Showing papers by "Moscow Institute of Physics and Technology published in 2017"

CatBoost: unbiased boosting with categorical features

Abstract: This paper presents the key algorithmic techniques behind CatBoost, a new gradient boosting toolkit. Their combination leads to CatBoost outperforming other publicly available boosting implementations in terms of quality on a variety of datasets. Two critical algorithmic advances introduced in CatBoost are the implementation of ordered boosting, a permutation-driven alternative to the classic algorithm, and an innovative algorithm for processing categorical features. Both techniques were created to fight a prediction shift caused by a special kind of target leakage present in all currently existing implementations of gradient boosting algorithms. In this paper, we provide a detailed analysis of this problem and demonstrate that proposed algorithms solve it effectively, leading to excellent empirical results.

Particle-flow reconstruction and global event description with the CMS detector

Abstract: The CMS apparatus was identified, a few years before the start of the LHC operation at CERN, to feature properties well suited to particle-flow (PF) reconstruction: a highly-segmented tracker, a fine-grained electromagnetic calorimeter, a hermetic hadron calorimeter, a strong magnetic field, and an excellent muon spectrometer. A fully-fledged PF reconstruction algorithm tuned to the CMS detector was therefore developed and has been consistently used in physics analyses for the first time at a hadron collider. For each collision, the comprehensive list of final-state particles identified and reconstructed by the algorithm provides a global event description that leads to unprecedented CMS performance for jet and hadronic τ decay reconstruction, missing transverse momentum determination, and electron and muon identification. This approach also allows particles from pileup interactions to be identified and enables efficient pileup mitigation methods. The data collected by CMS at a centre-of-mass energy of 8\TeV show excellent agreement with the simulation and confirm the superior PF performance at least up to an average of 20 pileup interactions.

INTEGRAL Detection of the First Prompt Gamma-Ray Signal Coincident with the Gravitational-wave Event GW170817

Abstract: We report the INTernational Gamma-ray Astrophysics Laboratory (INTEGRAL) detection of the short gamma-ray burst GRB 170817A (discovered by Fermi-GBM) with a signal-to-noise ratio of 4.6, and, for the first time, its association with the gravitational waves (GWs) from binary neutron star (BNS) merging event GW170817 detected by the LIGO and Virgo observatories. The significance of association between the gamma-ray burst observed by INTEGRAL and GW170817 is 3.2σ, while the association between the Fermi-GBM and INTEGRAL detections is 4.2σ. GRB 170817A was detected by the SPI-ACS instrument about 2 s after the end of the GW event. We measure a fluence of (1.4 ± 0.4 ± 0.6) × 10(−)(7) erg cm(−)(2) (75–2000 keV), where, respectively, the statistical error is given at the 1σ confidence level, and the systematic error corresponds to the uncertainty in the spectral model and instrument response. We also report on the pointed follow-up observations carried out by INTEGRAL, starting 19.5 hr after the event, and lasting for 5.4 days. We provide a stringent upper limit on any electromagnetic signal in a very broad energy range, from 3 keV to 8 MeV, constraining the soft gamma-ray afterglow flux to <7.1 × 10(−)(11) erg cm(−)(2) s(−)(1) (80–300 keV). Exploiting the unique capabilities of INTEGRAL, we constrained the gamma-ray line emission from radioactive decays that are expected to be the principal source of the energy behind a kilonova event following a BNS coalescence. Finally, we put a stringent upper limit on any delayed bursting activity, for example, from a newly formed magnetar.

druGAN: An Advanced Generative Adversarial Autoencoder Model for de Novo Generation of New Molecules with Desired Molecular Properties in Silico

Abstract: Deep generative adversarial networks (GANs) are the emerging technology in drug discovery and biomarker development. In our recent work, we demonstrated a proof-of-concept of implementing deep generative adversarial autoencoder (AAE) to identify new molecular fingerprints with predefined anticancer properties. Another popular generative model is the variational autoencoder (VAE), which is based on deep neural architectures. In this work, we developed an advanced AAE model for molecular feature extraction problems, and demonstrated its advantages compared to VAE in terms of (a) adjustability in generating molecular fingerprints; (b) capacity of processing very large molecular data sets; and (c) efficiency in unsupervised pretraining for regression model. Our results suggest that the proposed AAE model significantly enhances the capacity and efficiency of development of the new molecules with specific anticancer properties using the deep generative models.

An integrated expression atlas of miRNAs and their promoters in human and mouse.

Abstract: MicroRNAs (miRNAs) are short non-coding RNAs with key roles in cellular regulation. As part of the fifth edition of the Functional Annotation of Mammalian Genome (FANTOM5) project, we created an integrated expression atlas of miRNAs and their promoters by deep-sequencing 492 short RNA (sRNA) libraries, with matching Cap Analysis Gene Expression (CAGE) data, from 396 human and 47 mouse RNA samples. Promoters were identified for 1,357 human and 804 mouse miRNAs and showed strong sequence conservation between species. We also found that primary and mature miRNA expression levels were correlated, allowing us to use the primary miRNA measurements as a proxy for mature miRNA levels in a total of 1,829 human and 1,029 mouse CAGE libraries. We thus provide a broad atlas of miRNA expression and promoters in primary mammalian cells, establishing a foundation for detailed analysis of miRNA expression patterns and transcriptional control regions.

A White Paper on keV sterile neutrino Dark Matter

Abstract: We present a comprehensive review of keV-scale sterile neutrino Dark Matter, collecting views and insights from all disciplines involved—cosmology, astrophysics, nuclear, and particle physics—in each case viewed from both theoretical and experimental/observational perspectives. After reviewing the role of active neutrinos in particle physics, astrophysics, and cosmology, we focus on sterile neutrinos in the context of the Dark Matter puzzle. Here, we first review the physics motivation for sterile neutrino Dark Matter, based on challenges and tensions in purely cold Dark Matter scenarios. We then round out the discussion by critically summarizing all known constraints on sterile neutrino Dark Matter arising from astrophysical observations, laboratory experiments, and theoretical considerations. In this context, we provide a balanced discourse on the possibly positive signal from X-ray observations. Another focus of the paper concerns the construction of particle physics models, aiming to explain how sterile neutrinos of keV-scale masses could arise in concrete settings beyond the Standard Model of elementary particle physics. The paper ends with an extensive review of current and future astrophysical and laboratory searches, highlighting new ideas and their experimental challenges, as well as future perspectives for the discovery of sterile neutrinos.

Measurement of the τ Lepton Polarization and R (D * ) in the Decay B ̄ →D * τ - ν ̄ τ

Abstract: We report the first measurement of the tau lepton polarization P-tau(D*) in the decay (B) over bar -> D* tau(-) (v) over bar (tau) as well as a newmeasurement of the ratio of the branching fractions R(D*) = B((B) over bar -> D* tau(-) (v) over bar (tau)) / B((B) over bar -> D* l(-) (v) over bar (l)), where l(-) denotes an electron or a muon, and the tau is reconstructed in the modes tau(-) -> pi(-) v(tau) and tau(-) -> rho(-) v(tau). We use the full data sample of 772 x 10(6) B (B) over bar pairs recorded with the Belle detector at the (KEKB) over bar electron-positron collider. Our results, P-tau(D*) = -0.38 +/- 0.51 (stat)(-0.16)(+0.21) (syst) and R(D*) = 0.270 +/- 0.035 (stat)(- 0.025)(+0.028) (syst), are consistent with the theoretical predictions of the standard model.

Lepton-Flavor-Dependent Angular Analysis of B→K^{*}ℓ^{+}ℓ^{-}

Abstract: We present a measurement of angular observables and a test of lepton flavor universality in the B -> K(+)l(+)l(-) decay, where l is either e or mu. The analysis is performed on a data sample corresponding to an integrated luminosity of 711 fb(-1) containing 772 x 10(6) B (B) over bar pairs, collected at the Upsilon(4S) resonance with the Belle detector at the asymmetric-energy e(+)e(-) collider KEKB. The result is consistent with standard model (SM) expectations, where the largest discrepancy from a SM prediction is observed in the muon modes with a local significance of 2.6 sigma.

Search for new high-mass phenomena in the dilepton final state using 36 fb−1 of proton-proton collision data at √s=13 TeV with the ATLAS detector

Abstract: A search is conducted for new resonant and non-resonant high-mass phenomena in dielectron and dimuon fi nal states. The search uses 36 : 1 fb(-1) of proton-proton collision data, collected at root ...

Deep Reinforcement Learning for De-Novo Drug Design

Abstract: We propose a novel computational strategy for de novo design of molecules with desired properties termed ReLeaSE (Reinforcement Learning for Structural Evolution). Based on deep and reinforcement learning approaches, ReLeaSE integrates two deep neural networks - generative and predictive - that are trained separately but employed jointly to generate novel targeted chemical libraries. ReLeaSE employs simple representation of molecules by their SMILES strings only. Generative models are trained with stack-augmented memory network to produce chemically feasible SMILES strings, and predictive models are derived to forecast the desired properties of the de novo generated compounds. In the first phase of the method, generative and predictive models are trained separately with a supervised learning algorithm. In the second phase, both models are trained jointly with the reinforcement learning approach to bias the generation of new chemical structures towards those with the desired physical and/or biological properties. In the proof-of-concept study, we have employed the ReLeaSE method to design chemical libraries with a bias toward structural complexity or biased toward compounds with either maximal, minimal, or specific range of physical properties such as melting point or hydrophobicity, as well as to develop novel putative inhibitors of JAK2. The approach proposed herein can find a general use for generating targeted chemical libraries of novel compounds optimized for either a single desired property or multiple properties.

Charged-particle nuclear modification factors in PbPb and pPb collisions at √sNN=5.02 TeV

Abstract: we acknowledge the enduring support for the construction and operation of the LHC and the CMS detector provided by the following funding agencies: BMWFW and FWF (Austria); FNRS and FWO (Belgium); CNPq, CAPES, FAPERJ, and FAPESP (Brazil); MES (Bulgaria); CERN; CAS, MoST, and NSFC (China); COLCIENCIAS (Colombia); MSES and CSF (Croatia); RPF (Cyprus); SENESCYT (Ecuador); MoER, ERC IUT and ERDF (Estonia); Academy of Finland, MEC, and HIP (Finland); CEA and CNRS/IN2P3 (France); BMBF, DFG, and HGF (Germany); GSRT (Greece); OTKA and NIH (Hungary); DAE and DST (India); IPM (Iran); SFI (Ireland); INFN (Italy); MSIP and NRF (Republic of Korea); LAS (Lithuania); MOE and UM (Malaysia); BUAP, CINVESTAV, CONACYT, LNS, SEP, and UASLP-FAI (Mexico); MBIE (New Zealand); PAEC (Pakistan); MSHE and NSC (Poland); FCT (Portugal); JINR (Dubna); MON, RosAtom, RAS and RFBR (Russia); MESTD (Serbia); SEIDI and CPAN (Spain); Swiss Funding Agencies (Switzerland); MST (Taipei); ThEPCenter, IPST, STAR and NSTDA (Thailand); TUBITAK and TAEK (Turkey); NASU and SFFR (Ukraine); STFC (United Kingdom); DOE and NSF (U.S.A.).

Measurements of properties of the Higgs boson decaying into the four-lepton final state in pp collisions at √s=13 TeV

Abstract: Properties of the Higgs boson are measured in the H → ZZ → 4l (l = e, μ) decay channel. A data sample of proton-proton collisions at $ \sqrt{s}=13 $ TeV, collected with the CMS detector at the LHC and corresponding to an integrated luminosity of 35.9 fb$^{−1}$ is used. The signal strength modifier μ, defined as the ratio of the observed Higgs boson rate in the H → ZZ → 4l decay channel to the standard model expectation, is measured to be μ = 1.05$_{− 0.17}^{+ 0.19}$ at m$_{H}$ = 125.09 GeV, the combined ATLAS and CMS measurement of the Higgs boson mass. The signal strength modifiers for the individual Higgs boson production modes are also measured. The cross section in the fiducial phase space defined by the requirements on lepton kinematics and event topology is measured to be 2. 92$_{− 0.44}^{+ 0.48}$ (stat)$_{− 0.24}^{+ 0.28}$ (syst)fb, which is compatible with the standard model prediction of 2.76 ± 0.14 fb. Differential cross sections are reported as a function of the transverse momentum of the Higgs boson, the number of associated jets, and the transverse momentum of the leading associated jet. The Higgs boson mass is measured to be m$_{H}$ = 125.26 ± 0.21 GeV and the width is constrained using the on-shell invariant mass distribution to be Γ$_{H}$ < 1.10 GeV, at 95% confidence level.

A stable compound of helium and sodium at high pressure

Abstract: Helium is generally understood to be chemically inert and this is due to its extremely stable closed-shell electronic configuration, zero electron affinity and an unsurpassed ionization potential. It is not known to form thermodynamically stable compounds, except a few inclusion compounds. Here, using the ab initio evolutionary algorithm USPEX and subsequent high-pressure synthesis in a diamond anvil cell, we report the discovery of a thermodynamically stable compound of helium and sodium, Na2He, which has a fluorite-type structure and is stable at pressures >113 GPa. We show that the presence of He atoms causes strong electron localization and makes this material insulating. This phase is an electride, with electron pairs localized in interstices, forming eight-centre two-electron bonds within empty Na8 cubes. We also predict the existence of Na2HeO with a similar structure at pressures above 15 GPa.

Optical constants and structural properties of thin gold films

Abstract: We report a comprehensive experimental study of optical and electrical properties of thin polycrystalline gold films in a wide range of film thicknesses (from 20 to 200 nm). Our experimental results are supported by theoretical calculations based on the measured morphology of the fabricated gold films. We demonstrate that the dielectric function of the metal is determined by its structural morphology. Although the fabrication process can be absolutely the same for different films, the dielectric function can strongly depend on the film thickness. Our studies show that the imaginary part of the dielectric function of gold, which is responsible for optical losses, rapidly increases as the film thickness decreases for thicknesses below 80 nm. At the same time, we do not observe a noticeable dependence of optical constants on the film thickness for thicker samples. These findings establish design rules for thin-film plasmonic and nanophotonic devices.

Search for new phenomena in dijet events using 37 fb-1 of pp collision data collected at √s=13 TeV with the ATLAS detector

Abstract: Dijet events are studied in the proton-proton collision dataset recorded at root s = 13 TeV with the ATLAS detector at the Large Hadron Collider in 2015 and 2016, corresponding to integrated lumino ...

Links of gut microbiota composition with alcohol dependence syndrome and alcoholic liver disease.

Abstract: Alcohol abuse has deleterious effects on human health by disrupting the functions of many organs and systems. Gut microbiota has been implicated in the pathogenesis of alcohol-related liver diseases, with its composition manifesting expressed dysbiosis in patients suffering from alcoholic dependence. Due to its inherent plasticity, gut microbiota is an important target for prevention and treatment of these diseases. Identification of the impact of alcohol abuse with associated psychiatric symptoms on the gut community structure is confounded by the liver dysfunction. In order to differentiate the effects of these two factors, we conducted a comparative “shotgun” metagenomic survey of 99 patients with the alcohol dependence syndrome represented by two cohorts—with and without liver cirrhosis. The taxonomic and functional composition of the gut microbiota was subjected to a multifactor analysis including comparison with the external control group. Alcoholic dependence and liver cirrhosis were associated with profound shifts in gut community structures and metabolic potential across the patients. The specific effects on species-level community composition were remarkably different between cohorts with and without liver cirrhosis. In both cases, the commensal microbiota was found to be depleted. Alcoholic dependence was inversely associated with the levels of butyrate-producing species from the Clostridiales order, while the cirrhosis—with multiple members of the Bacteroidales order. The opportunist pathogens linked to alcoholic dependence included pro-inflammatory Enterobacteriaceae, while the hallmarks of cirrhosis included an increase of oral microbes in the gut and more frequent occurrence of abnormal community structures. Interestingly, each of the two factors was associated with the expressed enrichment in many Bifidobacterium and Lactobacillus—but the exact set of the species was different between alcoholic dependence and liver cirrhosis. At the level of functional potential, the patients showed different patterns of increase in functions related to alcohol metabolism and virulence factors, as well as pathways related to inflammation. Multiple shifts in the community structure and metabolic potential suggest strong negative influence of alcohol dependence and associated liver dysfunction on gut microbiota. The identified differences in patterns of impact between these two factors are important for planning of personalized treatment and prevention of these pathologies via microbiota modulation. Particularly, the expansion of Bifidobacterium and Lactobacillus suggests that probiotic interventions for patients with alcohol-related disorders using representatives of the same taxa should be considered with caution. Taxonomic and functional analysis shows an increased propensity of the gut microbiota to synthesis of the toxic acetaldehyde, suggesting higher risk of colorectal cancer and other pathologies in alcoholics.

Coherent perfect absorbers: linear control of light with light

Abstract: Absorption of electromagnetic energy by a material is a phenomenon that underlies many applied problems, including molecular sensing, photocurrent generation and photodetection. Commonly, the incident energy is delivered to the system through a single channel, for example by a plane wave incident on one side of an absorber. However, absorption can be made much more efficient by exploiting wave interference. A coherent perfect absorber is a system in which complete absorption of electromagnetic radiation is achieved by controlling the interference of multiple incident waves. Here, we review recent advances in the design and applications of such devices. We present the theoretical principles underlying the phenomenon of coherent perfect absorption and give an overview of the photonic structures in which it can be realized, including planar and guided-mode structures, graphene-based systems, parity- and time-symmetric structures, 3D structures and quantum-mechanical systems. We then discuss possible applications of coherent perfect absorption in nanophotonics and, finally, we survey the perspectives for the future of this field.

Searches for invisible decays of the Higgs boson in pp collisions at √s = 7, 8, and 13 TeV

Abstract: Searches for invisible decays of the Higgs boson are presented. The data collected with the CMS detector at the LHC correspond to integrated luminosities of 5.1, 19.7, and 2.3 fb−1 at centre-of-mass energies of 7, 8, and 13 TeV, respectively. The search channels target Higgs boson production via gluon fusion, vector boson fusion, and in association with a vector boson. Upper limits are placed on the branching fraction of the Higgs boson decay to invisible particles, as a function of the assumed production cross sections. The combination of all channels, assuming standard model production, yields an observed (expected) upper limit on the invisible branching fraction of 0.24 (0.23) at the 95% confidence level. The results are also interpreted in the context of Higgs-portal dark matter models.

Coherent perfect absorbers: linear control of light with light

Abstract: The absorption of electromagnetic energy by a material is a phenomenon that underlies many applications, including molecular sensing, photocurrent generation and photodetection. Typically, the incident energy is delivered to the system through a single channel, for example, by a plane wave incident on one side of an absorber. However, absorption can be made much more efficient by exploiting wave interference. A coherent perfect absorber is a system in which the complete absorption of electromagnetic radiation is achieved by controlling the interference of multiple incident waves. Here, we review recent advances in the design and applications of such devices. We present the theoretical principles underlying the phenomenon of coherent perfect absorption and give an overview of the photonic structures in which it can be realized, including planar and guided-mode structures, graphene-based systems, parity-symmetric and time-symmetric structures, 3D structures and quantum-mechanical systems. We then discuss possible applications of coherent perfect absorption in nanophotonics, and, finally, we survey the perspectives for the future of this field.

Precise Measurement of the e+e- →π+π-J /ψ Cross Section at Center-of-Mass Energies from 3.77 to 4.60 GeV

Abstract: The cross section for the process e(+)e(-)-> pi(+) pi(-) J/psi is measured precisely at center-of-mass energies from 3.77 to 4.60 GeV using 9 fb(-1) of data collected with the BESIII detector operating at the BEPCII storage ring. Two resonant structures are observed in a fit to the cross section. The first resonance has a mass of (222.0 +/- 3.1 +/- 1.4) MeV/ c(2) and a width of (44.1 +/- 4.3 +/- 2.0)MeV, while the second one has a mass of (4320.0 +/- 10.4 +/- 7.0)MeV/c(2) and a width of (101.4(- 19.7)(+25.3) +/- 10.2) MeV, where the first errors are statistical and second ones are systematic. The first resonance agrees with the Y(4260) resonance reported by previous experiments. The precision of its resonant parameters is improved significantly. The second resonance is observed in e(+)e(-)-> pi(+) pi(-) J/psi for the first time. The statistical significance of this resonance is estimated to be larger than 7.6 sigma. The mass and width of the second resonance agree with the Y(4360) resonance reported by the BABAR and Belle experiments within errors. Finally, the Y(4008) resonance previously observed by the Belle experiment is not confirmed in the description of the BESIII data.

Microfluidic droplet platform for ultrahigh-throughput single-cell screening of biodiversity

Abstract: Ultrahigh-throughput screening (uHTS) techniques can identify unique functionality from millions of variants. To mimic the natural selection mechanisms that occur by compartmentalization in vivo, we developed a technique based on single-cell encapsulation in droplets of a monodisperse microfluidic double water-in-oil-in-water emulsion (MDE). Biocompatible MDE enables in-droplet cultivation of different living species. The combination of droplet-generating machinery with FACS followed by next-generation sequencing and liquid chromatography-mass spectrometry analysis of the secretomes of encapsulated organisms yielded detailed genotype/phenotype descriptions. This platform was probed with uHTS for biocatalysts anchored to yeast with enrichment close to the theoretically calculated limit and cell-to-cell interactions. MDE-FACS allowed the identification of human butyrylcholinesterase mutants that undergo self-reactivation after inhibition by the organophosphorus agent paraoxon. The versatility of the platform allowed the identification of bacteria, including slow-growing oral microbiota species that suppress the growth of a common pathogen, Staphylococcus aureus, and predicted which genera were associated with inhibitory activity.

Efficient Second-Harmonic Generation in Nanocrystalline Silicon Nanoparticles

Abstract: Recent trends to employ high-index dielectric particles in nanophotonics are motivated by their reduced dissipative losses and large resonant enhancement of nonlinear effects at the nanoscale. Because silicon is a centrosymmetric material, the studies of nonlinear optical properties of silicon nanoparticles have been targeting primarily the third-harmonic generation effects. Here we demonstrate, both experimentally and theoretically, that resonantly excited nanocrystalline silicon nanoparticles fabricated by an optimized laser printing technique can exhibit strong second-harmonic generation (SHG) effects. We attribute an unexpectedly high yield of the nonlinear conversion to a nanocrystalline structure of nanoparticles supporting the Mie resonances. The demonstrated efficient SHG at green light from a single silicon nanoparticle is 2 orders of magnitude higher than that from unstructured silicon films. This efficiency is significantly higher than that of many plasmonic nanostructures and small silicon nan...

Structural insights into ion conduction by channelrhodopsin 2

Abstract: INTRODUCTION Ion channels are integral membrane proteins that upon stimulation modulate the flow of ions across the cell or organelle membrane. The resulting electrical signals are involved in biological functions such as electrochemical transmission and information processing in neurons. Channelrhodopsins (ChRs) appear to be unusual channels. They belong to the large family of microbial rhodopsins, seven-helical transmembrane proteins containing retinal as chromophore. Photon absorption initiates retinal isomerization resulting in a photocycle, with different spectroscopically distinguishable intermediates, thereby controlling the opening and closing of the channel. In 2003, it was demonstrated that light-induced currents by heterologously expressed ChR2 can be used to change a host’s membrane potential. The concept was further applied to precisely control muscle and neural activity by using light-induced depolarization to trigger an action potential in neurons expressing ChR2. This optogenetic approach with ChR2 and other ChRs has been widely used for remote control of neural cells in culture and in living animals with high spatiotemporal resolution. It is also used in biomedical studies aimed to cure severe diseases. RATIONALE Despite the wealth of biochemical and biophysical data, a high-resolution structure and structural mechanisms of a native ChR2 (and other ChRs) have not yet been known. A step forward was the structure of a chimera (C1C2). However, recent electrophysiological and Fourier transform infrared data showed that C1C2 exhibits light-induced responses that are functionally and mechanistically different from ChR2. Given that ChR2 is the most frequently used tool in optogenetics, a high-resolution structure of ChR2 is of high importance. Deciphering the structure of the native channel would shed light on how the light-induced changes at the retinal Schiff base (RSB) are linked to the channel operation and may make engineering of enhanced optogenetic tools more efficient. RESULTS We expressed ChR2 in LEXSY and used in the meso crystallization approach to determine the crystal structure of the wild-type ChR2 and C128T slow mutant at 2.4 and 2.7 A, respectively (C, cysteine; T, threonine). Two different dark-state conformations of ChR2 in the two protomers in the asymmetric unit were resolved. The overall structure alignment of the protomers does not show a visible difference in backbone conformation. However, the conformation of some amino acids and the position of water molecules are not the same. The dimerization is strong and provided mainly through the interaction of helices 3 and 4 and the N termini. In addition, the protomers are connected with a disulfide bond, C34/C36′. In both protomers, we identified ion conduction pathway comprising four cavities [extracellular cavity 1 (EC1), EC2, intracellular cavity 1 (IC1), and IC2] that are separated by three gates [extracellular gate (ECG), central gate (CG), and intracellular gate (ICG)] (figure, panel A). Arginines R120 and R268 are the cores of ECG and ICG, respectively, in all ChRs. The Schiff base is hydrogen-bond–connected to E123 and D253 amino acids (E, glutamic acid; D, aspartic acid) and is a key part of the CG that is further connected with two other gates through an extended H-bond network mediated by numerous water molecules (figure, panel B). The DC gate is separate from the gates in the channel pathway and is bridged by hydrogen bonds through the water molecule w5. Hydrogen bonding of the DC pair (C128 and D156) has two important consequences. It stabilizes helices 3 and 4 and provides connection from D156, a possible proton donor, to the RSB. The presence of the hydrogen bonds provides structural insights into how the DC gate controls ChR2 gating lifetime. CONCLUSION The determined structures of ChR2 and its C128T mutant present the molecular basis for the understanding of ChR functioning. They provide insights into mechanisms of channel opening and closing. A plausible scenario is that the disruption of the H-bonds between E123 and D253 and the Schiff base and the protonation of D253 upon retinal isomerization trigger rearrangements in the extended hydrogen-bonded networks, stabilizing the ECG and CG and also rearranging the H-bonding network in the cavities. Upon retinal isomerization, these two gates are opened and the network is broken. This leads to the reorientation of helix 2. Additional changes in helices 6 and 7 induced by the isomerization could help with opening the ICG and channel pore formation.

Mechanism of transmembrane signaling by sensor histidine kinases

Abstract: One of the major and essential classes of transmembrane (TM) receptors, present in all domains of life, is sensor histidine kinases (HKs), parts of two-component signaling systems (TCS). The structural mechanisms of transmembrane signaling by these sensors are poorly understood. We present here crystal structures of the periplasmic sensor domain, the TM domain and the cytoplasmic HAMP domain of the Escherichia coli nitrate/nitrite sensor HK NarQ in the ligand-bound and mutated ligand-free states. The structures reveal that the ligand binding induces significant rearrangements and piston-like shifts of TM helices. The HAMP domain protomers undergo lever-like motions and convert the piston-like motions into helical rotations. Our findings provide the structural framework for complete understanding of TM TCS signaling and for development of antimicrobial treatments targeting TCS.

INTEGRAL Detection of the First Prompt Gamma-Ray Signal Coincident with the Gravitational Wave Event GW170817

Abstract: We report the e INTernational Gamma-ray Astrophysics Laboratory (INTEGRAL) detection of the short gamma-ray burst GRB 170817A (discovered by Fermi-GBM) with a signal-to-noise ratio of 4.6, and, for the first time, its association with the gravitational waves (GWs) from binary neutron star (BNS) merging event GW170817 detected by the LIGO and Virgo observatories. The significance of association between the gamma-ray burst observed by INTEGRAL and GW170817 is 3.2 $\sigma$, while the association between the Fermi-GBM and INTEGRAL detections is 4.2 $\sigma$. GRB 170817A was detected by the SPI-ACS instrument about 2 s after the end of the gravitational wave event. We measure a fluence of $(1.4 \pm 0.4 \pm 0.6) \times$10$^{-7}$ erg cm$^{-2})$ (75--2000 keV), where, respectively, the statistical error is given at the 1 $\sigma$ confidence level, and the systematic error corresponds to the uncertainty in the spectral model and instrument response. We also report on the pointed follow-up observations carried out by INTEGRAL, starting 19.5 h after the event, and lasting for 5.4 days. We provide a stringent upper limit on any electromagnetic signal in a very broad energy range, from 3 keV to 8 MeV, constraining the soft gamma-ray afterglow flux to $<7.1\times$10$^{-11}$ erg cm$^{-2}$ s$^{-1}$ (80--300 keV). Exploiting the unique capabilities of INTEGRAL, we constrained the gamma-ray line emission from radioactive decays that are expected to be the principal source of the energy behind a kilonova event following a BNS coalescence. Finally, we put a stringent upper limit on any delayed bursting activity, for example from a newly formed magnetar.

Enlargement of optical Schrödinger's cat states

Abstract: Superpositions of macroscopically distinct quantum states, introduced in Schrodinger's famous Gedankenexperiment, are an epitome of quantum ‘strangeness’ and a natural tool for determining the validity limits of quantum physics. The optical incarnation of Schrodinger's cat (SC)—the superposition of two opposite-amplitude coherent states—is also the backbone of continuous-variable quantum information processing. However, the existing preparation methods limit the amplitudes of the component coherent states, which curtails the state's usefulness for fundamental and practical applications. Here, we convert a pair of negative squeezed SC states of amplitude 1.15 to a single positive SC state of amplitude 1.85 with a success probability of ∼0.2. The protocol consists in bringing the initial states into interference on a beamsplitter and a subsequent heralding quadrature measurement in one of the output channels. Our technique can be realized iteratively, so arbitrarily high amplitudes can, in principle, be reached. The amplitude of a Schrodinger's cat (SC) state — superposed coherent state — is increased using a homodyne measurement. A pair of negative SC states with amplitude of 1.15 is probabilistically converted to a single positive SC state with amplitude of 1.85.

Relativistic Axions from Collapsing Bose Stars.

Abstract: The substructures of light bosonic (axionlike) dark matter may condense into compact Bose stars. We study the collapse of critical-mass stars caused by attractive self-interaction of the axionlike particles and find that these processes proceed in an unexpected universal way. First, nonlinear self-similar evolution (called "wave collapse" in condensed matter physics) forces the particles to fall into the star center. Second, interactions in the dense center create an outgoing stream of mildly relativistic particles which carries away an essential part of the star mass. The collapse stops when the star remnant is no longer able to support the self-similar infall feeding the collisions. We shortly discuss possible astrophysical and cosmological implications of these phenomena.