Culture

CHAMPAIGN, Ill. -- Researchers have developed the first computational model of a human cell and simulated its behavior for 15 minutes - the longest time achieved for a biological system of this complexity. In a new study, simulations reveal the effects of spatial organization within cells on some of the genetic processes that control the regulation and development of human traits and some human diseases.

The study, which produced a new computational platform that is available to any researcher, is published in the journal PLOS Computational Biology.

"This is the first program that allows researchers to set up a virtual human cell and change chemical reactions and geometries to observe cellular processes in real time," said Zhaleh Ghaemi, a research scientist at the University of Illinois at Urbana-Champaign and lead author of the study.

Working off the notion the insides of cells are packed with various organelles and molecules, the group, led by U. of I. chemistry professor Zaida Luthey-Schulten, focuses on how the movement of individual molecules around the many obstacles affects the chemical reactions inside cells.

To test the new model, the team performed simulations of a process called RNA splicing, which is one of the most complex cellular processes and a hallmark of human cellular biology, the researchers said.

"RNA splicing changes the messenger RNA molecules that carry information needed from DNA to form proteins," Ghaemi said. "The process uses a complex cellular machine - called a spliceosome - that requires the trafficking of precursor and mature components around the highly compartmentalized parts of a cell. This makes RNA splicing ideal for studying how spatial arrangement affects the various chemical reactions that take place in cells."

The new simulations revealed a rationale for why precursors of the spliceosome move between the nucleus and cytoplasm compartments, the researchers said.

"Even though this movement seems somewhat inefficient and counterintuitive at first glance, our simulations indicate that they are essential to the proper RNA splicing, and therefore protein synthesis," said Martin Gruebele, a chemistry professor and study co-author. "When protein synthesis goes awry, it can lead to disease, including cancer,"

The researchers designed the computational platform to model a variety of cellular processes while being fully customizable by the researcher using it. "For example, we could use this model to observe what types of proteins will form if the RNA-splicing process were to remove only two parts of a DNA sequence instead of three," Luthey-Schulten said. "This could provide insights into how different proteins form and influence the development of cancer cells."

Although the most comprehensive human cell model to date, the computational model still has ample room for advancement and customization to study other cellular processes, the researchers said.

"This simulation allowed us to observe the RNA splicing for 15 minutes," Gruebele said. "Ultimately, we would like to be able to run the program for much longer and include all of the proteins that are required for gene replication, allowing us to observe cell division in real-time. The possibilities for our group - and others because the program is open access - are endless."

Nationwide survey data on more than 230,000 U.S. adolescents over the period 2005 to 2018 suggest that anxiety, depression, suicidal thoughts, and other "internalizing" problems account for an increasing share of the adolescent mental health burden, according to a study from researchers at Johns Hopkins Bloomberg School of Public Health and Columbia University.

The study, to be published online March 25 in JAMA Psychiatry, also found that the percentage of adolescent girls seeking mental health care each year rose significantly during the period, as did the use of outpatient mental health care services by adolescent girls.

"We aren't sure why this is occurring, but it is clear from this evidence and other epidemiological studies that anxiety, depression, and other internalizing problems are becoming more prevalent among adolescents relative to other types of mental health problems," says study lead author Ramin Mojtabai, MD, PhD, MPH, a professor in the Department of Mental Health at the Bloomberg School.

Much of what is known about rates of depression and other mental health problems among U.S. adolescents comes from the U.S. Substance Abuse and Mental Health Services Administration's National Survey of Drug Use and Health (NSDUH), an annual nationwide survey of tens of thousands of Americans age 12 and up. NSDUH data have shown, for example, that at the time of the 2017 survey, 20 percent of adolescent girls ages 12 to 17 reported having had at least one major depressive episode in the prior year, compared to 8.7 percent of adult women.

In the new study, Mojtabai and co-author Mark Olfson, MD, PhD, of Columbia University's Vagelos College of Physicians and Surgeons, examined long-term trends in NSDUH data on adolescents with an analysis of survey data from January 1, 2005 to December 31, 2018. The researchers grouped the 14 annual surveys into seven sets of two consecutive surveys, to address short-term variability in the data and make longer-term trends more evident.

During the 2005 to 2018 period, 203,070 adolescents had been interviewed, and of these 47,090 (19.7 percent) reported prior-year treatment or counseling for mental health problems. Mojtabai and Olfson found that the percentage of surveyed adolescents who reported treatment or counseling didn't change significantly from 2005-06 to 2017-18. However, the proportion of adolescent girls reporting treatment or counseling did rise significantly, from an average of 22.8 percent in the 2005-06 surveys to 25.4 percent in 2017-18, an 11.4 percent increase, while the proportion of boys reporting treatment or counseling declined from 17.8 percent to 16.4 percent, a decrease of 7.9 percent, over the same interval. Most of those changes occurred after 2011-12.

The mental health problems were categorized by researchers into several categories including internalizing problems (anxiety, depression, suicidal thinking, somatization disorders), externalizing problems (conduct and substance-use problems), relationship problems, and problems at school. Mojtabai and Olfson found that internalizing problems accounted for an increasing proportion of the total during the study window--from 48.3 percent in 2005-06 to 57.8 percent in 2017-18, a 19.7 percent increase. Among internalizing problems, suicidal thoughts or attempts increased most sharply, by 63.3 percent, from 15.0 percent to 24.5 percent of the total.

"These trends in the types of reported problems were seen across different care settings, from school counseling to inpatient mental health services," Mojtabai says.

There were also trends in the types of services reported by the survey respondents; in particular, the researchers found a 15.8 percent increase in reliance on outpatient mental health services--such as psychiatric and psychotherapy clinics--which 67.3 percent of respondents reported using in 2017-18 vs. 58.1 percent in 2005-06. There was a corresponding drop in the reported use of school counseling services, from 49.1 percent to 45.4 percent, a decrease of 7.5 percent. Changes in the use of inpatient mental health care and general medical services were slight.

The authors did not attempt to address these trends in this study, although they did note that other research suggests a link between internet social media use and texting, on the one hand, and increased rates of depression on the other. Increased use of psychiatic drugs for children, and decreased exposure to environmental lead compounds--which are known to cause neurological problems associated with aggressive behavior--are two other factors noted that might explain declines in externalizing problems.

Psychiatrists have long observed that mental health problems are more likely to manifest in girls and women as internalizing problems, and in boys and men as externalizing problems. The increased proportion of girls reporting mental health problems during 2005-18 is thus a potential factor underlying the observed increase in internalizing problems. However, Mojtabai and Olfson found that this trend remains in place even when adjusting for sex and other factors. "This trend cannot be completely explained by the larger proportion of girls seeking treatment in later years," he says.

He adds that policymakers, education system planners, and the medical profession should be aware of the observed trends in the uses of different mental health services, in particular the shift away from school counseling towards more use of outpatient mental health services.

A transport protein that is used by the human pathogen Mycobacterium tuberculosis to import vitamin B12 turns out to be very different from other transport proteins. It contains a huge water-filled cavity, in which hydrophilic substances are transported across the cell membrane. This discovery, which changes our understanding of bacterial physiology, was made by imaging the transport protein using cryo-electron microscopy. The results were published in the journal Nature on 26 March.

The tuberculosis bacterium has all the genes required to produce vitamin B12 but, for some reason, it still needs to import this vitamin for successful cell division. To do so, it uses a transport protein that is part of a large family of ATP-binding cassette (ABC) transporters. Interestingly, the vitamin B12 transporter is also implicated in the transport of antimicrobial peptides such as bleomycin. 'And it is very odd to have a single transporter for two very different types of molecules,' says Professor of Biochemistry Dirk Slotboom.

Cavity

Slotboom and his team, together with their colleague Albert Guskov, set out to elucidate the protein structure of the enigmatic transporter. 'This was a long process but we finally cracked it using cryo-electron microscopy,' says Slotboom. This was performed at the SLAC National Accelerator Laboratory, Menlo Park, CA, USA. The structure revealed a major surprise: a water-filled cavity that spans the entire cell membrane, measuring a massive 7,700 cubic Angstrom. 'That is as big as seven vitamin B12 molecules.'

This cavity appears to simply transport water together with any substances that might be in it. 'You could compare it with a sluice,' explains Slotboom. 'You let the water in and everything that is in it.' It does explain why the transporter can handle both antibiotic peptides and vitamin B12. Since it is non-selective, it must be an inefficient transport system. This does not matter for the uptake of vitamin B12 by Mycobacterium tuberculosis, as the cells only need to take up very few of these molecules during their reproductive cycle, which lasts around 24 hours.

Antibiotics

The non-selective transport system is totally different from known transporters. 'As such, it changes the way that we look at the physiology of bacteria. There are strong indications that other bacterial species have a similar system, which means that they pick up random molecules from their environment.' It also offers an interesting perspective on the treatment of tuberculosis: 'If we could stimulate the activity of this transporter, it might import antibiotics more efficiently, making it easier to kill these cells. We realize, though, that this may not be straightforward, as the bacterium uses effective strategies to keep antibiotics out.'

The next step is to find out how the transporter works. 'We expect that inside the cell, the sluice is emptied by binding and hydrolysing ATP. But we do not know how it opens on the outside, to let new molecules in.' The transport protein is a dimer and the two halves appear to protrude on the outside - where they may somehow open up to let fresh cargo in. 'Maybe we can find a way to loosen this cap and let more antibiotics in.'

Human cells

There is also a distinct possibility that a similar sluice-type transporter is present in human cells, says Slotboom. In our intestines, vitamin B12 is first bound to a peptide called intrinsic factor and then taken up by epithelial cells. 'It ends up in lysosomes, vesicles full of enzymes, where the intrinsic factor is degraded. Next, the vitamin B12 is released from the lysosome into the cells. I strongly suspect that this involves a similar non-specific transporter.'

What The Study Did: This observational study of 416 patients in Wuhan, China, with confirmed coronavirus disease 2019 (COVID-19) reports that cardiac injury is a common condition among hospitalized patients with COVID-19 and it is associated with higher risk of in-hospital mortality.

Authors: Bo Yang, M.D., Ph.D., and He Huang, M.D., Ph.D., of Renmin Hospital of Wuhan University in China, are the corresponding authors.

To access the embargoed study: Visit our For The Media website at this link https://media.jamanetwork.com/ 

(doi:10.1001/jamacardio.2020.0950)

Editor's Note: The article includes funding/support disclosures. Please see the articles for additional information, including other authors, author contributions and affiliations, conflicts of interest and financial disclosures, and funding and support.

What The Study Did: Researchers examined changes over time in the kinds of mental health problems for which adolescents in the United States received care and where they got that care in this survey study with findings that should be interpreted within the context of several limitations including self-reported information.

Authors: Ramin Mojtabai, M.D., Ph.D., M.P.H., of the  Johns Hopkins Bloomberg School of Public Health in Baltimore, is the corresponding author.

To access the embargoed study: Visit our For The Media website at this link https://media.jamanetwork.com/

(10.1001/jamapsychiatry.2020.0279)

Editor's Note: Please see the article for additional information, including other authors, author contributions and affiliations, financial disclosures, funding and support, etc.

CRISPR-Cas9 gene editing technology is best known for its potential role in correcting genetic diseases. But it can also be used as a tool to find genes that act as supporting players, making the disease better or worse. Such genes might make good targets for new treatments.

A new study led by Louis Kunkel, PhD, and research fellow Angela Lek, PhD at Boston Children's Hospital used CRISPR-Cas9 to better understand facioscapulohumeral muscular dystrophy (FSHD) and explore potential treatments. FSHD causes muscle weakness in the face, shoulder blades, and upper arms, and currently has no treatment other than supportive care.

In FSHD, the gene DUX4, normally active mainly during fetal development, is inappropriately "turned on." This causes toxic DUX4 protein to be produced in muscle cells when it shouldn't be, leading to cell death and muscle weakness.

Kunkel, Lek, and colleagues wondered if other genes could be targeted to prevent or compensate for this problem. They decided to use CRISPR-Cas9 to systematically mutate every gene in the genome. Their goal: to find genes that, when knocked out, enable human muscle cells to survive even when the DUX4 protein is being made.

"We essentially utilized the CRISPR screen technique as a shortcut to illuminate 'druggable' pathways for FSHD," says Lek, the paper's first author.

Preventing muscle cells from dying

The CRISPR-Cas9 screening process yielded about a half-dozen strong "hits." Among them were several genes that play a role in the cellular response to low-oxygen conditions, or hypoxia. That, it turns out, is the main driver of cell death caused by DUX4. When the team exposed muscle cells to compounds known to inhibit this hypoxia response, the cells stayed alive.

"Our results show that knockout of key genes involved in hypoxia signaling can desensitize cells to toxicity from DUX4, and prevent them from dying," says Kunkel.

Going a step further, the team created muscle cell lines from actual patients with FSHD. When treated with the same compounds, these cells showed fewer of the known biomarkers of the disease.

Finally, the researchers created two live zebrafish models of FSHD. When they exposed the fish to compounds that inhibit hypoxia signaling, the fish showed improvements in muscle structure and function and more swimming activity.

Moving forward

Kunkel and Lek have filed a patent application covering their discoveries. Lek, now at the Yale School of Medicine, is moving the drug experiments into mouse models of FSHD, while Kunkel plans further zebrafish studies at Boston Children's.

"The most encouraging finding about this study is that we discovered that there are FDA-approved drugs that can overcome DUX4's toxic effect," says Lek. "We now have a collection of drugs to test and figure out which is most suitable for long-term dosing in patients with FSHD."

Kunkel believes the process used in this study could be applied to many other diseases.

"Our approach could provide an accelerated path to understanding complex genetic diseases, discovering therapeutic targets, and testing potential treatments," he says.

New artifacts uncovered at the Waim archaeological site in the highlands of New Guinea - including a fragment of the earliest symbolic stone carving in Oceania - illustrate a shift in human behavior between 5050 and 4200 years ago in response to the widespread emergence of agriculture, ushering in a regional Neolithic Era similar to the Neolithic in Eurasia. The location and pattern of the artifacts at the site suggest a fixed domestic space and symbolic cultural practices, hinting that the region began to independently develop hallmarks of the Neolithic about 1000 years before Lapita farmers from Southeast Asia arrived in New Guinea. While scientists have known that wetland agriculture originated in the New Guinea highlands between 8000 and 4000 years ago, there has been little evidence for corresponding social changes like those that occurred in other parts of the world. To better understand what life was like in this region as agriculture spread, Ben Shaw et al. excavated and examined a trove of artifacts from the recently identified Waim archaeological site. "What is truly exciting is that this was the first time these artifacts have been found in the ground, which has now allowed us to determine their age with radiocarbon dating," Shaw said. The researchers analyzed a stone carving fragment depicting the brow ridge of a human or animal face, a complete stone carving of a human head with a bird perched on top (recovered by Waim residents), and two ground stone pestle fragments with traces of yam, fruit and nut starches on their surfaces. They also identified an obsidian core that provides the first evidence for long-distance, off-shore obsidian trade, as well as postholes where house posts may have once stood.

In this post-industrialization age, electricity has become the backbone of our society. However, using fossil fuels to generate it is not the best option because of their limited availability and harmful nature. In the last two decades, significant efforts have been made to develop techniques to foster sustainable energy. Against this backdrop, solid oxide fuel cells (SOFCs) have risen as a clean and highly efficient alternative that can generate electrical energy. However, a major drawback of SOFCs is their high operating temperatures, restricting their widespread usage.

Various previous studies have attempted to overcome this drawback by improving conductivity at high temperatures using fluorite type oxides like CeO2-δ. Normally, these fluorite oxides are available in porous form, and their mechanism of conductivity is believed to be dependent on the surface adsorption of water molecules, which is the process of adhesion of atoms or molecules to a surface.

A team of scientists from Tokyo University of Science, led by Dr Tohru Higuchi, took this research one step forward. In their new study published in Nanoscale Research Letters, the researchers explored the effect of "doping," which is the process of adding impurities to alter their conductivity, on these oxides, which are a very good candidate for SOFCs. Researchers "doped" the oxide with a metal called Samarium (Sm). Then, they deposited thin films of this doped oxide on a substrate of Aluminium oxide (Al2O3) in a specific direction known to enhance the conductivity. Dr Higuchi considers this an advantage, stating, "When considering practical devices, thin film forms are more suitable than porous or nanocrystalline forms."

Then, the research team characterized the crystalline quality and electronic structure of the novel film. They also compared the difference in conductivity between this novel film and thick ceramic oxides commonly used in the industry. Their findings revealed that the ceramic sample exhibited poor crystallinity and had poor proton conductivity compared to the thin film sample.

What's more, the "resistivity"--or the resistance to electrical flow--of the thin film was found to decrease with increasing humidity due to the "proton conduction" in fluorite type oxides, as explained by Grotthuss mechanism. A water molecule consists of two atoms of oxygen and one atom of hydrogen. The molecules of water have bonds between them, called "hydrogen bonds." The Grotthuss mechanism (or the "hop-turn" mechanism) allows the water molecules to be split into ions that increase the conductivity, and hence they move from one hydrogen bond to another. The novel film was found to exhibit surface protonic conduction in the low temperature region below 100°C.

This novel film, with its high conductivity at room temperatures, is sure to have several applications in the future. As far as SOFCs are concerned, Dr Higuchi concludes, "Our study on electrolyte membranes presents radical findings that can help lower the operating temperature of SOFCs, and may be an alternative system for making more practical devices using fluorite type oxides in SOFCs, and open up new avenues for nuclear and thermal power generation in the future."

Most people know about the painkiller paracetamol, commonly used against headaches and ingested orally.

However, in hospitals, paracetamol is administered intravenously. In this way, doctors and nurses can help critically ill patients who are unable to swallow one or more pills.

Furthermore, the substance acts much faster intravenously, and the method allows healthcare professionals to control the doses and the timing of their effect very precisely.

Nevertheless, the intravenous paracetamol has a serious side effect: namely, a temporary large drop in blood pressure.

'Previous studies suggest it is quite a sizable drop. We are, for example, talking about drops in the range of 25-30 mm Hg from a systolic pressure of 120, and we now believe that we know the mechanism underlying this dangerous side effect', says Assistant Professor Thomas Qvistgaard Jepps from the Department of Biomedical Sciences.

He adds that the drop in blood pressure is found in both common and critically ill patients. In the latter category, six out of ten have been reported to experience the side effect. One third of these to such an extent that it requires medical intervention.

This research is rather timely, given the unprecedented COVID-19 crisis and dramatic increase in critically ill patients that maybe receiving intravenous paracetamol in the hospitals to help with pain and fever management.

Different kinds of metabolism
Despite the statistics, intravenous paracetamol is considered to be a relatively stable drug that is used increasingly in the healthcare system, even though many doctors and nurses are aware of the potential side effects.

On this background, Thomas Qvistgaard Jepps and his team set out to find a cause for the steep drop in blood pressure. As the first in the world, they have now succeeded through studies in rats.

'Paracetamol bypasses the liver when administered intravenously, therefore it is metabolised differently to when you ingest it orally', says Thomas Qvistgaard Jepps, adding:

'It still gets metabolised, but it happens elsewhere in the body, where the subsequent chemicals can cause an effect that wouldn't normally happen, if the drug was taken orally'.

The Assistant Professor emphasises that most people should not be afraid to take painkillers as usual. As long as you still stay within the maximum recommended dose.

The solution to the pressure drop
More precisely, it appears that the residual products of the painkiller affect some of the potassium channels, which, among other things, regulate how your blood vessels contract and relax, thereby controlling your blood pressure.

By using drugs that block these potassium channels, specifically, the research team subsequently succeeded in reducing the side effect of the large drop in blood pressure in the test rats.

'Because we have identified the mechanism of how the side effect occurs, we believe we are able to offer a potential pharmaceutical design for a new kind of co-therapy: A type of paracetamol infused with another drug that prevents the drop in blood pressure', says Thomas Qvistgaard Jepps.

'However, blockers of the potassium channels we have investigated are not yet approved for human consumption and need to be developed and tested properly. We wouldn't want to replace one side effect with another'.

The next step of the research group is therefore to investigate how drugs that block the potassium channels may be adapted for humans. They are also investigating alternatives for blocking the potassium channels, for example, by affecting the enzymes involved in metabolising paracetamol outside the liver.

CAMBRIDGE, MA -- Researchers at MIT and the University of Colorado at Denver have proposed a stopgap measure that they believe could help Covid-19 patients who are in acute respiratory distress. By repurposing a drug that is now used to treat blood clots, they believe they could help people in cases where a ventilator is not helping, or if a ventilator is not available.

Three hospitals in Massachusetts and Colorado are developing plans to test this approach in severely ill Covid-19 patients. The drug, a protein called tissue plasminogen activator (tPA), is commonly given to heart attack and stroke victims. The approach is based on emerging data from China and Italy that Covid-19 patients have a profound disorder of blood clotting that is contributing to their respiratory failure.

"If this were to work, which I hope it will, it could potentially be scaled up very quickly, because every hospital already has it in their pharmacy," says Michael Yaffe, a David H. Koch Professor of Science at MIT. "We don't have to make a new drug, and we don't have to do the same kind of testing that you would have to do with a new agent. This is a drug that we already use. We're just trying to repurpose it."

Yaffe, who is also a member of MIT's Koch Institute for Integrative Cancer Research and an intensive care physician at Boston's Beth Israel Deaconess Medical Center/Harvard Medical School, is the senior author of a paper describing the new approach.

The paper, which appears in the Journal of Trauma and Acute Care Surgery, was co-authored by Christopher Barrett, a surgeon at Beth Israel Deaconess and a visiting scientist at MIT; Hunter Moore, Ernest Moore, Peter Moore, and Robert McIntyre of the University of Colorado at Denver; Daniel Talmor of Beth Israel Deaconess; and Frederick Moore of the University of Florida.

Breaking up clots

In one large-scale study of the Covid-19 outbreak in Wuhan, China, it was found that 5 percent of patients required intensive care and 2.3 percent required a ventilator. Many doctors and public health officials in the United States worry that there may not be enough ventilators for all Covid-19 patients who will need them. In China and Italy, a significant number of the patients who required a ventilator went on to die of respiratory failure, despite maximal support, indicating that there is a need for additional treatment approaches.

The treatment that the MIT and University of Colorado team now proposes is based on many years of research into what happens in the lungs during respiratory failure. In such patients, blood clots often form in the lungs. Very small clots called microthrombi can also form in the blood vessels of the lungs. These tiny clots prevent blood from reaching the airspaces of the lungs, where blood normally becomes oxygenated.

The researchers believe that tPA, which helps to dissolve blood clots, may help patients in acute respiratory distress. A natural protein found in our bodies, tPA converts plasminogen to an enzyme called plasmin, which breaks down clots. Larger amounts are often given to heart attack patients or stroke victims to dissolve the clot causing the heart attack or stroke.

Animal experiments, and one human trial, have shown potential benefits of this approach in treating respiratory distress. In the human trial, performed in 2001, 20 patients who were in respiratory failure following trauma or sepsis were given drugs that activate plasminogen (urokinase or streptokinase, but not tPA). All of the patients in the trial had respiratory distress so severe that they were not expected to survive, but 30 percent of them survived following treatment.

That is the only study using plasminogen activators to treat respiratory failure in humans to date, largely because improved ventilator strategies have been working well. This appears not to be the case for many patients with Covid-19, Yaffe says.

The idea to try this treatment in Covid-19 patients arose, in part, because the Colorado and MIT research team has spent the last several years studying the inflammation and abnormal bleeding that can occur in the lungs following traumatic injuries. It turns out that Covid-19 patients also suffer from inflammation-linked tissue damage, which has been seen in autopsy results from those patients and may contribute to clot formation.

"What we are hearing from our intensive care colleagues in Europe and in New York is that many of the critically ill patients with Covid-19 are hypercoagulable, meaning that they are clotting off their IVs, and having kidney and heart failure from blood clots, in addition to lung failure. There's plenty of basic science to support the idea that this concept should be beneficial," Yaffe says. "The tricky part, of course, is figuring out the right dose and route of administration. But the target we are going after is well-validated."

Potential benefits

The researchers will test tPA in patients under the FDA's "compassionate use" program, which allows experimental drugs to be used in cases where there are no other treatment options. If the drug appears to help in an initial set of patients, its use could be expanded further, Yaffe says.

"We learned that the clinical trial will be funded by BARDA [the Biomedical Advanced Research and Development Authority], and that Francis Collins, the NIH director, was briefed on the approach yesterday afternoon," he says. "Genentech, the manufacturer of tPA, has already donated the drug for the initial trial, and indicated that they will rapidly expand access if the initial patient response is encouraging."

Based on the latest data from their colleagues in Colorado, these groups plan to deliver the drug both intravenously and/or instill it directly into the airways. The intravenous route is currently used for stroke and heart attack patients. Their idea is to give one dose rapidly, over a two-hour period, followed by an equivalent dose given more slowly over 22 hours. Applied BioMath, a company spun out by former MIT researchers, is now working on computational models that may help to refine the dosing schedule.

"If it were to work, and we don't yet know if it will, it has a lot of potential for rapid expansion," Yaffe says. "The public health benefits are obvious. We might get people off ventilators quicker, and we could potentially prevent people from needing to go on a ventilator."

The hospitals planning to test this approach are Beth Israel Deaconess, the University of Colorado Anschultz Medical Campus, and Denver Health. The research that led to this proposal was funded by the National Institutes of Health and the Department of Defense Peer Reviewed Medical Research Program.

The study, conducted by Imperial College London on data from 2009 to 2018, looked at a third of a million passenger responses to Customer Satisfaction Surveys (CSSs) from 28 cities across four continents.

They found that on average, women are ten per cent more likely than men to feel unsafe on metro trains (trains that go underground) and six per cent more likely than men to feel unsafe on buses.

The largest difference between women and men's perceptions of safety was in Europe, where women were 12 per cent more likely to report feeling unsafe than men.

The smallest difference was in South America, where women were nine per cent more likely to report feeling unsafe than men.
The researchers say the findings highlight an important social issue that could be preventing some women from thriving both personally and professionally.

Lead author Laila Ait Bihi Ouali, of Imperial's Department of Civil and Environmental Engineering, said: "Feeling unsafe can lead to social, professional, economic, and health problems for those affected. In this case, women who feel unsafe on public transport might turn down shift work at certain times of day, or avoid social or work events that require travelling a certain route."

"Our study was conducted on data from before the coronavirus outbreak, but its message will be just as important when life resumes as normal."

The results are published today in Journal of the Royal Statistical Society: Series A.

Safety and satisfaction

Public transport operators send online CSSs every year to passengers that are designed to measure general feelings of satisfaction with their networks. The surveys ask passengers their level of agreement with various statements about availability, time, information, comfort, security, customer care, accessibility, environment, and overall satisfaction.

The response options are usually: agree strongly; agree; neither agree nor disagree; disagree; or disagree strongly.

To carry out the study, the researchers looked at 327,403 completed responses to CSSs from 2009 to 2018.

As well as measuring overall satisfaction scores, they focussed on responses to three questions [see notes to Eds] pertaining to feelings of 'security' and assigned numbers from one to five for each potential response (one for 'agree strongly; five for 'disagree strongly') to quantify the responses.

They then compared the scores between men and women, and looked at whether they differed alongside characteristics of the transport network like rates of violence on the network, numbers of cars per train, and busyness of vehicles and stations.

They found that around half of women surveyed felt safe on urban public transport (45 per cent felt safe in metro trains and stations; 55 per cent felt safe in buses), but that women were ten per cent more likely than men to report feeling unsafe in metro trains and stations, and six per cent more likely than men to feel unsafe in buses.

The study also showed that women were overall less satisfied than men with public transport services, but the gap between genders for satisfaction was far less than for safety (gap of three per cent gap for satisfaction on metros; 2.5 per cent gap for satisfaction on buses). The researchers say that this demonstrates that safety is an important part of overall passenger satisfaction.

Carriage characteristics

The team found that having more staff on metro trains doesn't seem to be correlated with feelings of safety, but that more staff at stations were correlated with increased feelings of safety, as were metro trains, metro stations, and buses with more passengers onboard.

Higher rates of violence on transport networks - particularly robberies - were linked to decreased feelings of safety, as were having more carriages per train, and carriages that were larger.

The researchers say that quantifying feelings of safety on public transport with operators' own data could help contribute towards creating tangible goals, which operators could use to improve people's feelings of safety.

Laila said: "Our research exposes a gap in passenger safety levels that's often overlooked. We hope that by putting a figure on feelings of safety, urban metro and bus companies can take measures to boost women's feelings of safety and reduce the gap between genders."

Study co-author Professor Dan Graham, also of Imperial's Department of Civil and Environmental Engineering, said: "Feeling unsafe on public transport can prevent people from living as they otherwise would at certain times or on certain routes. We hope our results will highlight the gender gap in feelings of safety and nudge transport companies to implement changes to help women feel safer using public transport."

Next, the researchers will look more closely at the links between transport characteristics and feelings of safety to try to decipher which characteristics companies might change to boost feelings of safety in passengers.
They will also look at how far the gap between men and women's perceptions of safety reflects the wider urban environment.

COLUMBUS, Ohio - During the COVID-19 pandemic, every frequently touched surface outside our home seems as dangerous as a hot pot right out of the oven. We won't get burned if we touch it, but we might get infected with a potentially dangerous virus.

A recent study suggests that even organized efforts to clean surfaces can fall short, a reminder for us all that keeping our surroundings clean may require some additional work.

For 5 ½ weeks, researchers tagged surfaces of a small-animal veterinary practice daily with a fluorescent dye visible only under black light. They checked tagged surfaces 24 hours later to see if the marks were showing. Surfaces were considered cleaned if the dye was completely removed.

Results showed that overall, only half of all surfaces were adequately cleaned during the study period. Human-touch surfaces - such as medical instruments, dog run handles, and computer mice and keyboards - were cleaned less frequently than areas touched primarily by animals. The results were similar to studies from other veterinary clinics.

The researchers recommended creating checklists of surfaces that need to be regularly cleaned and educating all staff on the importance of proper cleaning to protect animal and human health.

"The concept of infectious diseases is around us all the time, but now it's more important than ever to take steps to protect ourselves," said senior study author Jason Stull, assistant professor of veterinary preventive medicine at The Ohio State University.

"A recent study concluded the coronavirus causing COVID-19 has the ability to survive on certain types of surfaces for hours to a few days. At veterinary practices, other businesses and certainly human hospitals, surface cleaning and disinfection is extremely important. People come in and may contaminate an area and that area potentially can serve as a source of infection for other people."

The study is published in the February issue of the Journal of Small Animal Practice.

Stull specializes in veterinary infection control, including prevention of diseases that animals can share with each other or pass to humans - such as Salmonella, E. coli and parasites.

For the current work, Stull and colleagues assessed almost 5,000 surfaces over the course of the study. On average, 50 percent of surfaces were cleaned, with broad variations by type of surface and hospital location. The human-touch surfaces were the least likely to be cleaned.

The study assessed everyday cleaning practices in a place where people spend lots of time with different animals and different people. It's not too much of a stretch to apply some lessons to what we're experiencing now with COVID-19, Stull said.

"Plenty of industries and groups outside of human health care have ramped up their efforts to clean and disinfect common-touch surfaces. The take-home messages from our study can have important parallels for others, such as other veterinary clinics, but also groups such as grocery stores.

"Our study also highlights that, despite our best efforts, 100 percent cleaning and disinfection is unlikely to occur. This is important to remember, as regardless of where you visit, it's also best to assume surfaces may be contaminated - and before you come back into your home, you should follow the recommendations to clean your hands and clean items you've handled."

At home, Stull said, it makes sense to concentrate on cleaning common-touch surfaces like doorknobs and countertops.

"For the average person, it's thinking about your list of things in your own home and ensuring that in some way that you're actually hitting those pieces with reasonable effort," he said.

On a normal day, people who have touched commonly shared surfaces should wash their hands before eating or scratching their noses. But will we remain diligent about this level of personal cleanliness - and community health - once the worst of the coronavirus threat is behind us?

"People have a tendency to swing from extremes," Stull said. "Changing the innate behaviors of people is always difficult, and we've struggled in human and veterinary health care to change these everyday practices.

"The hard part is continuing these efforts. When we get to the end of this, and at some point that will happen, you will likely see people revert back to their norm. What we need is a culture shift, so people recognize that infection control through hand-washing and thorough cleaning of shared surfaces is a critically important thing we can all do all the time, and it has measurable impact."

The cover for issue 12 of Oncotarget features Figure 11, "Global analyses of the RNA-Seq data of LNCaP empty vector and LNCaP cells overexpressing hPCL3S (Clone 12)" by Abdelfettah, et al.

These proteins contain a TUDOR domain binding H3K36me3, two PHD domains and a Winged-helix domain involved in GC-rich DNA binding.

The human PCL3 locus encodes the full-length hPCL3L protein and a shorter isoform, hPCL3S containing the TUDOR and PHD1 domains only.

A mutant hPCL3S unable to bind H3K36me3 increased proliferation and migration of LNCa P similarly to wt hPCL3S whereas inactivation of its PHD1 domain decreased proliferation.

Dr. Dominique Leprince from the University de Lille, CNRS, Institut Pasteur de Lille, UMR 8161m M3T, Mechanisms of Tumorigenesis and Targeted Therapies, F-59000 Lille, France said, "Prostate cancer (PCa) is the second most common type of cancer diagnosed worldwide and is still a leading cause of death despite recent research advances."

"Prostate cancer (PCa) is the second most common type of cancer diagnosed worldwide and is still a leading cause of death despite recent research advances"

- Dr. Dominique Leprince, University de Lille, CNRS, Institut Pasteur de Lille, UMR 8161m M3T, Mechanisms of Tumorigenesis and Targeted Therapies

Two of most commonly used prostate cancer cell lines LNCa P and PC3 are representative of prostatic adenocarcinoma and of Small Cell Neuroendocrine Carcinomas, respectively.

These proteins share a structured N-terminal domain consisting of a TUDOR domain, two PHD domains followed by a Winged-helix domain involved in GC-rich DNA binding and a C-terminal reverse Chromodomain.

Indeed, PHF1 through its PHD1 domain is the only human Polycomb-like protein capable of inducing cell quiescence by interacting with P53 to stabilize it independently of its TUDOR domain and thus of its binding at chromatin.

In this study, the authors have quantified the expression levels of both hPCL3 isoforms in primary prostate tumors as well as in the hormone-dependent LNCa P and hormone-independent DU145 and PC3 prostate cancer cell lines.

Collectively, their results provide insights into a new mechanism whereby AR-independent prostate cancer cell lines acquire heightened ability to proliferate and migrate and highlight hPCL3S targeting as a new potential interventional strategy against castration resistant prostate cancers.

The Leprince Research Team concluded in their Oncotarget Research Paper, "we demonstrated that overexpression of hPCL3S promoted proliferation, anchorage-independent growth and migration in human LNCaP prostate cancer cells whereas silencing of endogenous hPCL3S in DU145 and PC3 prostate cancer cells impaired these effects. Furthermore, our results suggested that hPCL3S did not act through the perturbation of PRC2 activity but rather mainly through chromatin-independent effects relying on its PHD1 domain. Therefore, our studies could have identified the overexpression of hPCL3S as a new alteration contributing to tumor progression in prostate cancer through the emergence of a rapidly growing cell population of neuroendocrine-like cells."

In the treatment of tumors, microenvironment plays an important role. It often contains immune cells that are so changed that they promote tumor growth. In the journal Angewandte Chemie, scientists have introduced a method by which cell samples from tumors and their surroundings can rapidly (under 1 hour) be cycled through staining, destaining, and then restaining with fluorescent antibodies--through attachment of a "black hole quencher" (fluorescence quencher) by means of "click chemistry".

To effectively and precisely fight a tumor, it is important to specifically characterize not only the cells of the tumor but also those in its microenvironment, including tumor-infiltrating immune cells. Until now, analyses of these dynamic changes with conventional biopsies and tissue sections could take days to weeks, or not occur at all prior to treatment. One alternative method is fine needle aspiration, in which only a few thousand cells are taken from different parts of a tumor and its surroundings. This method has few risks and is faster because it does not require embedding or sectioning. However, to obtain a representative estimate of the immune cell populations in the tumor's microenvironment, many different stains must be carried out. Because the number of cells is so small, this means that the same sample must be repeatedly stained, destained, and stained again. However, the cells are too delicate for conventional, harsh destaining, and the procedures would take too long.

A team headed by Jonathan Carlson and Ralph Weissleder at the Massachusetts General Hospital Research Institute and Harvard Medical School (Boston, MA, USA) has now developed an ultrafast, highly efficient, and gentle cyclic method for multiplexed protein profiling of individual cells, which allows for numerous different stainings. Instead of splitting off the dye or bleaching it, the fluorescence of the stain is simply "switched off" with a black hole quencher. Black hole quenchers absorb the energy of a fluorescence dye over the entire visible spectrum and convert it to heat as soon as they get near enough. This switches off the glow of the dye.

The method goes like this: using a connector that contains a trans-cyclooctene group, a fluorescent dye is attached to antibodies that specifically recognize the characteristic marker molecules of the cells. If the target marker is in a given sample, the antibody binds to it and the fluorescence can be detected. Then the quencher carrying a tetrazine group is added. Using this tetrazine group and the trans-cyclooctene, the quencher can simply be attached by being "clicked" on as though with a snap (hence the term click chemistry for this type of reaction). The quencher is thus site-specifically and very quickly and efficiently brought near to the dye, immediately quenching its fluorescence. The rapidity of this click reaction is remarkable, running orders of magnitude faster than expected. The reason for this may be the strong interaction between the fluorescence dye and the quencher.

The next fluorescent antibody can be applied immediately after the fluorescence quenching. The researchers were able to stain twelve different marker molecules in a sample within one hour. This makes it possible to rapidly characterize the immune cell populations in tumors to select the most suitable treatments.

A recent study from North Carolina State University finds that people who manage to balance living in the moment with planning for the future are best able to weather daily stress without succumbing to negative moods.

"It's well established that daily stressors can make us more likely to have negative affect, or bad moods," says Shevaun Neupert, a professor of psychology at NC State and corresponding author of a paper on the recent work. "Our work here sheds additional light on which variables influence how we respond to daily stress."

Specifically, the researchers looked at two factors that are thought to influence how we handle stress: mindfulness and proactive coping.

Mindfulness is when people are centered and living in the moment, rather than dwelling in the past or worrying about the future. Proactive coping is when people engage in planning to reduce the likelihood of future stress.

To see how these factors influence responses to stress, the researchers looked at data from 223 study participants. The study included 116 people between the ages of 60 and 90, and 107 people between the ages of 18 and 36. All of the study participants were in the United States.

All of the study participants were asked to complete an initial survey in order to establish their tendency to engage in proactive coping. Participants were then asked to complete questionnaires for eight consecutive days that explored fluctuations in mindfulness. On those eight days, participants were also asked to report daily stressors and the extent to which they experienced negative mood.

The researchers found that engaging in proactive coping was beneficial at limiting the effect of daily stressors, but that this advantage essentially disappeared on days when a participant reported low mindfulness.

"Our results show that a combination of proactive coping and high mindfulness result in study participants of all ages being more resilient against daily stressors," Neupert says. "Basically, we found that proactive planning and mindfulness account for about a quarter of the variance in how stressors influenced negative affect.

"Interventions targeting daily fluctuations in mindfulness may be especially helpful for those who are high in proactive coping and may be more inclined to think ahead to the future at the expense of remaining in the present."

The paper, "Thinking Ahead and Staying in the Present: Implications for Reactivity to Daily Stressors," is published in the journal Personality and Individual Differences. First author of the paper is Melody Polk, an undergraduate at NC State. The paper was co-authored by Emily Smith and Ling-Rui Zhang, graduate students at NC State. The work was done with support from NC State's College of Humanities and Social Sciences.