CHARLOTTESVILLE, Va., Dec. 7, 2021 /PRNewswire/ — A large-scale systematic investigation to replicate high-impact, preclinical cancer biology experiments identified barriers to conducting replications and observed weaker evidence for the findings compared with the original experiments. Unnecessary friction in the research process may be slowing the advancement of knowledge, solutions, and treatments.
Today, eLife publishes the final outputs of the Reproducibility Project: Cancer Biology, an 8-year effort to replicate experiments from 53 high-impact papers published between 2010 and 2012. Tim Errington, the Director of Research at the Center for Open Science and project leader said: “The purpose of the project was to transparently assess the extent to which there are challenges for conducting replications and obtaining similar evidence of published findings in cancer biology research.”
Launched in 2013, the Reproducibility Project: Cancer Biology was a collaboration between the Center for Open Science, a nonprofit culture change organization with a mission to improve openness, integrity, and reproducibility of research, and Science Exchange, the world’s first online R&D marketplace whose mission is to accelerate scientific discovery. With support from Arnold Ventures (formerly the Laura and John Arnold Foundation), the team conducted a systematic process to select high-impact cancer research papers published between 2010 and 2012. Based on the selection criteria, most of the papers came from high-profile journals such as Nature, Science, and Cell. A total of 193 experiments were selected for replication.
The team designed replication experiments of key findings from each paper by reviewing the methodology and requesting information about protocols and availability of reagents. Then, appropriate expertise for conducting the experiments was sourced through the Science Exchange marketplace.
For each paper the detailed protocols for the replication experiments were written up as a Registered Report and submitted to eLife for peer review; moreover, work on the replication experiments could not begin until the Registered Report had been accepted for publication. The completed replication experiments were then written up as a Replication Study, peer reviewed and published in eLife. Two of the papers published today are capstone summaries of the entire project.
The first paper “Challenges for Assessing Replicability in Preclinical Cancer Biology” reports on the challenges confronted when preparing and conducting replications of 193 experiments from 53 papers. None of the experiments were described in sufficient detail to design a replication without seeking clarifications from the original authors. Some authors (26%) were extremely helpful and generous with feedback, and some authors (32%) were not at all helpful or did not respond to requests. During experimentation, about two-thirds of the experiments required some modification to the protocols because, for example, model systems behaved differently than originally reported. Ultimately, 50 replication experiments from 23 papers were completed, a small proportion of what were planned. Errington noted, “We had challenges at every stage of the research process to design and conduct the replications. It was hard to understand what was originally done, we could not always get access to the original data or reagents to conduct the experiments, and model systems frequently did not behave as originally reported. The limited transparency and incomplete reporting made the efforts to replicate the findings much harder than was necessary.”
The second paper, “Investigating the Replicability of Preclinical Cancer Biology“, reports a meta-analysis of the results of the 50 replication experiments that did get completed. Many of these experiments involved measuring more than one effect (e.g., measuring the influence of an intervention on both the tumor burden and overall survival), and the 50 experiments that were completed included a total of 158 effects. Most of these effects (136) were reported as positive effects in the original papers, with 22 being reported as null effects. The meta-analysis also had to take into account that 41 of the effects were reported as images rather than as numerical values in the original papers. Replications provided much weaker evidence for the findings compared to the original experiments. For example, for original positive results, replication effect sizes were 85% smaller than the original effect sizes on average.
The team also used a number of binary criteria to assess whether a replication was successful or not. A total of 112 effects could be assessed by five of these criteria, and 18% succeeded on all five, 15% succeeded on four, 13% succeeded on three, 21% succeeded on two, 13% succeeded on one, and 20% failed on all five. Collectively, 46% of the replications were successful on more criteria than they failed and 54% of the replications failed on more criteria than they succeeded.
Summarizing, Errington noted, “Of the replication experiments we were able to complete, the evidence was much weaker on average than the original findings even though all the replications underwent peer review before conducting the experiments to maximize their quality and rigor. Our findings suggest that there is room to improve replicability in preclinical cancer research.”
Brian Nosek, Executive Director from the Center for Open Science and co-author added, “Science is making substantial progress in addressing global health challenges. The evidence from this project suggests that we could be doing even better. There is unnecessary friction in the research process that is interfering with advancing knowledge, solutions, and treatments. Investing in improving transparency, sharing, and rigor of preclinical research could yield huge returns on investment by removing sources of friction and accelerating science. For example, open sharing of data, materials, and code will make it easier to understand, critique, and build upon each other’s work. And, preregistration of experiments and analysis plans will reduce the negative effects of publication bias and distinguish between planned tests and unplanned discoveries.”
These papers identify substantial challenges for cancer research, but they occur amid a reformation in science to address dysfunctional incentives, improve the research culture, increase transparency and sharing, and improve rigor in design and conduct of research. Science is at its best when it confronts itself and identifies ways to improve the quality and credibility of research findings. The Reproducibility Project: Cancer Biology is just one contribution in an ongoing self-examination of research practices and opportunities for improvement.
Additional supporting information about the project is also available via this OSF link. This includes a fact sheet, background information, a list of independent researchers that have agreed to be listed as possible contacts for interviews, and a guide with links to navigating the content of the RP:CB papers, reviews, and supporting information.
The previously published Registered Reports, Replication Studies, and related commentaries are all available on eLife’s Reproducibility Project: Cancer Biology Collection page, and all data, code, and supporting materials are available in COS’s Reproducibility Project: Cancer Biology Collection. Also summary information about the project and links to key resources are available at http://cos.io/rpcb.
About Center for Open Science
Founded in 2013, COS is a nonprofit technology and culture change organization with a mission to increase openness, integrity, and reproducibility of scientific research. COS pursues this mission by building communities around open science practices, supporting metascience research, and developing and maintaining free, open source software tools, including the Open Science Framework (OSF). For more information, visit cos.io.
About Science Exchange
Founded in 2011 with the goal to accelerate scientific discovery, Science Exchange is an online marketplace powering scientific outsourcing for the R&D industry – providing companies with instant access to scientific services from a trusted network of contract research organizations. Science Exchange’s R&D marketplace simplifies scientific outsourcing and eliminates contracting delays so scientists can access innovation without the administrative burdens. Since 2011, Science Exchange has raised more than $70 million from Norwest Venture Partners, Maverick Ventures, Union Square Ventures, Collaborative Fund, Windham Ventures, OATV, the YC Continuity Fund, and others. For more information, visit scienceexchange.com.
eLife is a non-profit organisation created by funders and led by researchers. Our mission is to accelerate discovery by operating a platform for research communication that encourages and recognises the most responsible behaviours. We review selected preprints in all areas of biology and medicine, while exploring new ways to improve how research is assessed and published. eLife receives financial support and strategic guidance from the Howard Hughes Medical Institute, the Knut and Alice Wallenberg Foundation, the Max Planck Society and Wellcome. Learn more at elifesciences.org/about.
About Arnold Ventures
Arnold Ventures is a philanthropy dedicated to tackling some of the most pressing problems in the United States. We invest in sustainable change, building it from the ground up based on research, deep thinking, and a strong foundation of evidence. We drive public conversation, craft policy, and inspire action through education and advocacy. For more information, visit arnoldventures.org.
SOURCE Center for Open Science
Are the northern lights caused by 'particles from the Sun'? Not exactly – Phys.org
What a spectacle a big aurora is, its shimmering curtains and colorful rays of light illuminating a dark sky. Many people refer to aurora as the northern lights (the aurora borealis), but there are southern lights too (the aurora australis). Either way, if you’re lucky enough to catch a glimpse of this phenomenon, it’s something you won’t soon forget.
The aurora is often explained simply as “particles from the Sun” hitting our atmosphere. But that’s not technically accurate except in a few limited cases. So what does happen to create this natural marvel?
We see the aurora when energetic charged particles—electrons and sometimes ions—collide with atoms in the upper atmosphere. While the aurora often follows explosive events on the Sun, it’s not quite true to say these energetic particles that cause the aurora come from the Sun.
Earth’s magnetism, the force that directs the compass needle, dominates the motions of electrically charged particles in space around Earth. The magnetic field near the surface of Earth is normally steady, but its strength and direction fluctuate when there are displays of the aurora. These fluctuations are caused by what’s called a magnetic substorm—a rapid disturbance in the magnetic field in near-Earth space.
To understand what happens to trigger a substorm, we first need to learn about plasma. Plasma is a gas in which a significant number of the atoms have been broken into ions and electrons. The gas of the uppermost regions of Earth’s atmosphere is in the plasma state, as is the gas that makes up the Sun and other stars. A gas of plasma flows away continuously from the Sun: this is called the solar wind.
Plasma behaves differently from those gases we meet in everyday life. Wave a magnet around in your kitchen and nothing much happens. The air of the kitchen consists overwhelmingly of electrically neutral atoms, so it’s quite undisturbed by the moving magnet. In a plasma, however, with its electrically charged particles, things are different. So if your house was filled with plasma, waving a magnet around would make the air move.
When solar wind plasma arrives at the earth it interacts with the planet’s magnetic field (as illustrated below—the magnetic field is represented by the lines that look a bit like a spider). Most of the time, plasma travels easily along the lines of the magnetic field, but not across them. This means that solar wind arriving at Earth is diverted around the planet and kept away from the Earth’s atmosphere. In turn, the solar wind drags the field lines out into the elongated form seen on the night side, called the magnetotail.
Sometimes moving plasma brings magnetic fields from different regions together, causing a local breakdown in the pattern of magnetic field lines. This phenomenon, called magnetic reconnection, heralds a new magnetic configuration, and, importantly, unleashes a huge amount of energy.
These events happen fairly often in the Sun’s outer atmosphere, causing an explosive energy release and pushing clouds of magnetized gas, called coronal mass ejections, away from the Sun (as seen in the image above).
If a coronal mass ejection arrives at Earth it can in turn trigger reconnection in the magnetotail, releasing energy that drives electrical currents in near-Earth space: the substorm. Strong electric fields that develop in this process accelerate electrons to high energies. Some of these electrons may have come from the solar wind, allowed into near-Earth space by reconnection, but their acceleration in the substorm is essential to their role in the aurora.
These particles are then funneled by the magnetic field towards the atmosphere high above the polar regions. There they collide with the oxygen and nitrogen atoms, exciting them to glow as the aurora.
Now you know exactly what causes the northern lights, how do you optimize your chances of seeing it? Seek out dark skies far from cities and towns. The further north you can go the better but you don’t need to be in the Arctic Circle. We see them from time to time in Scotland, and they’ve even been spotted in the north of England—although they’re still better seen at higher latitudes.
Websites such as AuroraWatch UK can tell you when it’s worth heading outside. And remember that while events on the Sun can give us a few days warning, these are indicative, not foolproof. Perhaps part of the magic lies in the fact that you need a little bit of luck to see the aurora in all its glory.
Are the northern lights caused by ‘particles from the Sun’? Not exactly (2022, January 21)
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Hubble telescope spots a black hole fostering baby stars in a dwarf galaxy – Space.com
Black holes can not only rip stars apart, but they can also trigger star formation, as scientists have now seen in a nearby dwarf galaxy.
At the centers of most, if not all, large galaxies are supermassive black holes with masses that are millions to billions of times that of Earth’s sun. For instance, at the heart of our Milky Way galaxy lies Sagittarius A*, which is about 4.5 million solar masses in size.
Astronomers have previously seen giant black holes shred apart stars. However, researchers have also detected supermassive black holes generating powerful outflows that can feed the dense clouds from which stars are born.
Black hole-driven star formation was previously seen in large galaxies, but the evidence for such activity in dwarf galaxies was scarce. Dwarf galaxies are roughly analogous to what newborn galaxies may have looked like soon after the dawn of the universe, so investigating how supermassive black holes in dwarf galaxies can spark the birth of stars may in turn offer “a glimpse of how young galaxies in the early universe formed a portion of their stars,” study lead author Zachary Schutte, an astrophysicist at Montana State University in Bozeman, told Space.com.
In a new study, the scientists investigated the dwarf galaxy Henize 2-10, located about 34 million light-years from Earth in the southern constellation Pyxis. Recent estimates suggest the dwarf galaxy has a mass about 10 billion times that of the sun. (In contrast, the Milky Way has a mass of about 1.5 trillion solar masses.)
A decade ago, study senior author Amy Reines at Montana State University discovered radio and X-ray emissions from Henize 2-10 that suggested the dwarf galaxy’s core hosted a black hole about 3 million solar masses in size. However, other astronomers suggested this radiation may instead have come from the remnant of a star explosion known as a supernova.
In the new study, the researchers focused on a tendril of gas from the heart of Henize 2-10 about 490 light-years long, in which electrically charged ionized gas is flowing as fast as 1.1 million mph (1.8 million kph). This outflow was connected like an umbilical cord to a bright stellar nursery about 230 light-years from Henize 2-10’s core.
This outflow slammed into the dense gas of the stellar nursery like a garden hose spewing onto a pile of dirt, leading water to spread outward. The researchers found newborn star clusters about 4 million years old and upwards of 100,000 times the mass of the sun dotted the path of the outflow’s spread, Schutte said.
With the help of high-resolution images from the Hubble Space Telescope, the scientists detected a corkscrew-like pattern in the speed of the gas in the outflow. Their computer models suggested this was likely due to the precessing, or wobbling, of a black hole. Since a supernova remnant would not cause such a pattern, this suggests that Henize 2-10’s core does indeed host a black hole.
“Before our work, supermassive black hole-enhanced star formation had only been seen in much larger galaxies,” Schutte said.
In the future, the researchers would like to investigate more dwarf galaxies with similar black hole-triggered star formation. However, this is difficult for many reasons — “systems like Henize 2-10 are not common; obtaining high quality observations is difficult; and so on,” Schutte said. However, when the James Webb Space Telescope hopefully comes online in the near future, “we will have new tools to search for these systems,” he noted.
Schutte and Reines detailed their findings in the Jan. 19 issue of the journal Nature.
Massive Iceberg Released Over 150 Billion Tons of Fresh Water Into Ocean As It Scraped Past South Georgia – SciTechDaily
Scientists monitoring the giant A68A Antarctic iceberg from space reveal that a huge amount of fresh water was released as it melted around the sub-Antarctic island of South Georgia.
152 billion tonnes of fresh water – equivalent to 20 x Loch Ness or 61 million Olympic sized swimming pools, entered the seas around the sub-Antarctic island of South Georgia when the megaberg A68A melted over 3 months in 2020/2021, according to a new study.
In July 2017, the A68A iceberg snapped off the Larsen-C Ice Shelf on the Antarctic Peninsula and began its epic 3.5 year, 4000 km journey across the Southern Ocean. At 5719 square kilometers in extent – quarter the size of Wales –, it was the biggest iceberg on Earth when it formed and the sixth largest on record. Around Christmas 2020, the berg received widespread attention as it drifted worryingly close to South Georgia, raising concerns it could harm the island’s fragile ecosystem.
Researchers from the Centre for Polar Observation and Modelling (CPOM) and British Antarctic Survey (BAS) used satellite measurements to chart the A68A iceberg’s area and thickness change throughout its life cycle. The authors show that the berg had melted enough as it drifted to avoid damaging the sea floor around South Georgia by running aground. However, a side effect of the melting was the release of a colossal 152 billion tonnes of fresh water in close proximity to the island – a disturbance that could have a profound impact on the island’s marine habitat.
For the first two years of its life, A68A stayed close to Antarctica in the cold waters of the Weddell Sea and experienced little in the way of melting. However, once it began its northwards journey across Drake Passage it traveled through increasingly warm waters and began to melt. Altogether, the iceberg thinned by 67 meters from its initial 235 m thickness, with the rate of melting rising sharply as the berg drifted in the Scotia Sea around South Georgia.
Laura Gerrish, GIS and mapping specialist at BAS and co-author of the study said:
“A68 was an absolutely fascinating iceberg to track all the way from its creation to its end. Frequent measurements allowed us to follow every move and break-up of the berg as it moved slowly northwards through iceberg alley and into the Scotia Sea where it then gained speed and approached the island of South Georgia very closely.”
Thinning and breakage of the A68A iceberg over time. Melt rates increase sharply once the iceberg is drifting in open ocean north of the Antarctic peninsula. Iceberg thickness was derived from satellite altimetry data from Cryosat-2 and ICESat-2. Iceberg shape and size were sourced from Sentinel-1, Sentinel-3 and MODIS satellite data. Credit: Anne Braakmann-Folgmann CPOM
If an iceberg’s keel is too deep it can get stuck on the sea floor. This can be disruptive in several different ways; the scour marks can destroy fauna, and the berg itself can block ocean currents and predator foraging routes. All of these potential outcomes were feared when A68A approached South Georgia. However, this new study reveals that it collided only briefly with the sea floor and broke apart shortly afterward, making it less of a risk in terms of blockage. By the time it reached the shallow waters around South Georgia, the iceberg’s keel had reduced to 141 meters below the ocean surface, shallow enough to avoid the seabed which is around 150 meters deep.
Nevertheless, the ecosystem and wildlife around South Georgia will certainly have felt the impact of the colossal iceberg’s visit. When icebergs detach from ice shelves, they drift with the ocean currents and wind while releasing cold fresh meltwater and nutrients as they melt. This process influences the local ocean circulation and fosters biological production around the iceberg. At its peak, the iceberg was melting at a rate of 7 meters per month, and in total it released a staggering 152 billion tonnes of fresh water and nutrients.
Anne Braakmann-Folgmann, a researcher at CPOM and PhD candidate at the University of Leeds’ School of Earth and Environment, is lead author of the study. She said:
“This is a huge amount of melt water, and the next thing we want to learn is whether it had a positive or negative impact on the ecosystem around South Georgia.
“Because A68A took a common route across the Drake Passage, we hope to learn more about icebergs taking a similar trajectory, and how they influence the polar oceans.”
The journey of A68A has been charted using observations from 5 different satellites. The iceberg’s area change was recorded using a combination of Sentinel-1, Sentinel-3, and MODIS imagery. Meanwhile, the iceberg’s thickness change was measured using CryoSat-2 and ICESat-2 altimetry. By combining these measurements, the iceberg’s area, thickness, and volume change were determined.
Tommaso Parrinello, CryoSat Mission Manager at the European Space Agency, said:
“Our ability to study every move of the iceberg in such detail is thanks to advances in satellite techniques and the use of a variety of measurements. Imaging satellites record the location and shape of the iceberg and data from altimetry missions add a third dimension as they measure the height of surfaces underneath the satellites and can therefore observe how an iceberg melts.”
Reference: “Observing the disintegration of the A68A iceberg from space” by A. Braakmann-Folgmann, A. Shepherd, L. Gerrish, J. Izzard and A. Ridout, 10 January 2022, Remote Sensing of Environment.
COVID-19 in Nova Scotia, Jan. 21: weekly recap, 94 hospitalized, 601 new cases – Halifax Examiner
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Sask. RCMP issue Canada-wide warrant for anti-vaccine dad charged with abducting daughter, 7 – CBC.ca
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