A step towards AI-based precision medicine

Mika Gustafsson and David Martínez hope that AI-based models could eventually be used in precision medicine to develop treatments and preventive strategies tailored to the individual. 
Photo Credit: Thor Balkhed

Artificial intelligence, AI, which finds patterns in complex biological data could eventually contribute to the development of individually tailored healthcare. Researchers at LiU have developed an AI-based method applicable to various medical and biological issues. Their models can for instance accurately estimate people’s chronological age and determine whether they have been smokers or not.

There are many factors that can affect which out of all our genes are used at any given point in time. Smoking, dietary habits and environmental pollution are some such factors. This regulation of gene activity can be likened to a power switch determining which genes are switched on or off, without altering the actual genes, and is called epigenetics.

Researchers at Linköping University (LiU) have used data with epigenetic information from more than 75,000 human samples to train a large number of AI neural network models. They hope that such AI-based models could eventually be used in precision medicine to develop treatments and preventive strategies tailored to the individual. Their models are of the autoencoder type, that self-organizes the information and finds interrelation patterns in the large amount of data.

Antigen testing can reduce, but not eliminate, the risk of COVID-19 clusters according to mathematical model

Illustration Credit: Kojima Kyoko

A research group has created a new model to calculate the probability of the occurrence of localized clusters caused by novel coronavirus infections. Led by Shingo Iwami at Nagoya University with collaborators in the United Kingdom and South Korea model, they revealed that screening of infected persons by antigen testing is effective in significantly reducing the probability of cluster occurrence. However, their findings also suggest that it is not sufficient to prevent clusters caused by highly infectious mutant strains, such as Omicron.  

With the availability of COVID-19 vaccines and population immunity, countries around the world are seeking to resume social activities while also trying to prevent the spread of infection. However, outbreaks of new strains of the coronavirus, associated with increased infectiousness and evasion of existing immunity, continue to be a threat. In several countries, new infections are increasing as the northern hemisphere enters the autumn and winter months.

Rivers may not recover from drought for years

Low water levels in rivers
Photo Credit: Manh Tuan Nguyen

Lack of rainfall is not the only measure of drought. New UC Riverside research shows that despite a series of storms, the impact of drought can persist in streams and rivers for up to 3.5 years.

There are two measures of drought in streams. One measure is the total water level, which is impacted by snowmelt and rainfall. Many researchers examine this measurement. Another measure is baseflow, which is the portion of streamflow fed by groundwater.

Fewer researchers examine baseflow droughts, and there was not previously an accurate way to measure them. Because baseflow is strongly tied to groundwater, and because the lack of it has significant impacts on water management and ecosystem services, the UCR team decided to examine baseflow more closely.

“People often just use rain as an indicator of drought because it’s easier to measure. But there are other kinds of drought that each have their own impacts,” said Hoori Ajami, corresponding study author and associate professor of groundwater hydrology at UCR. “We needed a new way to see how long it takes for one form of drought to become another form.”

Tens of thousands of endangered sharks and rays caught off Congo

Shark catch from one boat after a week at sea.
Photo Credit: Phil Doherty

Tens of thousands of endangered sharks and rays are caught by small-scale fisheries off the Republic of the Congo each year, new research shows.

Scientists surveyed fish brought ashore at Songolo, which is home to more than 60% of the country’s “artisanal” fishers (small boats, small engines, hand-hauled lines and nets).

In three years, the team – led by the University of Exeter in partnership with the Wildlife Conservation Society (WCS) Congo Program and the Republic of the Congo’s fisheries department – recorded more than 73,000 sharks and rays landed.

Most were juveniles, and 98% of individuals were of species listed as vulnerable, endangered or critically endangered on the IUCN Red List.

The researchers highlighted good news from the study: it shows the area is rich in sharks and rays, including two species previously thought to be locally absent – the African wedgefish and the smoothback angelshark.

Making hydropower plants more environmentally friendly

Dr. Melanie Müller, Dr. Joachim Pander and Prof. Jürgen Geist (from left) investigated the ecological impact of eight hydropower plants.
Photo Credit: Andreas Heddergott / TUM 

A research team from the Chair of Aquatic Systems Biology at the Technical University of Munich (TUM) has analyzed the harm caused to fish, changes in their behavior and the impact on the aquatic habitat at the shaft power plant in the Loisach, a river in Bavaria. This study was part of a large-scale research project looking into the ecological impact of different types of hydroelectric power plant. It has highlighted a number of factors that should be considered in the construction of future shaft power plants to minimize the environmental impact as far as possible.

Developed in recent years, the shaft power plant is a novel type of hydropower installation. A shaft housing the turbine and generator is installed in the riverbed upstream of a weir. Water flows into the shaft, drives the turbine and is then directed back into the river by the weir. A smaller proportion of the water flows over the shaft and the weir. The weir features openings, which are designed to allow fish to migrate downstream. This design aims to ensure that, unlike in other types of hydropower plants, only a small number of fish are harmed by traveling into the turbine. Conventional fish ladders also allow fish to migrate upstream.

Land use: produce more food and store more carbon at the same time

Optimized land use could still significantly increase yields taking climatic conditions into account, keeping land use within limits.
Photo Credit: Anita Bayer

Double food production, save water and at the same time increase carbon storage - that sounds paradoxical, but would be theoretically possible, at least according to the biophysical potential of the earth. However, a radical spatial reorganization in land use would be necessary. Researchers from the Karlsruhe Institute of Technology (KIT) and the Heidelberg Institute for Geoinformation Technology (HeiGIT), an affiliated institute of Heidelberg University, found this out. They have their results in the Proceedings of the National Academy of Sciences.

How people use the surface of the earth, including for the production of food, has changed a lot in the past centuries. Today, more and more people live on earth, more food is needed and food can be transported around the world in a short time. However, as the study shows, the historically grown systems of food production do not reflect the biophysical potential of our ecosystems. Food is therefore not produced where there is area, water and CO2- would be the most efficient in terms of technology. Instead, according to the authors of the study, forests for arable and pasture land continue to be cleared and fields in arid areas irrigated - measures that have a massive negative impact on water availability and carbon storage.

Illuminating the dance of RNA with ultrabright X-rays

Researchers demonstrated the ability to observe fine details, right down to angstrom-scale features in RNA at SLAC’s Linac Coherent Light Source (LCLS).   
Photo Credit: Olivier Bonin/SLAC National Accelerator Laboratory

DNA, RNA, and proteins are three pillars of molecular biology. While DNA holds genetic instructions and proteins put these plans to action, RNA serves as the messenger and interpreter. DNA is transcribed to RNA, which then decodes those instructions to synthesize proteins. But large portions of RNA don't proceed to produce proteins, with a vast majority remaining just as RNA. What these molecules do or why they exist in such a state is still not fully understood.

Now, scientists have developed a promising method to uncover RNA’s secrets. Using X-ray free-electron laser sources such as the Linac Coherent Light Source at the Department of Energy’s SLAC National Accelerator Laboratory, researchers can now observe fine details, right down to angstrom-scale features, in RNA that is freely dispersed in solution so that large scale structural changes can occur – just as they would in our bodies. Not only does this research shed light on RNA's behavior, but the techniques developed can also be applied to other biological molecules. The implications are far-reaching, from better understanding diseases to designing new therapeutics. The results were published last week in Science Advances.

New Study Points to New Possibilities for Treating Lung Cancer Patients

Illustration Credit: Rawpixel

Currently, researchers from different institutions in the world are testing a drug against obesity and diabetes, and now a Danish research team reports that the same substance has had a beneficial effect on mice with experimental lung cancer.

The substance is the short-chain fatty acid propionate, which is naturally produced by bacteria in our gut. From there, it is distributed throughout the body, and this new research study shows that treating mice with lung cancer with propionate can reduce the occurrence of metastases.

The study also demonstrates a role for propionate in increasing the effectiveness of Cisplatin, a commonly used drug for lung cancer patients. This was shown by lab experiments carried out in cancer cells derived from patients.

Exploring Parameter Shift for Quantum Fisher Information

Image Credit: Scientific Frontline stock image

Quantum computing uses quantum mechanics to process and store information in a way that is different from classical computers. While classical computers rely on bits like tiny switches that can be either 0 or 1, quantum computers use quantum bits (qubits). Qubits are unique because they can be in a mixture of 0 and 1 simultaneously - a state referred to as superposition. This unique property enables quantum computers to solve specific problems significantly faster than classical ones.

In a recent publication in EPJ Quantum Technology, Le Bin Ho from Tohoku University's Frontier Institute for Interdisciplinary Sciences has developed a technique called "Time-dependent Stochastic Parameter Shift" in the realm of quantum computing and quantum machine learning. This breakthrough method revolutionizes the estimation of gradients or derivatives of functions, a crucial step in many computational tasks.

Typically, computing derivatives requires dissecting the function and calculating the rate of change over a small interval. But even classical computers cannot keep dividing indefinitely. In contrast, quantum computers can accomplish this task without having to discrete the function. This feature is achievable because quantum computers operate in a realm known as "quantum space," characterized by periodicity, and no need for endless subdivisions.

Microbial Metabolites: A New Link to Parkinson's Disease?

Photo Credit: Rawpixel

Researchers from the University of Vienna, University of Konstanz, and Albert Einstein College of Medicine uncover a potential environmental trigger for Parkinson's disease.

Published in Environment International, a groundbreaking study from the Institute of Biological Chemistry and Centre for Microbiology and Environmental Systems Science (CeMESS) at the University of Vienna, in collaboration with the University of Konstanz and the Albert Einstein College of Medicine, reveals a microbial metabolite's role in inducing Parkinson's-like symptoms. This discovery could reshape our understanding of the environmental triggers of Parkinson's disease.

The underlying causes of Parkinson's disease, a debilitating neurodegenerative condition, are not well understood. While genetic mutations are known to cause Parkinson's, a staggering 90% of cases are sporadic, with no clear genetic origin. Scientists suspect environmental factors could play a role – and substances like pesticides and industrial chemicals have been investigated for potential links to neurodegeneration. Among the possible culprits are microbial metabolites.

Recent studies highlight the gut-brain axis's importance, suggesting that our microbiome might influence neurodegenerative diseases. Notably, the gut microbiome of Parkinson's patients differs from that of healthy individuals. Some microbial metabolites have even been shown to specifically target dopamine-producing neurons, which are crucially affected in Parkinson's disease.

Killing remains a threat to Bornean orangutans

Photo Credit: Simone Millward

University of Queensland research has found despite considerable conservation efforts, the illegal killing of critically endangered orangutans on Borneo may be an ongoing threat to the species.  

PhD candidate Emily Massingham from UQ’s Faculty of Science managed a team of researchers which visited 79 villages across the Bornean orangutan range in Kalimantan, conducting face to face interviews with 431 people.

“Our study builds on previous research which indicated killing was one of the key reasons for orangutan population decline, alongside habitat loss,” Ms. Massingham said.

“The aim of our project was to understand whether orangutans have been killed in recent times, to look at whether conservation projects are effectively preventing killing, and to gain insights into community perceptions and the motivations behind it.

“It has been almost 15 years since the previous study, and we did not find a clear decrease in killings despite Indonesia’s commendable efforts to reduce habitat loss.

Scientists Call for Real-Time Forecasting of Tropical Cyclones in Light of Climate Change

Satellite view of Hurricane Ian
Photo Credit: NASA

The need for quick and “real-time” forecasting of tropical cyclones is more necessary than ever given the impact of climate change on rainfall amounts. Two climate scientists who believe this take the notion further by suggesting a storyline case study of Hurricane Ian in 2022 can be used as a blueprint for rapid operational climate change attribution statements about extreme storms. Their premise is detailed in a paper published in the journal Environmental Research: Climate.

Co-authors Kevin A. Reed, professor and associate dean of Research in the School of Marine and Atmospheric Sciences at Stony Brook University, and Michael F. Wehner, of Lawrence Berkeley National Laboratory in California, note that tropical cyclones such as Hurricane Ian are devastating events worldwide, endangering lives and causing damage costing billions of dollars to repair. Therefore, the public, media and governmental leaders affected by such extreme storms turn to scientists to understand more about the weather event and how climate change may have affected it.

Discovery reveals fragile X syndrome begins developing even before birth

The energy-making organelles called mitochondria (shown in green) that work inside cells to make energy aren’t working as they should in the neurons (shown in red) of people with fragile X syndrome. UW–Madison researchers have identified a protein and gene involved in this mitochondrial dysfunction, as well as a potential treatment.
Image Credit: Minjie Shen

Fragile X syndrome, the most common form of inherited intellectual disability, may be unfolding in brain cells even before birth, despite typically going undiagnosed until age 3 or later.

A new study published today in the journal Neuron by researchers at the University of Wisconsin–Madison showed that FMRP, a protein deficient in individuals with fragile X syndrome, has a role in the function of mitochondria, part of a cell that produces energy, during prenatal development. Their results fundamentally change how scientists understand the developmental origins of fragile X syndrome and suggest a potential treatment for brain cells damaged by the dysfunction.

Xinyu Zhao is a neuroscience professor and neurodevelopmental diseases researcher at UW–Madison’s Waisman Center. Four postdoctoral fellows in her lab led the study.

Stellar fountain of youth with turbulent formation history in the center of our galaxy

A multi-wavelength view of the surroundings of the supermassive black hole SgrA * (yellow X). The stars are red, the dust is blue. Many of the young stars in the IRS13 star cluster are covered by dust or covered by the bright stars.
Credits: Florian Peißker / University of Cologne

An international team led by Dr Florian Peißker at the University of Cologne’s Institute of Astrophysics has analyzed in detail a young star cluster in the immediate vicinity of the super massive black hole Sagittarius A* (Sgr A*) in the center of our galaxy and showed that it is significantly younger than expected. This cluster, known as IRS13, was discovered more than twenty years ago, but only now has it been possible to determine the cluster members in detail by combining a wide variety of data – taken with various telescopes over a period of several decades. The stars are a few 100,000 years old and therefore extraordinarily young for stellar conditions. By comparison, our sun is about 5 billion years old. Due to the high-energy radiation as well as the tidal forces of the galaxy, it should in fact not be possible for such a large number of young stars to be in the direct vicinity of the super massive black hole. The study was conducted under the title ‘The Evaporating Massive Embedded Stellar Cluster IRS 13 Close to Sgr A*. I. Detection of a Rich Population of Dusty Objects in the IRS13 Cluster’ and has now appeared in The Astrophysical Journal.

Lethal Climate Change Millions of Years Ago Was Due to Volcanic Eruptions, Scientists Conclude

Earth’s Geological History Tied to Astronomical Motions—Not Just the Planet’s Interior
Illustration Credit: Scientific Frontline

Climate change that has occurred over the past 260 million years and brought about mass extinctions of life during these periods was due to massive volcanic eruptions and subsequent environmental crises, concludes a team of scientists.

Its analysis, which appears in the journal Earth-Science Reviews, shows that these eruptions released large amounts of carbon dioxide into the Earth’s atmosphere, leading to extreme greenhouse climate warming and bringing about near-lethal or lethal conditions to our planet.

Significantly, these phenomena—which occur every 26 to 33 million years—coincided with critical changes in the planet’s orbit in the solar system that follow the same cyclical patterns, the researchers add.

“The Earth’s geologic processes, long considered to be strictly determined by events within the planet’s interior, may in fact be controlled by astronomical cycles in the solar system and the Milky Way Galaxy,” says Michael Rampino, a professor in New York University’s Department of Biology and the paper’s senior author. “Crucially, these forces have converged many times in the Earth’s past to foreshadow drastic changes to our climate.”