Tuesday, April 25, 2023

Research collaboration aims to improve nationwide water quality, restore wetlands


Researchers from the University of South Florida and EPA developed a new classification system that will help improve methods for targeting wetland restoration and protection

Peer-Reviewed Publication

UNIVERSITY OF SOUTH FLORIDA

wetlands 

IMAGE: AERIAL VIEW OF WETLANDS IN ALASKA, NEAR KATMAI AND LAKE CLARK NATIONAL PARKS. view more 

CREDIT: MARK RAINS, USF

TAMPA, Fla. (April 20, 2023) – Wetlands, such as swamps and marshes, are home to some of the planet’s most valuable ecosystems.

They act as sponges, preventing pollution from seeping into streams and other bodies of water, yet the depth of their federal protection is murky. In collaboration with the U.S. Environmental Protection Agency, a University of South Florida geologist has developed the first-ever classification system for wetland connectivity, helping improve water quality and management nationwide.

The new classification system, published recently in Nature Water, demonstrates the effects wetlands have on water quality at a continental scale – invaluable data that can be used to better define whether wetlands are federally regulated under the U.S. Clean Water Act.

“Since the Clean Water Act was established in 1972, we have continued to debate what constitutes our ‘nation’s waters,’ and wetlands continue to be lost due to draining and filling, despite their immense value in controlling the water quality in our major waterways,” said USF geology Professor Mark Rains, who was appointed by the state in 2021 to serve as Florida’s chief science officer. “However we define the ‘nation’s waters’ will have a huge influence on whether we continue to protect the remaining wetlands or if we will lose more.”

The researchers categorized freshwater wetlands into four classes based on their proximity to streams and whether water flows between them at or below the surface. They then used the new classification system to show that wetlands play important roles in controlling a stream’s water quality.

The goal is to provide a better understanding of how wetlands contribute to the chemical, physical and biological integrity of downstream waters, especially nutrient runoff that can cause damaging algal blooms.

“It’s the disruption of these processes that has led to many of the water quality challenges we face today,” Rains said. “My hope is this will be the start of change for the way we think about wetlands, especially those not directly adjacent to streams. This was the most rewarding collaboration of my career – it was a great group of people who were really committed to doing science that serves the public.”

The EPA plans to make this classification system available for researchers to download and use. In addition to its impact on water quality, the system provides researchers and resource managers insight into improved methods for spatially targeting wetland restoration and protection.

“Until now, there hasn’t been a way to classify how wetlands connect to other waters at large scales,” EPA Research Ecologist Scott Leibowitz said. “This has limited our ability to understand how wetland connectivity might contribute to water quality in watersheds.”

Rains says the research doesn’t stop here, as this classification system will likely lead to more projects in the near future. “We still have much to learn about how wetlands connect to downstream waters in different geographic regions,” Rains said. “This classification system gives us a place to start.”

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About the University of South Florida

The University of South Florida, a high-impact global research university dedicated to student success, generates an annual economic impact of more than $6 billion. Over the past 10 years, no other public university in the country has risen faster in U.S. News and World Report’s national university rankings than USF. Serving more than 50,000 students on campuses in Tampa, St. Petersburg and Sarasota-Manatee, USF is designated as a Preeminent State Research University by the Florida Board of Governors, placing it in the most elite category among the state’s 12 public universities. USF has earned widespread national recognition for its success graduating under-represented minority and limited-income students at rates equal to or higher than white and higher income students. USF is a member of the American Athletic Conference. Learn more at www.usf.edu.

How and when do athletes seek mental health support?

Peer-Reviewed Publication

UNIVERSITY OF BIRMINGHAM

Athletes’ experience of using mental health support – and their attitudes towards these services – could be better understood with a more robust approach to research.

Experts at the University of Birmingham’s School of Sport, Exercise and Rehabilitation Sciences, plan to assess current studies on athletes’ mental health help-seeking, suggesting that research to consolidate existing knowledge was a necessary next step.

Athletes are less likely to seek help for mental health issues than non-athletes, and can also face challenges including a lack of access to services or previous negative experiences when seeking help.

While researchers understand the sources of support available – including those available in healthcare, sporting contexts and higher education systems, how athletes access these and their experience of them is less well understood.

Since athletes’ help-seeking for mental health is a relatively new area of research, a review of existing studies that could inform future research directions would be an important next step as new evidence is emerging continually.

The protocol, published in BMJ Open, outlines plans for a scoping review, leading to clearer identification of gaps in the knowledge base and suggestions for further research.

Kirsty Brown, who led the research, said: “Athletes are known to have similar rates of issues such as anxiety, depression and eating disorders as the general population, yet they have lower rates of help-seeking for mental health. It’s likely, therefore, that a significant proportion of athletes are not getting the help they need and so it’s really important that we understand how and when athletes are looking for help, and what their experience of using services is.”

The BMJ protocol sets out clear stages for a comprehensive programme of research which includes an investigation of how easy athletes  believe it is to access services; how willing they are to seek out support and whether the preference would be to get help from inside the sport environment or turn to coaches for help.

Advance care planning produces trend toward less aggressive and more comfort-focused care for patients with cancer

Peer-Reviewed Publication

REGENSTRIEF INSTITUTE

INDIANAPOLIS – A meta-analysis of studies involving 33,541 cancer patients evaluates the relationship between advance care planning and aggressive vs. comfort-focused end-of-life care. The study, led by Kristin Levoy, PhD, MSN, RN, of the Regenstrief Institute and Indiana University School of Nursing, found a general trend toward less aggressive and more comfort-focused end-of-life care among cancer patients who had engaged in advance care planning, compared to those who did not do so.


Advance care planning is a dynamic process to help prepare people for future decision-making with the goal of ensuring that individuals receive care at the end-of-life that is consistent with their preferences. Rather than a simple process of providing forms to be filled out and never reviewed, the research team noted the importance of the communication that takes place as a part the ongoing approach to advance care planning across disease trajectories.


“Our findings demonstrated that efforts to directly engage patients and caregivers in the communication components of advance care planning were a crucial aspect of improving the end-of-life care that patients with cancer received,” said Dr. Levoy.


“You could think of advance care planning as similar to having car insurance,” she added. “The idea of advance care planning is that you're protecting yourself for future eventualities that may or may not occur, and you're documenting what your healthcare preferences would be if you were to lose decision-making capacity and were unable to speak for yourself. The intention is that any healthcare we deliver should be patient-centered, that is, guided by the patients’ preferences and goals and consistent with their values.”


Cancer often is characterized by a protracted chronic illness with fairly high levels of functioning and a steep decline in capabilities and increase in symptoms in the last six months of life. Patients generally have time to prepare for the end-of-life and can do so in the form of advance care planning to later inform decisions.


“Advance care planning works in this illness population,” Dr. Levoy noted. “We found it positively impacted the decision of patients and caregivers facing cancer to avoid hospital and intensive care unit admissions and to complete do not resuscitate orders at the end-of-life. So, it worked. Compiling findings from studies involving tens of thousands of patients with cancer allows us to understand the value that advance care planning provides for patients and caregivers across the disease trajectory.”


Cancer patients who engaged in advance care planning were 50 percent more likely to complete do not resuscitate orders than those who did not.


The meta-analysis found advance care planning also was associated with significantly lower odds of various indicators of “aggressive” end-of-life:

• chemotherapy
• intensive care
• hospital admissions
• delayed hospice referrals
• hospital death


The meta-analysis revealed the following outcomes were not impacted by advance care planning:
• hospice use
• cardiopulmonary resuscitation
• emergency department admissions
• mechanical ventilation


End of life preferences are highly individualized. The study authors note that evidence suggests that persons with serious illnesses generally prefer comfort-focused care and desire to avoid aggressive interventions.


“This meta-analysis is important because it provides clear evidence that advance care planning helps patients with cancer receive goal concordant care,” said Regenstrief Institute Interim President and Chief Executive Officer Susan Hickman, PhD, a study co-author and an expert on advance care planning. “While there is still a lot of work that needs to be done to improve advance care planning implementation, our findings confirm that ongoing conversations about goals, values, and preferences are essential to help prepare patients and their caregivers for end-of-life decision-making.”


“Don't Throw the Baby Out with the Bathwater: Meta-Analysis of Advance Care Planning and End-of-life Cancer” is published in the peer-reviewed Journal of Pain and Symptom Management.


Authors and affiliations
Kristin Levoy 1 , Suzanne S. Sullivan 2 , Jesse Chittams 3 , Ruth L. Myers 4 , Susan E. Hickman 5 , Salimah H. Meghani 6


1 Department of Community and Health Systems; Indiana University School of Nursing; Indianapolis, IN; United States; Indiana University Center for Aging Research; Regenstrief Institute; Indianapolis, IN; United States; Indiana University Melvin and Bren Simon Comprehensive Cancer Center; Indianapolis, IN; United States.
2 School of Nursing; University at Buffalo; State University of New York; Buffalo, NY; United States.
3 BECCA (Biostatistics, Evaluation, Collaboration, Consultation & Analysis) Lab, Office of Nursing Research; University of Pennsylvania School of Nursing; Philadelphia, PA; United States.
4 Department of Community and Health Systems; Indiana University School of Nursing; Indianapolis, IN; United States.5 Department of Community and Health Systems; Indiana University School of Nursing; Indianapolis, IN; United States; Indiana University Center for Aging Research; Regenstrief Institute; Indianapolis, IN; United States; Indiana University Melvin and Bren Simon Comprehensive Cancer Center; Indianapolis, IN; United States.
6 New Courtland Center for Transitions and Health, Department of Biobehavioral Health Sciences; University of Pennsylvania School of Nursing; Philadelphia, PA; United States; Leonard Davis Institute of Health Economics; University of Pennsylvania; Philadelphia, PA; United States.


Funding
During the conduct of this study, Dr. Levoy was supported, in part, by a Future of Nursing Scholars Award from the Robert Wood Johnson Foundation, a Doctoral Degree Scholarship in Cancer Nursing (131753-DSCN-18-072-SCN) from the American Cancer Society, and a National Institutes of Health’s National Institute of Nursing Research’s Ruth L. Kirschstein National Research Service Award program (T32 NR009356). Dr. Sullivan was also supported, in part, by a NIH/NINR Ruth L. Kirschstein Predoctoral Individual National Research Service Award (F31 NR016394), the National Library of Medicine National Institute of Aging Institutional Grants for Research Training in Biomedical Informatics (T15 LM012495), and an NIH/NIA award R03 AG067159. Dr. Hickman is currently supported by NIH/NIA awards R33 AG057353, R01 AG057733 and R01 AG056618. Dr. Meghani is currently supported by NIH/NINR award R01 NR017853 and NIH/NCI award R01 CA270483.


About Kristin Levoy, PhD, MSN, RN
In addition to her role as a research scientist in the IU Center for Aging Research at Regenstrief Institute, Dr. Levoy is an assistant professor at IU School of Nursing and a researcher at the IU Melvin and Bren Simon Comprehensive Cancer Center.


About Susan Hickman, Ph.D.
In addition to serving as interim president and CEO of the Regenstrief Institute and leading the IU Center for Aging Research at Regenstrief Institute, Susan Hickman, PhD, is a professor at Indiana University School of Nursing, a professor and Cornelius and Yvonne Pettinga Chair of Aging Research at IU School of Medicine, and the co-director of the IUPUI Research in Palliative and End-of-Life Communicating and Training (RESPECT) Signature Center.


About Regenstrief Institute
Founded in 1969 in Indianapolis, Regenstrief Institute is a local, national and global leader dedicated to a world where better information empowers people to end disease and realize true health. A key research partner to Indiana University, Regenstrief and its research scientists are responsible for a growing number of major healthcare innovations and studies. Examples range from the development of global health information technology standards that enable the use and interoperability of electronic health records to improving patient-physician communications, to creating models of care that inform practice and improve the lives of patients around the globe.

Sam Regenstrief, a nationally successful entrepreneur from Connersville, Indiana, founded the institute with the goal of making healthcare more efficient and accessible for everyone. His vision continues to guide the institute’s research mission.


About IU School of Nursing
Indiana University School of Nursing was established in 1914 with the opening of Long Hospital in Indianapolis, Indiana. The School unites into a core structure with three campus locations: Bloomington, Indianapolis (IUPUI), and Fort Wayne. Almost 23,000 alumni across the globe are leaders in clinical practice, research, education, and innovation. The Master’s and DNP programs were named to the 2023 U.S. News & World Report Best Graduate Nursing Schools and in 2023 U.S. News & World Report Best Online Programs ranked the Master’s #10 in the nation. The National League for Nursing has designated the School as a Center of Excellence in Nursing Education in two areas. Academic programs include three tracks in the undergraduate program, nine
tracks in the master’s program, post-master’s options, a post-masters DNP, and a PhD. The School is known for a robust program of research focused on quality of life in chronic illness, nursing education, and cancer prevention and control.

Two qudits fully entangled

A new way to entangle high-dimensional quantum systems

Peer-Reviewed Publication

UNIVERSITY OF INNSBRUCK

Surface trap 

IMAGE: VACUUM CHAMBER WITH A MICROFABRICATED SURFACE TRAP view more 

CREDIT: MARTIN VAN MOURIK

In the world of computing, we typically think of information as being stored as ones and zeros – also known as binary encoding. However, in our daily life we use ten digits to represent all possible numbers. In binary the number 9 is written as 1001 for example, requiring three additional digits to represent the same thing.

The quantum computers of today grew out of this binary paradigm, but in fact the physical systems that encode their quantum bits (qubit) often have the potential to also encode quantum digits (qudits), as recently demonstrated by a team led by Martin Ringbauer at the Department of Experimental Physics at the University of Innsbruck. According to experimental physicist Pavel Hrmo at ETH Zurich: “The challenge for qudit-based quantum computers has been to efficiently create entanglement between the high-dimensional information carriers.”

In a study published in the journal Nature Communications the team at the University of Innsbruck now reports, how two qudits can be fully entangled with each other with unprecedented performance, paving the way for more efficient and powerful quantum computers.

Thinking like a quantum computer

The example of the number 9 shows that, while humans are able calculate 9 x 9 = 81 in one single step, a classical computer (or calculator) has to take 1001 x 1001 and perform many steps of binary multiplication behind the scenes before it is able to display 81 on the screen. Classically, we can afford to do this, but in the quantum world where computations are inherently sensitive to noise and external disturbances, we need to reduce the number of operations required to make the most of available quantum computers.

Crucial to any calculation on a quantum computer is quantum entanglement. Entanglement is one of the unique quantum features that underpin the potential for quantum to greatly outperform classical computers in certain tasks. Yet, exploiting this potential requires the generation of robust and accurate higher-dimensional entanglement.

The natural language of quantum systems

The researchers at the University of Innsbruck were now able to fully entangle two qudits, each encoded in up to 5 states of individual Calcium ions. This gives both theoretical and experimental physicists a new tool to move beyond binary information processing, which could lead to faster and more robust quantum computers.

Martin Ringbauer explains: “Quantum systems have many available states waiting to be used for quantum computing, rather than limiting them to work with qubits.” Many of today's most challenging problems, in fields as diverse as chemistry, physics or optimisation, can benefit from this more natural language of quantum computing.

The research was financially supported by the Austrian Science Fund FWF, the Austrian Research Promotion Agency FFG, the European Research Council ERC, the European Union and the Federation of Austrian Industries Tyrol, among others.

Publication: Native qudit entanglement in a trapped ion quantum processor. Pavel Hrmo, Benjamin Wilhelm, Lukas Gerster, Martin W. van Mourik, Marcus Huber, Rainer Blatt, Philipp Schindler, Thomas Monz, Martin Ringbauer. Nature Communications 14, 2242 (2023) (Open Access) https://doi.org/10.1038/s41467-023-37375-2

Tuberculosis breakthrough should lead to a new range of anti-TB inhibitors

New research by a team of scientists will support further development of much-needed additional treatment options for Tuberculosis (TB) one of the deadliest infectious diseases worldwide

Peer-Reviewed Publication

DIAMOND LIGHT SOURCE

Close-up of the x-ray crystal structure of the Mtb CYP125 enzyme bound to one of the leading inhibitor compounds. 

IMAGE: THE SYNTHETIC EXPANSION OF A CHEMICAL STRUCTURE IN TWO DIRECTIONS DESIGNED TO FIT INTO THE ACTIVE SITE OF MTB CHOLESTEROL OXIDASE ENZYMES TO GENERATE A NEW RANGE OF INHIBITORS AND POTENTIAL ANTI-TB DRUGS. THE RIGHT-HAND IMAGE SHOWS A CLOSE-UP OF THE X-RAY CRYSTAL STRUCTURE OF THE MTB CYP125 ENZYME BOUND TO ONE OF THE LEADING INHIBITOR COMPOUNDS. view more 

CREDIT: UNIVERSITY OF HUDDERSFIELD

Tuberculosis (TB) is one of the deadliest infectious diseases worldwide that is spread in the air like the common cold. TB is caused by the bacterium Mycobacterium tuberculosis (Mtb) and was responsible for approximately 1.6 million deaths in 2021. Mtb will usually attack the lungs but can attack any part of the body. Drug resistant TB strains are spreading and present a major concern. New work and a paper by a team of scientists from Manchester, Cambridge and Huddersfield Universities using a structure-guided approach, combined with biophysical characterization obtained a series of compounds with activity against clinically relevant drug-resistant isolates. These will support further development of much-needed additional treatment options against Mtb.

During infection the TB bacteria can utilize lipids (cholesterol and fatty acids) from the human host to act as nutrients to maintain and fuel the infectious state.  The teams’ paper, just published in Chemistry Europe, outlines this collaborative project and the results of their research into a set of enzymes involved in a key step in the breakdown of host cholesterol used by the TB bacteria.  Called Structure Based Discovery of Inhibitors of CYP125 and CYP142 from Mycobacterium tuberculosis,” (https://doi.org/10.1002/chem.202203868) ; their work involves characterising the enzymes using the UK’s national synchrotron, Diamond Light Source X-ray macromolecular crystallography beamlines to view their structures in molecular detail. 

Corresponding author, Dr Kirsty McLean Senior Lecturer in Cell Biology/Biochemistry in the Department of Biological and Geographical Sciences, University of Huddersfield explained that these enzyme structures are used to design inhibitor molecules that can bind to the enzymes and prevent them doing their job - essential for TB infection. The inhibitors molecules initially came from screening a library of small chemical compounds and were then gradually built up and synthesised chemically designing them to sit specifically into the enzyme structure. This process iteratively combines protein structure knowledge and chemical synthesis to design a succession of better inhibitors. The leading compounds were tested against clinically active and drug resistant strains of Mycobacterium tuberculosis and revealed anti-TB activity.

“Using a structure-guided approach, combined with biophysical characterization, compounds with micromolar range in-cell activity against clinically relevant drug-resistant isolates were obtained. These will support further development of much-needed additional treatment options and provide routes to probe the role of CYP125 and CYP142 in Mtb pathogenesis. This study should incite further development of an alternative range of anti-TB inhibitors,”  adds Dr McLean.

Dave Hall, Science Group Leader for Diamond’s Macromolecular Crystallography Group concludes; “Much of the team’s X-ray diffraction data was collected and managed using tools for remote access to our beamlines and new shift modes. Our staff worked closely with the group across various of our beamlines including I03, I04, I04-1 and I24. We are delighted to have helped move this important research on to the next stage.”

With the emergence of extensive drug resistance, novel therapeutic agents are urgently needed, and continued drug discovery efforts required. Host-derived lipids such as cholesterol support Mtb growth, and are also suspected to function in immunomodulation, with links to persistence and immune evasion. Mtb cytochrome P450 (CYP) enzymes facilitate key steps in cholesterol catabolism and thus present potential targets for inhibition. The authors present a series of compounds based on an ethyl 5-(pyridin-4-yl)-1H-indole-2-carboxylate pharmacophore which bind strongly to both Mtb cholesterol oxidases CYP125 and CYP142.

-ENDS-

Image shows: The synthetic expansion of a chemical structure in two directions designed to fit into the active site of Mtb cholesterol oxidase enzymes to generate a new range of inhibitors and potential anti-TB drugs. The right-hand image shows a close-up of the x-ray crystal structure of the Mtb CYP125 enzyme bound to one of the leading inhibitor compounds. Credit – University of Huddersfield

X-ray data collection and structure solution: X-ray diffraction data was collected at various beamlines at Diamond Light Source in Oxfordshire UK, and was indexed and integrated using the DIALS pipeline.

The Paper and authors: Chemistry Europe – March, Structure Based Discovery of Inhibitors of CYP125 and CYP142 from Mycobacterium tuberculosis,” (https://doi.org/10.1002/chem.202203868)

Mona M. KatariyaMatthew SneeRichard B. TunnicliffeMadeline E. KavanaghHelena I. M. BoshoffCecilia N. AmadiColin W. LevyAndrew W. MunroChris AbellDavid Leys … See all authors

March 2023

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For further information please contact Diamond Communications: Lorna Campbell +44 7836 625999 or Isabelle Boscaro-Clarke +44 1235 778130   Diamond Light Source: www.diamond.ac.uk  Twitter: @DiamondLightSou  

Diamond Light Source provides industrial and academic user communities with access to state-of-the-art analytical tools to enable world-changing science. Shaped like a huge ring, it works like a giant microscope, accelerating electrons to near light speeds, to produce a light 10 billion times brighter than the Sun, which is then directed off into 33 laboratories known as ‘beamlines’. In addition to these, Diamond offers access to several integrated laboratories including the world-class Electron Bio-imaging Centre (eBIC) and the Electron Physical Science Imaging Centre (ePSIC).  

Diamond serves as an agent of change, addressing 21st century challenges such as disease, clean energy, food security and more. Since operations started, more than 16,000 researchers from both academia and industry have used Diamond to conduct experiments, with the support of approximately 760 world-class staff. Almost 12,000 scientific articles have been published by our users and scientists.  

Funded by the UK Government through the Science and Technology Facilities Council (STFC), and by the Wellcome Trust, Diamond is one of the most advanced scientific facilities in the world, and its pioneering capabilities are helping to keep the UK at the forefront of scientific research.  

Diamond was set-up as an independent not for profit company through a joint venture, between the UKRI’s Science and Technology Facilities Council and one of the world’s largest biomedical charities, the Wellcome Trust - each respectively owning 86% and 14% of the shareholding.