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Physiology

PhysIQs Proprietary Personalized Analytics to be Used for COVID-19 Care with Newly Broadened FDA Labeling – Yahoo Finance

PhysIQ announces FDA-sanctioned labeling to address the COVID-19 public health emergency with its proprietary Multivariate Change Index (MCI)

Deployed within the pinpointIQ continuous remote monitoring solution, physIQs MCI will be used to proactively monitor homebound patients with or vulnerable to COVID-19

The sophisticated, machine learning-based algorithm uses multiple continuous vital signs from wearable sensors to detect subtle changes in physiology that may offer early detection of COVID-19-related clinical deterioration

The Food and Drug Administration (FDA) has sanctioned labeling for pinpointIQ, physIQs continuous remote monitoring system for use in the COVID-19 pandemic, including application of its proprietary Multivariate Change Index (MCI). During this pandemic, pinpointIQ may be used to provide continuous physiologic remote monitoring to homebound or quarantined patients with confirmed or suspected COVID-19 or those whose high-risk profile that requires continuous remote monitoring, for example, those with heart failure, COPD, or hypertension. By passively collecting wearable sensor data and applying advanced analytics, pinpointIQ may ease burden on hospitals and other healthcare facilities and reduce the risk of exposure for patients and healthcare providers to SARS-CoV-2 and conserve resources for the very sickest.

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PhysIQ announces FDA-sanctioned labeling to address the COVID-19 public health emergency with its proprietary Multivariate Change Index (MCI) ) (Photo: Business Wire)

Recently, physIQ announced the results of a VA-sponsored clinical study published in Circulation Heart Failure of 100 patients with congestive heart failure that was able to detect subtle physiologic changes predictive of hospitalization one week in advance. This study serves as a model for the potential utility of our artificial intelligence (AI)-powered devices to detect similar cardiovascular changes that may emerge in COVID-19 cases. The viability of pinpointIQ is substantiated by the work physIQ has done with USAID during the Ebola epidemic. This supports the solution and the previously stated use cases for how this platform/product can aid in the COVID-19 crisis mitigation.

Story continues

"Our entire healthcare infrastructure is about to become completely overwhelmed by COVID-19," said Gary Conkright, CEO of physIQ. "We will have more patients than hospital beds and our only option is to find ways to better care for patients at home. With clinical grade wearable sensors and our proprietary, FDA-cleared analytics, we are providing hospitals with personalized physiologic visibility into their homebound high-risk COVID-19 patients. We believe this will not only free up hospital capacity, but also reduce clinician exposure to this highly virulent disease."

PhysIQ is pursuing multiple clinical use cases including COVID-19 positive patients, patients with chronic diseases such as heart failure or COPD, patients on chemotherapy or other immune-suppressive therapy, and to surveille healthcare providers who are at elevated risk of getting infected themselves. With the system, patients are mailed a kit that provides all components required for continuous remote monitoring including FDA-cleared clinical-grade wearable sensors and a phone for data transmission with data plan. The system is deployed directly to patients home, requiring no direct physical contact from a clinician. Data continuously streams to the cloud where physIQs proprietary FDA-cleared analytics detect subtle changes in physiology that may offer early warning of clinical deterioration related to COVID-19.

About physIQ

PhysIQ is a leading digital medicine company dedicated to generating unprecedented health insight using continuous wearable biosensor data and advanced analytics. Our enterprise-ready cloud platform continuously collects and processes data from any wearable biosensor using a deep portfolio of FDA-cleared analytics. We have published one of the most rigorous clinical studies to date in digital medicine and are pioneers in developing, validating, and achieving regulatory approval of Artificial Intelligence-based analytics. With applications in both healthcare and clinical trial support, physIQ is transforming continuous physiological data into insight for health systems, payers, and pharmaceutical companies. For more information, please visit http://www.physIQ.com. Follow us on Twitter and LinkedIn.

View source version on businesswire.com: https://www.businesswire.com/news/home/20200326005087/en/

Contacts

Jodi PerkinsOutlook Marketing ServicesPh: 847-508-0877Jodi@outlookmarketingsrv.com

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PhysIQs Proprietary Personalized Analytics to be Used for COVID-19 Care with Newly Broadened FDA Labeling - Yahoo Finance

Physiology

‘I’m Losing My Mind.’ How to Counter Stress Response – Thrive Global

Have you ever wondered why people go a bit cray cray in times of deep stress? Its really out of our control

Well the huge demands (stessors) placed on people such as they may be experiencing now, with job losses, financial pressures and trying to keep themselves and their families healthy, starts a chain of events.

The brain reacts according to Harvard Health Publishing Harvard Medical School, in that the amygdala senses danger and sends a distress signal to the hypothalmus. This part of the brain is like a command centre communicating with the rest of the body through the nervous system.

When the hypothalmus receives a distress signal it activates our sympathetic nervous system. Stress hormones flood our body and it provides people with a burst of energy to respond to any perceived danger.

This allows people to activate the energy to fight or flight. This part of our brain controls our involuntary functions such as breathing, heart beat, heart rate, dilation of blood vessels and the like. This is why we show physiological signs when we feel stressed such as increased heart rate and headaches.

Our body becomes prepared to act in order to keep us safe. Stress hormone, cortisol is also activated and if not released from our body in a timely manner can cause problems to our health over time.

At the same time, a study by Amy. F. T. Arnstern National Institute of Health states that the pre-frontal cortex, which serves our highest cognitive function quickly suffers detrimentally to stress. It shuts down to conserve energy. Our thinking becomes impaired and we can lose our ability to think clearly. So the term Im losing my mind is kinda true!

Its important to know according to Harvard, that the sympathetic nervous system, our gas pedal and the parasympathetic nervous system, our brake cant function at the same time.

Our parasympathetic nervous system which controls our rest and digest functions responds to help us calm down post threat. It does the job of dampening down our stress response. Under normal circumstances cortisol levels will be reduced.

People with chronic stress however, behave differently. The body produces more cortisol than it can release, and that becomes a pre-cursor to a range of health problems. For example heart disease.

Countering our stress response with our natural brake is so important to our overall health and well being!

Relaxation methods activate the parasympathetic system and we can more easily dampen down.

So how does it work?

One of the best ways of returning to calm is by returning to your breath.

Dr. Herbert Benson M.D. in his book the relaxation response outlines its positive effects. He maintains one of the best things we can do for ourselves is learn deep relaxation to counter the flight fight response. When we breath in deeply it signals to our nervous system and our physiology we are safe and everything is ok.

So how do we do it?

Dr. Benson created his relaxation response technique over 25 years ago which you can find here

Today I want to show you The Backpack Meditation by Gabby Bernstein because you can literally do it anywhere, hence its name!

Its easy, feels great and its a quick way to reduce your stress response in one minute per day! To your best health and happiness.I hope youll give it a try.

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'I'm Losing My Mind.' How to Counter Stress Response - Thrive Global

Physiology

Are animals vulnerable to COVID-19? – The Ohio State University News

While theres no evidence so far that pets, livestock, or their owners can infect each other with COVID-19, there is also very little research about a potential crossover.

The novel coronavirus started with an animal, then mutated to transfer to people, but research hasnt yet shown if the virus has jumped back to animals, said Scott Kenney, a researcher at The Ohio State University College of Food, Agricultural, and Environmental Sciences (CFAES).

Viruses are constantly sampling and evolving, trying to find other hosts, said Kenney, who studies coronaviruses, including those that cross over from one species to another.

Quickly spreading among people across the world, COVID-19 is believed to have originated in bats, but the bat virus changed, altering surface proteins to be able to efficiently transfer from person to person. These surface proteins are different in the mutated bat virus, so COVID-19 is now less likely to affect the original bats. Whether other animals are susceptible to COVID-19 has yet to be tested, he said.

When viruses infect an animal, they produce billions of copies of themselves. Some of the copies tend to be slightly changed from the original virus. According to Kenney, while most of these irregular copies die, occasionally one has a change that is beneficial for the virus, such as altering its ability to infect a different species.

If the new species is exposed to this altered virus, it can now make many more copies of itself and potentially infect a whole new species, he said.

So far, the only research on COVID-19 and animals involves studies in China that showed two dogs tested positive for COVID-19. But neither of the infected dogs had symptoms of the virus, and researchers in those studies do not believe they transmitted the disease to any other animals or people.

Coronaviruses are a large family of viruses, with COVID-19 being the newest addition. Some coronaviruses cause illness in people, some cause illness in certain animals, and others sicken both people and animals. Severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) were both coronaviruses that started in animals and shifted to people, leading to outbreaks. Neither was as adept at transmitting to people as COVID-19.

COVID-19 has managed to hit a virus evolution sweet spot, Kenney said. Infected people can be either very sick or show few signs, leading to very rapid spread of the infection.

Coronaviruses are common among farm animals. If COVID-19 were to jump species again and be receptive to animals, a likely animal on the farm to catch it would be pigs, he said. Thats because pigs have a similar protein to humans that the SARS virus, a coronavirus cousin to COVID-19, uses to infect humans. Studies show that it may work in pigs too.

Among farm animals, pigs seem to be the most susceptible to coronaviruses, able to contract up to six different pig-specific coronaviruses.

Im not sure anyone really knows why, he said. Outside of bats, pigs and humans seem to be infected by the largest numbers of different coronaviruses.

More studies are needed to understand whether this is because of something in pigs physiology or genetic makeup, or just that humans and pigs encounter coronaviruses more frequently than other animals. That results in more virus spillovers.

One of the more devastating coronaviruses among livestock in recent years affected only pigs: the porcine epidemic diarrhea virus. During a 2013 outbreak, the virus killed significant numbers of pigs in the United States and China, all of them young pigs.

The virus continues to pop up and cause problems in many countries around the world, Kenney said.

Even if farmers have spent a lot of time around pigs or other livestock, including animals with coronaviruses, they do not have immunity to COVID-19, he said. Thats why it is still important to be cautious.

Any time youre around an animal, you should use good hygiene. There are many illnesses besides coronaviruses in animals that can be passed to humans, and vice versa

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Are animals vulnerable to COVID-19? - The Ohio State University News

Physiology

Outlook on the Cell Line Development Market to 2027 – Global Analysis and Forecasts – ResearchAndMarkets.com – Business Wire

DUBLIN--(BUSINESS WIRE)--The "Cell Line Development Market to 2027 - Global Analysis and Forecasts By Type; By Product; Application; and Geography" report has been added to ResearchAndMarkets.com's offering.

The global cell line development market is anticipated to reach US$ 11,161.35 Mn in 2027 from US$ 3,694.87 Mn in 2018. The cell line development market is expected to grow with a CAGR of 13.2% from 2019-2027.

Driving factors are increasing the adoption of regenerative medicines, rising prevalence of cancer across the globe, and increasing investments in R&D by pharmaceutical and biotechnology companies. However, risks associated with cell line contamination is expected to hamper the market during the forecast period.

The cell line is established cell culture, which gets increased numerous times when supplied with the growth medium and space for growth. Different cell lines can be made from different cells. The cell line plays a vital role in the study of cytology. The cell line enables stepwise alterations in the structure, physiology, and genetic makeup of cells under a customized environment.

The global cell line development market is bifurcated into type, product, and application. Based on type, the cell line development market is segmented into a primary cell line, hybridomas, continuous cell lines, and recombinant cell line. Based on product, the cell line development market is segmented into equipment, media and reagent. On the basis of application, the cell line development market is bifurcated into drug discovery, bioproduction, and tissue engineering. In 2018, the bioproduction segment held the largest share of the market. However, the drug discovery segment is expected to register the highest CAGR in the market during the forecast period.

Reasons to Buy

Key Topics Covered:

1. Introduction

2. Cell Line Development Market - Key Takeaways

3. Research Methodology

4. Cell Line Development - Market Landscape

4.1 Overview

4.2 PEST Analysis

4.3 Expert Opinion

5. Global Cell Line Development Market - Key Market Dynamics

5.1 Key Market Drivers

5.1.1 Increasing Adoption of Regenerative Medicines

5.1.2 Rising Prevalence of Cancer

5.1.3 Growing Investment in R&D by Pharmaceutical and Biotechnology Companies

5.2 Key Restraints

5.2.1 Risk Associated with Cell Line Contamination

5.3 Key Opportunity

5.3.1 Middle Income Countries Creating Development Opportunities

5.4 Future Trend

5.4.1 Consistent Research in Drug Discovery Activities

5.5 Impact Analysis

6. Cell Line Development Market - Global Analysis

6.1 Global Cell Line Development Market Revenue Forecast and Analysis

6.2 Global Cell Line Development Market, By Geography - Forecast and Analysis

6.3 Market Positioning of Key Players

6.3.1 Merck KGaA

6.3.2 Thermo Fisher Scientific Inc.

7. Cell Line Development Market - Revenue and Forecasts to 2027 - Type

7.1 Overview

7.2 Global Cell Line Development Market, by Type, 2018 & 2027 (% Share)

7.3 Primary Cell Line

7.4 Hybridomas

7.5 Continuous Cell Lines

7.6 Recombinant Cell Line

8. Cell Line Development Market Analysis and Forecasts to 2027 - Product

8.1 Overview

8.2 Global Cell Line Development Market, by Product, 2018 & 2027 (% Share)

8.3 Equipment

8.4 Media and Reagent

9. Cell Line Development Market Analysis and Forecasts to 2027 - Application

9.1 Overview

9.2 Global Cell Line Development Market Share by Application 2018 & 2027 (%)

9.3 Drug Discovery

9.4 Bioproduction

9.5 Tissue Engineering

10. Cell Line Development Market Revenue and Forecast to 2027 - Geographical Analysis

10.1 North America Cell Line Development Market, Revenue and Forecast to 2027

10.2 Europe Cell Line Development Market Revenue and Forecast to 2027

10.3 APAC Cell Line Development Market, Revenue and Forecast to 2027

10.4 MEA Cell Line Development Market, Revenue and Forecast to 2027

10.5 South and Central America Cell Line Development Market, Revenue and Forecast to 2027

11. Cell Line Development Market - Industry Landscape

11.1 Overview

11.2 Growth Strategies Done by the Companies in The Market, (%)

11.3 Organic Developments Done by The Companies in the Market

11.4 Inorganic Developments Done by The Companies in the Market

12. Cell Line Development Market- Key Company Profiles

12.1 Merck KGaA

12.2 Thermo Fisher Scientific, Inc.

12.3 Sartorius AG

12.4 SELEXIS

12.5 BioFactura, Inc.

12.6 WuXi AppTec

12.7 LakePharma, Inc.

12.8 General Electric

12.9 Lonza

12.10 Corning Incorporated

13. Appendix

For more information about this report visit https://www.researchandmarkets.com/r/j909g0

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Outlook on the Cell Line Development Market to 2027 - Global Analysis and Forecasts - ResearchAndMarkets.com - Business Wire

Physiology

Senior Lecturer/Lecturer Above the Bar Physiology (Skeletal Muscle & Ageing) Job with National University of Ireland, Galway – The Irish Times

Applications are invited for the following post:

College of Medicine, Nursing andHealth Sciences

Senior Lecturer/Lecturer Above the BarPhysiology (Skeletal Muscle & Ageing),Permanent

Applications are invited for the above permanent post in the Academic Discipline of Physiology at NUI, Galway. The appointment will be at the Senior lecturer/Lecturer Above the Bar level. Candidates should indicate the grade they are applying for i.e. Senior Lecturer or Lecturer above the bar or both.

The successful candidate is expected to have an established research profile commensurate with her/his career to date, in the field of skeletal muscle biology with particular reference to ageing. A combination of basic research and human research will be an advantage. The successful candidate will, in addition, be expected to teach physiology in a range of undergraduate and postgraduate courses and to contribute to a research programme within the Discipline of Physiology. The Discipline of Physiology is housed in the Human Biology Building, a new state-of-the-art building dedicated to teaching and research.

Closing date: 22nd April 2020

Application details/procedure:For further information and to make an online application for theabove posts please visit http://www.nuigalway.ie/about-us/jobs/

National University of Ireland, Galway isan equal opportunities employer.

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Senior Lecturer/Lecturer Above the Bar Physiology (Skeletal Muscle & Ageing) Job with National University of Ireland, Galway - The Irish Times

Genetics

The First Genetic Map of the Cerebral Cortex – Technology Networks

The cerebral cortex is the relatively thin, folded, outer gray matter layer of the brain crucial for thinking, information processing, memory, and attention. Not much has been revealed about the genetic underpinnings that influence the size of the cortexs surface area and its thickness, both of which have previously been linked to various psychiatric traits, including schizophrenia, bipolar disorder, depression, attention deficit hyperactivity disorder (ADHD), and autism.Now, for the first time, more 360 scientists from 184 different institutions including UNC-Chapel Hill have contributed to a global effort to find more than 200 regions of the genome and more than 300 specific genetic variations that affect the structure of the cerebral cortex and likely play important roles in psychiatric and neurological conditions.

The study was led by co-senior authors Jason Stein, PhD, assistant professor in the Department of Genetics at the UNC School of Medicine; Sarah Medland, PhD, senior research fellow at the QIMR Berghofer Medical Research Institute in Australia; and Paul Thompson, PhD, associate director of the Mark and Mary Stevens Neuroimaging and Informatics Institute at the University of Southern California. Ten years ago, these scientists cofounded the ENIGMA Consortium, an international research network that has brought together hundreds of imaging genomics researchers to understand brain structure, function, and disease based on brain imaging and genetic data.

This study was only possible due to a huge scientific collaboration of more than 60 sites involved in MRI scanning and genotyping participants, Stein said. This study is the crown jewel of the ENIGMA Consortium, so far.

The researchers studied MRI scans and DNA from more than 50,000 people to identify 306 genetic variants that influence brain structure in order to shed light on how genetics contribute to differences in the cerebral cortex of individuals. Genetic variants or variations are simply the slight genetic differences that make us unique. Generally speaking, some variants contribute to differences such as hair color or blood type. Some are involved in diseases. Most of the millions of genetic variants, though, have no known significance. This is why pinpointing genetic variants associated with cortex size and structure is a big deal. Stein and colleagues consider their new genetic roadmap of the brain a sort of Rosetta stone that will help translate how some genes impact physical brain structure and neurological consequences for individuals.

Among the findings of the research:

Most of our previous understanding of genes affecting the brain are from model systems, like mice, Stein said. With mice, we can find genes, knock out genes, or over express genes to see how they influence the structure or function of the brain. But there are a couple of problems with this.One problem is, quite simply, a mouse is not a human. There are many human-specific features that scientists can only study in the human brain.

The genetic basis for a mouse is very different than the genetic basis for humans, Stein said, especially in in the noncoding regions of the genome.

Genes contain DNA, the basic human code that, when translated into action, creates proteins that do things, such as help your finger muscles type or your heart beat or your liver process toxins. But only about 3 percent of the human genome codes for proteins. The vast majority of the human genome is called the noncoding genome. Much of this region is not shared between mice and humans. This noncoding genome consists of tiny molecular switches that can modulate the expression of other genes. These switches dont directly alter the function of a protein, but they can affect the amounts of a protein that is expressed. Turns out, most genetic variants associated with psychiatric disorders are found in the noncoding region of the genome.

These findings can now be a resource for scientists to help answer important questions about the genetic influences on the brain and how they relate to numerous conditions.ReferenceGrasby et al. (2020) The genetic architecture of the human cerebral cortex. Science. DOI: https://doi.org/10.1126/science.aay6690

This article has been republished from the following materials. Note: material may have been edited for length and content. For further information, please contact the cited source.

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The First Genetic Map of the Cerebral Cortex - Technology Networks

Genetics

Icelandic genetics company conducting mass testing for COVID-19 to provide data on the spread of the virus – WGN TV Chicago

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Kari Stefansson Neurologist, Decode Genetics Founder

Headquartered in Reykjavik, Iceland, deCODE is a global leader in analyzing and understanding the human genome. Using our unique expertise and population resources, deCODE has discovered key genetic risk factors for dozens of common diseases ranging from cardiovascular disease to cancer.

Find more information here

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Icelandic genetics company conducting mass testing for COVID-19 to provide data on the spread of the virus - WGN TV Chicago

Genetics

Global scientific collaboration produces first genetic map of the cerebral cortex – News-Medical.net

The cerebral cortex is the relatively thin, folded, outer "gray matter" layer of the brain crucial for thinking, information processing, memory, and attention. Not much has been revealed about the genetic underpinnings that influence the size of the cortex's surface area and its thickness, both of which have previously been linked to various psychiatric traits, including schizophrenia, bipolar disorder, depression, attention deficit hyperactivity disorder (ADHD), and autism.

Now, for the first time, more 360 scientists from 184 different institutions - including UNC-Chapel Hill - have contributed to a global effort to find more than 200 regions of the genome and more than 300 specific genetic variations that affect the structure of the cerebral cortex and likely play important roles in psychiatric and neurological conditions.

The study, published in Science, was led by co-senior authors Jason Stein, PhD, assistant professor in the Department of Genetics at the UNC School of Medicine; Sarah Medland, PhD, senior research fellow at the QIMR Berghofer Medical Research Institute in Australia; and Paul Thompson, PhD, associate director of the Mark and Mary Stevens Neuroimaging and Informatics Institute at the University of Southern California. Ten years ago, these scientists cofounded the ENIGMA Consortium, an international research network that has brought together hundreds of imaging genomics researchers to understand brain structure, function, and disease based on brain imaging and genetic data.

This study was only possible due to a huge scientific collaboration of more than 60 sites involved in MRI scanning and genotyping participants. This study is the crown jewel of the ENIGMA Consortium, so far."

Jason Stein, Ph.D., assistant professor, Department of Genetics, UNC School of Medicine

The researchers studied MRI scans and DNA from more than 50,000 people to identify 306 genetic variants that influence brain structure in order to shed light on how genetics contribute to differences in the cerebral cortex of individuals. Genetic variants or variations are simply the slight genetic differences that make us unique. Generally speaking, some variants contribute to differences such as hair color or blood type. Some are involved in diseases. Most of the millions of genetic variants, though, have no known significance. This is why pinpointing genetic variants associated with cortex size and structure is a big deal. Stein and colleagues consider their new genetic roadmap of the brain a sort of "Rosetta stone" that will help translate how some genes impact physical brain structure and neurological consequences for individuals.

Among the findings of the research published in Science:

One problem is, quite simply, a mouse is not a human. There are many human-specific features that scientists can only study in the human brain.

"The genetic basis for a mouse is very different than the genetic basis for humans," Stein said, "especially in in the noncoding regions of the genome."

Genes contain DNA, the basic human code that, when translated into action, creates proteins that "do" things, such as help your finger muscles type or your heart beat or your liver process toxins. But only about 3 percent of the human genome codes for proteins. The vast majority of the human genome is called the noncoding genome. Much of this region is not shared between mice and humans. This noncoding genome consists of tiny molecular switches that can modulate the expression of other genes. These switches don't directly alter the function of a protein, but they can affect the amounts of a protein that is expressed. Turns out, most genetic variants associated with psychiatric disorders are found in the noncoding region of the genome.

These findings can now be a resource for scientists to help answer important questions about the genetic influences on the brain and how they relate to numerous conditions.

Source:

Journal reference:

Grasby, K.L., et al. (2020) The genetic architecture of the human cerebral cortex. Science. doi.org/10.1126/science.aay6690.

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Global scientific collaboration produces first genetic map of the cerebral cortex - News-Medical.net

Genetics

The Enemy Is no Longer Invisible, Greek Professor of Genetics Says – The National Herald

By ANA March 27, 2020

Aristotle University of Thessaloniki. (Photo by Eurokinissi/ Vasilis Ververidis)

ATHENS The rapid analysis and now the knowledge of the SARS-CoV-2 genome is helping us to find quicker ways to deal with it, said Zacharias Skouras, Professor of Genetics at the Aristotle University of Thessaloniki (AUTH).

In an interview with the Athens-Macedonian News Agency, he explained that the enemy is no longer invisible, because it is visible through the progress made under the microscope, the penetration of the human eye into parts so tiny that we can see its image, its phenotype, the means of cultivating and identifying it in different environments, and even more so, its genotype and the analysis of its genetic information.

As for the behaviour of SARS-CoV-2, he noted that it is the seventh coronavirus, and despite its recent appearance, it has been extensively studied. He observed that it is a smart virus as it is invasive and spreads, that is, it survives better because it is not extremely lethal.

Based on studies of human-infecting coronaviruses, both clinically and molecularly, he agreed with the scientific conclusion that the virus did not escape from a laboratory, it was not genetically modified and it is probably a product of nature.

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The Enemy Is no Longer Invisible, Greek Professor of Genetics Says - The National Herald

Biochemistry

Coronavirus Massive Simulations Completed on Supercomputer – UC San Diego Health

A coronavirus envelope all-atom computer model is being developed by the Amaro Lab of UC San Diego on the NSF-funded Frontera supercomputer of TACC at UT Austin. Biochemist Rommie Amaro hopes to build on her recent success with all-atom influenza virus simulations (left) and apply them to the coronavirus (right). Credit: Lorenzo Casalino (UC San Diego), TACC

Scientists are preparing a massive computer model of the coronavirus that they expect will give insight into how it infects in the body. They've taken the first steps, testing the first parts of the model and optimizing code on the Frontera supercomputer at the University of Texas at Austin. The knowledge gained from the full model can help researchers design new drugs and vaccines to combat the coronavirus.

UC San Diegos Rommie Amaro is leading efforts to build the first complete all-atom model of the SARS-COV-2 coronavirus envelope, its exterior component.

Rommie Amaro, Professor of Chemistry and Biochemistry, University of California, San Diego.

If we have a good model for what the outside of the particle looks like and how it behaves, we're going to get a good view of the different components that are involved in molecular recognition, said Amaro, a professor of chemistry and biochemistry.

Molecular recognition involves how the virus interacts with the angiotensin converting enzyme 2 (ACE2) receptors and possibly other targets within the host cell membrane.

The coronavirus model is anticipated by Amaro to contain roughly 200 million atoms, a daunting undertaking, as the interaction of each atom with one another has to be computed. Her team's workflow takes a hybrid, or integrative modeling approach.

We're trying to combine data at different resolutions into one cohesive model that can be simulated on leadership-class facilities like Frontera, Amaro said. We basically start with the individual components, where their structures have been resolved at atomic or near atomic resolution. We carefully get each of these components up and running and into a state where they are stable. Then we can introduce them into the bigger envelope simulations with neighboring molecules.

On March 12-13, the Amaro Lab ran molecular dynamics simulations on up to 4,000 nodes, or about 250,000 processing cores, on Frontera at the Texas Advanced Computing Center at the University of Texas at Austin.

Amaro's work with the coronavirus builds on her success with an all-atom simulation of the influenza virus envelope, published in ACS Central Science, in February 2020. She said that the influenza work will have a remarkable number of similarities to what they're now pursuing with the coronavirus.

The NSF-funded Frontera supercomputer of the Texas Advanced Computing Center at UT Austin is ranked #5 fastest in the world and #1 for academic systems, according to the November 2019 Top500 rankings. (Credit: TACC)

It's a brilliant test of our methods and our abilities to adapt to new data and to get this up and running right off the fly, Amaro said. It took us a year or more to build the influenza viral envelope and get it up and running on the national supercomputers. For influenza, we used the Blue Waters supercomputer, which was in some ways the predecessor to Frontera. The work, however, with the coronavirus obviously is proceeding at a much, much faster pace. This is enabled, in part because of the work that we did on Blue Waters earlier.

According to Amaro, these simulations will provide new insights into the different parts of the coronavirus that are required for infectivity.

And why we care about that is because if we can understand these different features, scientists have a better chance to design new drugs; to understand how current drugs work and potential drug combinations work. The information that we get from these simulations is multifaceted and multidimensional and will be of use for scientists on the front lines immediately and also in the longer term, Amaro explained. Hopefully, the public will understand that there's many different components and facets of science to push forward to understand this virus. These simulations on Frontera are just one of those components, but hopefully an important and a gainful one.

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Coronavirus Massive Simulations Completed on Supercomputer - UC San Diego Health