Smelling in VR environment possible with new gaming technology

Peer-Reviewed Publication

STOCKHOLM UNIVERSITY

 

IMAGE: THE RESEARCH TEAM IS TESTING THE OLFACTOMETER IN THE LAB. view more 

CREDIT: JENS LASTHEIN

An odor machine, so-called olfactometer, makes it possible to smell in VR environments. First up is a “wine tasting game” where the user smells wine in a virtual wine cellar and gets points if the guess on aromas in each wine is correct. The new technology that can be printed on 3D printers has been developed in collaboration between Stockholm University and Malmö University. The research, funded by the Marianne and Marcus Wallenberg Foundation, was recently published in the International Journal of Human - Computer Studies.

“We hope that the new technical possibilities will lead to scents having a more important role in game development, says Jonas Olofsson, professor of psychology and leader of the research project at Stockholm University.

In the past, computer games have focused mostly on what we can see – moving images on screens. Other senses have not been present. But an interdisciplinary research group at Stockholm University and Malmö University has now constructed a scent machine that can be controlled by a gaming computer. In the game, the participant moves in a virtual wine cellar, picking up virtual wine glasses containing different types of wine, guessing the aromas. The small scent machine is attached to the VR system's controller, and when the player lifts the glass, it releases a scent.

“The possibility to move on from a passive to a more active sense of smell in the game world paves the way for the development of completely new smell-based game mechanics based on the players' movements and judgments,” says Simon Niedenthal, interaction and game researcher at Malmö University.

The olfactometer consists of four different valves each connected to a channel. In the middle there is a fan sucking the air into a tube. With the help of the computer, the player can control the four channels so that they open to different degrees and provide different mixtures of scent. Scent blends that can mimic the complexity of a real wine glass. The game has different levels of difficulty with increasing levels of complexity.

“In the same way that a normal computer game becomes more difficult the better the player becomes; the scent game can also challenge players who already have a sensitive nose. This means that the scent machine can even be used to train wine tasters or perfumers,” says Jonas Olofsson.

All code, blueprints and instructions for the machine are openly available online, as is code for the virtual wine tasting game. The research group, Sensory Cognitive Interaction Laboratory, which is located at the Department of Psychology, Stockholm University, now hopes that scented computer games can become useful for other purposes.

“For those who, for example, lost their sense of smell after COVID-19 or for other reasons, the new technology can mean an opportunity to regain their sense of smell with the help of game-based training,” says Jonas Olofsson, research team leader.

Smell training is a method recommended by doctors for those who lose their sense of smell after colds and other viruses, but according to Jonas Olofsson, many people stop training because it becomes too boring.

“I hope that the fact that drawings and code are openly available as "open source" will lead to an opportunity for game companies to start creating new, commercial products for scent training using the new technology,” says Jonas Olofsson.

According to Simon Niedenthal, “open source” leads to promoting accessibility, reproducibility and comparison of results in research. It also contributes to creating a cohesive research and design community within the game development field.

“But it also means that the costs of the equipment are greatly reduced, which makes it available to more people. To us that is important,” says Simon Niedenthal.

“We believe in open science, that research results should be made available to the public and that other researchers should be able to repeat our results. With the help of our research, others can build scent machines and explore new ways of using scents in games,” says Jonas Olofsson.

The technology for the olfactometer has been developed by Peter Lundén, research engineer at Stockholm University and member of the research team at SCI LAB.

CAPTION

The olfactometer

CREDIT

William Fredborg

CAPTION

Servo motors (1–4) and stepless valves (a). A diagrammatic illustration of the functionality of the olfactory display and the control of its airflow (b).

CREDIT

SCI LAB

CAPTION

The game environment in the wine tasting game.

CREDIT

SCI LAB

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DOI

10.1016/j.ijhcs.2022.102928 

SUBJECT OF RESEARCH

Not applicable

ARTICLE TITLE

A graspable olfactory display for virtual reality

The State of Open Data Report 2022: Researchers need more support to assist with open data mandates

New findings provide update on researchers’ attitudes towards open data

Reports and Proceedings

DIGITAL SCIENCE

 

IMAGE: ONE OF THE KEY FINDINGS OF THE 2022 STATE OF OPEN DATA REPORT view more 

CREDIT: FIGSHARE/DIGITAL SCIENCE

Researchers worldwide will need further assistance to help comply with an increasing number of open data mandates, according to the authors of a new report.

The State of Open Data Report 2022 – the latest in an annual collaborative series from Digital Science, Figshare and Springer Nature – is released today.

Based on a global survey, the report is now in its seventh year and provides insights into researchers’ attitudes towards and experiences of open data. With more than 5,400 respondents, the 2022 survey is the largest since the COVID-19 pandemic began.

This year’s report also includes guest articles from open data experts at the National Institutes of Health (NIH), the White House Office of Science and Technology Policy (OSTP), the Chinese Academy of Sciences (CAS), publishers and universities.

Founder and CEO of Figshare Mark Hahnel says: “This year’s State of Open Data Report comes at a unique point in time when we’re seeing a growing number of open data mandates from funding organizations and policymakers, most notably the NIH and OSTP in the United States, but also recently from the National Health and Medical Research Council (NHMRC) in Australia, and in Europe and the UK.

“What is clear from the findings of our report is that while most researchers embrace the concepts of open data and open science, they also have some reasonable misgivings about how open data policies and practices impact on them. In an environment where open data mandates are increasing, funding organizations would benefit from working even more closely with researchers and providing them with additional support to help smooth the transition to a fully open data future.

“We all have a role to play in driving a better future for open data and accessible research, and one way we can do that through this report is by listening to the voices of researchers, funders, institutions, and publishers,” he says.

 

CAPTION

A comment from NIH contributors to the 2022 State of Open Data report

CREDIT

Figshare/Digital Science

Primary findings from this year’s report indicated that:

• There is a growing trend in researchers being in favour of data being made openly available as common practice (4 out of every five researchers were in agreement with this), supported somewhat by now over 70% of respondents being required to follow a policy on data sharing.
• However, researchers still cite a key need in helping them to share their data as being more training or information on policies for access, sharing and reuse (55%) as well as long-term storage and data management strategies (52%).
• Credit and recognition were once again a key theme for researchers in sharing their data. Of those who had previously shared data, 66% had received some form of recognition for their efforts – most commonly via full citation in another article (41%) followed by co-authorship on a paper that had used the data.
• Researchers are more inclined to share their research data where it can have an impact on citations (67%) and the visibility of their research (61%), rather than being motivated by public benefit or journal/publisher mandate (both 56%).

Graham Smith, Open Data Program Manager, Springer Nature, says: “For the past seven years these surveys have helped paint a picture of researcher perspectives on open data. The report shows us not only the progress made but the steps that still need to be taken on the journey towards an open data future in support of the research community. Whether it’s the broad support of researchers for making research data openly available as common practice or the changing attitudes to open data mandates, we must learn from and deliver concrete steps forward to address what the community is telling us.

“Springer Nature is firmly committed to this and we continue to work closely with our partners, such as Figshare and Digital Science, to create better understanding around data sharing.”

Daniel Hook, CEO of Digital Science, says: “Digital Science is committed to making open, collaborative and inclusive research possible, as we believe this environment will lead to the greatest benefit for society. Now in its seventh year, while the articles in The State of Open Data Report represent a unique set of snapshots marking the evolution of attitudes about Open Data in our community, the data behind the survey constitutes a valuable resource to track researcher sentiment regarding open data and their experiences of data sharing. I believe that these data represent an amazing opportunity to understand the challenges and needs of our community so that we can collectively build better infrastructure to support research.”

The full report can be accessed on Figshare: https://doi.org/10.6084/m9.figshare.21276984

Join in the conversation at #StateOfOpenData

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Key findings via theme of the report

Support for open data

• Four out of every five respondents are in favour of research data being made openly available as common practice.
• 74% of respondents reported sharing their data during publication.
• Approximately one fifth of respondents reported having no concerns about sharing data openly – this proportion has been steadily growing since 2018.
• 88% of researchers surveyed are supportive of making research articles open access (OA) as a common scholarly practice.

Motivations and benefits

• When it comes to researchers sharing their data, citations of research papers (67%) and increased impact and visibility of papers (61%) outweigh public benefit or journal/publisher mandate (both 56%) as motivation.
• Of those who had previously shared data, 66% had received some form of recognition for their efforts – most commonly via full citation in another article (41%) followed by co-authorship on a paper that had used the data.
• A third of respondents indicated they had been involved in a research collaboration as a result of data they had previously shared.

Open data mandates

• 70% of respondents were required to follow a policy on data sharing for their most recent piece of research.
• More than two-thirds of respondents are supportive “to some extent” of a national mandate for making research data openly available. This number has been declining since 2019.
• Just over half (52%) of respondents in the 2022 survey felt that sharing data should be a part of the requirement for awarding research grants. Again, this number has been declining since 2019.

Drawbacks

• Only 19% of respondents believe that researchers get sufficient credit for sharing their data, while 75% say they receive too little credit.
• Just under a quarter of respondents indicated that they had previously received support with planning, managing or sharing their research data
• The greatest concern among respondents is misuse of their data (35%).
• The key needs of researchers which were felt more training or information would improve were better understanding and definitions for policies for access, sharing and reuse (55%) as well as long-term storage and data management strategies (52%) – things that impact both ends of the research cycle.

Key demographics of respondents

• Researchers from China now comprise 11% of all respondents, equal with that of the United States. China and the US are the two countries with the biggest response to the survey, followed by India, Japan, Germany, Italy, UK, Canada, Brazil, France and Spain.

• 31% of respondents were early career researchers (ECRs), while a further 31% classed themselves as senior researchers.

• Most respondents (42%) were from medicine & life sciences; 38% from mathematics, physics and applied sciences; and 17% from humanities and social sciences (an increase of 3%).

• Respondents were broadly categorised as: Open science advocates (32%), Open publishing advocates (26%), Cautiously pro open science (25%), Open science agnostics (11%), and Non-believers of open science (6%).

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About Figshare
Figshare is a leading provider of out-of-the-box, cloud repository software for research data, papers, theses, teaching materials, conference outputs, and more. Research outputs become more discoverable and impactful with search engine indexing and usage metrics including citations and altmetrics. Figshare provides a proficient platform for all types of research data to be shared and showcased in a FAIR way whilst enabling researchers to receive credit. Visit knowledge.figshare.com and follow @figshare on Twitter.

 

About Springer Nature
For over 180 years Springer Nature has been advancing discovery by providing the best possible service to the whole research community. We help researchers uncover new ideas, make sure all the research we publish is significant, robust and stands up to objective scrutiny, that it reaches all relevant audiences in the best possible format, and can be discovered, accessed, used, re-used and shared. We support librarians and institutions with innovations in technology and data; and provide quality publishing support to societies. As a research publisher, Springer Nature is home to trusted brands including Springer, Nature Portfolio, BMC, Palgrave Macmillan and Scientific American. For more information, please visit springernature.com and @SpringerNature

 

About Digital Science
Digital Science is a technology company working to make research more efficient. We invest in, nurture and support innovative businesses and technologies that make all parts of the research process more open and effective. Our portfolio includes admired brands including Altmetric, Dimensions, Figshare, ReadCube, Symplectic, IFI CLAIMS, Overleaf, Ripeta and Writefull. We believe that together, we can help researchers make a difference. Visit www.digital-science.com and follow @digitalsci on Twitter.

 

Media contacts

David Ellis, Press, PR & Social Manager, Digital Science: Mobile +61 447 783 023,  d.ellis@digital-science.com

Simon Linacre, Head of Content, Brand & Press, Digital Science: Mobile: +44 7484 381477, s.linacre@digital-science.com

Sam Sule, Communications Officer, Springer Nature: +44 203 192 2149, sam.sule@springernature.com

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DOI

10.6084/m9.figshare.21276984 

ARTICLE TITLE

The State of Open Data 2022

Heaviest element yet detected in an exoplanet atmosphere

Peer-Reviewed Publication

ESO

 

IMAGE: THIS ARTIST’S IMPRESSION SHOWS AN ULTRA-HOT EXOPLANET, A PLANET BEYOND OUR SOLAR SYSTEM, AS IT IS ABOUT TO TRANSIT IN FRONT OF ITS HOST STAR. WHEN THE LIGHT FROM THE STAR PASSES THROUGH THE PLANET’S ATMOSPHERE, IT IS FILTERED BY THE CHEMICAL ELEMENTS AND MOLECULES IN THE GASEOUS LAYER. WITH SENSITIVE INSTRUMENTS, THE SIGNATURES OF THOSE ELEMENTS AND MOLECULES CAN BE OBSERVED FROM EARTH. USING THE ESPRESSO INSTRUMENT OF ESO’S VERY LARGE TELESCOPE, ASTRONOMERS HAVE FOUND THE HEAVIEST ELEMENT YET IN AN EXOPLANET'S ATMOSPHERE, BARIUM, IN THE TWO ULTRA-HOT JUPITERS WASP-76 B AND WASP-121 B. view more 

CREDIT: ESO/M. KORNMESSER

Using the European Southern Observatory’s Very Large Telescope (ESO’s VLT), astronomers have discovered the heaviest element ever found in an exoplanet atmosphere — barium. They were surprised to discover barium at high altitudes in the atmospheres of the ultra-hot gas giants WASP-76 b and WASP-121 b — two exoplanets, planets which orbit stars outside our Solar System. This unexpected discovery raises questions about what these exotic atmospheres may be like.

“The puzzling and counterintuitive part is: why is there such a heavy element in the upper layers of the atmosphere of these planets?” says Tomás Azevedo Silva, a PhD student at the University of Porto and the Instituto de Astrofísica e Ciências do Espaço (IA) in Portugal who led the study published today in Astronomy & Astrophysics.

WASP-76 b and WASP-121 b are no ordinary exoplanets. Both are known as ultra-hot Jupiters as they are comparable in size to Jupiter whilst having extremely high surface temperatures soaring above 1000°C. This is due to their close proximity to their host stars, which also means an orbit around each star takes only one to two days. This gives these planets rather exotic features; in WASP-76 b, for example, astronomers suspect it rains iron.

But even so, the scientists were surprised to find barium, which is 2.5 times heavier than iron, in the upper atmospheres of WASP-76 b and WASP-121 b. “Given the high gravity of the planets, we would expect heavy elements like barium to quickly fall into the lower layers of the atmosphere,” explains co-author Olivier Demangeon, a researcher also from the University of Porto and IA.

“This was in a way an ‘accidental’ discovery,” says Azevedo Silva. “We were not expecting or looking for barium in particular and had to cross-check that this was actually coming from the planet since it had never been seen in any exoplanet before.”

The fact that barium was detected in the atmospheres of both of these ultra-hot Jupiters suggests that this category of planets might be even stranger than previously thought. Although we do occasionally see barium in our own skies, as the brilliant green colour in fireworks, the question for scientists is what natural process could cause this heavy element to be at such high altitudes in these exoplanets. ​​“At the moment, we are not sure what the mechanisms are,” explains Demangeon.

In the study of exoplanet atmospheres ultra-hot Jupiters are extremely useful. As Demangeon explains: “Being gaseous and hot, their atmospheres are very extended and are thus easier to observe and study than those of smaller or cooler planets”.

Determining the composition of an exoplanet’s atmosphere requires very specialised equipment. The team used the ESPRESSO instrument on ESO’s VLT in Chile to analyse starlight that had been filtered through the atmospheres of WASP-76 b and WASP-121 b. This made it possible to clearly detect several elements in them, including barium.

These new results show that we have only scratched the surface of the mysteries of exoplanets. With future instruments such as the high-resolution ArmazoNes high Dispersion Echelle Spectrograph (ANDES), which will operate on ESO’s upcoming Extremely Large Telescope (ELT), astronomers will be able to study the atmospheres of exoplanets large and small, including those of rocky planets similar to Earth, in much greater depth and to gather more clues as to the nature of these strange worlds.

More information

This research was presented in the paper “Detection of Barium in the atmospheres of ultra-hot gas giants WASP-76b & WASP-121b” to appear in Astronomy & Astrophysics (doi: 10.1051/0004-6361/202244489).

The team is composed of T. Azevedo Silva (Instituto de Astrofísica e Ciências do Espaço, Universidade do Porto, Portugal [IA/UPorto, CAUP] and Departamento de Física e Astronomia Faculdade de Ciências, Universidade do Porto, Portugal [FCUP]), O. D. S. Demangeon (IA/UPorto, CAUP and FCUP), N. C. Santos (IA/UPorto, CAUP and FCUP), R. Allart (Department of Physics, and Institute for Research on Exoplanets, Université de Montréal, Canada and Observatoire astronomique de l’Université de Genève, Switzerland [UNIGE]), F. Borsa (INAF – Osservatorio Astronomico di Brera, Italy) , E. Cristo (IA/UPorto, CAUP and FCUP) , E. Esparza-Borges (Instituto de Astrofísica de Canarias, Spain [IAC] and Departamento de Astrofísica, Universidad de La Laguna, Tenerife, Spain [IAC-ULL]) , J. V. Seidel (European Southern Observatory, Chile [ESO Chile]) , E. Palle (IAC) , S. G. Sousa (IA/UPorto), H. M. Tabernero (Centro de Astrobiología, CSIC-INTA, Spain [CSIC-INTA]), M. R. Zapatero Osorio (CSIC-INTA), S. Cristiani (INAF – Osservatorio Astronomico di Trieste, Italy [INAF Trieste]), F. Pepe (UNIGE) , R. Rebolo (IAC and IAC-ULL) , V. Adibekyan (IA/UPorto and FCUP), Y. Alibert (Physikalisches Institut, University of Bern,, Switzerland), S. C. C. Barros (IA/UPorto and FCUP), V. Bourrier (UNIGE) , P. Di Marcantonio (INAF Trieste), V. D’Odorico (INAF Trieste, Scuola Normale Superiore, Italy and Institute for Fundamental Physics of the Universe, Trieste, Italy [IFPU]), D. Ehrenreich (UNIGE and Centre Vie dans l’Univers, Faculté des sciences de l’Université de Genève, Switzerland), P. Figueira (UNIGE and IA/UPorto), J. I. González Hernández (IAC and Universidad de La Laguna, Departamento de Astrofísica, Spain), C. J. A. P. Martins (UA/UPorto and Centro de Astrofísica da Universidade do Porto, Portugal), A. Mehner (ESO Chile) , G. Micela (INAF – Osservatorio Astronomico di Palermo, Italy), P. Molaro (INAF Trieste and IFPU), D. Mounzer (UNIGE), N. J. Nunes (Instituto de Astrofísica e Ciências do Espaço, Faculdade de Ciências da Universidade de Lisboa and Departamento de Física, Faculdade de Ciências da Universidade de Lisboa, Portugal), A. Sozzetti (INAF - Osservatorio Astrofisico di Torino, Italy), A. Suárez Mascareño (IAC and IAC-ULL), and S. Udry (UNIGE).

The European Southern Observatory (ESO) enables scientists worldwide to discover the secrets of the Universe for the benefit of all. We design, build and operate world-class observatories on the ground — which astronomers use to tackle exciting questions and spread the fascination of astronomy — and promote international collaboration in astronomy. Established as an intergovernmental organisation in 1962, today ESO is supported by 16 Member States (Austria, Belgium, the Czech Republic, Denmark, France, Finland, Germany, Ireland, Italy, the Netherlands, Poland, Portugal, Spain, Sweden, Switzerland and the United Kingdom), along with the host state of Chile and with Australia as a Strategic Partner. ESO’s headquarters and its visitor centre and planetarium, the ESO Supernova, are located close to Munich in Germany, while the Chilean Atacama Desert, a marvellous place with unique conditions to observe the sky, hosts our telescopes. ESO operates three observing sites: La Silla, Paranal and Chajnantor. At Paranal, ESO operates the Very Large Telescope and its Very Large Telescope Interferometer, as well as survey telescopes such as VISTA. Also at Paranal ESO will host and operate the Cherenkov Telescope Array South, the world’s largest and most sensitive gamma-ray observatory. Together with international partners, ESO operates APEX and ALMA on Chajnantor, two facilities that observe the skies in the millimetre and submillimetre range. At Cerro Armazones, near Paranal, we are building “the world’s biggest eye on the sky” — ESO’s Extremely Large Telescope. From our offices in Santiago, Chile we support our operations in the country and engage with Chilean partners and society.

Links

• Research paper
• Photos of the VLT
• Find out more about ESO's Extremely Large Telescope
• For journalists: subscribe to receive our releases under embargo in your language
• For scientists: got a story? Pitch your research

Contacts

Tomás Azevedo Silva
Instituto de Astrofisica e Ciências do Espaço, Faculdade de Ciências, Universidade do Porto
Porto, Portugal
Email: Tomas.Silva@astro.up.pt

Olivier Demangeon
Instituto de Astrofisica e Ciências do Espaço, Faculdade de Ciências, Universidade do Porto
Porto, Portugal
Tel: +351 226 089 855
Email: olivier.demangeon@astro.up.pt

Nuno Santos
Instituto de Astrofisica e Ciências do Espaço, Faculdade de Ciências, Universidade do Porto
Porto, Portugal
Email: Nuno.Santos@astro.up.pt

María Rosa Zapatero Osorio
Centro de Astrobiología (CSIC-INTA)
Madrid, Spain
Email: mosorio@cab.inta-csic.es

Hugo Tabernero
Centro de Astrobiología (CSIC-INTA)
Madrid, Spain
Email: htabernero@cab.inta-csic.es

Jonay González Henández
Instituto de Astrofísica de Canarias
Tenerife, Spain
Email: jonay@iac.es

Alejandro Suárez Mascareño
Instituto de Astrofísica de Canarias
Tenerife, Spain
Email: alejandro.suarez.mascareno@iac.es

Paolo Molaro
INAF Osservatorio Astronomico di Trieste
Trieste, Italy
Email: paolo.molaro@inaf.it

Baptiste Lavie
University of Geneva
Geneva, Switzerland
Email: Baptiste.Lavie@unige.ch

Juan Carlos Muñoz Mateos
ESO Media Officer
Garching bei München, Germany
Tel: +49 89 3200 6176
Email: press@eso.org

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JOURNAL

Astronomy and Astrophysics

DOI

10.1051/0004-6361/202244489 

Anti-anaerobic antibiotics associated with increased risk of mortality in critically ill patients

Study by U-M researchers shows early treatment with specific antibiotics depletes the body of gut anaerobes that protect against pneumonia, organ failure, and mortality.

Peer-Reviewed Publication

MICHIGAN MEDICINE - UNIVERSITY OF MICHIGAN

ANN ARBOR, MI – A common clinical practice may be inadvertently harming patients, according to new research published October 13 in the European Respiratory Journal. The team of Michigan Medicine researchers behind the study suggest that administration of antibiotics with activity against anaerobic bacteria has a profound effect on the gut microbiome and, ultimately, an adverse impact on critically ill patients.  

“We talk about the gut microbiome as a metabolic and immune ‘organ,’ and when we give patients anti-anerobic antibiotics, I worry we are causing a hidden form of organ failure,” said senior author Robert Dickson, M.D., Associate Professor in Pulmonary and Critical Care Medicine and Deputy Director at the Weil Institute for Critical Care Research and Innovation at the University of Michigan. “Our research suggests that depleting the gut of these ‘good bugs’ may be contributing to worse clinical outcomes.”

In the paper, researchers found that, in critically ill patients, the practice of early administration of anti-anaerobic antibiotics is commonplace – about two-thirds of the 3,032 patients observed in the study’s cohort received such treatment.

“For sick patients in the Emergency Department and Intensive Care Unit, there has been a lot of focus on ‘time-to-antibiotics’ as a quality improvement measure,” said Dickson. “Our results demonstrate that antibiotics really can’t be considered a single entity, as they have widely different impacts on the microbiome and on our patients. Patients who received anti-anaerobic antibiotics did far worse than patients who didn’t. We think that which antibiotic is given probably matters more than how quickly they are administered.”

With support from the Weil Institute, along with funding from the National Institutes of Health, the researchers conducted a retrospective single-center cohort study of 3,032 critically ill patients, comparing those who did and did not receive early anti-anaerobic antibiotics. By comparing ICU outcomes in all patients, and changes in gut microbiota in 116 of the patients, they found that those who received anti-anaerobic antibiotics early in their hospital course had worse outcomes, whether measured in overall survival, infection-free survival, or pneumonia-free survival.

The authors also found dramatic consequences of these antibiotics on the gut microbiome – during hospitalization, patients who received anti-anaerobic antibiotics had decreased initial gut bacterial density, followed by increased expansion and domination of the microbiome Enterobacteriaceae (a genus of common bacteria, many of which are pathogenic and cause opportunistic infections in immunocompromised hosts). These findings confirm that anti-anaerobic antibiotics have a dramatic effect on gut bacterial communities.

While the primary findings were from an observational study in humans, the team confirmed the results using animal modeling. In two different mouse models (pneumonia and oxygen-induced lung injury), animals who were treated with anti-anaerobic antibiotics did worse. Anti-anaerobic antibiotics increased the susceptibility of mice to pneumonia due to Enterobacteriaceae and increased their mortality from oxygen toxicity.

Co-author Rishi Chanderraj, M.D., a Clinical Lecturer in Infectious Diseases at U-M, was the lead researcher on the initial project and will be carrying the work forward in future studies.

“In observational studies, there is always a risk that a mortality difference is due to confounding; maybe the patients who received anti-anaerobic antibiotics were just sicker,” he said. “But the fact that we were able to recapitulate these findings in two different animal models gives us confidence that these findings are real.”

“No one wants to withhold antibiotics from patients with life-threatening infections,” said Chanderraj. “But our study confirms that the risk of overtreating with antibiotics isn’t just theoretical. I’m concerned that we’re harming our patients.”

Paper cited: “In critically ill patients, anti-anaerobic antibiotics increase risk of adverse clinical outcomes,” European Respiratory Journal. DOI: 10.1183/13993003.00910-2022

Project team: Rishi Chanderraj1,2, Jennifer M. Baker3,4, Stephen G. Kay3, Christopher A. Brown3,5, Kevin J. Hinkle3, Daniel J. Fergle3, Roderick A. McDonald3, Nicole R. Falkowski3, Joseph D. Metcalf3, Keith S. Kaye6, Robert J. Woods1,2,7, Hallie C. Prescott3,8,9, Michael W. Sjoding3,7,8,10, Robert P. Dickson3,4,10

Affiliations:

1. Division of Infectious Diseases, Department of Internal Medicine, University of Michigan

Medical School, Ann Arbor, MI, USA.

2. Medicine Service, Infectious Diseases Section, Veterans Affairs (VA) Ann Arbor Healthcare

System, Ann Arbor, Michigan, USA.

3. Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine,

University of Michigan Medical School, Ann Arbor, MI, USA.

4. Department of Microbiology and Immunology, University of Michigan Medical School, Ann

Arbor, MI, USA.

5. Institute for Research on Innovation and Science, Institute for Social Research, University of

Michigan

6. Division of Infectious Diseases, Department of Medicine, Rutgers-New Jersey Medical

School

7. Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann

Arbor, MI, USA.

8. Institute for Healthcare Policy and Innovation, University of Michigan, Ann Arbor, Michigan.

9. VA Center for Clinical Management Research, Ann Arbor, Michigan.

10. Weil Institute for Critical Care Research & Innovation; Ann Arbor, Michigan

About the Weil Institute, formerly MCIRCC

The team at the Max Harry Weil Institute for Critical Care Research and Innovation (formerly the Michigan Center for Integrative Research in Critical Care) is dedicated to pushing the leading edge of research to develop new technologies and novel therapies for the most critically ill and injured patients. Through a unique formula of innovation, integration and entrepreneurship that was first imagined by Weil, their multi-disciplinary teams of health providers, basic scientists, engineers, data scientists, commercialization coaches, donors and industry partners are taking a boundless approach to re-imagining every aspect of critical care medicine. For more information, visit weilinstitute.med.umich.edu

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JOURNAL

European Respiratory Journal

DOI

10.1183/13993003.00910-2022 

Study questions the medical privacy of forensic samples

SF State researchers say databases used by law enforcement could contain private information about individuals, including crime victims

Peer-Reviewed Publication

SAN FRANCISCO STATE UNIVERSITY

Watch any episode of “CSI,” and a character will use forensic DNA profiling to identify a criminal. A new study from San Francisco State University suggests that these forensic profiles may indirectly reveal medical information — perhaps even those of crime victims — contrary to what the legal field has believed for nearly 30 years. The findings could have ethical and legal implications.

“The central assumption when choosing those [forensic] markers was that there wouldn’t be any information about the individuals whatsoever aside from identification. Our paper challenges that assumption,” said first author Mayra Bañuelos (B.S., ’19), who started working on the project as a San Francisco State undergraduate and is now a Ph.D. student at Brown University.

Law enforcement uses the Combined DNA Index System (CODIS), a system organizing criminal justice DNA databases that uses specific genetic markers to identify individuals. Crime labs from national, state and local levels contribute to these databases and provide profiles from samples collected from crime scene evidence, convicted offenders, felony arrestees, missing persons and more. Law officials can use the database to try to match samples found in an investigation to profiles already stored in the database.

CODIS profiles consist of an individual’s genetic variants as a set of short tandem repeats (STRs), sequences of DNA that repeat at various frequencies among individuals. Since the ’90s, 20 STRs have been chosen for forensic CODIS profiling specifically because it was believed they did not relay medical information. If these profiles contained any trait information, then there could be issues about medical privacy.

“But that assumption hasn’t had much investigation in a long time, and we know a lot more about the genome now than we did back then,” explained SF State Associate Professor of Biology Rori Rohlfs, who led this project.

The assumption that only criminals are sampled is also not completely accurate. “It actually also includes victims of crime and people that may have been at crime scenes. You have these huge databases including a lot of people that are not necessarily criminals,” Bañuelos said. “I believe also that accessibility to these databases varies a lot according to a jurisdiction.”

The researchers explained that other papers have found associations between other (non-CODIS) STRs and disease or gene expression. With that in mind, the SF State team wanted to understand the relationship between the CODIS STR markers and gene expression.

Rohfls’ lab used publicly available data (1000 Genome Project) and genetic models to investigate the relationship between CODIS markers and gene expression. Of the 20 CODIS markers, they found six associations between CODIS markers and gene expression of nearby genes in white blood cell lines from more than 400 unrelated individuals in the database.

“In some genes, gene expression change has been associated with medical conditions,” Bañuelos explained, citing prior research. “[In this study,] we indirectly know there is an association between these CODIS genotypes and some change in genes that can lead to illness.”

The authors note three associations to genes (CSF1R, LARS2, KDSR) that were particularly interesting. Prior literature shows that mutations and changes in gene expression of CSF1R can be tied to psychiatric conditions (depression and schizophrenia). Mutations and gene expression changes in the other genes have been connected to Perrault syndrome, MELAS syndrome, severe skin and platelet conditions and more, the scientists note in the PNAS (Proceedings of the National Academy of Sciences) paper. If CODIS markers can be connected to the expression of genes linked to disease and health, then it means that the data in the CODIS database could compromise an individual’s medical privacy.

“Our paper in some ways is like the tip of the iceberg,” Rohlfs said, admitting that she was surprised to find associations in a relatively small sample size. The project itself simply started as an undergraduate exploration project. Eight of the 11 authors were, like Bañuelos, undergraduates at SF State when the project began.

“It raises the question: If we did a more expansive [genetic] study, would we find even more information that would be revealed by CODIS profiles?” Rohlfs asked.

Bañuelos and Rohlfs are curious to know what they’d find if they looked at a larger dataset of more diverse populations — their current dataset is predominantly European. Their analysis was also limited to white blood cells. What relationships would they find if they looked in other tissues?

These are important lines of inquiry because the current dataset doesn’t represent the general population. Furthermore, Latino and African American communities are overrepresented in these CODIS databases, Bañuelos explained.

Additional studies are needed to better flush out the relationship between CODIS and medical information. However, the researchers point out that if CODIS profiles contain medical information, there could be major implications.

“If [these CODIS profiles] contain medical information, then their treatment would need to be consistent with the way we protect medical information in the United States. We would have to have policies that regulate the seizure, storage and sharing of these profiles,” Rohlfs added.

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JOURNAL

Proceedings of the National Academy of Sciences

DOI

10.1073/pnas.2121024119 

ARTICLE TITLE

Associations between forensic loci and expression levels of neighboring genes may compromise medical privacy

Variation in Research Experiences and Publications During Medical School by Sex and Race and Ethnicity

Mytien Nguyen, MS¹; Sarwat I. Chaudhry, MD²; Emmanuella Asabor, MPhil¹; et alMayur M. Desai, PhD, MPH³; Elle Lett, PhD, MA^4,5; Jose E. Cavazos, MD, PhD⁶; Hyacinth R. C. Mason, PhD⁷; Dowin Boatright, MD, MBA, MHS⁸

Author Affiliations Article Information

JAMA Netw Open. 2022;5(10):e2238520. doi:10.1001/jamanetworkopen.2022.38520

Original Investigation 

Medical Education

October 25, 2022

Key Points

Question  Are student sex and racial and ethnic identity associated with publication rate during medical school?

Findings  This cohort study of 31 474 medical school graduates found a significant disparity in publication rates across sex and race and ethnicity, with women and Black and Hispanic students reporting lower publication rates compared with men and White students. Sex and racial and ethnic disparities in research persisted at both National Institutes of Health top 40 and non–top 40 research-intensive schools.

Meaning  These findings suggest that inequities in the physician-scientist workforce began early in training, as exposure to research and research productivity are critical for a successful career as a physician-scientist.

Abstract

Importance  Diverse research teams are critical to solving complex health problems and producing high-quality medical research.

Objective  To examine the associations of student sex and racial and ethnic identity with publication rates during medical school.

Design, Setting, and Participants  This cohort study assessed individual-level data of US MD graduates from medical school who matriculated in academic years 2014 to 2015 and 2015 to 2016. Data were obtained from the Association of American Medical Colleges and analyzed from October 2021 to January 2022.

Main Outcomes and Measures  Outcomes of interest included students’ self-reported participation in unique research experiences, number of publications, and computed publications per research experience. Poisson regressions were constructed to determine the association of sex and racial and ethnic identity with research outcomes using adjusted rate ratios (aRRs).

Results  Among 31 474 graduates, 15 159 (48.2%) identified as women and 4344 (13.8%) identified as underrepresented in medicine by race and ethnicity (URIM; including American Indian, Alaska Native, Black, Hawaiian Native, Hispanic/Latinx, and Pacific Islander individuals). Students who attended National Institutes of Health (NIH) top 40 research-ranked schools reported higher number of research experiences and publication counts, resulting in a higher publication rate compared with students from non–top 40 schools (median [IQR] 1.60 [1.00-3.00] vs 1.25 [0.50-2.33]; P < .001). Women reported a higher number of research experiences than men but a significantly lower number of publications (top 40 schools: aRR, 0.89; 95% CI, 0.87-0.90; non–top 40 schools: aRR, 0.93; 95% CI, 0.92-0.95). This resulted in a significantly lower publication rate among women (top 40 schools: aRR, 0.85; 95% CI, 0.83-0.86; non–top 40 schools: aRR, 0.91; 95% CI, 0.90-0.92). Compared with White students, Asian students had higher publication rates at both NIH top 40 schools (aRR, 1.10; 95% CI, 1.08-1.12) and non–top 40 schools (aRR, 1.07; 95% CI, 1.05-1.08), while lower publication rates were reported among Black students (top 40 schools: aRR, 0.83; 95% CI, 0.80-0.86; non–top 40 schools: aRR, 0.88; 95% CI, 0.85-0.95) and Hispanic students attending non–top 40 schools (aRR, 0.93; 95% CI, 0.90-0.95).

Conclusions and Relevance  These findings illustrate that inequities in the physician-scientist workforce began early in training and highlight key areas for intervention, such as funding support and mentorship training during undergraduate medical education, that may promote the future success of a diverse physician-scientist workforce.

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