bluuebunny/crossref_metadata_2025 huggingface dataset:
Control of dielectric surface energy by dry surface treatment for high performance organic thin film transistor based on dibenzothiopheno[6,5-b:6′,5′-f]thieno[3,2-b]thiophene semiconductor
Authors: Choi Ajeong , Kwon Young-Nam , Chung Jong Won , Yun Youngjun , Park Jeong-Il , Lee Yong Uk
Published: February 2020

We studied organic thin film transistors using vacuum-deposited para-sexiphenyl (p-6P) as a sublayer to reduce the surface energy of the dielectric material. The correlation between the growth mode of a thin film of the organic semiconductor dibenzothiopheno[6,5-b:6′,5′-f]thieno[3,2-b]thiophene and the number of p-6P sublayers could be explained by a surface energy difference resulting from molecular orientation changes in the p-6P layer. A local surface energy difference was confirmed by measuring the adhesion force using a nanomechanical force measurement method.
Scaling and conformal symmetries for plane gravitational waves
Authors: Zhang P.-M. , Cariglia M. , Elbistan M. , Horvathy P. A.
Published: February 2020

The isometries of an exact plane gravitational wave are symmetries for both massive and massless particles. Their conformal extensions are, in fact, chrono-projective transformations {introduced earlier by Duval et al. [Classical Quantum Gravity 3, 461 (1986); Classical Quantum Gravity 32(17), 175006 (2015)]} and are symmetries for massless particles. Homotheties are universal chrono-projective symmetries for any profile. Chrono-projective transformations also generate new conserved quantities for the underlying non-relativistic systems in the Bargmann framework. Homotheties play a similar role for the lightlike “vertical” coordinate as isometries play for the transverse coordinates.
Freestanding ultra-thin silica
Authors: Zhao Rui , Kim Hongyeun , Stapleton Joshua , Liu Zi-Kui , Robinson Joshua
Published: February 2020

Silica (SiOx) thin films are promising for a wide range of applications, including catalysis, separation technology, biomedicine, or transparent super-hydrophilic films. Here, we present a study demonstrating a unique way of producing ultra-thin, freestanding silica films via silicon etching. This method utilizes silicon wafers with thermally oxidized surfaces and two common inorganic elements (sulfur and tellurium), which leads to high-rate chemical etching of the Si substrate, leaving behind freestanding silica layers. Thermodynamic calculations of the tellurium–silicon–sulfur (Te–Si–S) ternary phase diagram suggest that the removal of the Si substrate from the silica layers is due to chemical reactions that result in liquid/vapor formation of Si–S and Si–Te phases. Importantly, the chemical and physical properties of the silica film post-etch are comparable to those of the starting material. The process described here provides a route to produce large area, flexible glass substrates with widely tunable thicknesses from tens to thousands of nanometers.
Simulation of β-Ga2O3 vertical Schottky diode based photodetectors revealing average hole mobility of 20 cm2 V−1 s−1
Authors: Akyol Fatih
Published: February 2020

With a wide bandgap of ∼4.85 eV, high chemical and thermal stability, and melt growth availability, β-Ga2O3 has been found in a large number of solar blind photodetector (SBP) applications including missile guidance, flame detection, water purification, and intersatellite communication. The modelling of a Schottky diode (SD) based SBPs is crucial in order to reach high external quantum efficiency (EQE), especially for self-powered applications and also to extract hole mobility in these devices. The EQE performance of β-Ga2O3 vertical SD SBPs with various Schottky contact finger spacings is obtained using highly controversial hole mobility values reported in the literature. By modelling experimentally demonstrated EQE values of the existing β-Ga2O3 vertical SD SBPs, average nonequilibrium hole mobility value of ∼20 cm2 V−1 s−1 is extracted, which is quite higher than the claimed theoretical value of 1 × 10−6 cm2 V−1 s−1 and motivates for the efforts of technologically important p-type β-Ga2O3. By modelling the efficiency of full Schottky metal covered vertical SD SBPs by using hole mobility value of 20 cm2 V−1 s−1, internal quantum efficiency of 92% is obtained at an optimum n-type doping concentration of 1 × 1016 cm−3.
Molecular relaxations in supercooled liquid and glassy states of amorphous gambogic acid: Dielectric spectroscopy, calorimetry, and theoretical approach
Authors: Phan Anh D. , Thu Thuy Tran Thi , Kim An Nguyen Thi , Knapik-Kowalczuk Justyna , Paluch Marian , Wakabayashi Katsunori
Published: February 2020

The relaxation dynamics and thermodynamic properties of supercooled and glassy gambogic acid are investigated using both theory and experiment. We measure the temperature dependence of the relaxation times in three polymorphs (α-, β-, and γ-form). To gain insight into the relaxation processes, we propose a theoretical approach to quantitatively understand the nature of these three relaxations. The α-relaxation captures cooperative motions of molecules, while the β-process is mainly governed by the local dynamics of a single molecule within the cage formed by its nearest neighbors. Based on quantitative agreement between theory and experimental data, our calculations clearly indicate that the β-process is a precursor of the structural relaxation and intramolecular motions are responsible for the γ-relaxation. Moreover, the approach is exploited to study the effects of the heating process on alpha relaxation. We find that the heating rate varies logarithmically with Tg and 1000/Tg. These variations are qualitatively consistent with many prior studies.
Experimental and simulation study of the high-pressure behavior of squalane and poly-α-olefins
Authors: Prentice Iain J. , Liu Xiaojiao , Nerushev Oleg A. , Balakrishnan Sashi , Pulham Colin R. , Camp Philip J.
Published: February 2020

The equation of state, dynamical properties, and molecular-scale structure of squalane and mixtures of poly-α-olefins at room temperature are studied with a combination of state-of-the-art, high-pressure experiments and molecular-dynamics simulations. Diamond-anvil cell experiments indicate that both materials are non-hydrostatic media at pressures above ∼1 GPa. The equation of state does not exhibit any sign of a first-order phase transition. High-pressure x-ray diffraction experiments on squalane show that there are no Bragg peaks, and hence, the apparent solidification occurs without crystallization. These observations are complemented by a survey of the equation of state and dynamical properties using simulations. The results show that molecular diffusion is essentially arrested above about 1 GPa, which supports the hypothesis that the samples are kinetically trapped in metastable amorphous-solid states. The shear viscosity becomes extremely large at very high pressures, and the coefficient governing its increase from ambient pressure is in good agreement with the available literature data. Finally, simulated radial distribution functions are used to explore the evolution of the molecular-scale structure with increasing pressure. Subtle changes in the short-range real-space correlations are related to a collapse of the molecular conformations with increasing pressure, while the evolution of the static structure factor shows excellent correlation with the available x-ray diffraction data. These results are of indirect relevance to oil-based lubricants, as the pressures involved are comparable to those found in engines, and hence, the ability of lubricating thin films to act as load-bearing media can be linked to the solidification phenomena studied in this work.
Calculation of optical response functions of dilute-N GaPAsN lattice-matched to Si
Authors: Zou Y. , Goodnick S. M.
Published: February 2020

Dilute-N GaPAsN alloys have great potential for optoelectronics lattice-matched to Si. However, there is a lack of systematic calculation of the optical response of these alloys. The present paper uses the sp3d5s∗sN tight-binding model to calculate the fullband electronic structure of dilute-N GaPAsN and then calculate the optical response functions considering direct transitions within the electric dipole approximation. Good agreement is obtained for the dielectric function in comparison to available optical data for dilute nitrides. To achieve this, the sp3d5s∗ parameters for GaP and GaAs are optimized for their optical properties in comparison to published data, which are then used as the basis for the sp3d5s∗sN parameters for dilute-N GaPN and GaAsN. The calculated absorption between the valence band and the newly formed lowest conduction band of the dilute nitrides increases as the N fraction increases, in agreement with experiments, mainly due to the net increase in their coupling in the entire Brillouin zone, supported by the calculated momentum matrix element in the present work.
Local and global approaches to treat the torsional barriers of 4-methylacetophenone using microwave spectroscopy
Authors: Herbers Sven , Fritz Sean M. , Mishra Piyush , Nguyen Ha Vinh Lam , Zwier Timothy S.
Published: February 2020

The Fourier transform microwave spectrum of 4-methylacetophenone recorded from 8 GHz to 18 GHz under jet-cooled conditions has revealed large tunneling splittings arising from a low barrier to internal rotation of the ring methyl group and small splittings from a high torsional barrier of the acetyl methyl group. The large splittings are especially challenging to model, while the small splittings are difficult to analyze due to the resolution limit of 120 kHz. The combination of two methyl groups undergoing internal rotations caused each rotational transition to split into five torsional species, which were resolved and fitted using a modified version of the XIAM code and the newly developed ntop code to a root-mean-square deviation close to measurement accuracy, providing an estimate of the V3 potential barriers of about 22 cm−1 and 584–588 cm−1 for the ring and the acetyl methyl groups, respectively. The assignment was aided by separately fitting the five torsional species using odd-power order operators. Only one conformer in which all heavy atoms are located on a symmetry plane could be identified in the spectrum, in agreement with results from conformation analysis using quantum chemical calculations.
A facile urea-hydrolysis calcination process for the preparation of

α

-Fe2O3 nanoparticles and

α

-Fe2O3 nanorods and their fabrication mechanisms
Authors: Chen Jianhong , Huang Wei , Pan Shuai , Liu Ruijiang
Published: February 2020

A facile urea-hydrolysis calcination process for the preparation of α-Fe2O3 nanoparticles and α-Fe2O3 nanorods was introduced. The effects of hydrolysis temperature, Fe3+ concentration, and the molar ratio of urea and Fe3+ on nanorod-like precursors and α-Fe2O3 nanomaterials were investigated. The average length and diameter of the nanorod precursors increased with the increasing hydrolysis temperature, Fe3+ concentration, and molar ratio of urea and Fe3+. When the molar ratio of urea and Fe3+ was not less than 5, the α-Fe2O3 nanoparticles were produced. However, when the molar ratio was not greater than 4, the α-Fe2O3 nanorods could be obtained. In addition, the average diameter of the α-Fe2O3 nanoparticles was the largest when the hydrolysis temperature was 85 °C. With the increase in Fe3+ concentration, the average diameter of the α-Fe2O3 nanoparticles was enlarged. The average length and diameter of the α-Fe2O3 nanorods increased with the increase in hydrolysis temperature and Fe3+ concentration. All the results suggested that the rod-like structure of the precursors provided a possibility and the template for the fabrication of α-Fe2O3 nanorods, and the content of Fe3+ in the rod-like precursors played the decisive role in the morphology of the α-Fe2O3 nanomaterials.
On-site tuning of the carrier lifetime in silicon for on-chip THz circuits using a focused beam of helium ions
Authors: Zimmermann P. , Holleitner A. W.
Published: February 2020

In this study, we demonstrate that a focused helium ion beam allows the local adjustment and optimization of the carrier lifetime in silicon-based photoswitches integrated in ultrafast on-chip terahertz-circuits. Starting with a carrier lifetime of 5.3 ps for as-grown silicon on sapphire, we monotonously reduce the carrier lifetime in integrated switches to a minimum of ∼0.55 ps for a helium ion fluence of 20 × 1015 ions/cm2. By introducing an analytical model for the carrier lifetimes in the photoswitches, we particularly demonstrate that the carrier lifetime can be adjusted locally even within single photoswitches. In turn, the demonstrated on-site tuning allows optimizing ultrafast high-frequency circuits, into which radiation-sensitive nanoscale materials, such as two-dimensional materials, are embedded.
Two-dimensional series connected photovoltaic cells defined by ferroelectric domains
Authors: Wu Guangjian , Wang Xudong , Chen Yan , Wu Shuaiqin , Shen Hong , Lin Tie , Ge Jun , Hu Weida , Zhang Shan-Tao , Meng X. J. , Chu Junhao , Wang Jianlu
Published: February 2020

Recently, a large amount of effort has been devoted to bringing p- and n-type two-dimensional (2D) materials in close contact to promise a p–n junction for photodetectors and photovoltaic devices. However, all solar cells based on 2D materials are single p–n junctions so far, where the open circuit voltage is usually limited by the bandgap of semiconductor materials. Here, by using a scanning-probe domain patterning method to polarize the ferroelectric film, we demonstrate a series connected MoTe2 photovoltaic cell with an additive open circuit voltage and output electrical power. The nonvolatile MoTe2 p–n diodes exhibit a rectification ratio of 100. As a photodetector, the device presents a responsivity of 220 mA/W and an external quantum efficiency of 41% without any gate or bias voltages. The open circuit voltage increases linearly with the number of series connected p–n junctions and can be beyond the bandgap of the multilayer MoTe2.
Development of a silicon–diamond interface on (111) diamond
Authors: Schenk A. K. , Sear M. J. , Dontschuk N. , Tsai A. , Rietwyk K. J. , Tadich A. , Cowie B. C. C. , Ley L. , Stacey A. , Pakes C. I.
Published: February 2020

We report the preparation of a silicon terminated (111) diamond surface. Low energy electron diffraction and core level photoemission demonstrate that this surface is highly ordered and homogeneous and possesses a negative electron affinity. Our analysis suggests that the surface reconstruction begins with the formation of silicon trimers that coalesce into a rhombohedral 2D silicon layer reminiscent of rhombohedral silicene.
Synthesis of Fatty Alcohol Ether Carboxylic Ester Surfactant and its Performance in an Anionic/Non-Ionic Mixed System
Authors: Wu Zhifang , Li Yunling , Wang Mengwei , Li Jun , Wang Zhifei
Published: February 2020

A salt-type fatty alcohol ether carboxylic ester (AECE-Na) surfactant with both anionic and non-ionic characteristics was synthesised using a fatty alcohol ether (AEO) and succinic anhydride. Compared with traditional synthetic methods, neither irritating substances (chloroacetic acid and chloroacetate) nor precious metals (Pt and Pd) were used in the synthesis, which is a simple, economic, and green method. FT-IR and 1H NMR spectroscopies and MALDI TOF mass spectrometry were used to prove the molecular structure of the target product AECE-Na. In addition, the surface activities, intermolecular interactions, application properties, and aggregation behaviours of the individual systems (AEO and AECE-Na) and the anionic/non-ionic mixed system (AECE-Na/AEO) were investigated. The results showed that AECE-Na/AEO exhibits synergistic effects in terms of surface tension reduction efficiency, wetting, emulsification, foaming, and detergency compared with the individual systems.
Recommended methodologies to determine Australian Indigenous community members' perceptions of their health needs: a literature review
Authors: Smith Rosetta Lillian , Devine Sue , Preston Robyn
Published: February 2020

When addressing disparities in health status of Indigenous Australians, it is necessary to consult with Indigenous people to explore their health needs. The process of improving health outcomes is complex; it requires acknowledgement of underlying cultural and social determinants of health and active engagement of Indigenous people to define the issues and identify solutions. The aim of this study is to explore the most appropriate research methodologies to determine Australian Indigenous community members’ perceptions of their health needs. A scoping review was conducted in BioMed Central, CINAHL, Informit Health, MEDLINE Ovid, ProQuest and Scopus databases and Google Scholar for all relevant literature published between 2009 and 2018. Extensive manual searches of reference lists were also undertaken. The limited number of articles relating to needs assessment with Indigenous community members prescribed broadening the scope of the review to include articles that describe methodologies to enhance Indigenous people’s engagement in the research process. Twelve papers met the inclusion criteria. Three major themes emerged: (1) the imperative to develop and implement Indigenist research methodologies; (2) participatory action research (PAR) and community-based participatory research (CBPR) as appropriate methodologies to conduct research with Indigenous community members; and (3) yarning or storytelling as a culturally appropriate Indigenous method of data collection.
Post-wildfire moss colonisation and soil functional enhancement in forests of the southwestern USA
Authors: Grover Henry S. , Bowker Matthew A. , Fulé Peter Z. , Doherty Kyle D. , Sieg Carolyn H. , Antoninka Anita J.
Published: February 2020

Fire mosses, including Ceratodon purpureus, Funaria hygrometrica and Bryum argenteum, can achieve high cover within months to years after high-severity fire, but do so heterogeneously across space and time. We conducted a survey of moss cover and erosion-related functions after 10 wildfires in Pinus ponderosa and mixed-conifer forests of the southwestern USA. We sampled 65 plots in high-severity patches, stratifying by elevation and insolation over each fire. Using three landscape-scale predictor variables and one temporal predictor, we explained 37% of the variance in fire moss cover using a random forest model. The predictors in order of importance were: equinox insolation (sunlight/day), pre-fire vegetation type, pre-fire soil organic carbon and time since fire. Within each plot we examined differences between bare and moss-covered soil surface microsites and found moss-covered microsites had a mean increase of 55% water infiltration, 106% shear strength, 162% compressive strength and 195% aggregate stability. We tested a suite of nutrients, finding 35% less manganese in the moss-covered soil. This research demonstrated that post-fire colonisation by moss is predictable and that colonisation improves soil surface erosion resistance and hydrological function, with implications for managing severely burned landscapes.
Timing and magnitude of Southern Ocean sea ice/carbon cycle feedbacks
Authors: Stein Karl , Timmermann Axel , Kwon Eun Young , Friedrich Tobias
Published: February 2020

Significance

Atmospheric carbon was sequestered in the ocean during glacial periods, but the processes responsible are not understood. Southern Ocean (SO) sea ice has been proposed as a link between several processes of carbon sequestration. This study analyzes the effect of SO sea ice on ocean ventilation in a 784,000-y climate model simulation. The results show that SO sea ice can dramatically reduce ocean ventilation by reducing the atmospheric exposure time of surface waters and by decreasing the vertical mixing of deep ocean waters. Sensitivity tests of the two mechanisms with a carbon cycle model show a 40-ppm reduction of atmospheric

C
O

2

, half the glacial/interglacial difference, with ocean stratification playing the leading role in both magnitude and timing.
Oncostatin M-induced astrocytic tissue inhibitor of metalloproteinases-1 drives remyelination
Authors: Houben Evelien , Janssens Kris , Hermans Doryssa , Vandooren Jennifer , Van den Haute Chris , Schepers Melissa , Vanmierlo Tim , Lambrichts Ivo , van Horssen Jack , Baekelandt Veerle , Opdenakker Ghislain , Baron Wia , Broux Bieke , Slaets Helena , Hellings Niels
Published: February 2020

Significance

The loss of myelin around axons is a main pathological hallmark of various neurological diseases. In early disease stages, this myelin sheath is restored through a process called remyelination. Later, remyelination fails and becomes the major driver of disease progression. Despite a clear demand for remyelination-enhancing therapies, the need is currently unmet. Here we present oncostatin M receptor signaling and its downstream effector molecule tissue inhibitor of metalloproteinases-1 as decisive mediators of successful remyelination, providing novel therapeutic opportunities for demyelinating disorders.
Chromatin remodeling factor ARID2 suppresses hepatocellular carcinoma metastasis via DNMT1-Snail axis
Authors: Jiang Hao , Cao Hui-Jun , Ma Ning , Bao Wen-Dai , Wang Jing-Jing , Chen Tian-Wei , Zhang Er-Bin , Yuan Yan-Mei , Ni Qian-Zhi , Zhang Feng-Kun , Ding Xu-Fen , Zheng Qian-Wen , Wang Yi-Kang , Zhu Min , Wang Xiang , Feng Jing , Zhang Xue-Li , Cheng Shu-Qun , Ma Dan-Jun , Qiu Lin , Li Jing-Jing , Xie Dong
Published: February 2020

Significance

In this study, we find that ARID2 expression is negatively correlated with HCC metastasis and positively associated with prognosis of HCC patients. We demonstrate that ARID2 inhibits metastasis of HCC cells by recruiting DNMT1 to the promoter of Snail, which elevates DNA methylation and suppresses Snail transcription. Notably, we discover a C2H2 truncated mutation (3817C > T) in metastatic HCC tissue. We further reveal that C2H2 domain is required for ARID2–DNMT1 interaction and find loss-of-function ARID2 mutants with disrupted C2H2 domain are positively associated with HCC metastasis and poor survival of HCC patients. Taken together, our study not only expands comprehensive understanding of ARID2 and its mutations in HCC, but also provides indication for treatment of ARID2-deficient HCC.
The MYCL and MXD1 transcription factors regulate the fitness of murine dendritic cells
Authors: Anderson David A. , Murphy Theresa L. , Eisenman Robert N. , Murphy Kenneth M.
Published: February 2020

We previously found that MYCL is required by a
Batf3
-dependent classical dendritic cell subset (cDC1) for optimal CD8 T cell priming, but the underlying mechanism has remained unclear. The MAX-binding proteins encompass a family of transcription factors with overlapping DNA-binding specificities, conferred by a C-terminal basic helix-loop-helix domain, which mediates heterodimerization. Thus, regulation of transcription by these factors is dependent on divergent N-terminal domains. The MYC family, including MYCL, has actions that are reciprocal to the MXD family, which is mediated through the recruitment of higher-order activator and repressor complexes, respectively. As potent proto-oncogenes, models of MYC family function have been largely derived from their activity at supraphysiological levels in tumor cell lines. MYC and MYCN have been studied extensively, but empirical analysis of MYCL function had been limited due to highly restricted, lineage-specific expression in vivo. Here we observed that
Mycl
is expressed in immature cDC1s but repressed on maturation, concomitant with
Mxd1
induction in mature cDC1s. We hypothesized that MYCL and MXD1 regulate a shared, but reciprocal, transcriptional program during cDC1 maturation. In agreement, immature cDC1s in
Mycl

−/−

-deficient mice exhibited reduced expression of genes that regulate core biosynthetic processes. Mature cDC1s from
Mxd1
−/−
mice exhibited impaired ability to inhibit the transcriptional signature otherwise supported by MYCL. The present study reveals LMYC and MXD1 as regulators of a transcriptional program that is modulated during the maturation of
Batf3
-dependent cDC1s.
Proteins containing ubiquitin-like (Ubl) domains not only bind to 26S proteasomes but also induce their activation
Authors: Collins Galen A. , Goldberg Alfred L.
Published: February 2020

Significance

Most protein degradation in eukaryotic cells is catalyzed by the 26S proteasome, which digests proteins marked for destruction by a chain of ubiquitin molecules. Typically, 26S proteasomes are present in cells as inactive particles that can become active when a ubiquitylated substrate binds. Proteasomes are usually viewed as containing a characteristic set of subunits, but, in cells, many important proteins associate transiently with proteasomes to deliver substrates or provide additional activities. Here, we show that a major class of proteasome-binding proteins that contain a ubiquitin-like (Ubl) domain can also enhance the 26S proteasome’s multiple enzymatic activities that are critical for protein degradation. Thus Ubl-containing proteins, in addition to their other functions, have this unexpected regulatory role.
Sequential activation of necroptosis and apoptosis cooperates to mediate vascular and neural pathology in stroke
Authors: Naito Masanori Gomi , Xu Daichao , Amin Palak , Lee Jinwoo , Wang Huibing , Li Wanjin , Kelliher Michelle , Pasparakis Manolis , Yuan Junying
Published: February 2020

Significance

Necroptosis has been defined as a regulated cell death mechanism that can be activated under apoptosis deficient conditions. Here we show that necroptosis can be activated under brain ischemic conditions without inhibition of apoptosis. Furthermore, neuronal necroptosis can be followed by delayed apoptosis after the reduction of TAK1 under ischemic conditions. Our study demonstrates the complex interaction of apoptosis and necroptosis after ischemic brain insult and suggests the therapeutic targeting of RIPK1 kinase for the treatment of stroke.
Phage liquid crystalline droplets form occlusive sheaths that encapsulate and protect infectious rod-shaped bacteria
Authors: Tarafder Abul K. , von Kügelgen Andriko , Mellul Adam J. , Schulze Ulrike , Aarts Dirk G. A. L. , Bharat Tanmay A. M.
Published: February 2020

The opportunistic pathogenPseudomonas aeruginosais a major cause of antibiotic-tolerant infections in humans.P. aeruginosaevades antibiotics in bacterial biofilms by up-regulating expression of a symbiotic filamentous inoviral prophage, Pf4. We investigated the mechanism of phage-mediated antibiotic tolerance using biochemical reconstitution combined with structural biology and high-resolution cellular imaging. We resolved electron cryomicroscopy atomic structures of Pf4 with and without its linear single-stranded DNA genome, and studied Pf4 assembly into liquid crystalline droplets using optical microscopy and electron cryotomography. By biochemically replicating conditions necessary for antibiotic protection, we found that phage liquid crystalline droplets form phase-separated occlusive compartments around rod-shaped bacteria leading to increased bacterial survival. Encapsulation by these compartments was observed even when inanimate colloidal rods were used to mimic rod-shaped bacteria, suggesting that shape and size complementarity profoundly influences the process. Filamentous inoviruses are pervasive across prokaryotes, and in particular, several Gram-negative bacterial pathogens includingNeisseria meningitidis,Vibrio cholerae,andSalmonella entericaharbor these prophages. We propose that biophysical occlusion mediated by secreted filamentous molecules such as Pf4 may be a general strategy of bacterial survival in harsh environments.
Tyrosine phosphorylation of the AMPA receptor subunit GluA2 gates homeostatic synaptic plasticity
Authors: Yong Adeline J. H. , Tan Han L. , Zhu Qianwen , Bygrave Alexei M. , Johnson Richard C. , Huganir Richard L.
Published: February 2020

Significance

Throughout an organism’s life span, neural circuits mediate sensory and cognitive processing via synaptic plasticity, which involves synapse-specific Hebbian plasticity and network-level homeostatic plasticity. Synaptic strengthening and weakening are finely tuned by changes in postsynaptic α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) -type glutamate receptors (AMPARs). We have elucidated a biochemical regulation of AMPARs that is specific to homeostatic synaptic plasticity while sparing Hebbian plasticity mechanisms. Specifically, phosphorylation of the AMPAR subunit, GluA2, at tyrosine-876 is required for homeostatic synaptic strengthening by dictating GluA2 binding to glutamate receptor interacting protein 1 (GRIP1), a scaffolding protein crucial for synaptic upscaling. This finding elucidates a mechanism through which neurons can maintain a range of synaptic signaling while not compromising their responsiveness to subsequent synaptic activity.
Local lattice distortions and dynamics in extremely overdoped superconducting YSr
2
Cu
2.75
Mo
0.25
O
7.54
Authors: Conradson Steven D. , Geballe Theodore H. , Gauzzi Andrea , Karppinen Maarit , Jin Changqing , Baldinozzi Gianguido , Li Wenmin , Cao Lipeng , Gilioli Edmondo , Jiang Jack M. , Latimer Matthew , Mueller Oliver , Nasretdinova Venera
Published: February 2020

Significance

We show that a second-phase diagram is needed to describe “overdoped” cuprates prepared by high-pressure oxygen methods. The transition temperatures of HPO compounds continue to increase past the values of O stoichiometry and Cu charge where the superconductivity in conventional materials terminates. The Mo and Cu maintain their preferred geometries despite the higher Cu charge via clustering of the Mo. The principal effect of the Mo and excess O is therefore nanophase separation into Mo- and Cu-enriched domains. The high degree of similarity between the HPO and normal structures, including a Cu2-apical O two-site distribution, therefore suggests that the elevated
T

c

of YSCO–Mo may originate in a combination of this nanoscale heterogeneity and the dynamical properties.
Why East Asians but not South Asians are underrepresented in leadership positions in the United States
Authors: Lu Jackson G. , Nisbett Richard E. , Morris Michael W.
Published: February 2020

Well-educated and prosperous, Asians are called the “model minority” in the United States. However, they appear disproportionately underrepresented in leadership positions, a problem known as the “bamboo ceiling.” It remains unclear why this problem exists and whether it applies to all Asians or only particular Asian subgroups. To investigate the mechanisms and scope of the problem, we compared the leadership attainment of the two largest Asian subgroups in the United States: East Asians (e.g., Chinese) and South Asians (e.g., Indians). Across nine studies (n= 11,030) using mixed methods (archival analyses of chief executive officers, field surveys in large US companies, student leader nominations and elections, and experiments), East Asians were less likely than South Asians and whites to attain leadership positions, whereas South Asians were more likely than whites to do so. To understand why the bamboo ceiling exists for East Asians but not South Asians, we examined three categories of mechanisms—prejudice (intergroup), motivation (intrapersonal), and assertiveness (interpersonal)—while controlling for demographics (e.g., birth country, English fluency, education, socioeconomic status). Analyses revealed that East Asians faced less prejudice than South Asians and were equally motivated by work and leadership as South Asians. However, East Asians were lower in assertiveness, which consistently mediated the leadership attainment gap between East Asians and South Asians. These results suggest that East Asians hit the bamboo ceiling because their low assertiveness is incongruent with American norms concerning how leaders should communicate. The bamboo ceiling is not an Asian issue, but an issue of cultural fit.
Metalinguistic discourses on translanguaging and
multimodality
Authors: Makoni Busi
Published: February 2020

This article explores metalinguistic discourses of black African
immigrants (BAIs) in Johannesburg on how they mobilize multilingual and
multimodal resources in their communicative practices to pass as South Africans
(SAs), concealing their identities as non-SAs to avert violent xenophobic
attacks. Drawing data from semi-structured interviews and group discussions with
BAIs, the article investigates how BAIs report on creatively, strategically
using translanguaging and multimodality in performance of ingroup membership as
local black SAs, blurring the boundaries between “outsiders” and “insiders.”
BAIs use passing as a social identity management strategy, to negotiate their
putative identity and resist ascription of the foreigner-outsider categorization
and attendant social meanings. Besides language(s), BAIs use modes of corporeal
practice (embodiment, clothing semiosis, skin-bleaching) as legitimating markers
of belonging. The article argues that using passing unsettles the distinction
between local/insider/citizen and migrant/outsider/non-citizen – concepts framed
around a nation-state – revealing tensions, contradictions, and complexities in
the politics of identity in Johannesburg.
Defining the subcellular distribution and metabolic channeling of phosphatidylinositol
Authors: Pemberton Joshua G. , Kim Yeun Ju , Humpolickova Jana , Eisenreichova Andrea , Sengupta Nivedita , Toth Daniel J. , Boura Evzen , Balla Tamas
Published: February 2020

Phosphatidylinositol (PI) is an essential structural component of eukaryotic membranes that also serves as the common precursor for polyphosphoinositide (PPIn) lipids. Despite the recognized importance of PPIn species for signal transduction and membrane homeostasis, there is still a limited understanding of the relationship between PI availability and the turnover of subcellular PPIn pools. To address these shortcomings, we established a molecular toolbox for investigations of PI distribution within intact cells by exploiting the properties of a bacterial enzyme, PI-specific PLC (PI-PLC). Using these tools, we find a minor presence of PI in membranes of the ER, as well as a general enrichment within the cytosolic leaflets of the Golgi complex, peroxisomes, and outer mitochondrial membrane, but only detect very low steady-state levels of PI within the plasma membrane (PM) and endosomes. Kinetic studies also demonstrate the requirement for sustained PI supply from the ER for the maintenance of monophosphorylated PPIn species within the PM, Golgi complex, and endosomal compartments.
The mechanisms shaping CA2 pyramidal neuron action potential bursting induced by muscarinic acetylcholine receptor activation
Authors: Robert Vincent , Therreau Ludivine , Davatolhagh M. Felicia , Bernardo-Garcia F. Javier , Clements Katie N. , Chevaleyre Vivien , Piskorowski Rebecca A.
Published: February 2020

Recent studies have revealed that hippocampal area CA2 plays an important role in hippocampal network function. Disruption of this region has been implicated in neuropsychiatric disorders. It is well appreciated that cholinergic input to the hippocampus plays an important role in learning and memory. While the effect of elevated cholinergic tone has been well studied in areas CA1 and CA3, it remains unclear how changes in cholinergic tone impact synaptic transmission and the intrinsic properties of neurons in area CA2. In this study, we applied the cholinergic agonist carbachol and performed on-cell, whole-cell, and extracellular recordings in area CA2. We observed that under conditions of high cholinergic tone, CA2 pyramidal neurons depolarized and rhythmically fired bursts of action potentials. This depolarization depended on the activation of M1 and M3 cholinergic receptors. Furthermore, we examined how the intrinsic properties and action-potential firing were altered in CA2 pyramidal neurons treated with 10 µM carbachol. While this intrinsic burst firing persisted in the absence of synaptic transmission, bursts were shaped by synaptic inputs in the intact network. We found that both excitatory and inhibitory synaptic transmission were reduced upon carbachol treatment. Finally, we examined the contribution of different channels to the cholinergic-induced changes in neuronal properties. We found that a conductance from Kv7 channels partially contributed to carbachol-induced changes in resting membrane potential and membrane resistance. We also found that D-type potassium currents contributed to controlling several properties of the bursts, including firing rate and burst kinetics. Furthermore, we determined that T-type calcium channels and small conductance calcium-activated potassium channels play a role in regulating bursting activity.
How stomatin stops ASIC3 gating
Authors: Short Ben
Published: February 2020

JGP study suggests that stomatin may trap the acid-sensing ASIC3 channel in its desensitized state.
Unsupervised identification of topological phase transitions using predictive models
Authors: Greplova Eliska , Valenti Agnes , Boschung Gregor , Schäfer Frank , Lörch Niels , Huber Sebastian D
Published: February 2020

Machine-learning driven models have proven to be powerful tools for the identification of phases of matter. In particular, unsupervised methods hold the promise to help discover new phases of matter without the need for any prior theoretical knowledge. While for phases characterized by a broken symmetry, the use of unsupervised methods has proven to be successful, topological phases without a local order parameter seem to be much harder to identify without supervision. Here, we use an unsupervised approach to identify boundaries of the topological phases. We train artificial neural nets to relate configurational data or measurement outcomes to quantities like temperature or tuning parameters in the Hamiltonian. The accuracy of these predictive models can then serve as an indicator for phase transitions. We successfully illustrate this approach on both the classical Ising gauge theory as well as on the quantum ground state of a generalized toric code.
Quantum coherence and correlation dynamics of two-qubit system in spin bath environment*
Authors: Yang Hao , Qin Li-Guo , Tian Li-Jun , Ma Hong-Yang
Published: February 2020

The quantum entanglement, discord, and coherence dynamics of two spins in the model of a spin coupled to a spin bath through an intermediate spin are studied. The effects of the important physical parameters including the coupling strength of two spins, the interaction strength between the intermediate spin and the spin bath, the number of bath spins and the temperature of the system on quantum coherence and correlation dynamics are discussed in different cases. The frozen quantum discord can be observed whereas coherence does not when the initial state is the Bell-diagonal state. At finite temperature, we find that coherence is more robust than quantum discord, which is better than entanglement, in terms of resisting the influence of environment. Therefore, quantum coherence is more tenacious than quantum correlation as an important resource.
Sentinel-1 observation frequency significantly increases burnt area detectability in tropical SE Asia
Authors: Carreiras Joao M B , Quegan Shaun , Tansey Kevin , Page Susan
Published: February 2020

Frequent cloud cover in the tropics significantly affects the observation of the surface by satellites. This has enormous implications for current approaches that estimate greenhouse gas (GHG) emissions from fires or map fire scars. These mainly employ data acquired in the visible to middle infrared bands to map fire scars or thermal data to estimate fire radiative power and consequently derive emissions. The analysis here instead explores the use of microwave data from the operational Sentinel-1A (S-1A) in dual-polarisation mode (VV and VH) acquired over Central Kalimantan during the 2015 fire season. Burnt areas were mapped in three consecutive periods between August and October 2015 using the random forests machine learning algorithm. In each mapping period, the omission and commission errors of the unburnt class were always below 3%, while the omission and commission errors of the burnt class were below 20% and 5% respectively. Summing the detections from the three periods gave a total burnt area of ∼1.6 million ha, but this dropped to ∼1.2 million ha if using only a pair of pre- and post-fire season S-1A images. Hence the ability of Sentinel-1 to make frequent observations significantly increases fire scar detection. Comparison with burnt area estimates from the Moderate Resolution Imaging Spectroradiometer (MODIS) burnt area product at 5 km scale showed poor agreement, with consistently much lower estimates produced by the MODIS data-on average 14%–51% of those obtained in this study. The method presented in this study offers a way to reduce the substantial errors likely to occur in optical-based estimates of GHG emissions from fires in tropical areas affected by substantial cloud cover.
The Combination of Non-dipper Heart Rate and High Brain Natriuretic Peptide Predicts Cardiovascular Events: The Japan Morning Surge-Home Blood Pressure (J-HOP) Study
Authors: Ogoyama Yukako , Kabutoya Tomoyuki , Hoshide Satoshi , Kario Kazuomi
Published: February 2020

BACKGROUND

We hypothesized that the association between the dipping heart rate (HR) pattern and cardiovascular (CV) events differs according to the brain natriuretic peptide (BNP) level.

METHODS

We examined a subgroup of 1,369 patients from the Japan Morning Surge Home Blood Pressure study; these were patients who had CV risk factors and had undergone ambulatory blood pressure (BP) monitoring. HR non-dipping status was defined as (awake HR − sleep HR)/awake HR <0.1, and high BNP was defined as ≥35 pg/ml. We divided the patients into four groups according to their HR dipper status (dipping or non-dipping) and BNP level (normal or high).

RESULTS

The mean follow-up period was 60 ± 30 months. The primary endpoints were fatal/nonfatal CV events (myocardial infarction, angina pectoris, stroke, hospitalization for heart failure, and aortic dissection). During the follow-up period, 23 patients (2.8%) in the dipper HR with normal BNP group, 8 patients (4.4%) in the non-dipper HR with normal BNP group, 24 patients (9.5%) in the dipper HR with high-BNP group, and 25 patients (21.0%) in the non-dipper HR with high-BNP group suffered primary endpoints (log rank 78.8, P < 0.001). Non-dipper HR was revealed as an independent predictor of CV events (hazard ratio, 2.13; 95% confidence interval, 1.35–3.36; P = 0.001) after adjusting for age, gender and smoking, dyslipidemia, diabetes mellitus, chronic kidney disease, BNP, non-dipper BP, 24-h HR, and 24-h systolic blood pressure.

CONCLUSIONS

The combination of non-dipper HR and higher BNP was associated with a higher incidence of CV events.
Proline: an efficient and user-friendly software suite for large-scale proteomics
Authors: Bouyssié David , Hesse Anne-Marie , Mouton-Barbosa Emmanuelle , Rompais Magali , Macron Charlotte , Carapito Christine , Gonzalez de Peredo Anne , Couté Yohann , Dupierris Véronique , Burel Alexandre , Menetrey Jean-Philippe , Kalaitzakis Andrea , Poisat Julie , Romdhani Aymen , Burlet-Schiltz Odile , Cianférani Sarah , Garin Jerome , Bruley Christophe
Published: February 2020

Motivation

The proteomics field requires the production and publication of reliable mass spectrometry-based identification and quantification results. Although many tools or algorithms exist, very few consider the importance of combining, in a unique software environment, efficient processing algorithms and a data management system to process and curate hundreds of datasets associated with a single proteomics study.

Results

Here, we present Proline, a robust software suite for analysis of MS-based proteomics data, which collects, processes and allows visualization and publication of proteomics datasets. We illustrate its ease of use for various steps in the validation and quantification workflow, its data curation capabilities and its computational efficiency. The DDA label-free quantification workflow efficiency was assessed by comparing results obtained with Proline to those obtained with a widely used software using a spiked-in sample. This assessment demonstrated Proline’s ability to provide high quantification accuracy in a user-friendly interface for datasets of any size.

Availability and implementation

Proline is available for Windows and Linux under CECILL open-source license. It can be deployed in client–server mode or in standalone mode at http://proline.profiproteomics.fr/#downloads.

Supplementary information

Supplementary data are available at Bioinformatics online.
A probabilistic graphical model for system-wide analysis of gene regulatory networks
Authors: Kotiang Stephen , Eslami Ali
Published: February 2020

Motivation

The inference of gene regulatory networks (GRNs) from DNA microarray measurements forms a core element of systems biology-based phenotyping. In the recent past, numerous computational methodologies have been formalized to enable the deduction of reliable and testable predictions in today’s biology. However, little focus has been aimed at quantifying how well existing state-of-the-art GRNs correspond to measured gene-expression profiles.

Results

Here, we present a computational framework that combines the formulation of probabilistic graphical modeling, standard statistical estimation, and integration of high-throughput biological data to explore the global behavior of biological systems and the global consistency between experimentally verified GRNs and corresponding large microarray compendium data. The model is represented as a probabilistic bipartite graph, which can handle highly complex network systems and accommodates partial measurements of diverse biological entities, e.g. messengerRNAs, proteins, metabolites and various stimulators participating in regulatory networks. This method was tested on microarray expression data from the M3D database, corresponding to sub-networks on one of the best researched model organisms, Escherichia coli. Results show a surprisingly high correlation between the observed states and the inferred system’s behavior under various experimental conditions.

Availability and implementation

Processed data and software implementation using Matlab are freely available at https://github.com/kotiang54/PgmGRNs. Full dataset available from the M3D database.
Phage protein receptors have multiple interaction partners and high expressions
Authors: Zhang Zheng , Yu Fen , Zou Yuanqiang , Qiu Ye , Wu Aiping , Jiang Taijiao , Peng Yousong
Published: February 2020

Motivation

Receptors on host cells play a critical role in viral infection. How phages select receptors is still unknown.

Results

Here, we manually curated a high-quality database named phageReceptor, including 427 pairs of phage–host receptor interactions, 341 unique viral species or sub-species and 69 bacterial species. Sugars and proteins were most widely used by phages as receptors. The receptor usage of phages in Gram-positive bacteria was different from that in Gram-negative bacteria. Most protein receptors were located on the outer membrane. The phage protein receptors (PPRs) were highly diverse in their structures, and had little sequence identity and no common protein domain with mammalian virus receptors. Further functional characterization of PPRs in Escherichia coli showed that they had larger node degrees and betweennesses in the protein–protein interaction network, and higher expression levels, than other outer membrane proteins, plasma membrane proteins or other intracellular proteins. These findings were consistent with what observed for mammalian virus receptors reported in previous studies, suggesting that viral protein receptors tend to have multiple interaction partners and high expressions. The study deepens our understanding of virus–host interactions.

Availability and implementation

phageReceptor is publicly available from: http://www.computationalbiology.cn/phageReceptor/index.html.

Supplementary information

Supplementary data are available at Bioinformatics online.