Posts about open access paper

Should Giant Viruses Be Included on the Tree of Life?

A new study of giant viruses supports the idea that viruses are ancient living organisms and not inanimate molecular remnants. The study may reshape the universal family tree, adding a fourth major branch to the three that most scientists agree represent the fundamental domains of life. But I am not sure that makes sense. The reason given for viruses not being “life” is that they cannot reproduce themselves – they hijack living cells to reproduce. The research in the past history of viruses as they evolved into current viruses is interesting but I don’t see the reason to classify current viruses as life.

The researchers used a relatively new method to peer into the distant past. Rather than comparing genetic sequences, which are unstable and change rapidly over time, they looked for evidence of past events in the three-dimensional, structural domains of proteins. These structural motifs, called folds, are relatively stable molecular fossils that Рlike the fossils of human or animal bones Рoffer clues to ancient evolutionary events, said University of Illinois crop sciences and Institute for Genomic Biology professor Gustavo Caetano-Anoll̩s, who led the analysis.

“Just like paleontologists, we look at the parts of the system and how they change over time,” Caetano-Anollés said. Some protein folds appear only in one group or in a subset of organisms, he said, while others are common to all organisms studied so far.

“We make a very basic assumption that structures that appear more often and in more groups are the most ancient structures,” he said.

Most efforts to document the relatedness of all living things have left viruses out of the equation, Caetano-Anollés said.

“We’ve always been looking at the Last Universal Common Ancestor by comparing cells,” he said. “We never added viruses. So we put viruses in the mix to see where these viruses came from.”

The researchers conducted a census of all the protein folds occurring in more than 1,000 organisms representing bacteria, viruses, the microbes known as archaea, and all other living things. The researchers included giant viruses because these viruses are large and complex, with genomes that rival Рand in some cases exceed Рthe genetic endowments of the simplest bacteria, Caetano-Anoll̩s said.

Related: Plants, Unikonts, Excavates and SARsBacteriophages: The Most Common Life-Like Form on Earth8 Percent of the Human Genome is Old Virus GenesMicrobes Retroviruses

Open access paper: Giant Viruses Coexisted With the Cellular Ancestors and Represent a Distinct Supergroup Along With Superkingdoms Archaea, Bacteria and Eukarya

The discovery of giant viruses with genome and physical size comparable to cellular organisms, remnants of protein translation machinery and virus-specific parasites (virophages) have raised intriguing questions about their origin. Evidence advocates for their inclusion into global phylogenomic studies and their consideration as a distinct and ancient form of life.

Results call for a change in the way viruses are perceived. They likely represent a distinct form of life that either predated or coexisted with the last universal common ancestor (LUCA) and constitute a very crucial part of our planet’s biosphere.

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A single spot in the Sahara that provides huge amounts of nutrients to the Amazon

The Bodélé depression: a single spot in the Sahara that provides most of the mineral dust to the Amazon forest

About 40 million tons of dust are transported annually from the Sahara to the Amazon basin. Saharan dust has been proposed to be the main mineral source that fertilizes the Amazon basin, generating a dependence of the health and productivity of the rain forest on dust supply from the Sahara. Here we show that about half of the annual dust supply to the Amazon basin is emitted from a single source: the Bodélé depression located northeast of Lake Chad, approximately 0.5% of the size of the Amazon or 0.2% of the Sahara. Placed in a narrow path between two mountain chains that direct and accelerate the surface winds over the depression, the Bodélé emits dust on 40% of the winter days, averaging more than 0.7 million tons of dust per day.

Even understanding how connected the global ecosystem is, research like this provides amazing reminders of those connections.

Related: The Amazon Rainforest Would Not Be Without Saharan Dust (podcast interview)Ancient Whale Uncovered in Egyptian DesertNigersaurusThe Sahara Wasn’t Always a DesertElusive Saharan cheetah and Sandcat

Scientific Inquiry Process Finds More Evidence Supporting Einstein’s Theory

As scientists have been able to see farther and deeper into the universe, the laws that govern its expansion have been revealed to be under the influence of an unexplained force.

In a paper on the arXiv, Astrophysical Tests of Modified Gravity: Constraints from Distance Indicators in the Nearby Universe, are a vindication of Einstein’s theory of gravity. Having survived several decades of tests in the solar system, it has passed this new test in galaxies beyond our own as well.

In 1998, astrophysicists made an observation that turned gravity on its ear: the universe’s rate of expansion is speeding up. If gravity acts the same everywhere, stars and galaxies propelled outward by the Big Bang should continuously slow down, like objects thrown from an explosion do here on Earth.

This observation used distant supernovae to show that the expansion of the universe was speeding up rather than slowing down. This indicated that something was missing from physicists’ understanding of how the universe responds to gravity, which is described by Einstein’s theory of general relativity. Two branches of theories have sprung up, each trying to fill its gaps in a different way.

One branch — dark energy — suggests that the vacuum of space has an energy associated with it and that energy causes the observed acceleration. The other falls under the umbrella of “scalar-tensor” gravity theories, which effectively posits a fifth force (beyond gravity, electromagnetism and the strong and weak nuclear forces) that alters gravity on cosmologically large scales.

“These two possibilities are both radical in their own way,” University of Pennsylvania astrophysicist Bhuvnesh Jain said. “One is saying that general relativity is correct, but we have this strange new form of energy. The other is saying we don’t have a new form of energy, but gravity is not described by general relativity everywhere.”

Jain’s research is focused on the latter possibility; he is attempting to characterize the properties of this fifth force that disrupts the predictions general relativity makes outside our own galaxy, on cosmic length scales. Jain’s recent breakthrough came about when he and his colleagues realized they could use the troves of data on a special property of a common type of star as an exquisite test of gravity.

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Bacteria In Cave Isolated for 4 Million Years Highly Resistant to Many Antibiotics

PLoS published an interesting open access research paper on bacteria and their resistance to antibiotics. I am surprised how widespread and strong the antibiotic resistance was is the isolated bacteria that were studied. It raises more interesting questions about the important area of antibiotics.

The lead researcher on this study, Gerry Wright, previously published on antibiotic properties of bacteria found in soil.

Abstract of Antibiotic Resistance Is Prevalent in an Isolated Cave Microbiome

Antibiotic resistance is a global challenge that impacts all pharmaceutically used antibiotics. The origin of the genes associated with this resistance is of significant importance to our understanding of the evolution and dissemination of antibiotic resistance in pathogens. A growing body of evidence implicates environmental organisms as reservoirs of these resistance genes; however, the role of anthropogenic use of antibiotics in the emergence of these genes is controversial.

We report a screen of a sample of the culturable microbiome of Lechuguilla Cave, New Mexico, in a region of the cave that has been isolated for over 4 million years. We report that, like surface microbes, these bacteria were highly resistant to antibiotics; some strains were resistant to 14 different commercially available antibiotics. Resistance was detected to a wide range of structurally different antibiotics including daptomycin, an antibiotic of last resort in the treatment of drug resistant Gram-positive pathogens.

Enzyme-mediated mechanisms of resistance were also discovered for natural and semi-synthetic macrolide antibiotics via glycosylation and through a kinase-mediated phosphorylation mechanism. Sequencing of the genome of one of the resistant bacteria identified a macrolide kinase encoding gene and characterization of its product revealed it to be related to a known family of kinases circulating in modern drug resistant pathogens. The implications of this study are significant to our understanding of the prevalence of resistance, even in microbiomes isolated from human use of antibiotics. This supports a growing understanding that antibiotic resistance is natural, ancient, and hard wired in the microbial pangenome.

Related: Alligator Blood Provides Strong Resistance to Bacteria and VirusesBacteria Survive On All Antibiotic DietClay Versus MRSA Superbug

Nature Uses Stem Cells from Fetus to Repair Health of Mother

Science shows us so many amazing things. Scientists have learned mice use stem cells from the fetus to repair damage to the mother in the event of things like heart attacks. And there is evidence people do the same thing. Very cool. Nature beat us to the idea of using stem cells to treat health problems.

Helpful Mouse Fetuses Naturally Send Stem Cells to Mom to Fix Her Damaged Heart

When the scientists examined the female mice’s heart tissue two weeks after the heart attacks, they found lots of glowing green tissue—cells that came from the fetus—in the mom’s heart. Mice who had heart attacks had eight times as many cells from the fetus in their hearts as mice who hadn’t had a heart attack did, meaning the high volume of fetal cells was a response to the heart attack.

What’s more, the embryo’s stem cells had differentiated into various types of heart tissue, including cardiomyocytes, the rhythmically contracting muscle cells that produce a heartbeat.

The hearts of two women who suffered from severe heart weakness were later found to contain cells derived from the cells of a male fetus years after they gave birth to their sons.

The same thing seems to hold true for other organs. When pregnant women have damage in other organs, including the brain, lung, and liver, earlier studies have shown, fetal cells show up there, too.

It makes sense for a fetus to try and aid the mother but it is amazing the evolution found such solutions. Given how many challenges the fetus creates for the mother giving some benefits can help increase the odds of a health birth.

Related: Researchers Explain How Rotifers Thrive Despite Forgoing SexMaking Embryonic Stem CellsStructure and Function of RibosomeWhy People Often Get Sicker When They’re Stressed

Faster Than Light Speed Anomaly Reported by CERN

The OPERA result is based on the observation of over 15000 neutrino events measured at Gran Sasso, and appears to indicate that the neutrinos travel at a velocity 20 parts per million above the speed of light, nature’s cosmic speed limit. Given the potential far-reaching consequences of such a result, independent measurements are needed before the effect can either be refuted or firmly established. This is why the OPERA collaboration has decided to open the result to broader scrutiny. The collaboration’s result is available on the preprint server

The OPERA measurement is at odds with well-established laws of nature, though science frequently progresses by overthrowing the established paradigms. For this reason, many searches have been made for deviations from Einstein’s theory of relativity, so far not finding any such evidence. The strong constraints arising from these observations makes an interpretation of the OPERA measurement in terms of modification of Einstein’s theory unlikely, and give further strong reason to seek new independent measurements.

“This result comes as a complete surprise,” said OPERA spokesperson, Antonio Ereditato of the University of Bern. “After many months of studies and cross checks we have not found any instrumental effect that could explain the result of the measurement. While OPERA researchers will continue their studies, we are also looking forward to independent measurements to fully assess the nature of this observation.”

“When an experiment finds an apparently unbelievable result and can find no artefact of the measurement to account for it, it’s normal procedure to invite broader scrutiny, and this is exactly what the OPERA collaboration is doing, it’s good scientific practice,” said CERN Research Director Sergio Bertolucci. “If this measurement is confirmed, it might change our view of physics, but we need to be sure that there are no other, more mundane, explanations. That will require independent measurements.” This is a great reminder of the proper application of the scientific inquiry process. Our understanding moves forward based on evidence and incredible results require a high burden of proof before we accept them.

In order to perform this study, the OPERA Collaboration teamed up with experts in metrology from CERN and other institutions to perform a series of high precision measurements of the distance between the source and the detector, and of the neutrinos’ time of flight. The distance between the origin of the neutrino beam and OPERA was measured with an uncertainty of 20 cm over the 730 km travel path. The neutrinos’ time of flight was determined with an accuracy of less than 10 nanoseconds by using sophisticated instruments including advanced GPS systems and atomic clocks. The time response of all elements of the CNGS beam line and of the OPERA detector has also been measured with great precision.

“We have established synchronization between CERN and Gran Sasso that gives us nanosecond accuracy, and we’ve measured the distance between the two sites to 20 centimetres,” said Dario Autiero, the CNRS researcher who will give this afternoon’s seminar. “Although our measurements have low systematic uncertainty and high statistical accuracy, and we place great confidence in our results, we’re looking forward to comparing them with those from other experiments.”

“The potential impact on science is too large to draw immediate conclusions or attempt physics interpretations. My first reaction is that the neutrino is still surprising us with its mysteries.” said Ereditato. “Today’s seminar is intended to invite scrutiny from the broader particle physics community.”

The OPERA experiment was inaugurated in 2006, with the main goal of studying the rare transformation (oscillation) of muon neutrinos into tau neutrinos. One first such event was observed in 2010, proving the unique ability of the experiment in the detection of the elusive signal of tau neutrinos.

This is great stuff, wether it turns out to be an amazing result that changes our understanding of physics or even if it doesn’t (if it turns out the apparent result is not what it seems). It is great to see us attempt to learn. My guess is that we find some explanation for the anomaly that does avoids something traveling faster than the speed of light.

Brian Cox on the BBC 6: “This is the way science works, we go away and do it again and check, and then do it again and check. If it is confirmed then it will be the most significant discovery in physics in the last, at least, 100 years.”

Related: full press releaseThe Sun is a Miasma of Incandescent PlasmaGravity and the Scientific MethodMore Mysterious Space PhenomenonNeutrino particle traveling faster than light? Two ways it could rewrite physics

Large Crabs Invading Antarctic as Waters Warm

photo of giant red king crab

Giant red king crabs

Large crabs are invading the Antarctic environment and due to their numbers and practices could cause havoc. They look yummy though. And eating them would be doing nature a favor unlike the overfishing of the oceans. Abstract of the open access article, A large population of king crabs in Palmer Deep on the west Antarctic Peninsula shelf and potential invasive impacts:

Lithodid crabs (and other skeleton-crushing predators) may have been excluded from cold Antarctic continental shelf waters for more than 14 Myr [million years]. The west Antarctic Peninsula shelf is warming rapidly and has been hypothesized to be soon invaded by lithodids. A remotely operated vehicle survey in Palmer Deep, a basin 120 km onto the Antarctic shelf, revealed a large, reproductive population of lithodids, providing the first evidence that king crabs have crossed the Antarctic shelf. DNA sequencing and morphology indicate the lithodid is Neolithodes yaldwyni Ahyong & Dawson, previously reported only from Ross Sea waters. We estimate a N. yaldwyni population density of 10 600 km−2 and a population size of 1.55 × 106 in Palmer Deep, a density similar to lithodid populations of commercial interest around Alaska and South Georgia. The lithodid occurred at depths of more than 850 m and temperatures of more than 1.4°C in Palmer Deep, and was not found in extensive surveys of the colder shelf at depths of 430–725 m. Where N. yaldwyni occurred, crab traces were abundant, megafaunal diversity reduced and echinoderms absent, suggesting that the crabs have major ecological impacts. Antarctic Peninsula shelf waters are warming at approximately 0.01°C yr−1; if N. yaldwyni is currently limited by cold temperatures, it could spread up onto the shelf (400–600 m depths) within 1–2 decades. The Palmer Deep N. yaldwyni population provides an important model for the potential invasive impacts of crushing predators on vulnerable Antarctic shelf ecosystems.

Related: Giant Star Fish and More in Antarctica2,000 Species New to Science (600 of them crabs) from One IslandAntarctic Fish “Hibernate” in Winter

Is Dark Matter an Illusion?

Open access letter asks – Is dark matter an illusion created by the gravitational polarization of the quantum vaccum? by Dragan Slavkov Hajdukovic, CERN

Assuming that a particle and its antiparticle have the gravitational charge of the opposite sign, the physical vacuum may be considered as a fluid of virtual gravitational dipoles. Following this hypothesis, we present the first indications that dark matter may not exist and that the phenomena for which it was invoked might be explained by the gravitational polarization of the quantum vacuum by the known baryonic matter.

Let us start with a major unresolved problem. The measured galaxy rotation curves remain roughly constant at large radii. Faster than expected orbits, require a larger central force, which, in the framework of our theory of gravity, cannot be explained by the existing baryonic matter. The analogous problem persists also at the scale of clusters of galaxies.

The favoured solution is to assume that our current theory of gravity is correct, but every galaxy resides in a halo of dark matter made of unknown non-baryonic particles (for a brief review on dark matter see for instance: Einasto, 2010). A full list of the proposed dark matter particles would be longer than this letter; let us mention only weekly interacting massive particles and axions. In spite of the significant efforts dark particles have never been detected…

The scientific inquiry process continues to be used to try and explain the evidence we gather. Unsettled areas of science show how difficult the discovery process is. Once we have settled on theories it is so easy to explain why basic truths of evolution, geology, chemistry… result in what the evidence shows. But getting to the scientific consensus is a challenging process.

Dark Matter Is an Illusion, New Antigravity Theory Says

Physicist David Evans called the new study a “very interesting theoretical exercise,” but he said he isn’t ready to abandon dark matter just yet. “The evidence for dark matter is now very compelling,” said Evans, of the University of Birmingham, who leads the U.K. team for the ALICE detector at CERN’s Large Hadron Collider.

For example, in 2006 astronomers unveiled a photo of two colliding galaxies known as the Bullet cluster that purportedly showed the separation of matter from dark matter. A similar effect was observed in the Pandora cluster earlier this summer, said Evans, who was not involved in the study.

Hajdukovic said he is currently expanding his theory to account for these observations. His preliminary calculations, he said, suggest that “what is observed in the Bullet cluster and more recently at the Pandora cluster may be understood in the framework of the gravitational polarization of the quantum vacuum.”

CERN physicist Michael Doser agreed that Hajdukovic’s ideas are “unorthodox” but did not immediately dismiss the new theory…
“In a few years,” Doser said, “we should definitely be in a position to confirm or refute [Hajdukovic’s] hypothesis.”

Related: The Mystery of Empty SpaceWhy do we Need Dark Energy to Explain the Observable Universe?Dark Matter Experiment ResultsLooking for Signs of Dark Matter Over Antarctica

Cutting the Boarding Time of Planes in Half

I thought I wrote about this several years ago, but I guess I didn’t (I can’t find it, if I did). Experimental test of airplane boarding methods:

The Ste en method, on the other hand, orders the passengers in such a way that adjacent passengers in line are sitting in corresponding seats two rows apart from each other (e.g., 12A, 10A, 8A, 6A, etc.). This method trades a small number of aisle interferences at the front of the cabin, for the benefit of having multiple passengers stowing their luggage simultaneously. Other methods, such as Wilma and the Reverse Pyramid also realize parallel use of the aisle in a natural way as adjacent passengers are frequently sitting in widely separated rows.

We have seen experimentally that there is a marked difference in the time required to board an aircraft depending upon the boarding method used. The evidence strongly supports the heuristic argument from Ste en that methods that parallelize the boarding process by more efficiently utilizing the aisle (having more passengers stow their luggage simultaneously) will board more quickly than those that do not. The relative benefit of the application of this theory will grow with the length of the aircraft. Here, we used a 12-row mock airplane, but a more typical airplane with twice that number of rows will gain more by the implementation of parallelized boarding methods.

How this improvement scales with the cabin length is different for each method. For the Ste en method, the benefit will scale almost linearly. If the airplane is twice as long, the time savings will be nearly twice as much since the density of luggage-stowing passengers will remain the same and the boarding will still be maximally parallel. For Wilma and random boarding the benefit will not be as strong since the benefits of parallel boarding are randomly distributed along the length of the cabin instead of being regularly distributed.

I am not optimistic that airlines will even test out this method. People tend to think companies apply sensible, proven concepts and methods. But that is much less likely to be done than people think. The failure of many places to use simple queuing theory improvement (customers should form one line and be served the next available person not form many individual lines) is one example of failures by companies to apply decades old proven better methods. The poor adoption of multivariate designed experiments is another. Applying better ideas is a process that is not done very efficiently in business, health care, education or even science and engineering – in fact in any human endeavor. This is a waste that impacts each of us every day. It is also an opportunity for you to gain advantages just by applying all the good ideas lying around that others are ignoring. You need to test the ideas out in your setting (using the PDSA cycle in an organizational context a good method).

Related: Engineering the Boarding of AirplanesSuccessful Emergency Plane Landing in the Hudson RiverChecklists Save LivesImproving Engineering Education

Insightful Problem Solving in an Asian Elephant

Another example of very cool animal behavior. This Asian Elephant, seemed to consider the problem, devise a solution and then go get a stool to reach food that could not be reached without a tool.

Insightful Problem Solving in an Asian Elephant

The “aha” moment or the sudden arrival of the solution to a problem is a common human experience. Spontaneous problem solving without evident trial and error behavior in humans and other animals has been referred to as insight. Surprisingly, elephants, thought to be highly intelligent, have failed to exhibit insightful problem solving in previous cognitive studies. We tested whether three Asian elephants (Elephas maximus) would use sticks or other objects to obtain food items placed out-of-reach and overhead. Without prior trial and error behavior, a 7-year-old male Asian elephant showed spontaneous problem solving by moving a large plastic cube, on which he then stood, to acquire the food. In further testing he showed behavioral flexibility, using this technique to reach other items and retrieving the cube from various locations to use as a tool to acquire food. In the cube’s absence, he generalized this tool utilization technique to other objects and, when given smaller objects, stacked them in an attempt to reach the food. The elephant’s overall behavior was consistent with the definition of insightful problem solving. Previous failures to demonstrate this ability in elephants may have resulted not from a lack of cognitive ability but from the presentation of tasks requiring trunk-held sticks as potential tools, thereby interfering with the trunk’s use as a sensory organ to locate the targeted food.

Further inspired by Köhler’s chimpanzee studies, in experiment 4 we conducted 8 additional sessions to investigate whether Kandula would stack items to reach food. For these sessions, the baited branches were hung at a height that could be reached by stacking three butcher block cutting boards or by the use of other objects. In addition, the elephant was given sticks and other enrichment items. Kandula first touched several items and then moved two items, a plastic disk and a block under the suspended branches, placing one front foot on each in an unsuccessful attempt to reach for the branch. He solved the problem in an unexpected novel manner, moving and standing on the object closest in size to the absent cube, a large ball. Standing on unstable platforms such as this had not been previously observed. He repeated this behavior 9 times during this session. During the session’s last minutes, Kandula picked up a block ~2 m from the food and placed it directly on top of a block that he placed under the food in a previous attempt. He stood on the stacked blocks and attempted to reach the food but was unsuccessful. He stacked two blocks again in the second and sixth sessions but each time his trunk was several inches from the food.

This is very cool research. I do wonder why they didn’t provide more videos (and in a more user-friendly format than .mov files). I made them available via YouTube.

It seems like a very interesting area to have more experiments with more elephants (and continuing to work with Kandula: he seems to be very curious elephant, good for him).

Related: Orangutan Attempts to Hunt Fish with SpearBird Using Bait to Catch FishCrows Transferring Their Understanding to Novel ProblemCapuchin Monkeys Using Stone ToolsFighting Elephant Poaching With SciencePhoto of Fish Using a Rock to Open a Clam
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MIT Scientists Find New Drug That Could Cure Nearly Any Viral Infection

New drug could cure nearly any viral infection

The drug works by targeting a type of RNA produced only in cells that have been infected by viruses. “In theory, it should work against all viruses,” says Todd Rider, a senior staff scientist in Lincoln Laboratory‘s Chemical, Biological, and Nanoscale Technologies Group who invented the new technology.

There are a handful of drugs that combat specific viruses, such as the protease inhibitors used to control HIV infection, but these are relatively few in number and susceptible to viral resistance.

Rider drew inspiration for his therapeutic agents, dubbed DRACOs (Double-stranded RNA Activated Caspase Oligomerizers), from living cells’ own defense systems. When viruses infect a cell, they take over its cellular machinery for their own purpose — that is, creating more copies of the virus. During this process, the viruses create long strings of double-stranded RNA (dsRNA), which is not found in human or other animal cells.

As part of their natural defenses against viral infection, human cells have proteins that latch onto dsRNA, setting off a cascade of reactions that prevents the virus from replicating itself. However, many viruses can outsmart that system by blocking one of the steps further down the cascade.

Rider had the idea to combine a dsRNA-binding protein with another protein that induces cells to undergo apoptosis (programmed cell suicide) — launched, for example, when a cell determines it is en route to becoming cancerous. Therefore, when one end of the DRACO binds to dsRNA, it signals the other end of the DRACO to initiate cell suicide.

Combining those two elements is a “great idea” and a very novel approach, says Karla Kirkegaard, professor of microbiology and immunology at Stanford University. “Viruses are pretty good at developing resistance to things we try against them, but in this case, it’s hard to think of a simple path pathway to drug resistance,” she says.

Each DRACO also includes a “delivery tag,” taken from naturally occurring proteins, that allows it to cross cell membranes and enter any human or animal cell. However, if no dsRNA is present, DRACO leaves the cell unharmed.

Very cool stuff and potentially hugely beneficial. Just a reminder: this works against viruses – not bacteria (just as antibiotics do not work against viruses).

image showing the results of cultures treated with DRACO v. those not treated

Related: Science Explained: RNA Interference8 Percent of the Human Genome is Old Virus GenesVirus Engineered To Kill Deadly Brain Tumors
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