a Phase II clinical trial conducted at Cedars-Sinai demonstrated that a new procedure reduced recurrent stroke rates from 37% to 10.7%. Encephaloduroarteriosynangiosis, or EDAS for short, is a new procedure that was used and recently published in the journal Neurosurgery.

“The EDAS procedure is unique in that it involves rerouting arteries from the scalp and membranes that cover the brain, to segments of the brain at risk of stroke,” said Nestor Gonzalez, MD, director of the Cedars-Sinai Neurovascular Laboratory. “Similar to gardening, over time, new blood vessels form and create a fresh path for blood oxygen to reach the brain.”

This gardening-like surgical technique differs from current, conventional approaches to reduce recurrent stroke, which include intensive medical management and various procedures, ranging from angioplasty and stenting to direct bypass surgery.

“Your brain needs a steady supply of oxygen-rich blood in order to function properly,” said Keith Black, MD, professor and chair of the Department of Neurosurgery. “This work is an important step in increasing the vital vessels in the brain and ensuring that patients with this complex condition have an innovative and minimally invasive option for care.”

The Neurovascular Center and Department of Neurosurgery at Cedars-Sinai provide personalized care for aneurysms, strokes and other neurovascular problems, using state-of-the-art imaging technology, a dedicated intensive care unit, advanced therapies and new surgical techniques.

As a next step, Gonzalez and his team are working with the National Institutes of Health—a funder of this work—to launch a large, multicenter Phase III clinical trial at medical centers across the nation. These sites will allow willing patients with atherosclerotic disease to participate in clinical research.

“Clinical research is a critical component and a necessary step to advance the science and treatments available to patients with this unique yet common condition,” said Gonzalez. “As the trial expands from Los Angeles to other parts of the country, I hope patients consider participating in the study of this promising technique.”

Funding: This research was supported by the National Institute of Neurological Disorders and Stroke of the NIH under award no. K23NS079477. The content is solely the responsibility of the authors.

Featured image: Nestor Gonzalez, MD © Cedars Sinai


Reference: Miguel D Quintero-Consuegra, MD, Juan F Toscano, BA, Robin Babadjouni, MD, Peyton Nisson, MD, Mohammad N Kayyali, MD, Daniel Chang, MD, Eyad Almallouhi, MD, Jeffrey L Saver, MD, Nestor R Gonzalez, MD, Encephaloduroarteriosynangiosis Averts Stroke in Atherosclerotic Patients With Border-Zone Infarct: Post Hoc Analysis From a Performance Criterion Phase II Trial, Neurosurgery, 2021;, nyaa563, https://doi.org/10.1093/neuros/nyaa563


Provided by Cedars Sinai

A Gene Provides Both Protection and Destruction (Biology)

Researchers at Freiburg University discover new function of the widely disseminated, yet little understood ENDOU enzyme.

The family of ENDOU enzymes is found in most organisms, yet its functions are only poorly understood. In humans, it has been connected with cancer. RNA viruses, such as SARS-CoV2, contain a gene corresponding to ENDOU, and this is important for virus replication and the suppression of the immune response. However, so far only few details of the role of these enzymes are known. The research group led by the molecular geneticist Dr. Wenjing Qi from the University of Freiburg now contributes some more details to its function in a study published by the renowned scientific journal Nature Communications. They suggest that the gene ENDU-2 could be responsible for triggering tumors in the body from a distance. In addition, the team discovered a novel, seemingly contradictive response: Under stress, ENDU-2 can contribute both to the protection of the organism and to its destruction.

The researchers studied the nematode worm C. elegans, which is frequently used for such genetic investigations. More than 60 percent of the genes are similar in worms and humans, including one for ENDOU, which is called ENDU-2. The current theory of tumor development suggests that cells only become cancer cells when errors, called mutations, accumulate in their genes. These arise, for example, from radiation, certain chemicals, or during aging. Qi showed back in 2017 that such errors do not have to occur in the cancer cells themselves, but they can also arise elsewhere in the body. Cancer is therefore triggered remotely, so to speak. The researcher suspected that the damaged cells in this case send signals to accomplish this, which then reprogram the other tissues. They now discovered the signal for this: ENDU-2.

“ENDOU/ENDU-2 is not only selectively discharged from stressed cells and circulated throughout the body, but it can also bind to the messenger RNA (mRNA) of many genes at the site of origin and in the target cells”, Qi explains. These mRNAs are the working copies of genes and are needed as blueprints for the production of all proteins and enzymes. What surprised the researcher was that ENDU-2 can perform two different functions under stress: at the site of origin, it cuts and destroys the mRNA, which reduces metabolism and prevents the already stressed organism from making faulty new proteins. At the destination, the RNA remains intact, and ENDU-2 helps these cells to survive. For this, however, it must be dosed precisely; otherwise it can cause tumor formation.

One conclusion that can be drawn from this could be that the worm specifically protects the embryos, i.e. its offspring, in times of great stress. “In this way, it seems guaranteed that whenever the organism’s self-healing powers are not sufficient for mother and child, it at least ensures the survival of the progeny”, speculates Prof. Dr. Ralf Baumeister, who was also involved in the study and in whose department Qi leads a research group. The Freiburg scientists now know that the loss of ENDU-2 can also reprogram stem cells. These then lose their immortality within a few generations. Next, the team wants to explore which conditions cause ENDU-2 to distinguish between destruction and protection.

The German Research Foundation is funding the Freiburg scientists’ study. In addition, they are cooperating with BIOSS – Centre for Biological Signalling Studies and the Excellence Cluster CIBSS – Centre for Integrative Biological Signalling Studies at the University of Freiburg.

Featured image: The nematode C. elegans, which is only 1 millimeter in size, is remarkably similar to humans from a genetic standpoint. Scientists can use the worm to study human diseases, life expectancy and even addictive behavior. © Ralf Baumeister/University of Freiburg


Original Publication:

Qi, W., von Gromoff, E.D., Xu, F., Zhao, Q, Yang, W., Pfeifer, W., Maier, W., Long, L., and Baumeister, R. (2021) The secreted endoribonuclease ENDU-2 from the soma protects germline immortality in C. elegans. Nature Communications, DOI: 10.1038/s41467-021-21516-6


Provided by University of Freiburg

Research Shows How Single Celled Algae Rotate as They Swim Towards the Light (Maths)

Scientists have made a pivotal breakthrough in the quest to understand how single-cell green algae are able to keep track of the light as they swim.

A team of researchers from the University of Exeter’s flagship Living Systems Institute has discovered how the model alga Chlamydomonas is seemingly able to scan the environment by constantly spinning around its own body axis in a corkscrewing movement. This helps it respond to light, which it needs for photosynthesis.

The tiny alga, which is found abundantly in fresh-water ponds across the world, swims by beating its two flagella, hair-like structures that adopt a whip-like movement to move the cell. These flagella beat in much the same way as the cilia in the human respiratory system.

Chlamydomonas cells are able to sense light through a red eye spot and can react to it, known as phototaxis. The cell rotates steadily as it propels itself forwards using a sort of breaststroke, at a rate of about once or twice a second, so that its single eye can scan the local environment.

However, the intricate mechanism that allows the alga to achieve this helical swimming has been previously unclear.

IN the new study, the researchers first performed experiments which revealed that the two flagella in fact beat in planes that are slightly skewed away from each other.

Then, creating a sophisticated computer model of Chlamydomonas, they were able to simulate the flagella movement and reproduce the observed swimming behaviour.

The researchers discovered that the flagella were able to move the Chlamydomonas in a clockwise fashion with each power stroke, and then anticlockwise on the reverse stroke – akin to how a swimmer rocks back and forth when switching from one arm to another. Except here the cell feels no inertia.

Furthermore, they also deduced how simply by exerting slightly different forces on the two flagella, the alga can even steer, rather than just move in a straight line.

The researchers were able to show that by adding in an additional influence, such as light, the alga can navigate left or right by knowing which flagellum to stroke harder than the other.

Dr Kirsty Wan, who led the study said: “The question of how a cell makes these types of precise decisions can be a matter of life or death. It’s quite a remarkable feat of both physics and biology, that a single cell with no nervous system to speak of is able to do this…It’s an age-old mystery that my group is currently working hard to solve.”

For the study, the researchers were able to test various scenarios to determine which variables were influencing the trajectory. Their study showed that by varying different parameters, such as if one flagella is slightly stronger than another, the tilt plane of the flagella or its beat pattern, the algae can manipulate its own movement.

Team member Dr Dario Cortese added: “The agreement of our model with the experiments is surprising really, that we could effectively capture the complex 3D beat of the flagella with a very simple movement of a bead going around in circles.”

The study entitled “Control of Helical Navigation by Three-Dimensional Flagellar Beating” is published in the journal Physical Review Letters on Wednesday, February 24th 2021.

Featured image: The non-planar beat pattern of Chlamydomonas flagella (see SM Video 1). (a) Cells are aspirated onto pipettes and imaged from the anterior pole (AP). An eyespot is located ~ 45° from the mean beat plane. (b) Basal bodies have a pre-defined symmetry with respect to axonemal microtubule doublets, numbered 1 → 9. Dyneins are separated into two groups, those on doublets operate 2, 3, 4 for the power (p) stroke, but 6, 7, 8 for the recovery (r) stroke. (c) Wave-forms are tracked by optic flow (arrows show direction of tip rotation), showing the relative offset between the basal bodies and the tilted beat planes. The beat plane (defined by α) rotates periodically (d). Waveforms are ordered by phase and averaged over ~ 1000 consecutive cycles to show the phase-dependence of the non-planar beat pattern (e).


Provided by University of Exeter

Discovery Offers Potential For Stripping Tumors of T Cell Protection (Medicine)

St. Jude Children’s Research Hospital has discovered a mechanism that tumors use to switch on protective regulatory T cells, raising the potential for drug treatments that render tumors more vulnerable to cancer immunotherapy.

Immunologists at St. Jude Children’s Research Hospital have discovered that tumors use a unique mechanism to switch on regulatory T cells to protect themselves from attack by the immune system. Surprisingly, the mechanism does not affect regulatory T cell function outside the tumor and may therefore limit the immune-associated toxicities of targeting regulatory T cells.

The finding offers the promise of drug treatment to selectively shut down regulatory T cells in a tumor, rendering the tumor vulnerable to cancer immunotherapies that activate the immune system to kill the tumor. The researchers showed that blocking tumor-associated regulatory T cell activity eliminated tumors cells in mice and sensitized the cells to cancer immunotherapy called anti-PD-1 therapy.

The research appeared today in the journal Nature.

A tumor-controlled metabolic pathway to ward off the immune system

Regulatory T cells keep the immune system in check, preventing it from attacking the body’s own tissues in autoimmune diseases such as lupus and rheumatoid arthritis.

“There has certainly been a great deal of interest in targeting regulatory T cells for cancer therapy, because they are central to keeping the immune system in check in tumors,” said corresponding author Hongbo Chi, Ph.D., of the St. Jude Department of Immunology. “But the risk of such targeting is possibly inducing autoimmune disease because these T cells are crucial to balancing the body’s immune response.

“Our finding is exciting because we have identified a metabolic pathway that tumors use to independently reprogram regulatory T cells,” he said. “Thus, we believe there is the potential for inhibiting regulatory T-cell activation in tumors to unleash effective antitumor immune responses without triggering autoimmune toxicity.”

Tracking gene regulation to a surprise

Researchers discovered the pathway by challenging mice with melanoma cells and then analyzing which genes were switched on in regulatory T cells. Investigators compared tumor-infiltrating regulatory T cells with regulatory T cells in other tissues to compare gene activation.

The experiment revealed a master genetic switch that was activated only in regulatory T cells in the tumor microenvironment. The switch was a transcription factor family called SREBP.

“We were surprised to find this context-dependent pathway functioning selectively in the tumor microenvironment,” Chi said. Seon Ah Lim, Ph.D., a first author of the study, added, “It is incredible we can target metabolic pathways in regulatory T cells for cancer immunotherapy while maintaining immune homeostasis.”

The researchers determined that the tumor-specific regulatory T cell pathway was switched on in a range of cancers—melanoma, breast cancer and head and neck cancer. The tumor-specific pathway was not switched on in animal models of inflammation or autoimmune disease.

Genetically blocking the SREBP pathway selectively in regulatory T cells led to rapid clearance of tumor cells in mice with melanoma and colon adenocarcinoma. Targeting the pathway also reduced tumor growth in mice with established tumors. Blocking the pathway had no effect on the proliferation of regulatory T cells or their overall function in the body.

Blocking a pathway unleashes the anti-cancer immune response

Blocking the SREBP pathway also unleashed a potent antitumor response in mice with melanoma treated with immunotherapy called anti-PD-1. Anti-PD-1 treatment alone was otherwise ineffective in the mice. This form of immunotherapy inhibits the biochemical switch known as programmed cell death protein 1, or PD-1. PD-1 is a checkpoint switch that protects tumors by suppressing the immune response to them.

“Anti-PD-1 therapy currently works in only about 20% of cancer patients, although when it works, the response is durable in those cases,” Chi said. “Many pediatric cancers are not responsive to anti-PD-1. Our experiments showed that blocking this lipid pathway had quite a remarkable effect in sensitizing mice to the therapy.

“While we still have a long research path ahead of us, these findings suggest that if we can develop drugs to control this context-specific regulatory T cell pathway in cancer patients, we can make them even more responsive to immunological checkpoint therapies,” he said.

Jun Wei of St. Jude is the other first author. The other authors are Thanh-Long Nguyen, Hao Shi, Wei Su, Gustavo Palacios, Yogesh Dhungana, Nicole Chapman, Lingyun Long, Jordy Saravia and Peter Vogel, all of St. Jude.

The research was supported by in part by the National Institutes of Health (CA221290, CA250533, AI105887, AI131703, AI140761, AI150241 and AI150514) and ALSAC, the St. Jude fundraising and awareness organization.

Featured image: First author Seon Ah Lim, Ph.D., and corresponding author Hongbo Chi, Ph.D., both of St. Jude Immunology, contributed to research that raises the potential for treatments that render tumors more vulnerable to cancer immunotherapy. © St. Jude Children’s Research Institute


Read the full text of the article:

Lipid signaling enforces functional specialization of Treg cells in tumors.

Nature, Published February 24, 2021


Provided by St. Jude Children’s Research Hospital


About St. Jude Children’s Research Hospital

St. Jude Children’s Research Hospital is leading the way the world understands, treats and cures childhood cancer and other life-threatening diseases. It is the only National Cancer Institute-designated Comprehensive Cancer Center devoted solely to children. Treatments developed at St. Jude have helped push the overall childhood cancer survival rate from 20 percent to 80 percent since the hospital opened more than 50 years ago. St. Jude freely shares the breakthroughs it makes, and every child saved at St. Jude means doctors and scientists worldwide can use that knowledge to save thousands more children. Families never receive a bill from St. Jude for treatment, travel, housing and food — because all a family should worry about is helping their child live. To learn more, visit stjude.org or follow St. Jude on social media at @stjuderesearch.

Scientists Begin Building Highly Accurate Digital Twin of our Planet (Earth Science)

A digital twin of our planet is to simulate the Earth system in future. It is intended to support policy-​makers in taking appropriate measures to better prepare for extreme events. A new strategy paper by European scientists and ETH Zurich computer scientists shows how this can be achieved.

To become climate neutral by 2050, the European Union launched two ambitious programmes:  “Green Deal” and “DigitalStrategy“. As a key component of their successful implementation, climate scientists and computer scientists launched the “Destination Earth” initiative, which will start in mid-​2021 and is expected to run for up to ten years. During this period, a highly accurate digital model of the Earth is to be created, a digital twin of the Earth, to map climate development and extreme events as accurately as possible in space and time.

Observational data will be continuously incorporated into the digital twin in order to make the digital Earth model more accurate for monitoring the evolution and predict possible future trajectories. But in addition to the observation data conventionally used for weather and climate simulations, the researchers also want to integrate new data on relevant human activities into the model. The new “Earth system model” will represent virtually all processes on the Earth’s surface as realistically as possible, including the influence of humans on water, food and energy management, and the processes in the physical Earth system.

Information system for decision-​making

The digital twin of the Earth is intended to be an information system that develops and tests scenarios that show more sustainable development and thus better inform policies. “If you are planning a two-​metre high dike in The Netherlands, for example, I can run through the data in my digital twin and check whether the dike will in all likelihood still protect against expected extreme events in 2050,” says Peter Bauer, deputy director for Research at the European Centre for Medium-​Range Weather Forecasts (ECMWF) and co-​initiator of Destination Earth. The digital twin will also be used for strategic planning of fresh water and food supplies or wind farms and solar plants.

The driving forces behind Destination Earth are the ECMWF, the European Space Agency (ESA), and the European Organisation for the Exploitation of Meteorological Satellites (EUMETSAT). Together with other scientists, Bauer is driving the climate science and meteorological aspects of the Earth’s digital twin, but they also rely on the know-​how of computer scientists from ETH Zurich and the Swiss National Supercomputing Centre (CSCS), namely ETH professors Torsten Hoefler, from the Institute for High Performance Computing Systems, and Thomas Schulthess, Director of CSCS.

In order to take this big step in the digital revolution, Bauer emphasises the need for earth sciences to be married to the computer sciences. In a recent publication in Nature Computational Science, the team of researchers from the earth and computer sciences discusses which concrete measures they would like to use to advance this “digital revolution of earth-​system sciences”, where they see the challenges and what possible solutions can be found.

Weather and climate models as a basis

In their paper, the researchers look back on the steady development of weather models since the 1940s, a success story that took place quietly. Meteorologists pioneered, so to speak, simulations of physical processes on the world’s largest computers. As a physicist and computer scientist, CSCS’s Schulthess is therefore convinced that today’s weather and climate models are ideally suited to identify completely new ways for many more scientific disciplines how to use supercomputers efficiently.

In the past, weather and climate modelling used different approaches to simulate the Earth system. Whereas climate models represent a very broad set of physical processes, they typically neglect small-​scale processes, which, however, are essential for the more precise weather forecasts that in turn, focus on a smaller number of processes.  The digital twin will bring both areas together and enable high-​resolution simulations that depict the complex processes of the entire Earth system. But in order to achieve this, the codes of the simulation programmes must be adapted to new technologies promising much enhanced computing power.

With the computers and algorithms available today, the highly complex simulations can hardly be carried out at the planned extremely high resolution of one kilometre because for decades, code development stagnated from a computer science perspective. Climate research benefited from being able to gain higher performance by ways of new generations of processors without having to fundamentally change their programme. This free performance gain with each new processor generation stopped about 10 years ago. As a result, today’s programmes can often only utilise 5 per cent of the peak performance of conventional processors (CPU).

For achieving the necessary improvements, the authors emphasize the need of co-​design, i.e. developing hardware and algorithms together and simultaneously, as CSCS successfully demonstrated during the last ten years. They suggest to pay particular attention to generic data structures, optimised spatial discretisation of the grid to be calculated and optimisation of the time step lengths. The scientists further propose to separate the codes for solving the scientific problem from the codes that optimally perform the computation on the respective system architecture. This more flexible programme structure would allow a faster and more efficient switch to future architectures.

Profiting from artificial intelligence

The authors also see great potential in artificial intelligence (AI). It can be used, for example, for data assimilation or the processing of observation data, the representation of uncertain physical processes in the models and data compression. AI thus makes it possible to speed up the simulations and filter out the most important information from large amounts of data. Additionally, the researchers assume that the use of machine learning not only makes the calculations more efficient, but also can help describing the physical processes more accurately.

The scientists see their strategy paper as a starting point on the path to a digital twin of the Earth. Among the computer architectures available today and those expected in the near future, supercomputers based on graphics processing units (GPU) appear to be the most promising option. The researchers estimate that operating a digital twin at full scale would require a system with about 20,000 GPUs, consuming an estimated 20MW of power. For both economic and ecological reasons, such a computer should be operated at a location where CO2-neutralgenerated electricity is available in sufficient quantities.

Featured image: A di­gital twin of the Earth is to sim­u­late the Earth sys­tem com­pre­hens­ively and at high res­ol­u­tion and serve, for ex­ample, as a basis for guid­ing ad­apt­a­tion meas­ures to cli­mate change. (ESA)


References

(1) Bauer P, Dueben PD, Hoefler T, Quintino T, Schulthess TC, Wedi NP: The digital revolution of Earth-system science. Nat. Comput. Sci. 1, 104–113 (2021). doi: 10.1038/s43588-021-00023-0. https://www.nature.com/articles/s43588-021-00023-0 (2) Bauer, P, Stevens, B, Hazeleger, W. A digital twin of Earth for the green transition. Nat. Clim. Chang. 11, 80–83 (2021). doi: 10.1038/s41558-021-00986-y. https://www.nature.com/articles/s41558-021-00986-y


Provided by ETH Zurich

Quantum Systems Learn Joint Computing (Quantum)

MPQ researchers realize the first quantum-logic computer operation between two separate quantum modules in different laboratories.

Today’s quantum computers contain up to several dozen memory and processing units, the so-called qubits. Severin Daiss, Stefan Langenfeld, and colleagues from the Max Planck Institute of Quantum Optics in Garching have successfully interconnected two such qubits located in different labs to a distributed quantum computer by linking the qubits with a 60-meter-long optical fiber. Over such a distance they realized a quantum-logic gate – the basic building block of a quantum computer. It makes the system the worldwide first prototype of a distributed quantum computer.

The limitations of previous qubit architectures

Quantum computers are considerably different from traditional “binary” computers: Future realizations of them are expected to easily perform specific calculations for which traditional computers would take months or even years – for example in the field of data encryption and decryption. While the performance of binary computers results from large memories and fast computing cycles, the success of the quantum computer rests on the fact that one single memory unit – a quantum bit, also called “qubit” – can contain superpositions of different possible values at the same time. Therefore, a quantum computer does not only calculate one result at a time, but instead many possible results in parallel. The more qubits there are interconnected in a quantum computer; the more complex calculations it can perform.

The basic computing operations of a quantum computer are quantum-logic gates between two qubits. Such an operation changes – depending on the initial state of the qubits – their quantum mechanical states. For a quantum computer to be superior to a normal computer for various calculations, it would have to reliably interconnect many dozens, or even thousands of qubits for equally thousands of quantum operations. Despite great successes, all current laboratories are still struggling to build such a large and reliable quantum computer, since every additionally required qubit makes it much harder to build a quantum computer in just one single set-up. The qubits are implemented, for instance, with single atoms, superconductive elements, or light particles, all of which need to be isolated perfectly from each other and the environment. The more qubits are arranged next to one another, the harder it is to both isolate and control them from outside at the same time.

Data line and processing unit combined

One way to overcome the technical difficulties in the construction of quantum computers is presented in a new study in the journal Science by Severin Daiss, Stefan Langenfeld and colleagues from the research group of Gerhard Rempe at the Max Planck Institute of Quantum Optics in Garching. In this work supported by the Institute of Photonic Sciences (Castelldefels, Spain), the team succeeded in connecting two qubit modules across a 60-meter distance in such a way that they effectively form a basic quantum computer with two qubits. “Across this distance, we perform a quantum computing operation between two independent qubit setups in different laboratories,” Daiss emphasizes. This enables the possibility to merge smaller quantum computers to a joint processing unit.

First author, Severin Daiss, in front of part one of their distributed quantum computer. © Max Planck Gesellschaft

Simply coupling distant qubits to generate entanglement between them has been achieved in the past, but now, the connection can additionally be used for quantum computations. For this purpose, the researchers employed modules consisting of a single atom as a qubit that is positioned amidst two mirrors. Between these modules, they send one single light quanta, a photon, that is transported in the optical fiber. This photon is then entangled with the quantum states of the qubits in the different modules. Subsequently, the state of one of the qubits is changed according to the measured state of the “ancilla photon”, realizing a quantum mechanical CNOT-operation with a fidelity of 80 percent. A next step would be to connect more than two modules and to host more qubits in the individual modules.

Higher performance quantum computers through distributed computing

Team leader and institute director Gerhard Rempe believes the result will allow to further advance the technology: “Our scheme opens up a new development path for distributed quantum computing”. It could enable, for instance, to build a distributed quantum computer consisting of many modules with few qubits that are interconnected with the newly introduced method. This approach could circumvent the limitation of existing quantum computers to integrate more qubits into a single setup and could therefore allow more powerful systems.

Featured image: This picture shows the two qubit modules (red atom between two blue mirrors) that have been interconnected to implement a basic quantum computation (depicted as light blue symbol) over a distance of 60 meters. The modules reside in different laboratories of the same building and are connected by an optical fiber. The computation operation is mediated by a single photon (flying red sphere) that interacts successively with the two modules. © Stephan Welte, Severin Daiss (MPQ)


Reference: Severin Daiss, Stephan Langenfeld, Stephan Welte, Emanuele Distante, Philip Thomas, Lukas Hartung, Olivier Morin, Gerhard Rempe, “A Quantum-Logic Gate between Distant Quantum-Network Modules”, Science 05 Feb 2021: Vol. 371, Issue 6529, pp. 614-617. https://dx.doi.org/10.1126/science.abe3150 https://science.sciencemag.org/content/371/6529/614


Provided by Max Planck Institute of Quantum Optics

Human Lung and Brain Organoids Respond Differently to SARS-CoV-2 Infection in Lab Tests (Medicine)

Findings may help explain the wide variety in COVID-19 symptoms and aid search for therapies

COVID-19, the disease caused by the pandemic coronavirus SARS-CoV-2, is primarily regarded as a respiratory infection. Yet the virus has also become known for affecting other parts of the body in ways not as well understood, sometimes with longer-term consequences, such as heart arrhythmia, fatigue and “brain fog.”

Researchers at University of California San Diego School of Medicine are using stem cell-derived organoids — small balls of human cells that look and act like mini-organs in a laboratory dish — to study how the virus interacts with various organ systems and to develop therapies to block infection.

“We’re finding that SARS-CoV-2 doesn’t infect the entire body in the same way,” said Tariq Rana, PhD, professor and chief of the Division of Genetics in the Department of Pediatrics at UC San Diego School of Medicine and Moores Cancer Center. “In different cell types, the virus triggers the expression of different genes, and we see different outcomes.”

Rana’s team published their findings February 11, 2021 in Stem Cell Reports.

Like many organs, the team’s lung and brain organoids produce the molecules ACE2 and TMPRSS2, which sit like doorknobs on the outer surfaces of cells. SARS-CoV-2 grabs these doorknobs with its spike protein as a means to enter cells and establish infection.

Rana and team developed a pseudovirus — a noninfectious version of SARS-CoV-2 — and labeled it with green fluorescent protein, or GFP, a bright molecule derived from jellyfish that helps researchers visualize the inner workings of cells. The fluorescent label allowed them to quantify the binding of the virus’ spike protein to ACE2 receptors in human lung and brain organoids, and evaluate the cells’ responses.

The team was surprised to see approximately 10-fold more ACE2 and TMPRSS2 receptors and correspondingly much higher viral infection in lung organoids, as compared to brain organoids. Treatment with viral spike protein or TMPRSS2 inhibitors reduced infection levels in both organoids.

“We saw dots of fluorescence in the brain organoids, but it was the lung organoids that really lit up,” Rana said.

Besides differences in infectivity levels, the lung and brain organoids also differed in their responses to the virus. SARS-CoV-2-infected lung organoids pumped out molecules intended to summon help from the immune system — interferons, cytokines and chemokines. Infected brain organoids, on the other hand, upped their production of other molecules, such as TLR3, a member of the toll-like receptor family that plays a fundamental role in pathogen recognition and activation of innate immunity

Rana explained that, while it might seem at first like the brain organoid reaction is just another form of immune response, those molecules can also aid in programmed cell death. Rana’s team previously saw a similar brain cell response to Zika virus, an infection known to stunt neonatal brain development.

“The way we are seeing brain cells react to the virus may help explain some of the neurological effects reported by patients with COVID-19,” Rana said.

Of course, organoids aren’t exact replicas of human organs. They lack blood vessels and immune cells, for example. But they provide an important tool for studying diseases and testing potential therapies. According to Rana, organoids mimic the real-world human condition more accurately than cell lines or animal models that have been engineered to over-express human ACE2 and TMPRSS2.

“In animals over-expressing ACE2 receptors, you see everything light up with infection, even the brain, so everyone thinks this is the real situation,” Rana said. “But we found that’s likely not the case.”

In addition to their work with the pseudovirus, the team validated their findings by applying live, infectious SARS-CoV-2 to lung and brain organoids in a Biosafety Level-3 laboratory — a facility specially designed and certified to safely study high-risk microbes.

Now Rana and collaborators are developing SARS-CoV-2 inhibitors and testing how well they work in organoid models derived from people of a variety of racial and ethnic backgrounds that represent California’s diverse population. They were recently awarded new funding from the California Institute for Regenerative Medicine to support the work.

Co-authors of the study include: Shashi Kant Tiwari, Shaobo Wang, Davey Smith and Aaron Carlin, all at UC San Diego.

Featured image: UC San Diego School of Medicine researchers found approximately 10-fold higher SARS-CoV-2 infection (green) in lung organoids (left), compared to brain organoids (right). © UC San Diego Health Sciences


Reference: Shashi Kant Tiwari, Shaobo Wang et al., “Revealing tissue-specific SARS-CoV-2 infection and host responses using human stem cell-derived lung and cerebral organoids”, Stem Cell Reports, 2021. DOI: https://doi.org/10.1016/j.stemcr.2021.02.005


Provided by University of California San Diego