bluuebunny/crossref_metadata_2025 huggingface dataset:
Calculation of nonlocal EDF using a one-dimensional Boltzmann equation solver
Authors: Yuan C. , Yao J. , Bogdanov E. A. , Kudryavtsev A. A. , Rabadanov K. M. , Zhou Z.
Published: February 2019

A method for the calculation of the nonlocal electron distribution function (EDF) with programs commonly used for solving the one-dimensional Boltzmann kinetic equation (e.g., COMSOL Multiphysics) was proposed and implemented. The capabilities of the proposed method were illustrated using the example of the positive column plasma in argon. Significant differences between the local and nonlocal EDFs were observed, especially at the plasma periphery. This can result in significant differences in the electron transport coefficients and reaction rate constants for electron-induced processes. The proposed approach increases the precision of the numerical modeling of gas discharge devices and equipment.
Non-Hermiticity and exceptional points in coherently coupled vertical cavity laser diode arrays
Authors: Gao Zihe , Thompson Bradley J. , Dave Harshil , Fryslie Stewart T. M. , Choquette Kent D.
Published: February 2019

Coherently coupled laser arrays can be described by the temporal coupled mode theory in which the array modal behavior can be classified according to the coupling matrix, M¯¯. Accounting for a nonuniform gain/loss distribution in a laser array makes M¯¯ a non-Hermitian matrix, and experimentally we find phase-front tuning (beam steering) of the coherent supermode as a result of the non-Hermiticity. We report the experimental characterization of the supermodes in coherently coupled vertical cavity surface emitting laser diode arrays and demonstrate control of non-Hermiticity by spatially varying injection currents. Exceptional points are identified in these electrically injected microcavity diode arrays.
Method for improved voltage determination for pulsed power systems utilizing a magnetically insulated transmission line
Authors: Ottinger P. F. , Renk T. J. , Schumer J. W.
Published: February 2019

Because the voltage is difficult to measure in a magnetically insulated transmission line (MITL), the measurement of the currents flowing in the cathode and anode is often used with MITL theory to estimate the voltage in a given experiment. However, this estimate contains a space charge correction term whose magnitude depends on what is referred to as the g factor that describes the distribution of charge and current in the electron flow layer in the MITL. Typically, g is on the order of unity, but the accuracy of the voltage estimate depends on its actual value. While the space charge correction term is small when the MITL flow is strongly insulated, it is particularly important near self-limited MITL flow. System parameters that affect the distribution of electron flow are studied here at self-limited flow in order to illustrate this matter and develop a methodology to improve the voltage determination.
Dispersion in steady and time-oscillatory two-dimensional flows through a parallel-plate channel
Authors: Chu Henry C. W. , Garoff Stephen , Przybycien Todd M. , Tilton Robert D. , Khair Aditya S.
Published: February 2019

A multiple-scale perturbation theory is developed to analyze the advection-diffusion transport of a passive solute through a parallel-plate channel. The fluid velocity comprises a steady and a time-oscillatory component, which may vary spatially in the transverse and streamwise directions, and temporally on the fast transverse diffusion timescale. A long-time asymptotic equation governing the evolution of the transverse averaged solute concentration is derived, complemented with Taylor dispersion coefficients and advection speed corrections that are functions of the streamwise coordinate. We demonstrate the theory with a two-dimensional flow in a channel comprising alternating shear-free and no-slip regions. For a steady flow, the dispersion coefficient changes from zero to a finite value when the flow transitions from plug-like in the shear-free section to parabolic in the no-slip region. For an oscillatory flow, the dispersion coefficient due to an oscillatory flow can be negative and two orders of magnitude larger than that due to a steady flow of the same amplitude. This motivates us to quantify the relative magnitude of the steady and oscillatory flow such that there is an overall positive dispersion coefficient necessary for an averaged (macrotransport) equation. We further substitute the transport coefficients into the averaged equation to compute the evolution of the concentration profile, which agrees well with that obtained by solving the full two-dimensional advection-diffusion equation. In a steady flow, we find that while the shear-free section suppresses band broadening, the following no-slip section may lead to a wider band compared with the dispersion driven by the same pressure gradient in an otherwise homogeneously no-slip channel. In an unsteady flow, we demonstrate that a naive implementation of the macrotransport theory with a (localized) negative dispersion coefficient will result in an aphysical finite time singularity (or “blow-up solution”), in contrast to the well-behaved solution of the full advection-diffusion equation.
Molecular dynamics study of crystal formation and structural phase transition in Yukawa system for dusty plasma medium
Authors: Maity Srimanta , Das Amita
Published: February 2019

The layered crystal formation in dusty plasma medium depicted by the Yukawa interaction amidst dust grains has been investigated using molecular dynamics simulations. The multilayer structures are shown to form in the presence of a combined gravitational and external electric field force (representing the sheath field in experiments) along the ẑ direction. A detailed study of the dependence of the number of crystal layer formation, their width, etc., on various system parameters (viz., the external field profile and the screening length of the Yukawa interaction) has been analyzed. The structural properties of crystalline bilayers have been studied in detail identifying them with the help of pair correlation functions and Voronoi diagrams. It has been shown that the crystalline layers undergo a structural phase transition from hexagonal (often also referred to as triangular) to square lattice configurations when the three-dimensional effects arising from the interaction amidst particles in different layers become important. The simulations show a re-entrant phase transition from the hexagonal to square (and rhombic) structures.
Pulsation behavior of a bubble generated by a deep underwater explosion
Authors: Liang Haozhe , Zhang Qingming , Long Renrong , Ren Siyuan
Published: February 2019

This paper reports on experiments involving deep underwater explosion (UNDEX) that were conducted in a pressure container. The bubble pulsation behavior due to the deep UNDEX is recorded by a high-speed camera for equivalent depths up to 350 m. The bubble images show that although the shape of the explosive package affects the bubble shape at the initial moment, the bubble easily becomes spherical in shallow water which is 0.8m and 100m depth, but never becomes spherical during the whole first pulsation in deep water which is 200m, 300m and 350m in this paper. Solutions of the Rayleigh–Plesset equation fit well with the experimental data, and the value of the polytropic index γ of the gaseous detonation products changes from 1.25 to 1.3 as the depth is increased. Finally, empirical laws governing the pulsation of a deep-UNDEX bubble are established. The experimental pulsation period and that from the Rayleigh–Plesset equation agree with that obtained empirically, but the maximum radius is smaller than the empirical one. This phenomenon shows that the water depth not only creates a high hydrostatic pressure for the bubble but also changes the energy-release process of a deep UNDEX.
Thermodynamic properties of CH4, CCl4 and CF4 on the melting line. Theory and computer simulation
Authors: Yakub L. N. , Bodiul E. S.
Published: February 2019

Thermodynamic properties of the condensed phases of methane CH4, carbon tetrafluoride CF4 and carbon tetrachloride CCl4 on the melting line and in the high-pressure region were studied using the equations of state developed earlier for methane in the framework of the thermodynamic perturbation theory. We also present the results of Monte Carlo computer simulations of fcc phases of methane, carbon tetrachloride, and of the monoclinic tetrafluoromethane phase using a potential model that takes into account both the central and octupole–octupole interaction. The contribution of the octupole–octupole interaction to the thermodynamic properties of crystals are evaluated. The simulation results are compared with the available experimental data on the sublimation and melting lines, as well as to results of previous calculations based on the equations of state.
Role of short-range atom-atom forces in formation of the orientational structure of simple molecular crystals
Authors: Yakub E. S.
Published: February 2019

An attempt is made to explain the appearance of certain phases having different orientational and spatial structures in the phase diagram of crystals formed by tetrahedral molecules. The classical Monte Carlo method is applied to solid heavy methane CD4 and the role of various contributions to the non-central intermolecular interactions in formation of the orientational structure in simple molecular crystals is assessed.
Studies of charging mechanisms in impurity-helium condensates by means of impedance spectroscopy and current spectroscopy
Authors: Pelmenev A. A. , Bykhalo I. B. , Krushinskaya I. N. , Boltnev R. E.
Published: February 2019

A new simple experimental technique has been elaborated to test applicability of impedance spectroscopy for studying processes during destruction of impurity-helium condensates. Combination of methods of optical spectroscopy, impedance spectroscopy and current spectroscopy to study the destruction processes of impurity-helium condensates has been applied for the first time. Experimental data have demonstrated a rather good sensitivity of the technique and proved formation of charged clusters during a destruction stage of impurity-helium condensates.
Magnetic properties of hexamethylbenzene
Authors: Yen Fei
Published: February 2019

Magnetic susceptibility χ(T) measurements on hexamethylbenzene C6(CH3)6 (HMB) as well as its deuterated analogue C6(CD3)6 (HMB-d18) in the range of 2–300 K are presented. When cooling, an uptick is detected in χ(T) when the external magnetic field is applied along the direction of the molecular planes which coincide with the onset of intra-molecular coupling of the CH3 groups at T'C_H = 110.8 K for HMB and CD3 groups at T'C_D = 126.7 K for HMB-d18. Upon warming, the same discontinuities occur near TC_H = 117.8 K and TC_D = 132.2 K. Near 40 K, a peak anomaly is observed believed to be the system accessing its ground tunneling state. Near 20 K, the divergence of χ(T) suggests the establishment of long-range ordering, viz., inter-molecular gearing of the methyl group rotations. When the external magnetic field is applied perpendicular to the molecular planes, χ(T) is independent of temperature. Our findings reveal how correlated periodic motion of protons, a phenomenon inherent in many molecular solids, exhibits magnetic behavior that has been thus far overlooked.
Computational study of the stable atomic trapping sites in Ar lattice
Authors: Ozerov Georgiy K. , Bezrukov Dmitry S. , Buchachenko Alexei A.
Published: February 2019

Stable atomic trapping sites in the Lennard-Jones face-centered cubic Ar crystals are investigated by means of the global optimization strategy and convex hull concept for thermodynamic stability. Five generic site types are found in full accord with crystallographic intuition: interstitial within tetrahedral and octahedral hollows and substitutions, single, tetra- and hexavacancy. Their identities are established by radial distribution function analysis. Stability regions of these sites are mapped into the space of Lennard-Jones parameters of the guest–host interatomic interaction. Predictions made for the number and types of the stable sites for selected atoms (H, Mn, Na, Yb, Eu, Ba) are found to be in line with the results of more sophisticated models and matrix isolation spectroscopy experiments.
Absorption-desorption of carbon dioxide in carbon honeycombs at elevated temperatures
Authors: Krainyukova Nina V. , Bogdanov Yuri , Kuchta Bogdan
Published: February 2019

The recently synthesized honeycomb carbon allotrope has numerous potential applications, in particular for storage of gases inside carbon matrices. In this work this carbon form was experimentally studied in its denser form in order to estimate the upper temperature limit for keeping a gas inside the cellular structure. Along with the previously reported random honeycombs of a zigzag type we have also revealed the densest armchair structure. The mechanism of absorption-desorption of carbon dioxide studied by means of high energy electron diffraction at low temperatures showed the two — stage character of the observed desorption at elevated temperatures. This effect is associated to the weaker or stronger bonding of molecules with pore walls depending on the specific configuration of channels with different sizes. We have found that complete desorption of CO2 does not occur even at the temperatures about three times higher as compared with the sublimation point of carbon dioxide in our vacuum conditions.
Microwave spectroscopy of superfluid He II
Authors: Chishko K. A. , Rybalko A. S.
Published: February 2019

Experimentally observed with dielectric disc resonator technique the resonant microwave absorption- amplification in superfluid He II below λ-point has been interpreted theoretically as a phenomenon in electrically active dielectric medium with low-energy excitations which exist near the ground state of the He–He interatomic bond due to fine structure of spin subsystem in condensed helium phase. The experimentally registered microwave resonant absorption line with fres = 180.3 GHz at T = 1.4 K and fres = 150.0 GHz at T = 2.1 K is closely related to the standard value of roton gap Δ/kB = 8.64 K (179.36 GHz). The measured temperature dependence of the resonant absorption demonstrates an excellent agreement with the corresponding neutron diffraction data for Δ(T) known from different literature sources. From the common point of view the obtained resonant absorption provides a typical example of the microwave spectroscopy which occurs widely among molecular systems with rotational and vibrational degrees of freedom, but for the first time discovered on as simple atomic matter as a superfluid helium. We explain the phenomenon as an effect of spin-phonon interaction within superfluid He II phase, and our theoretical estimation gives an upper limit ∼ 250 GHz for the microwave resonant response of the system at T = 0. We interpret the dielectric 4He superfluid as an electrically active working substance for low temperature MASER, and clarify the atomic mechanism of microwave absorption– amplification in the condensed helium phases.
Phylogeography and species delimitation of Cherax destructor (Decapoda: Parastacidae) using genome-wide SNPs
Authors: Unmack P. J. , Young M. J. , Gruber B. , White D. , Kilian A. , Zhang X. , Georges A.
Published: February 2019

Cherax is a genus of 58 species of decapod crustaceans that are widespread across Australia and New Guinea. We use single-nucleotide polymorphisms (SNPs) to examine phylogeographic patterns in the most widespread species of Cherax, namely, C. destructor, and test the distinctiveness of one undescribed species, two C. destructor subspecies, previously proposed evolutionarily significant units, and management units. Both the phylogenetic analyses and the analysis of fixed allelic differences between populations support the current species-level taxonomy of C. setosus, C. depressus, C. dispar and C. destructor, the distinctiveness of C. destructor albidus and C. d. destructor and the existence of one undescribed species. The two populations of C. d. albidus from the Glenelg and Wimmera rivers were significantly distinct, with eight diagnostic differences (<1% fixed differences, null expectation is four fixed differences), but this low level of divergence is interpreted as within the range that might be expected of management units, that is, among allopatric populations of a single species or subspecies. A southern clade of C. d. destructor comprising the Murray River and its tributaries upstream from its confluence with the Darling River is genetically distinct from a northern clade comprising populations from the Lake Eyre Basin, the northern half of the Murray–Darling Basin (Darling River catchment) and the Lower Murray River below the Darling confluence.
Relationship between soil properties and enzyme activities with soil water repellency
Authors: Simpson Robert M. , Mason Karen , Robertson Kyle , Müller Karin
Published: February 2019

Soil water repellency (SWR) is a common phenomenon observed throughout the world. It has a significant impact on water infiltration, altering soil hydrology and consequently the soil microbial community and nutrient cycling. Despite the importance of this phenomenon, the processes involved in the development and breakdown of SWR are poorly understood. The importance of the microbial community for SWR is becoming increasingly apparent. In this study, relationships between microbial activities and SWR were investigated by utilising the patchy occurrence of SWR to select both repellent and wettable soils in six locations of the east coast of the North Island of New Zealand. Samples were from directly adjacent locations in mid spring and late summer, and a range of soil physico-chemical properties and enzyme activities were measured. The degree and potential persistence of SWR did not change between the two sampling times, whereas actual persistence of SWR increased. Soil moisture decreased between the two times, and although there was an inverse relationship between moisture and actual persistence of SWR in late summer, unexpectedly, it was a positive relationship in spring. Phosphatase, arylsulfatase and polysaccharide degrading enzyme activities increased with increasing SWR, whereas peroxidase activity decreased. The possible effects of increasing temperature and decreasing water content were modelled, and the observed relationships were strengthened. Arylsulfatase activity was strongly correlated with the degree of SWR, as was extractable organic sulfate, suggesting that the breakdown of sulfate-esters within humic material in soil may be involved in the release and accumulation of SWR-inducing hydrophobic compounds.
Nonlinear dynamics underlying sensory processing dysfunction in schizophrenia
Authors: Lainscsek Claudia , Sampson Aaron L. , Kim Robert , Thomas Michael L. , Man Karen , Lainscsek Xenia ,   The COGS Investigators, Swerdlow Neal R. , Braff David L. , Sejnowski Terrence J. , Light Gregory A. , Light Gregory A. , Swerdlow Neal R. , Thomas Michael L. , Green Michael F. , Greenwood Tiffany A. , Gur Raquel E. , Gur Ruben C. , Lazzeroni Laura C. , Nuechterlein Keith H. , Radant Allen D. , Seidman Larry J. , Sharp Richard F. , Siever Larry J. , Silverman Jeremy M. , Sprock Joyce , Stone William S. , Sugar Catherine A. , Tsuang Debby W. , Tsuang Ming T. , Turetsky Bruce I. , Braff David L.
Published: February 2019

Significance

One of the fundamental challenges of neuroscience is to understand the seamless orchestration of many interconnected brain regions, which is needed to produce the integrated experience of cognition. This paper describes a method based on dynamical systems theory to identify important nonlinear features underlying brain signals. We show that this method can indeed detect unique dynamical states underlying normal and altered auditory information processing in large cohorts of healthy subjects and schizophrenia patients. These dynamical states correspond to network changes preceding well-known auditory–neurophysiological responses. Results indicate that brain signals can be analyzed using a rather unconventional method to extract important large-scale dynamical information that is not apparent from conventional methods commonly used in the study of neuropsychiatric disorders.
Quantitative zeptomolar imaging of miRNA cancer markers with nanoparticle assemblies
Authors: Qu Aihua , Sun Maozhong , Xu Liguang , Hao Changlong , Wu Xiaoling , Xu Chuanlai , Kotov Nicholas A. , Kuang Hua
Published: February 2019

Significance

Engineering of reconfigurable nanoparticle assemblies enabled the practical realization of multiplexed detection, monitoring, and in vivo imaging of miRNA in live cells and animals, which was previously impeded by the fast degradation of these essential epigenetic markers. Nanoparticle superstructures afford rapid quantitative assessment of the imaging results, facilitating proliferation of digital personalized medicine.
Antibiotic resistance and host immune evasion in
Staphylococcus aureus
mediated by a metabolic adaptation
Authors: Jiang Jhih-Hang , Bhuiyan Md Saruar , Shen Hsin-Hui , Cameron David R. , Rupasinghe Thusitha W. T. , Wu Chun-Ming , Le Brun Anton P. , Kostoulias Xenia , Domene Carmen , Fulcher Alex J. , McConville Malcolm J. , Howden Benjamin P. , Lieschke Graham J. , Peleg Anton Y.
Published: February 2019

Significance

Staphylococcus aureus
is one of the most significant human bacterial pathogens that has the capacity to cause serious infections and become highly resistant to antibiotics. In this study, we identified a metabolic adaptation mechanism used by
S. aureus
to simultaneously circumvent killing by one of the last-line antistaphylococcal antibiotics, daptomycin, and attack from host innate immune cells. This process led to enhanced bacterial survival and was mediated by a change in bacterial membrane phospholipid composition sufficient to impair daptomycin membrane penetration and significantly affect neutrophil chemotactic responses. These results highlight the importance of bacterial membrane lipid adaptation in bacterial pathogenesis and provide crucial insights into potentially novel therapeutic targeting.
Experimental support for alternative attractors on coral reefs
Authors: Schmitt Russell J. , Holbrook Sally J. , Davis Samantha L. , Brooks Andrew J. , Adam Thomas C.
Published: February 2019

Ecological theory predicts that ecosystems with multiple basins of attraction can get locked in an undesired state, which has profound ecological and management implications. Despite their significance, alternative attractors have proven to be challenging to detect and characterize in natural communities. On coral reefs, it has been hypothesized that persistent coral-to-macroalgae “phase shifts” that can result from overfishing of herbivores and/or nutrient enrichment may reflect a regime shift to an alternate attractor, but, to date, the evidence has been equivocal. Our field experiments in Moorea, French Polynesia, revealed the following: (
i
) hysteresis existed in the herbivory–macroalgae relationship, creating the potential for coral–macroalgae bistability at some levels of herbivory, and (
ii
) macroalgae were an alternative attractor under prevailing conditions in the lagoon but not on the fore reef, where ambient herbivory fell outside the experimentally delineated region of hysteresis. These findings help explain the different community responses to disturbances between lagoon and fore reef habitats of Moorea over the past several decades and reinforce the idea that reversing an undesired shift on coral reefs can be difficult. Our experimental framework represents a powerful diagnostic tool to probe for multiple attractors in ecological systems and, as such, can inform management strategies needed to maintain critical ecosystem functions in the face of escalating stresses.
Cortical route for facelike pattern processing in human newborns
Authors: Buiatti Marco , Di Giorgio Elisa , Piazza Manuela , Polloni Carlo , Menna Giuseppe , Taddei Fabrizio , Baldo Ermanno , Vallortigara Giorgio
Published: February 2019

Significance

Newborns show a remarkable ability to detect faces even minutes after birth, an ecologically fundamental skill that is instrumental for interacting with their conspecifics. What are the neural bases of this expertise? Using EEG and a slow oscillatory visual stimulation, we identified a reliable response specific to facelike patterns in newborns, for which underlying cortical sources overlap with the adult face-specific cortical circuit. This suggests that the development of face perception in infants might rely on an early cortical route specialized in face processing already shortly after birth.
Loss of MPC1 reprograms retinal metabolism to impair visual function
Authors: Grenell Allison , Wang Yekai , Yam Michelle , Swarup Aditi , Dilan Tanya L. , Hauer Allison , Linton Jonathan D. , Philp Nancy J. , Gregor Elizabeth , Zhu Siyan , Shi Quan , Murphy Joseph , Guan Tongju , Lohner Daniel , Kolandaivelu Saravanan , Ramamurthy Visvanathan , Goldberg Andrew F. X. , Hurley James B. , Du Jianhai
Published: February 2019

Significance

Mitochondrial pyruvate carrier (MPC) is responsible for transporting pyruvate from glycolysis into mitochondria for oxidative phosphorylation. In the vertebrate retinas, the majority of glucose is metabolized into lactate by glycolysis rather than being oxidized in the mitochondria. Here, we show that although a small percentage of glucose is transported through MPC, deletion of MPC impairs visual function, decreases the viability of photoreceptors, disrupts photoreceptor ultrastructure, and causes glial activation. We find that MPC is required for maintaining the retinal metabolism in amino acids, neurotransmitters, and ketone bodies.
Human complement factor H Y402H polymorphism causes an age-related macular degeneration phenotype and lipoprotein dysregulation in mice
Authors: Landowski Michael , Kelly Una , Klingeborn Mikael , Groelle Marybeth , Ding Jin-Dong , Grigsby Daniel , Bowes Rickman Catherine
Published: February 2019

Significance

The complement factor H (CFH) Y402H polymorphism (rs1061170) imparts the strongest risk for age-related macular degeneration (AMD), the leading cause of blindness in the elderly. Popular thinking holds that the CFH H402 variant increases complement activation in the eye, predisposing susceptibility to disease. However, clinical trials of complement inhibitors in AMD patients have failed. Here we provide an explanation, showing CFH variant-specific differences in the presentation of AMD-like pathologies. We show that aged mice expressing the human H402, but not Y402 variant, (i) develop AMD-like symptoms and (ii) display differences in their systemic and ocular lipoprotein levels, but not in their complement activation, after diet. These findings support targeting lipoproteins for the treatment of AMD.
PILS6 is a temperature-sensitive regulator of nuclear auxin input and organ growth in
Arabidopsis thaliana
Authors: Feraru Elena , Feraru Mugurel I. , Barbez Elke , Waidmann Sascha , Sun Lin , Gaidora Angelika , Kleine-Vehn Jürgen
Published: February 2019

Significance

High temperature (HT) strongly modulates plant growth and eventually threatens yield stability. HT induces biosynthesis of the phytohormone auxin, which in turn increases cellular auxin levels and growth rates in shoots. This mechanism does not control HT-induced root growth and, hence, the role of auxin in this process is currently controversial. Here we show that the putative auxin carrier PIN-LIKES 6 (PILS6) localizes to the endoplasmic reticulum, where it gates nuclear auxin accumulation and perception. HT decreases the abundance of PILS6 proteins, consequently increasing nuclear auxin signaling and root growth. Our data dismantle current controversy, revealing an alternative subcellular mechanism in roots, which links PILS6-dependent control of cellular auxin sensitivity with HT-induced organ growth.
Dynamically stiffened matrix promotes malignant transformation of mammary epithelial cells via collective mechanical signaling
Authors: Ondeck Matthew G. , Kumar Aditya , Placone Jesse K. , Plunkett Christopher M. , Matte Bibiana F. , Wong Kirsten C. , Fattet Laurent , Yang Jing , Engler Adam J.
Published: February 2019

Significance

Gradual stiffening of the native extracellular matrix has been implicated in promoting breast cancer progression through stiffness-mediated signaling. Herein, we probe mammary epithelial cell responses to substrate stiffness with a dynamically stiffened hydrogel, enabling investigation of how the change in substrate stiffness impacts collective cell behaviors. We demonstrate that signaling pathways, both paracrine and mechanosensing, impact mammary epithelial cell response to stiffening and act in concert to drive epithelial-mesenchymal plasticity. Interestingly, previous static stiffness hydrogel studies did not observe this interplay of signaling, highlighting the need for dynamic materials to recapitulate disease development. These responses can also be inhibited, individually and together, demonstrating how dynamic stiffening drives cancer progression.
Basolateral amygdala input to the medial prefrontal cortex controls obsessive-compulsive disorder-like checking behavior
Authors: Sun Tingting , Song Zihua , Tian Yanghua , Tian Wenbo , Zhu Chunyan , Ji Gongjun , Luo Yudan , Chen Shi , Wang Likui , Mao Yu , Xie Wen , Zhong Hui , Zhao Fei , Luo Min-Hua , Tao Wenjuan , Wang Haitao , Li Jie , Li Juan , Zhou Jiangning , Wang Kai , Zhang Zhi
Published: February 2019

Significance

The pathophysiology underlying obsessive-compulsive disorder (OCD) remains unclear, leading to major challenges in the treatment of OCD patients. Here, we defined a projection from the basolateral amygdala glutamate neurons to the medial prefrontal cortex glutamate and GABA neurons and described the putative importance of this circuit in manifesting the checking symptoms of OCD in mice. In addition, the above major findings were further verified in an fMRI mouse study. These findings raise the possibility of developing optimal treatments for OCD that involve the use of nondrug approaches, such as transcranial magnetic stimulation, that target the converging pathways.
Plasma lipidome reveals critical illness and recovery from human Ebola virus disease
Authors: Kyle J. E. , Burnum-Johnson K. E. , Wendler J. P. , Eisfeld A. J. , Halfmann Peter J. , Watanabe Tokiko , Sahr Foday , Smith R. D. , Kawaoka Y. , Waters K. M. , Metz T. O.
Published: February 2019

Ebola virus disease (EVD) often leads to severe and fatal outcomes in humans with early supportive care increasing the chances of survival. Profiling the human plasma lipidome provides insight into critical illness as well as diseased states, as lipids have essential roles as membrane structural components, signaling molecules, and energy sources. Here we show that the plasma lipidomes of EVD survivors and fatalities from Sierra Leone, infected during the 2014–2016 Ebola virus outbreak, were profoundly altered. Focusing on how lipids are associated in human plasma, while factoring in the state of critical illness, we found that lipidome changes were related to EVD outcome and could identify states of disease and recovery. Specific changes in the lipidome suggested contributions from extracellular vesicles, viremia, liver dysfunction, apoptosis, autophagy, and general critical illness, and we identified possible targets for therapies enhancing EVD survival.
YfmK is an N
ε
-lysine acetyltransferase that directly acetylates the histone-like protein HBsu in
Bacillus subtilis
Authors: Carabetta Valerie J. , Greco Todd M. , Cristea Ileana M. , Dubnau David
Published: February 2019

Significance

N
ε
-lysine acetylation is a dynamic regulatory posttranslational modification that affects hundreds of proteins in all three domains of life. In bacteria, acetylated proteins can be found in many essential pathways, and may also be important for virulence in pathogenic species. However, the biological relevance of the overwhelming majority of these acetylation events remains poorly characterized. Here, we discover that acetylation of the histone-like protein HBsu regulates its ability to control nucleoid compaction, and we identify the second protein acetyltransferase in
Bacillus subtilis
. Moving forward, the targeting of bacterial protein acetylation may be exploited to aid in the design of novel therapeutics, as it has been successful in the treatment of certain cancers and latent viral and fungal infections.
Rhizobium
induces DNA damage in
Caenorhabditis elegans
intestinal cells
Authors: Kniazeva Marina , Ruvkun Gary
Published: February 2019

Significance

An incredible diversity of microbial species inhabit the Earth. Many new interactions of bacteria with animals are only beginning to surface. We show that feeding a worm,
Caenorhabditis elegans,
with
Rhizobium
bacteria causes failed nuclear divisions in intestinal cells.
C. elegans
mutations compromising DNA damage repair pathways and exogenous reactive oxygen species cause similar failure in intestinal nuclear divisions, suggesting that
Rhizobium
may produce reactive oxygen species. In accordance, free radical scavenger chemicals suppress the response to
Rhizobium
. We propose that
Rhizobium
induces reactive oxygen species in its encounter with
C. elegans
. Our findings provide an insight into the interactions between microbes and animal cells.
Genomic and transcriptomic investigations of the evolutionary transition from oviparity to viviparity
Authors: Gao Wei , Sun Yan-Bo , Zhou Wei-Wei , Xiong Zi-Jun , Chen Luonan , Li Hong , Fu Ting-Ting , Xu Kai , Xu Wei , Ma Li , Chen Yi-Jing , Xiang Xue-Yan , Zhou Long , Zeng Tao , Zhang Si , Jin Jie-Qiong , Chen Hong-Man , Zhang Guojie , Hillis David M. , Ji Xiang , Zhang Ya-Ping , Che Jing
Published: February 2019

Viviparous (live-bearing) vertebrates have evolved repeatedly within otherwise oviparous (egg-laying) clades. Over two-thirds of these changes in vertebrate reproductive parity mode happened in squamate reptiles, where the transition has happened between 98 and 129 times. The transition from oviparity to viviparity requires numerous physiological, morphological, and immunological changes to the female reproductive tract, including eggshell reduction, delayed oviposition, placental development for supply of water and nutrition to the embryo by the mother, enhanced gas exchange, and suppression of maternal immune rejection of the embryo. We performed genomic and transcriptomic analyses of a closely related oviparous–viviparous pair of lizards (Phrynocephalus przewalskiiandPhrynocephalus vlangalii) to examine these transitions. Expression patterns of maternal oviduct through reproductive development of the egg and embryo differ markedly between the two species. We found changes in expression patterns of appropriate genes that account for each of the major aspects of the oviparity to viviparity transition. In addition, we compared the gene sequences in transcriptomes of four oviparous–viviparous pairs of lizards in different genera (Phrynocephalus,Eremias,Scincella, andSphenomorphus) to look for possible gene convergence at the sequence level. We discovered low levels of convergence in both amino acid replacement and evolutionary rate shift. This suggests that most of the changes that produce the oviparity–viviparity transition are changes in gene expression, so occasional reversals to oviparity from viviparity may not be as difficult to achieve as has been previously suggested.
Additive manufacturing of patterned 2D semiconductor through recyclable masked growth
Authors: Guo Yunfan , Shen Pin-Chun , Su Cong , Lu Ang-Yu , Hempel Marek , Han Yimo , Ji Qingqing , Lin Yuxuan , Shi Enzheng , McVay Elaine , Dou Letian , Muller David A. , Palacios Tomás , Li Ju , Ling Xi , Kong Jing
Published: February 2019

Significance

Traditional semiconductor fabrication methods, such as lithography and etching, have been sufficient for the needs of integrated circuits over past decades. Their applicability has also been demonstrated in emerging 2D materials, which offers facile processing over large lateral dimensions, while unique and remarkable properties due to the confinement within atomic thicknesses. Nevertheless, each fabrication step adds cost to the manufacturing and increases the possibility of quality degradation. Here, we developed a method to directly synthesize arbitrary monolayer molybdenum disulfide patterns with high spatial resolution, excellent homogeneity, and electrical performance on insulating SiO
2
/Si. Significantly, our on-demand method allows for the repeated growth of patterned 2D materials with preserved structural integrity and material qualities, paving the way for simpler and cost-effective fabrication.
Polar molecules catalyze CO insertion into metal-alkyl bonds through the displacement of an agostic C-H bond
Authors: Zhou Tian , Malakar Santanu , Webb Steven L. , Krogh-Jespersen Karsten , Goldman Alan S.
Published: February 2019

The insertion of CO into metal-alkyl bonds is the key C-C bond-forming step in many of the most important organic reactions catalyzed by transition metal complexes. Polar organic molecules (e.g., tetrahydrofuran) have long been known to promote CO insertion reactions, but the mechanism of their action has been the subject of unresolved speculation for over five decades. Comprehensive computational studies [density functional theory (DFT)] on the prototypical system Mn(CO)
5
(arylmethyl) reveal that the polar molecules do not promote the actual alkyl migration step. Instead, CO insertion (i.e. alkyl migration) occurs rapidly and reversibly to give an acyl complex with a sigma-bound (agostic) C-H bond that is not easily displaced by typical ligands (e.g. phosphines or CO). The agostic C-H bond is displaced much more readily, however, by the polar promoter molecules, even though such species bind only weakly to the metal center and are themselves then easily displaced; the facile kinetics of this process are attributable to a hydrogen bonding-like interaction between the agostic C-H bond and the polar promoter. The role of the promoter is to thereby catalyze isomerization of the agostic product of CO insertion to give an

η

2

-C,O-bound acyl product that is more easily trapped than the agostic species. This ability of such promoters to displace a strongly sigma-bound C-H bond and to subsequently undergo facile displacement themselves is without reported precedent, and could have implications for catalytic reactions beyond carbonylation.
Paneth cell α-defensins HD-5 and HD-6 display differential degradation into active antimicrobial fragments
Authors: Ehmann D. , Wendler J. , Koeninger L. , Larsen I. S. , Klag T. , Berger J. , Marette A. , Schaller M. , Stange E. F. , Malek N. P. , Jensen B. A. H. , Wehkamp J.
Published: February 2019

Significance

Paneth cells provide intestinal host defense against pathogens and control the healthy microbiota by secreting antimicrobial peptides. We show that the most abundant secreted Paneth cell products, human defensin HD-5 and HD-6, show a distinct susceptibility to proteolytic digestion by human duodenal fluid. While HD-5 is digested in many fragments, HD-6 is stable and still able to form nanonets. The occurring fragments of HD-5 were antimicrobially active against microorganisms. We provide proof of concept about microbiome modulating capacities in vivo, which includes an increase of
Akkermansia
sp. Our results indicate that fragmentation of defensins increases antimicrobial diversity and further adds to the complexity of host microbial interaction at interfaces. Fragmentation could lead to new antimicrobial peptides with possible therapeutic usage.
Redox traits characterize the organization of global microbial communities
Authors: Ramírez-Flandes Salvador , González Bernardo , Ulloa Osvaldo
Published: February 2019

Significance

Biological communities are conventionally described as assemblages of species, whose ecological roles are known or predictable from their observable morphology. In microbial ecology, such a taxonomic approach is hindered by limited capacity to discriminate among different microbes, which bear highly dynamic genomes and establish complex associations. Approaches based on culture-independent functional genes profiling might overcome these problems, but a set of usable established genes in a general situation is still lacking. We show that genes related to reduction-oxidation (redox) processes separate microbial communities into their corresponding biomes. This redox-based characterization is linked to the microbial energetics of ecosystems and to most biogeochemical cycles and might be useful for assessing the impact of environmental degradation on the ecosystem services, underpinned by microorganisms.
Human Cooperation When Acting Through Autonomous Machines
Authors: de Melo Celso M. , Marsella Stacy , Gratch Jonathan
Published: February 2019

Significance

Autonomous machines that act on our behalf—such as robots, drones, and autonomous vehicles—are quickly becoming a reality. These machines will face situations where individual interest conflicts with collective interest, and it is critical we understand if people will cooperate when acting through them. Here we show, in the increasingly popular domain of autonomous vehicles, that people program their vehicles to be more cooperative than they would if driving themselves. This happens because programming machines causes selfish short-term rewards to become less salient, and that encourages cooperation. Our results further indicate that personal experience influences how machines are programmed. Finally, we show that this effect generalizes beyond the domain of autonomous vehicles and we discuss theoretical and practical implications.
Crystal structure of MICU2 and comparison with MICU1 reveal insights into the uniporter gating mechanism
Authors: Kamer Kimberli J. , Jiang Wei , Kaushik Virendar K. , Mootha Vamsi K. , Grabarek Zenon
Published: February 2019

The mitochondrial uniporter is a Ca
2+
-channel complex resident within the organelle’s inner membrane. In mammalian cells the uniporter’s activity is regulated by Ca
2+
due to concerted action of MICU1 and MICU2, two paralogous, but functionally distinct, EF-hand Ca
2+
-binding proteins. Here we present the X-ray structure of the apo form of
Mus musculus
MICU2 at 2.5-Å resolution. The core structure of MICU2 is very similar to that of MICU1. It consists of two lobes, each containing one canonical Ca
2+
-binding EF-hand (EF1, EF4) and one structural EF-hand (EF2, EF3). Two molecules of MICU2 form a symmetrical dimer stabilized by highly conserved hydrophobic contacts between exposed residues of EF1 of one monomer and EF3 of another. Similar interactions stabilize MICU1 dimers, allowing exchange between homo- and heterodimers. The tight EF1–EF3 interface likely accounts for the structural and functional coupling between the Ca
2+
-binding sites in MICU1, MICU2, and their complex that leads to the previously reported Ca
2+
-binding cooperativity and dominant negative effect of mutation of the Ca
2+
-binding sites in either protein. The N- and C-terminal segments of the two proteins are distinctly different. In MICU2 the C-terminal helix is significantly longer than in MICU1, and it adopts a more rigid structure. MICU2’s C-terminal helix is dispensable in vitro for its interaction with MICU1 but required for MICU2’s function in cells. We propose that in the MICU1–MICU2 oligomeric complex the C-terminal helices of both proteins form a central semiautonomous assembly which contributes to the gating mechanism of the uniporter.
Genome replication affects transcription factor binding mediating the cascade of herpes simplex virus transcription
Authors: Dremel Sarah E. , DeLuca Neal A.
Published: February 2019

In herpes simplex virus type 1 (HSV-1) infection, the coupling of genome replication and transcription regulation has been known for many years; however, the underlying mechanism has not been elucidated. We performed a comprehensive transcriptomic assessment and factor-binding analysis for Pol II, TBP, TAF1, and Sp1 to assess the effect genome replication has on viral transcription initiation and elongation. The onset of genome replication resulted in the binding of TBP, TAF1, and Pol II to previously silent late promoters. The viral transcription factor, ICP4, was continuously needed in addition to DNA replication for activation of late gene transcription initiation. Furthermore, late promoters contain a motif that closely matches the consensus initiator element (Inr), which robustly bound TAF1 postreplication. Continued DNA replication resulted in reduced binding of Sp1, TBP, and Pol II to early promoters. Therefore, the initiation of early gene transcription is attenuated following DNA replication. Herein, we propose a model for how viral DNA replication results in the differential utilization of cellular factors that function in transcription initiation, leading to the delineation of kinetic class in HSV-productive infection.
The ubiquitin ligase UBE3B, disrupted in intellectual disability and absent speech, regulates metabolic pathways by targeting BCKDK
Authors: Cheon Solmi , Kaur Kiran , Nijem Nadine , Tuncay Islam Oguz , Kumar Pooja , Dean Milan , Juusola Jane , Guillen-Sacoto Maria J. , Bedoukian Emma , Ierardi-Curto Lynne , Kaplan Paige , Schaefer G. Bradley , Mishra Prashant , Chahrour Maria H.
Published: February 2019

Significance

UBE3B is a ubiquitin ligase disrupted in severe neurodevelopmental diseases (NDDs). Mechanistic studies on the function of UBE3B and its substrates have been lacking. Here, we show that deletion of
Ube3b
in mice causes neuroanatomical, behavioral, and metabolic abnormalities. Moreover, we identify BCKDK as a substrate UBE3B ubiquitinates.
BCKDK
is mutated in a spectrum of NDDs, and encodes a kinase that regulates several metabolic pathways. We show that
UBE3B
mutations are associated with metabolic disturbances in plasma from patients. Our findings place two NDD genes,
UBE3B
and
BCKDK
, in the same pathway, functionally validate the role of
UBE3B
in human disease, and identify both a disease mechanism in patients with
UBE3B
mutations and the downstream substrate that mediates this mechanism.
Morphogenesis of termite mounds
Authors: Ocko Samuel A. , Heyde Alexander , Mahadevan L.
Published: February 2019

Significance

Termite mounds are the result of the collective behavior of termites working to modify their physical environment, which in turn affects their behavior. During mound construction, environmental factors such as heat flow and gas exchange affect the building behavior of termites, and the resulting change in mound geometry in turn modifies the response of the internal mound environment to external thermal oscillations. Our study highlights the principles of self-organized animal architecture driven by the coupling of environmental physics to organismal behavior and might serve as a natural inspiration for the design of sustainable human architectures.
Mid-infrared feed-forward dual-comb spectroscopy
Authors: Chen Zaijun , Hänsch Theodor W. , Picqué Nathalie
Published: February 2019

Significance

Each molecule leaves characteristic absorptions, which enable one to unambiguously identify and quantify it, and to understand its structure and dynamics. Such fingerprints, strong in the mid-infrared region of the electromagnetic spectrum, can be accessed by measuring the intensity of light transmitted through a medium as a function of its frequency. Here, we describe a spectrometer for mid-infrared spectroscopy based on two frequency comb generators, light sources emitting narrow evenly spaced laser lines over a broad spectral bandwidth. Our instrument without moving parts simultaneously measures broad high-resolution spectra with calibration of the frequency scale directly to an atomic clock and precise spectral line shapes. These features are obtained from the experimental data without any need for corrective processing.