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News Article | May 10, 2017
Site: www.eurekalert.org

The survival of the human species in the face of high rates of genetic mutations has remained an important problem in evolutionary biology. While mutations provide a source of novelty for the species, a large fraction of these genetic changes can also be damaging. A newborn human is estimated to have ~70 new mutations that the parents did not have. In a project conducted by Brigham and Women's Hospital research geneticist Shamil Sunyaev, PhD, and University of Michigan professor Alexey Kondrashov, PhD, scientists studied natural selection in humans. Their findings are published in a new paper in Science, where they report that, as a species, humans are able to keep the accumulation of damaging mutations in check because each additional mutation that's added to a genome causes larger, and larger consequences, decreasing an individual's ability to pass on genetic material. A damaging mutation is one that likely interferes with the biological function that a gene has for the organism. The researchers studied population samples from Europe, Asia and Africa and found a significant depletion of individuals carrying a large number of highly damaging mutations overall. They inferred that if a new mutation occurs in a genome that already contains many damaging mutations, it has a stronger effect than if it occurred in a genome with just a few other damaging mutations. Thus, the more damaging mutations a genome carries, the less likely that individual will be able to contribute progeny to the next generation. "Our study suggests that natural selection against highly damaging genetic mutations is ongoing in humans, and that it is aided by synergistic interactions between different parts of the human genome," said Sunyaev. This observation is general and is not limited to the human species. The same effect was independently observed in fruit flies. The findings also help explain another long-standing conundrum in evolutionary biology, that of the evolutionary maintenance of sexual reproduction. Because sex shuffles two genomes together, it can generate some genomes with very few mutations, and other genomes with very many mutations every generation. If damaging mutations in a genome behave synergistically, genomes with a high number of damaging mutations are then very unlikely to leave progeny. Evolutionary theory, thus, holds that sexual reproducers may be more successful than asexual reproducers because they are able to purge multiple damaging mutations from the population with single genetic deaths post sex-induced genetic remixing. This is precisely what is observed in this study. "By showing that sexual reproducers, such as humans and fruit flies, have a much lower rate of individuals with a large number of highly damaging mutations, our study provides support to theories that suggest that sex has an evolutionary advantage in a deterministic sense," said lead author Mashaal Sohail, PhD candidate in systems biology at Harvard University "that is to say, sex had to come about in a species such as our own to allow for more effective natural selection because the mutation rate is too high to sustain otherwise." This work was conducted at Harvard Medical School's Department of Biomedical Informatics and Brigham and Women's Hospital's Division of Genetics in collaboration with the Institute for Information Transmission Problems (Kharkevich Institute) of the Russian Academy of Sciences in Russia, and the Department of Neurology and Neurosurgery at the University Medical Center Utrecht in the Netherlands. This project was supported by the National Institutes of Health and by the Russian Science Foundation.

News Article | August 31, 2016
Site: www.nature.com

Crowded streets in Moscow boast some unusual adverts. Instead of touting property or consumer goods, they offer services for improving one's h-index and other metrics that will boost the impact of published scientific papers. A thriving market of academic fraud is one ugly side of post-Soviet science. Lamenting former prowess in everything from space exploration to nuclear power is another. Over the past 15 years, Russia has doubled its total spend on research and development (R&D). But this increase has failed to make up for the calamitous decline in Russian science during the 1990s, following the disintegration of the Soviet Union. According to the Russian Academy of Sciences (RAS), total R&D spending in 2013 still hovered about 40% below 1990 levels. And in 2014, the country spent 1.19% of its gross domestic product (GDP) on R&D, according to estimates by the Organisation for Economic Co-operation and Development (OECD) — only a slight improvement on the 1.05% it invested in 2000, and well below the 2.38% OECD average. But funding issues alone cannot explain why Russia has been on the sidelines of the international research stage for years — a lack of competition, poor infrastructure and an inability to retain talent have all played their part. Now a stumbling economy threatens the modest recovery in science made in the past decades, and the chances of reform. In 2014, Russia's R&D spending rose to a post-Soviet high of US$38.2 billion (in 2010 dollars). But Victor Kalinushkin, head of the RAS's trade union and a laser researcher at the A. M. Prokhorov General Physics Institute in Moscow, says that the current level of funding “is a minimal survival level” that does not allow for development, “keeping up with the others or compensating the losses incurred in the 1990s”. Twenty-five years into a market economy, R&D is still a state-dominated affair: from 2000 to 2014, the government's share of funding rose by 14%, to 69%, but private funding dropped by a few per cent. By comparison, in countries such as the United States and China about 75% of R&D funding comes from non-government sources. “Regrettably, we have failed to create the stimuli needed for the private sector to at least maintain the level of investment,” says Irina Dezhina, a science-policy researcher at Moscow's Institute for the Economy in Transition. And we cannot change the situation without large-scale economic reforms, she says. Instead of setting new rules to distribute the additional government funds through competitive grants, “this new money started pouring into the old system”, says Mikhail Gelfand, deputy director of the Institute for Information Transmission Problems in Moscow. “It was spread thin,” he says. “We have failed to build a new system, and the one we have is inelastic relative to investment. Funding has increased significantly over the last 15 years, and productivity, however you choose to measure it, has hardly increased at all.” The transition to a competitive-grant-based funding model has been slow. In 2014, just 11.1% of total R&D spending went on research foundation grants, barely up from 9.5% in 2010. Most R&D money is allocated through institution budgets. Adding to funding woes is the fact that precious extra resources are often distributed through politicking rather than through a transparent process. An analysis of 2016 budget plans (go.nature.com/2aisci7, in Russian) by Evgeny Onishchenko, a trade-union activist and semiconductor researcher at the Lebedev Physical Institute in Moscow, revealed that the Kurchatov Institute will receive 40% more funding this year than it did in 2015. The institute is headed by physicist Mikhail Kovalchuk, who is the brother of the businessman Yury Kovalchuk — a close friend of Russian President Vladimir Putin. Alexei Khokhlov, vice-rector at Lomonosov Moscow State University and chair of the advisory council for the Russian Ministry of Education and Science, says that the Federal Agency for Scientific Organizations, which was created in a swift reform of the RAS in 2013 to manage the network of institutes, has been “timid” in its efforts to change the status quo of competitive funding. Khokhlov thinks that the amount of research funding is not the central issue. Instead, he says that the lingering Soviet idea that every scientist should have a permanent salaried position that is largely independent of job performance, known as a stavka and much like a tenured professorship, has prevented meaningful reforms. The bulk of research spending will be paying for “payroll for positions set years ago”, he says. He also notes that this rigid personnel structure means that labs lack autonomy, allowing little room for scientists to work in emerging fields. This is reflected in how Russian science is represented internationally: the bulk of articles indexed by Web of Science and Scopus are related to physics, astronomy, chemistry, engineering and maths — all areas with a strong Soviet legacy. But the country is poorly represented in disciplines such as medicine or neuroscience. In the past 20 years or so, an exodus of researchers from Russia has contributed to the scientific workforce falling by about one-third, to some 373,900 people. This follows a previous catastrophic loss between 1989 and 1994, when a similar decreased happened in just five years. Pinning down the scale of cross-border 'brain drain' is tricky: estimates range from 30,000 to 200,000 scientists having left since the early 1990s. A small proportion of the researchers have returned, encouraged by initiatives such as a mega-grant programme to establish new labs in universities and research institutes — a total of 162 projects have been supported since 2010, in areas such as metamaterials, climate change and stem-cell research. Gelfand thinks that, apart from money, the science community's biggest problem is the lack of “a set of career paths with clear rules” for researchers. He says that there are too few opportunities for researchers to establish independent research groups, as well as little mobility in a system that, owing to its inflexibility and red tape, “does not encourage changing research areas, labs or institutes”. RAS president Vladimir Fortov has publicly stated that a renewed outflow of younger researchers in the past couple of years is evidence of this problem, a sentiment shared by Gelfand and others. Konstantin Severinov, a molecular biologist at Rutgers University in New Brunswick, New Jersey, who returned to Moscow in 2004 to also work at the Skolkovo Institute of Technology, has compared working in Russia to “swimming in a pool without water”. He says that staying in the country precludes young and promising scientists from competing internationally. By 2015, Russia had planned to increase its Web of Science share to an inexplicably precise 2.44%, a target set by Putin's 2012 decree. This did not happen, but the focus on performance indicators is unlikely to go away. Dezhina says that Russia places too much importance on metrics. “Most science-led economies have already passed this stage and now have a stronger appreciation for the role of experts,” she says. Kalinushkin also questions whether replacing peer-review assessments with statistics and metrics is a good strategy for evaluating scientists work. Resistance to what is seen as excessive focus on 'scientometrics' has put a spotlight on those who exploit loopholes in the system. One recent case of fraud involved two senior researchers at a biophysics institute who added irrelevant references into student conference papers that they edited to boost their own metrics. The two were exploiting a national science-citation index, which was established in 2006 as a way to measure the impact of Russian science that was largely invisible to the international audience. One analysis showed that some 90% of papers published by Russian scientists in 2014 were not indexed in Web of Science or Scopus ( et al. The Economics of Science 1, 6–14 (2015); in Russian). With little reaction from governing bodies to cases of academic fraud and plagiarism, some scientists have taken it upon themselves to expose university boards that routinely rubber-stamp plagiarized or ghostwritten PhD dissertations. Gelfand, who co-manages Dissernet, a volunteer organization dedicated to exposing this fraud, says that the 'immune response' by government has been weak, and groups such as his are in an arms race with unscrupulous people who are abusing the systems designed to protect the integrity of science. “Reputation as a social institution has been destroyed in Russia,” he says. “Nothing is shameful.” During a panel discussion at the St. Petersburg International Economic Forum in June 2016, historian Loren Graham, of the Massachusetts Institute of Technology in Cambridge, was asked if Russia can compete with the rest of the world in science and innovation. He reiterated the “contradictory and strange” fact that Russians tend to be excellent inventors, able to come up with new ideas, but very poor innovators, not able to make commercial successes of those ideas. Russian leaders prohibit demonstrations, suppress political opponents and twist the legal system, creating a regressive authoritarian regime that does not encourage entrepreneurship, Graham told the forum audience. “They want the milk without the cow.” Until such policies change, he concluded, “the scientific genius of the Russian people, for which I have such respect, will remain economically unfulfilled”. But things may get worse before they get better, as the Russian recession looks likely to deepen. In June, the Moscow-based Higher School of Economics said that it could see no signs of recovery in the economy. The recent turbulence has led to a 10% cut in science spending in 2016, and further cuts are expected to follow. Limited funding will require better prioritizing. Khokhlov thinks that any attempt to do this should reflect challenges that are specific to Russia. The world in general “will do just fine without us”, he says. He cites a statement by the advisory council for the Russian Ministry of Education and Science, which calls for Russia to prioritize communications, transportation technologies that are appropriate for the country's size, and a transition to automation. Gelfand, however, highlights the importance of a more results-based approach. “I think there's one top priority in Russian science now,” he says. “And that is protecting everything that still has a heartbeat.” The country's leaders have paid lip service to the importance of research. Indeed, in a speech at the RAS, just two weeks after his first inauguration in a May 2000, Putin called science “a crucial resource for economic growth”. Sixteen years later, although the economy has grown, Russia's scientific enterprise has a long way to go to regain past glories.

Levitov L.,Massachusetts Institute of Technology | Falkovich G.,Weizmann Institute of Science | Falkovich G.,Institute for Information Transmission Problems
Nature Physics | Year: 2016

Quantum-critical strongly correlated electron systems are predicted to feature universal collision-dominated transport resembling that of viscous fluids. However, investigation of these phenomena has been hampered by the lack of known macroscopic signatures of electron viscosity. Here we identify vorticity as such a signature and link it with a readily verifiable striking macroscopic d.c. transport behaviour. Produced by the viscous flow, vorticity can drive electric current against an applied field, resulting in a negative nonlocal voltage. We argue that the latter may play the same role for the viscous regime as zero electrical resistance does for superconductivity. Besides offering a diagnostic that distinguishes viscous transport from ohmic currents, the sign-changing electrical response affords a robust tool for directly measuring the viscosity-to-resistivity ratio. A strongly interacting electron-hole plasma in high-mobility graphene affords a unique link between quantum-critical electron transport and the wealth of fluid mechanics phenomena. © 2016 Macmillan Publishers Limited.

Bylinkin A.A.,Institute of Theoretical and Experimental Physics | Rostovtsev A.A.,Institute for Information Transmission Problems
Nuclear Physics B | Year: 2014

A qualitative model for hadroproduction in high energy collisions considering two components ("thermal" and "hard") to hadroproduction is proposed. Inclusive pseudorapidity distributions, dσ/. dη, and transverse momentum spectra, d2σ/(dηdpT2), measured by different collaborations are considered in terms of this model. The shapes of the pseudorapidity distributions agree with that one can expect from the qualitative picture introduced. The model is used to provide predictions for the LHC. Data up to a centre-of-mass energy of 7 TeV are well described and predictions for higher energies await new data. Finally, the differences between charged particle spectra produced in inclusive and diffractive events are discussed and the absence of the "thermal" component in the latter is observed. © 2014 The Authors.

Falkovich G.,Weizmann Institute of Science | Falkovich G.,Institute for Information Transmission Problems | Frishman A.,Weizmann Institute of Science
Physical Review Letters | Year: 2013

We develop an analytic formalism and derive new exact relations that express the short-time dispersion of fluid particles via the single-time velocity correlation functions in homogeneous isotropic and incompressible turbulence. The formalism establishes a bridge between single-time Eulerian and long-time Lagrangian pictures of turbulent flows. In particular, we derive an exact formula for a short-term counterpart of the long-time Richardson law, and we identify a conservation law of turbulent dispersion which is true even in nonstationary turbulence. © 2013 American Physical Society.

Frishman A.,Weizmann Institute of Science | Falkovich G.,Weizmann Institute of Science | Falkovich G.,Institute for Information Transmission Problems
Physical Review Letters | Year: 2014

The turbulent energy flux through scales, remains constant and nonvanishing in the limit of zero viscosity, which results in the fundamental anomaly of time irreversibility. It was considered straightforward to deduce from this the Lagrangian velocity anomaly, du2/dt=-4 at t=0, where u↠is the velocity difference of a pair of particles, initially separated by a fixed distance. Here we demonstrate that this assumed first taking the limit tâ†0 and then Îâ†0, while a zero-friction anomaly requires taking viscosity to zero first. We find that the limits tâ†0 and Îâ†0 do not commute if particles deplete (accumulate) in shocks backward (forward) in time on the viscous time scale. We compute analytically the resultant Lagrangian anomaly for one-dimensional Burgers turbulence and find it completely altered: du2/dt has different values forward and backward in time. For incompressible flows, on the other hand, we show that the limits commute and the Lagrangian anomaly is still induced by the flux law, apparently due to a homogeneous distribution of fluid particles at all times. © 2014 American Physical Society.

Belan S.,Weizmann Institute of Science | Belan S.,Institute for Information Transmission Problems | Fouxon I.,Weizmann Institute of Science | Fouxon I.,Institute for Information Transmission Problems | And 2 more authors.
Physical Review Letters | Year: 2014

Small aerosols drift down a temperature or turbulence gradient since faster particles fly longer distances before equilibration. That fundamental phenomenon, called thermophoresis or turbophoresis, is widely encountered in nature and used in industry. It is universally believed that particles moving down the kinetic energy gradient must concentrate in minima (say, on walls in turbulence). Here, we show that this is incorrect: escaping minima is possible for inertial particles whose time of equilibration is longer than the time to reach the minimum. "The best way out is always through": particles escape by flying through minima or reflecting from walls. We solve the problem analytically and find the phase transition as a sign change of the mean velocity. That means separation: light particles concentrate in a minimum while heavy particles spread away from it (gravity can reverse the effect). That discovery changes our understanding of that fundamental phenomenon and may find numerous applications. © 2014 American Physical Society.

V'yugin V.,Institute for Information Transmission Problems
IEEE International Symposium on Information Theory - Proceedings | Year: 2011

An instability property of the Birkhoff's ergodic theorem and related asymptotic laws with respect to small violations of algorithmic randomness is studied. The Shannon-McMillan-Breiman theorem and all universal compression schemes are also among them. © 2011 IEEE.

Berkolaiko G.,Texas A&M University | Comech A.,Texas A&M University | Comech A.,Institute for Information Transmission Problems | Sukhtayev A.,Texas A&M University
Nonlinearity | Year: 2015

We study the linear stability of localized modes in self-interacting spinor fields, analysing the spectrum of the operator corresponding to linearization at solitary waves. Following the generalization of the Vakhitov-Kolokolov approach, we show that the bifurcation of real eigenvalues from the origin is completely characterized by the Vakhitov-Kolokolov condition d Q/dω = 0 and by the vanishing of the energy functional. We give the numerical data on the linear stability in the generalized Gross-Neveu model and the generalized massive Thirring model in the charge-subcritical, charge-critical and chargesupercritical cases, illustrating the agreement with the Vakhitov-Kolokolov and the energy vanishing conditions. © 2015 IOP Publishing Ltd & London Mathematical Society.

Borodin A.,California Institute of Technology | Borodin A.,Institute for Information Transmission Problems | Gorin V.,Moscow State University | Rains E.M.,California Institute of Technology
Selecta Mathematica, New Series | Year: 2010

We introduce elliptic weights of boxed plane partitions and prove that they give rise to a generalization of MacMahon's product formula for the number of plane partitions in a box. We then focus on the most general positive degenerations of these weights that are related to orthogonal polynomials; they form three 2-D families. For distributions from these families, we prove two types of results. First, we construct explicit Markov chains that preserve these distributions. In particular, this leads to a relatively simple exact sampling algorithm. Second, we consider a limit when all dimensions of the box grow and plane partitions become large and prove that the local correlations converge to those of ergodic translation invariant Gibbs measures. For fixed proportions of the box, the slopes of the limiting Gibbs measures (that can also be viewed as slopes of tangent planes to the hypothetical limit shape) are encoded by a single quadratic polynomial. © 2010 Springer Basel AG.

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