bluuebunny/crossref_metadata_2025 huggingface dataset:
An extended chiral surface coordination network based on Ag7-clusters
Authors: Svane Katrine L. , Baviloliaei Mahdi S. , Hammer Bjørk , Diekhöner Lars
Published: October 2018

We present an extended metal-coordinated structure obtained by deposition of trimesic acid (TMA) onto the Ag(111) surface under ultra-high vacuum conditions followed by annealing to 510 K. Scanning tunneling microscopy and density functional theory calculations reveal the structure to consist of metal clusters containing seven Ag atoms each, coordinated by six dehydrogenated TMA molecules. The molecules are asymmetrically arranged, resulting in a chiral structure. The calculations confirm that this structure has a lower free energy under the experimental conditions than the hydrogen-bonded structures observed after annealing at lower temperatures. We show that the formation of such large metal clusters is possible due to the low adatom formation energy on silver and the relatively strong Ag-O bond in combination with a good lattice match between the structure and the Ag surface.
Effect of epitaxial strain and vacancies on the ferroelectric-like response of CaTiO3 thin films
Authors: Sarantopoulos A. , Ong Wee-Liat , Malen Jonathan A. , Rivadulla F.
Published: October 2018

We report the effect of the epitaxial strain and deliberate incorporation of anionic/cationic defects on the ferroelectric-like response of CaTiO3 thin films. The role of the defect concentration and TiO6 octahedral rotation in the suppression or promotion of a ferroelectric phase is discussed. We demonstrate that a local electric field and/or mechanical force induce the local accumulation/depletion of oxygen vacancies, which change the surface potential and local volume similar to ferroelectric polarization. Our results demonstrate that reversible bi-stable states can be produced in CaTiO3 by electrical or mechanical means, opening interesting possibilities for ionic-based devices.
Simulation and measurement of water-induced liquid-liquid phase separation of imidazolium ionic liquid mixtures
Authors: Rocha M. Alejandra , Zhang Yong , Maginn Edward J. , Shiflett Mark B.
Published: October 2018

The miscibility of ionic liquid (IL) pairs with a common cation (1-ethyl-3-methylimidazolium [C2C1im]) and different anions (bis(trifluoromethylsulfonyl)amide [TFSI], acetate [OAc], and chloride [Cl]) was investigated at a wide range of water concentrations at room temperature. Molecular simulations predicted that the addition of water to the [C2C1im][TFSI]:[C2C1im][OAc] and [C2C1im][TFSI]:[C2C1im][Cl] mixtures would induce a liquid-liquid phase separation and that water addition to the [C2C1im][OAc]:[C2C1im][Cl] mixture would not produce a phase separation. The effect of water on the phase behavior of the IL mixtures was verified experimentally, and the IL and water concentrations were determined in each phase. Of particular importance is the analytical methodology used to determine the species’ concentration, where 1H NMR and a combination of 19F NMR, Karl Fischer titration, and ion chromatography techniques were applied.
Convective heat transport in two-phase superfluid/vapor 4He system
Authors: Urban P. , Hanzelka P. , Vlček I. , Schmoranzer D. , Skrbek L.
Published: October 2018

We have recently shown that under certain cryogenic conditions heat can flow from a colder but constantly heated body to a hotter but constantly cooled body. Specifically, we have provided experimental evidence that heat flows through normal liquid and gaseous phases of 4He from the constantly heated, but cooler, bottom plate of a Rayleigh–Bénard convection cell to its hotter, but constantly cooled, top plate. Here we report results of a modified experiment, where the bottom normal liquid helium layer is replaced by superfluid 4He, providing, together with a superfluid film covering the entire cell interior, an effective thermal short-circuit. Applied heat input of order 1 W to the bottom plate results in simultaneous heating of the entire cell: this physical process can be viewed, at least approximately, as a series of subsequent equilibrium states, until upon reaching the superfluid transition the non-equilibrium processes described in our previous study [Proc. Nat. Acad. Sci. USA 110, 8036 (2013)] are fully recovered.
Kinetics of low-temperature gas of hydrogen-like atoms in an external electromagnetic field
Authors: Zagorodny А. G. , Slyusarenko Yu. V. , Shulga S. N.
Published: October 2018

A microscopic approach for the construction of the kinetic theory of low-temperature hydrogen-like gases in an external electromagnetic field was developed. The approach is based on the formulation of secondary quantization in the presence of bound states of particles. It is suggested that the bound state (for example, a hydrogen-like atom of alkali metal) is formed by two charged fermions of different sorts — the valence electron and the ion core. The reduced description of relaxation processes establishes the basis for the formulation of the kinetic equations. Within the developed theoretical framework, the system of kinetic equations for Wigner’s distribution functions of free fermions of both sorts and their bound states, hydrogen-like atoms, is developed accounting for an external and self-consistent (intermediate) fields acting on the system. The obtained equations of motion for Wigner’s distribution functions serve as a basis for analyzing non-equilibrium effects and phenomena related to the influence of an external electromagnetic field on low-temperature gases of alkali metals.
Some features of the long-pulse propagation mode of a phonon sheet in superfluid 4He
Authors: Vovk R. V. , Williams C. D. H. , Wyatt A. F. G.
Published: October 2018

The angular distribution of the energy density of an anisotropic “phonon sheet” was studied during its propagation in superfluid 4He at pulse duration up to 300 ns. The presence of a flat segment on the angular dependencies of phonon signal is explained by the formation of a “hot” area in the central region of the sheet and by the process of generation of high-energy phonons in this central region. The saturation of width of a flat section at pulse durations near 300 ns is explained by implementation of the long-pulsed beam propagation mode.
Roton excitations in a condensed medium
Authors: Karasevskii A. I.
Published: October 2018

Here, it has been shown that the homogeneous state of the medium can be unstable in melts near the melting curve, in multicomponent liquids, in dense gases, as well as in superfluid helium. Nanoclusters may be spontaneously formed in the medium; their metastability is associated with the increase in orientational entropy during spontaneous rotation of the nanoparticles. With a positive energy of formation of nanoparticles, their concentration is determined by the increase in entropy of the system configuration. Like vacancies in crystals, roton clusters are structural defects of the melt.
Electric response induced by second sound in superfluid helium
Authors: Yayama Hideki , Nishimura Yugo , Uchiyama Hiroka , Kawai Hiroshi , van Woensel Jean-Paul , Hafez Ali G.
Published: October 2018

The electric response of superfluid helium was measured when a second sound standing wave was generated in a resonator cavity. The results were qualitatively in agreement with that of other research laboratories, but the normalized signal strength was one order of magnitude larger reflecting the difference in electrode structure. The temporal phase difference between the electric oscillation and the temperature oscillation was measured and compared with the analysis. The result excluded a hypothesis that the electric response was induced by the velocities of the relative motion of normal and superfluid components of liquid helium. We suggested a hypothetical explanation of the electric response based on the oscillation of chemical potential of electrons in helium atoms. The effect of an external dc electric field was examined and no effect was observed. The heater power dependence of the temperature oscillation and the electric oscillation showed the qualitative agreement with the original experiment.
Low-energy excitations in helium-like dimer within an exact diagonalization approach
Authors: Chishko K. A.
Published: October 2018

The non-relativistic quantum-mechanical problem on bound states of four interacting spinless electrons moving in the Coulomb field of two attractive point centers with Z0=2 spaced at fixed distance R0 (4He2 dimer within Born–Oppenheimer–Heitler–London approximation) has been solved rigorously through exact diagonalization (expansion on truncated orthonormalized basis) method. The four-spin-conditioned relativistic corrections (of order ∼1/c2) to the ground state level of the dimer have been calculated with exact diagonalization on spin cluster, the spectrum and eigenvectors of the spin problem have been obtained. It is shown that pair spin coupling is antiferromagnetic with exchange constant of 12 K (it provides antisymmetry of the spin-singlet ground-state wave function for isolated 4He atom with two fermions coupled within the unitary spatially symmetric shell), but within four-electron shell of 4He2 dimer this fact yields the quintet ground state of the four-spin cluster totally antisymmetric relative to pair permutations. The exchange within the interatomic bond depends on the interatomic distance, so that there is a coupling between spin and phonon degrees of freedom which leads to renormalization of phonon spectrum in condensed phase as compared to the corresponding spinless medium. This effect can be interpreted as a direct analog of translation-rotation interaction in molecular cryocrystals.
Dynamics of crystallization of solid ethanol
Authors: Efimov V. , Izotov A. , Rybchenko O.
Published: October 2018

Experimental studies of the kinetics of phase transitions of C2H5OH ethyl alcohol samples from amorphous to crystalline phase demonstrated that their transition rate and energy characteristics strongly depend on the size and composition of the samples (rectified alcohol, absolute alcohol). Almost all bulk amorphous samples of rectified alcohol that were several millimeters in size crystallized into the monoclinic phase within few hours at a temperature of T ∼ 125 K, while in amorphous nanocluster samples consisting of clusters of the order of tens nanometers in size, a similar transition was observed at T ∼ 110 K. Characteristic transition times from one crystalline phase to another also differed greatly. Temperatures at which the transition from the plastic to the monoclinic phase occurred for both bulk and nanoclusters samples of absolute alcohol were lower (100–105 K), and crystallization of nanocluster samples occurred much more rapidly. The exponent moduli in time dependence of x ∼ tn in the JMAK model (crystallization of an amorphous substance) strongly depended on temperature, and for nanocrystallites were of the order of one or less. However, for massive samples, the exponent modulus n turned out to be closer to two for both rectified and absolute alcohol.
Low-density polyethylene microplastics as a source and carriers of agrochemicals to soil and earthworms
Authors: Rodríguez-Seijo Andrés , Santos Bruna , Ferreira da Silva Eduardo , Cachada Anabela , Pereira Ruth
Published: October 2018

Environmental contextMicroplastics, long recognised as contaminants in aquatic ecosystems, are increasingly of environmental concern for terrestrial ecosystems. This study focuses on the potential of microplastics to act as carriers of agrochemicals and the subsequent effects on soil biota. The results indicate the need for further studies into how soil properties influence both the degradation of microplastics and their role as pollutant carriers.
AbstractMicroplastics (MPs) are of environmental concern to marine ecosystems owing to the evidence of their presence in and adverse effects on organisms, but studies to address this problem on soils and its biota are scarce. Several questions can arise related to this major environmental problem and its impact on terrestrial ecosystems, mainly, whether MPs can transport contaminants (e.g. pesticides) to the soil matrix and if they can be a carrier of pesticides to soil biota. To contribute to the understanding of these issues, earthworms (Eisenia fetida) were exposed for 14 days to soil containing two different sized MPs (5mm and 0.25 µm–1mm) that were either previously sprayed or not with chlorpyrifos (CPF). Acetylcholinesterase (AChE) activity and thiobarbituric acid reactive substances (TBARS) were measured to track the exposure of the earthworms to MPs, both non-sprayed and sprayed with CPF. The behaviour of the earthworms in the test containers and the movement of MPs in the soil were assessed. The concentration of CPF in soil at the end of the experiment differed between the treatments with MPs of different sizes (17.9ngg−1 and 2442ngg−1 for large and small MPs, respectively). Despite the ability of the MPs to release CPF to the soil, the earthworms avoided the contaminated MPs at the highest contaminant level. At a lower concentration of CPF (large MPs), the earthworms avoided the MPs, but the contact time with contaminated soil was higher, as shown by the enhanced level of TBARs and AChE inhibition. However, no evidence of MPs uptake was recorded, thus it was not demonstrated that MPs can be carriers of pesticides to earthworms.
The in silico human surfaceome
Authors: Bausch-Fluck Damaris , Goldmann Ulrich , Müller Sebastian , van Oostrum Marc , Müller Maik , Schubert Olga T. , Wollscheid Bernd
Published: October 2018

Significance

Despite the fundamental importance of the surfaceome as a signaling gateway to the cellular microenvironment, it remains difficult to determine which proteoforms reside in the plasma membrane and how they interact to enable context-dependent signaling functions. We applied a machine-learning approach utilizing domain-specific features to develop the accurate surfaceome predictor SURFY and used it to define the human in silico surfaceome of 2,886 proteins. The in silico surfaceome is a public resource which can be used to filter multiomics data to uncover cellular phenotypes and surfaceome markers. By our domain-specific feature machine-learning approach, we show indirectly that the environment (extracellular, cytoplasm, or vesicle) is reflected in the biochemical properties of protein domains reaching into that environment.
Nickel-hydrogen batteries for large-scale energy storage
Authors: Chen Wei , Jin Yang , Zhao Jie , Liu Nian , Cui Yi
Published: October 2018

Significance

Rechargeable batteries offer great opportunities to target low-cost, high-capacity, and highly reliable systems for large-scale energy storage. This work introduces an aqueous nickel-hydrogen battery by using a nickel hydroxide cathode with industrial-level areal capacity of ∼35 mAh cm
−2
and a low-cost, bifunctional nickel-molybdenum-cobalt electrocatalyst as hydrogen anode to effectively catalyze hydrogen evolution and oxidation reactions in alkaline electrolyte. The nickel-hydrogen battery exhibits an energy density of ∼140 Wh kg
−1
in aqueous electrolyte and excellent rechargeability without capacity decay over 1,500 cycles. The estimated cost of the nickel-hydrogen battery reaches as low as ∼$83 per kilowatt-hour, demonstrating attractive potential for practical large-scale energy storage.
Microfluidics in structured multimaterial fibers
Authors: Yuan Rodger , Lee Jaemyon , Su Hao-Wei , Levy Etgar , Khudiyev Tural , Voldman Joel , Fink Yoel
Published: October 2018

Significance

The development of microfluidics, or the study of fluid behavior and manipulation at the microscale, has largely been catalyzed by microfabrication techniques based on a planar chip format. While immensely powerful, planar fabrication methods have inherent restrictions that prevent the realization of relatively simple channel structures, such as nonrectangular cross-sectional geometries and arbitrary cross-sectional materials placement. This study introduces a microfluidics fabrication method based on a fiber format that enables the construction of microchannels with highly tunable cross-sectional geometries and a broad range of materials. This approach allows for degrees of freedom in the design and function of microfluidic systems, thereby extending the reach of realizable microfluidic devices.
Regulatory discrimination of mRNAs by FMRP controls mouse adult neural stem cell differentiation
Authors: Liu Botao , Li Yue , Stackpole Emily E. , Novak Annie , Gao Yu , Zhao Yinghua , Zhao Xinyu , Richter Joel D.
Published: October 2018

Fragile X syndrome (FXS) is caused by the loss of fragile X mental retardation protein (FMRP), an RNA binding protein whose deficiency impacts many brain functions, including differentiation of adult neural stem cells (aNSCs). However, the mechanism by which FMRP influences these processes remains unclear. Here, we performed ribosome profiling and transcriptomic analysis of aNSCs in parallel from wild-type and
Fmr1
knockout mice. Our data revealed diverse gene expression changes at both mRNA and translation levels. Many mitosis and neurogenesis genes were dysregulated primarily at the mRNA level, while numerous synaptic genes were mostly dysregulated at the translation level. Translational “buffering”, whereby changes in ribosome association with mRNA are compensated by alterations in RNA abundance, was also evident. Knockdown of NECDIN, an FMRP-repressed transcriptional factor, rescued neuronal differentiation. In addition, we discovered that FMRP regulates mitochondrial mRNA expression and energy homeostasis. Thus, FMRP controls diverse transcriptional and posttranscriptional gene expression programs critical for neural differentiation.
Haiti’s biodiversity threatened by nearly complete loss of primary forest
Authors: Hedges S. Blair , Cohen Warren B. , Timyan Joel , Yang Zhiqiang
Published: October 2018

Significance

The loss of forest from human activities is a global threat to biodiversity, continually diminishing populations of forest-dwelling species. However, species extinction usually is delayed until the last habitats disappear. Nonetheless, mass extinction may be imminent in a small number of tropical countries with low forest cover. Here, we find that Haiti has less than 1% of its original primary forest and is therefore among the most deforested countries in the world. Forty-two of the 50 highest and largest mountains have lost all primary forest. Our surveys of vertebrates on these mountaintops suggest that endemic species have been lost along with the loss of forest. This indicates that Haiti is already undergoing a mass extinction of its biodiversity because of deforestation.
Cell-autonomous requirement of TDP-43, an ALS/FTD signature protein, for oligodendrocyte survival and myelination
Authors: Wang Jia , Ho Wan Yun , Lim Kenneth , Feng Jia , Tucker-Kellogg Greg , Nave Klaus-Armin , Ling Shuo-Chien
Published: October 2018

Significance

TDP-43 is the defining pathological hallmark protein for two overlapping adult-onset neurodegenerative diseases, amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). TDP-43 proteinopathies are also found in other major neurodegenerative diseases, such as Alzheimer’s disease, further highlighting the pivotal role of TDP-43 in the nervous system. Curiously, TDP-43 aggregates are also found in oligodendrocytes, which provide myelination and metabolic support for the neurons. Here, we show that TDP-43 is indispensable, in a cell-autonomous manner, for the proper functioning of mature oligodendrocytes, in particular, myelination and cell survival. Specifically, TDP-43 depletion leads to RIPK1-mediated necroptosis of mature oligodendrocytes and down-regulation of myelin proteins that are essential for myelination but exerts no apparent toxicity on motor neurons.
Shear heating reconciles thermal models with the metamorphic rock record of subduction
Authors: Kohn Matthew J. , Castro Adrian E. , Kerswell Buchanan C. , Ranero César R. , Spear Frank S.
Published: October 2018

Significance

Thermal structure controls numerous aspects of subduction zone metamorphism, rheology, and melting. Many thermal models assume small or negligible coefficients of friction and underpredict pressure–temperature (P–T) conditions recorded by subduction zone metamorphic rocks by hundreds of degrees Celsius. Adding shear heating to thermal models simultaneously reproduces surface heat flow and the P–T conditions of exhumed metamorphic rocks. Hot dry rocks are denser than cold wet rocks, so rocks from young-hot subduction systems are denser and harder to exhume through buoyancy. Thus, the metamorphic record may underrepresent hot-young subduction and overrepresent old-cold subduction.
Switchable control over in vivo CAR T expansion, B cell depletion, and induction of memory
Authors: Viaud Sophie , Ma Jennifer S. Y. , Hardy Ian R. , Hampton Eric N. , Benish Brent , Sherwood Lance , Nunez Vanessa , Ackerman Christopher J. , Khialeeva Elvira , Weglarz Meredith , Lee Sung Chang , Woods Ashley K. , Young Travis S.
Published: October 2018

Significance

Chimeric antigen receptor (CAR) T cell therapy represents a powerful strategy in immuno-oncology. Nevertheless, associated life-threatening toxicities and chronic B cell aplasia have underscored the need to control engineered T cells in the patient. To address these challenges, we have previously developed a switchable CAR (sCAR) T cell platform that allows dose-titratable control over CAR T cell activity by using antibody-based switches. Here, we demonstrate in a syngeneic murine model that the switchable platform can impart antitumor efficacy while dissociating long-term persistence from chronic B cell aplasia. Further, the functional reversibility of the switchable platform can be leveraged to incorporate “rest” phases through cyclical dosing of the switch to enable the induction of a robust central memory population for in vivo, on-demand expansion of sCAR T cells.
Regulation of myelin structure and conduction velocity by perinodal astrocytes
Authors: Dutta Dipankar J. , Woo Dong Ho , Lee Philip R. , Pajevic Sinisa , Bukalo Olena , Huffman William C. , Wake Hiroaki , Basser Peter J. , SheikhBahaei Shahriar , Lazarevic Vanja , Smith Jeffrey C. , Fields R. Douglas
Published: October 2018

Significance

Proper communication between brain regions, via white matter tracts, allows us to carry out complex cognitive and motor tasks. Impulses traveling must arrive at relay points almost simultaneously for such communication to be effective. Myelin enables saltatory conduction of impulses and hence is a candidate for modulation of impulse conduction velocity. But myelin structure, once formed, has been considered static. In this study, we show that mature myelin structure is dynamic. The mature myelin sheath thickness and nodal gap length can be reversibly modulated to optimize the speed of axonal impulses. This modulation of myelin is regulated by exocytosis of thrombin protease inhibitors from astrocytes at the node of Ranvier.
Ab initio structure determination from experimental fluctuation X-ray scattering data
Authors: Pande Kanupriya , Donatelli Jeffrey J. , Malmerberg Erik , Foucar Lutz , Bostedt Christoph , Schlichting Ilme , Zwart Petrus H.
Published: October 2018

Significance

Fluctuation X-ray scattering is a biophysical structural characterization technique that overcomes low data-to-parameter ratios encountered in traditional X-ray methods used for studying noncrystalline samples. By collecting a series of ultrashort X-ray exposures on an ensemble of particles at a free-electron laser, information-dense experimental data can be extracted that ultimately result in structures with a greater level of detail than can be obtained using traditional X-ray scattering methods. In this article we demonstrate the practical feasibility of this technique by introducing data-processing techniques and advanced noise-filtering methods that reduce the required data collection time to less than a few minutes. This will ultimately allow one to visualize details of structural dynamics that may be inaccessible through traditional methods.
Agonists of growth hormone-releasing hormone (GHRH) inhibit human experimental cancers in vivo by down-regulating receptors for GHRH
Authors: Schally Andrew V. , Wang Haibo , He Jinlin , Cai Renzhi , Sha Wei , Popovics Petra , Perez Roberto , Vidaurre Irving , Zhang Xianyang
Published: October 2018

Significance

This study demonstrates that the growth hormone-releasing hormone (GHRH) agonist MR409 exerts agonistic action in cancer cells in vitro but, in vivo, suppresses tumor growth of human experimental lung cancers and other cancers. The inhibition of lung tumor growth by MR409 is accompanied by down-regulation of pituitary-type GHRH receptor and its splice-variant in pituitary glands and tumors. Our findings resemble well-known phenomena of the suppression of sex hormone-dependent cancers after the down-regulation of receptors for luteinizing hormone-releasing hormone (LHRH) by LHRH agonists. In addition to hinting at previously unknown approaches to possible uses of GHRH agonists, these findings may relieve serious concerns about stimulating growth of cancers with GHRH agonists in the course of therapy for other diseases and conditions.
Gene-guided discovery and engineering of branched cyclic peptides in plants
Authors: Kersten Roland D. , Weng Jing-Ke
Published: October 2018

Significance

In the past decade, the number of publicly available plant genomes and transcriptomes has steadily increased. Inspired by this genetic resource, we developed a genome-mining approach for the rapid discovery of plant ribosomal peptides from genome-sequenced plants. Herein, we introduce the hypotensive lyciumins as a class of branched cyclic ribosomal peptides in plants and show that they are widely distributed in crop and forage plants. Our results suggest that lyciumin biosynthesis is coupled to plant-specific BURP domains in their precursor peptides and that lyciumin peptide libraries can be generated
in planta
. This discovery sets the stage for gene-guided discovery of peptide chemistry in the plant kingdom and therapeutic and agrochemical applications of lyciumins.
Humanized cereblon mice revealed two distinct therapeutic pathways of immunomodulatory drugs
Authors: Gemechu Yohannes , Millrine David , Hashimoto Shigeru , Prakash Jaya , Sanchenkova Ksenia , Metwally Hozaifa , Gyanu Parajuli , Kang Sujin , Kishimoto Tadamitsu
Published: October 2018

Significance

Shortly after its appearance on the drug market, it was found out that thalidomide was highly teratogenic. Although thalidomide passed the safety check in pregnant mice, it was not safe among humans due to different actions of thalidomide among various species. Due to inactivity of immunomodulatory drugs (IMiDs) in mice, preclinical safety checks and clinical investigation of IMiDs is impossible in murine models. Here, we developed a murine model to study IMiDs in vivo and began to unravel the complex IMiD mechanism of action. This model may also permit investigation of the main safety concerns. We further investigated IMiD activity toward different substrates targeted by small molecules. Overall, our study provides an important insight into the study of IMiDs.
NRG1 functions downstream of EDS1 to regulate TIR-NLR-mediated plant immunity in
Nicotiana benthamiana
Authors: Qi Tiancong , Seong Kyungyong , Thomazella Daniela P. T. , Kim Joonyoung Ryan , Pham Julie , Seo Eunyoung , Cho Myeong-Je , Schultink Alex , Staskawicz Brian J.
Published: October 2018

Significance

Plants employ nucleotide-binding leucine-rich repeat (NLR) immune receptors to recognize pathogen effectors and to activate effector-triggered immunity (ETI). The Toll/IL-1 receptor-NLR (TNL) protein (Roq1) recognizes the effectors XopQ and HopQ1 in an Enhanced Disease Susceptibility 1 (EDS1)-dependent way in
Nicotiana benthamiana
. Interestingly, we found that the coiled-coil NLR protein N requirement gene 1 (NRG1) is required for activation of ETI by the TNLs Roq1 and Recognition of
Peronospora parasitica
1. NRG1 interacts with EDS1 and acts downstream of Roq1 and EDS1 to mediate XopQ/HopQ1-triggered ETI. In addition, Roq1, EDS1, and NRG1 mediate XopQ-triggered transcriptional changes in
N. benthamiana
and regulate resistance to
Xanthomonas
and
Pseudomonas
species that carry the effectors XopQ or HopQ1. This study suggests that NRG1 may be a conserved key component in TNL-mediated signaling pathways.
A critical review of research and practice in data-driven learning (DDL) in the academic writing classroom
Authors: Chen Meilin , Flowerdew John
Published: October 2018

Since the late 1980s, there has been a growing interest in the direct application of corpora, or data-driven learning (DDL), in language education. This relatively novel teaching approach has been particularly applied in the teaching and learning of English for Academic Purposes (EAP)/academic writing, especially since the turn of the century. This paper synthesizes and evaluates the research progress in the field of EAP/academic writing since the year 2000 by critically reviewing 37 empirical studies focussing on applications of DDL in this context. Based on the critical review and a discussion of some contentious issues, a set of five recommendations for the way forward in DDL research and practice for EAP/academic writing is presented.
A corpus-driven comparison of English and French Islamist extremist texts
Authors: Baker Paul , Vessey Rachelle
Published: October 2018

Using corpus linguistics and qualitative, manual discourse analysis, this paper compares English and French extremist texts to
determine how messages in different languages draw upon similar and distinct discursive themes and linguistic strategies. Findings
show that both corpora focus on religion and rewards (i.e. for faith) and strongly rely on othering strategies. However, the
English texts are concerned with world events whereas the French texts focus on issues specific to France. Also, while the English
texts use Arabic code-switching as a form of legitimation, the French texts use a formal register and quotation from scripture in
discussions of permissions, rights, obligations and laws. Finally, the English texts refer to and justify violence to a greater
extent than the French texts. This paper contributes to the field of terrorism studies and the field of corpus linguistics by
presenting a new approach to corpus-driven studies of discourse across more than one language.
Microtubule-severing enzymes: From cellular functions to molecular mechanism
Authors: McNally Francis J. , Roll-Mecak Antonina
Published: October 2018

Microtubule-severing enzymes generate internal breaks in microtubules. They are conserved in eukaryotes from ciliates to mammals, and their function is important in diverse cellular processes ranging from cilia biogenesis to cell division, phototropism, and neurogenesis. Their mutation leads to neurodegenerative and neurodevelopmental disorders in humans. All three known microtubule-severing enzymes, katanin, spastin, and fidgetin, are members of the meiotic subfamily of AAA ATPases that also includes VPS4, which disassembles ESCRTIII polymers. Despite their conservation and importance to cell physiology, the cellular and molecular mechanisms of action of microtubule-severing enzymes are not well understood. Here we review a subset of cellular processes that require microtubule-severing enzymes as well as recent advances in understanding their structure, biophysical mechanism, and regulation.
Dynein activator Hook1 is required for trafficking of BDNF-signaling endosomes in neurons
Authors: Olenick Mara A. , Dominguez Roberto , Holzbaur Erika L.F.
Published: October 2018

Axonal transport is required for neuronal development and survival. Transport from the axon to the soma is driven by the molecular motor cytoplasmic dynein, yet it remains unclear how dynein is spatially and temporally regulated. We find that the dynein effector Hook1 mediates transport of TrkB–BDNF-signaling endosomes in primary hippocampal neurons. Hook1 comigrates with a subpopulation of Rab5 endosomes positive for TrkB and BDNF, which exhibit processive retrograde motility with faster velocities than the overall Rab5 population. Knockdown of Hook1 significantly reduced the motility of BDNF-signaling endosomes without affecting the motility of other organelles. In microfluidic chambers, Hook1 depletion resulted in a significant decrease in the flux and processivity of BDNF-Qdots along the mid-axon, an effect specific for Hook1 but not Hook3. Hook1 depletion inhibited BDNF trafficking to the soma and blocked downstream BDNF- and TrkB-dependent signaling to the nucleus. Together, these studies support a model in which differential association with cargo-specific effectors efficiently regulates dynein in neurons.
Delta-secretase (AEP) mediates tau-splicing imbalance and accelerates cognitive decline in tauopathies
Authors: Wang Zhi-Hao , Liu Pai , Liu Xia , Yu Shan Ping , Wang Jian-Zhi , Ye Keqiang
Published: October 2018

SRPK2 is abnormally activated in tauopathies including Alzheimer’s disease (AD). SRPK2 is known to play an important role in pre–mRNA splicing by phosphorylating SR-splicing factors. Dysregulation of tau exon 10 pre–mRNA splicing causes pathological imbalances in 3R- and 4R-tau, leading to neurodegeneration; however, the role of SRPK2 in these processes remains unclear. Here we show that delta-secretase (also known as asparagine endopeptidase; AEP), which is activated in AD, cleaves SRPK2 and increases its nuclear translocation as well as kinase activity, augmenting exon 10 inclusion. Conversely, AEP-uncleavable SRPK2 N342A mutant increases exon 10 exclusion. Lentiviral expression of truncated SRPK2 increases 4R-tau isoforms and accelerates cognitive decline in htau mice. Uncleavable SRPK2 N342A expression improves synaptic functions and prevents spatial memory deficits in tau intronic mutant FTDP-17 transgenic mice. Hence, AEP mediates tau-splicing imbalance in tauopathies via cleaving SRPK2.
VarSome: the human genomic variant search engine
Authors: Kopanos Christos , Tsiolkas Vasilis , Kouris Alexandros , Chapple Charles E , Albarca Aguilera Monica , Meyer Richard , Massouras Andreas
Published: October 2018

VarSome.com is a search engine, aggregator and impact analysis tool for human genetic variation and a community-driven project aiming at sharing global expertise on human variants.

Availability and implementation

VarSome is freely available at http://varsome.com.

Supplementary information

Supplementary data are available at Bioinformatics online.
Long non-coding RNA LOC284454 promotes migration and invasion of nasopharyngeal carcinoma via modulating the Rho/Rac signaling pathway
Authors: Fan Chunmei , Tang Yanyan , Wang Jinpeng , Wang Yian , Xiong Fang , Zhang Shanshan , Li Xiayu , Xiang Bo , Wu Xu , Guo Can , Ma Jian , Zhou Ming , Li Xiaoling , Xiong Wei , Li Yong , Li Guiyuan , Zeng Zhaoyang
Published: October 2018

Nasopharyngeal carcinoma (NPC) is a unique malignant cancer with high metastasis. Because the early symptoms of NPC patients are not obvious, most patients have distant metastases when diagnosed, which makes treatment difficult. Long non-coding RNAs (lncRNAs) are emerging as important regulators in human carcinogenesis. LncRNAs have been increasingly identified but remain largely unknown in NPC. Therefore, we performed gene expression profiling to screen for altered expression of lncRNAs in NPC tissues and adjacent samples. One lncRNA, LOC284454, was upregulated and associated with poor prognosis in NPC. In in vivo and in vitro assays, LOC284454 promoted the migration and invasion capacity of NPC cells. Mass spectrometry combined with bioinformatics suggested that LOC284454 affected the cytoskeletal and adhesion-related Rho/Rac signaling pathways. LOC284454 may be a potential novel treatment target and is expected to be a new diagnostic and prognostic marker in patients with NPC.
Next-generation Diagnostics for Melioidosis: Evaluation of a Prototype i-STAT Cartridge to Detect Burkholderia pseudomallei Biomarkers
Authors: Schully Kevin L , Young Charles C , Mayo Mark , Connolly Amy L , Rigas Vanessa , Spall Ammarah , Chan Alyssa A , Salvador Mark G , Lawler James V , Opdyke Jason A , Clark Danielle V , Currie Bart J
Published: October 2018

Background

Infection with the gram-negative bacterium Burkholderia pseudomallei can result in melioidosis, a life-threatening disease that can be difficult to diagnose. Culture remains the gold standard for diagnosis but requires laboratory resources not available in many endemic regions. A lateral flow immunoassay has shown promise for POC diagnostics but suffers from low sensitivity when used on blood samples. PCR also has low sensitivity on blood, attributed to the low bacterial numbers in blood observed in melioidosis patients, even when bacteraemic.

Methods

A prototype i-STAT cartridge was developed to utilize the monoclonal antibody specific for the capsule of pathogenic Burkholderia species employed on the LFI. The resulting POC assay was evaluated on 414 clinical specimens from Darwin, Australia and Cambodia.

Results

The i-STAT assay accurately distinguished Australian blood culture positive melioidosis patients from Australian patients hospitalized with other infections (AUC = 0.91, 95% CI 0.817 - 1.0). We derived an assay cutoff with 76% sensitivity and 94% specificity that correctly classified 88% (n = 74) of the Australian patients. Interestingly, only 46% (6/13) of the culture-positive melioidosis patients in Cambodia were classified correctly. Of great importance however, the assay detected capsule from blood samples for 32% of blood culture negative melioidosis patients in both cohorts and previously undiagnosed melioidosis patients in Cambodia. In addition the assay showed high sensitivity and specificity for urine, pus and sputum.

Conclusions

Diagnostic tools that are not dependent upon the growth kinetics or the levels of bacteremia of B. pseudomallei represent the next-generation of diagnostics and must be pursued further.
The Atacama Cosmology Telescope: two-season ACTPol extragalactic point sources and their polarization properties
Authors: Datta Rahul , Aiola Simone , Choi Steve K , Devlin Mark , Dunkley Joanna , Dünner Rolando , Gallardo Patricio A , Gralla Megan , Halpern Mark , Hasselfield Matthew , Hilton Matt , Hincks Adam D , Ho Shuay-Pwu P , Hubmayr Johannes , Huffenberger Kevin M , Hughes John P , Kosowsky Arthur , López-Caraballo Carlos H , Louis Thibaut , Lungu Marius , Marriage Tobias , Maurin Loïc , McMahon Jeff , Moodley Kavilan , Naess Sigurd K , Nati Federico , Niemack Michael D , Page Lyman A , Partridge Bruce , Prince Heather , Staggs Suzanne T , Switzer Eric R , Wollack Edward J , Farren Gerrit
Published: October 2018

We report on measurements of the polarization of extragalactic sources at 148 GHz made during the first two seasons of the Atacama Cosmology Telescope Polarization (ACTPol) survey. The survey covered 680 deg2 of the sky on the celestial equator. Polarization measurements of 169 intensity-selected sources brighter than 30 mJy, that are predominantly active galactic nuclei, are presented. Above a total flux of 215 mJy where the noise bias removal in the polarization measurement is reliable, we detect 26 sources, 14 of which have a detection of linear polarization at greater than 3σ significance. The distribution of the fractional polarization as a function of total source intensity is analysed. Our result is consistent with the scenario that the fractional polarization of our measured radio source population is independent of total intensity down to the limits of our measurements and well described by a Gaussian distribution with a mean fractional polarization pm = 0.028 ± 0.005 and standard deviation $\sigma _{\mathrm{p_{m}}}$ = 0.054, truncated at p = 0. Extrapolating this model for the distribution of source polarization below the ACTPol detection threshold, we predict that one could get a clean measure of the E-mode polarization power spectrum of the microwave background out to $\ell \approx 6000$ with 1 $\mu$K-arcminute maps over ${10\!{\ \rm \%}}$ of the sky from a future survey. We also study the spectral energy distribution of the total and polarized source flux densities by cross-matching with low radio frequency catalogues. We do not find any correlation between the spectral indices for total flux and polarized flux.
The tight empirical relation between dark matter halo mass and flat rotation velocity for late-type galaxies
Authors: Katz Harley , Desmond Harry , McGaugh Stacy , Lelli Federico
Published: October 2018

We present a new empirical relation between galaxy dark matter halo mass (Mhalo) and the velocity along the flat portion of the rotation curve (Vflat), derived from 120 late-type galaxies from the SPARC data base. The orthogonal scatter in this relation is comparable to the observed scatter in the baryonic Tully–Fisher relation (BTFR), indicating a tight coupling between total halo mass and galaxy kinematics at r ≪ Rvir. The small vertical scatter in the relation makes it an extremely competitive estimator of total halo mass. We demonstrate that this conclusion holds true for different priors on M*/L[3.6$\mu$] that give a tight BTFR, but requires that the halo density profile follow DC14 rather than NFW. We provide additional relations between Mhalo and other velocity definitions at smaller galactic radii (i.e. V2.2, Veff, and Vmax) which can be useful for estimating halo masses from kinematic surveys, providing an alternative to abundance matching. Furthermore, we constrain the dark matter analogue of the radial acceleration relation and also find its scatter to be small, demonstrating the fine balance between baryons and dark matter in their contribution to galaxy kinematics.
Biased Policy Professionals
Authors: Banuri Sheheryar , Dercon Stefan , Gauri Varun
Published: October 2018

Although the decisions of policy professionals are often more consequential than those of individuals in their private capacity, there is a dearth of studies on the biases of policy professionals: those who prepare and implement policy on behalf of elected politicians. Experiments conducted on a novel subject pool of development policy professionals (public servants of the World Bank and the Department for International Development in the UK) show that policy professionals are indeed subject to decision-making traps, including the effects of framing outcomes as losses or gains, and, most strikingly, confirmation bias driven by ideological predisposition, despite having an explicit mission to promote evidence-informed and impartial decision making. These findings should worry policy professionals and their principals in governments and large organizations, as well as citizens themselves. A further experiment, in which policy professionals engage in discussion, shows that deliberation may be able to mitigate the effects of some of these biases.
Operative Strategies for Perforated Diverticulitis: A Systematic Review and Meta-analysis
Authors: Acuna Sergio A. , Wood Trevor , Chesney Tyler R. , Dossa Fahima , Wexner Steven D. , Quereshy Fayez A. , Chadi Sami A. , Baxter Nancy N.
Published: October 2018

BACKGROUND:

The traditional approach for perforated diverticulitis, the Hartmann procedure, has considerable morbidity and the challenge of stoma reversal. Alternative procedures, including primary resection and anastomosis and laparoscopic lavage, have been proposed but remain controversial.

OBJECTIVE:

The purpose of this study was to compare operative strategies for perforated diverticulitis.

DATA SOURCES:

MEDLINE, Embase, Cochrane Library, and the grey literature were searched from inception to October 2017.

STUDY SELECTION:

We included randomized clinical trials evaluating operative strategies for perforated diverticulitis.

INTERVENTIONS:

Hartmann procedure, primary resection and anastomosis, and laparoscopic lavage were included.

MAIN OUTCOME MEASURES:

Data were independently extracted by 2 investigators. Risk of bias was evaluated using the Cochrane risk-of-bias tool. Pooled risk ratios for major complications, reoperation, and mortality were determined using random-effects models.

RESULTS:

Six trials including 626 patients with perforated diverticulitis were identified. Laparoscopic lavage and sigmoidectomy had comparable rates of early reoperation and postoperative mortality; major complications (Clavien–Dindo >IIIa) were more frequent after laparoscopic lavage (RR = 1.68 (95% CI, 1.10–2.56); 3 trials, 305 patients). Comparing approaches for sigmoidectomy, primary resection and anastomosis had similar rates of major complications (RR = 0.88 (95% CI, 0.49–1.55); 3 trials, 255 patients) and postoperative mortality (RR = 0.58 (95% CI, 0.20–1.70); 3 trials, 254 patients) compared with the Hartmann procedure. However, patients who underwent primary resection and anastomosis were more likely to be stoma free at 12 months compared with the Hartmann procedure (RR = 1.40 (95% CI, 1.18–1.67); 4 trials, 283 patients) and to experience fewer major complications related to the stoma reversal procedure (RR = 0.26 (95% CI, 0.07–0.89); 4 trials, 186 patients).

LIMITATIONS:

There were no limitations to this study.

CONCLUSIONS:

Laparoscopic lavage is associated with increased risk of major complications versus primary resection for Hinchey III diverticulitis. The lower rate of stoma reversal and higher rate of complications after the Hartmann procedure suggest primary resection and anastomosis as the optimal management of perforated diverticulitis.
Factors Associated With Weight Intervention Participation Among People With Serious Mental Illness
Authors: Bennett Lauren L. , Cohen Amy N. , Young Alexander S.
Published: October 2018

Evidence-based practices effectively reduce weight in people with serious mental illness (SMI), yet participation is limited. Positive relationships between self-efficacy (SE), readiness to change (RtC), and subsequent participation in weight loss interventions have been demonstrated in the general population. The role of SE and RtC in predicting participation in individuals with SMI is explored. A total of 82 participants recruited from a county mental health clinic and a Veterans Affairs mental health clinic were randomly assigned to a weight management intervention or usual care. RtC and SE were assessed at baseline. Intervention participation rates were gathered. SE significantly correlated with intervention participation (p< 0.02). RtC did not predict significantly over and above SE. A linear combination of all measures was significantly related to participation (p< 0.05). To improve weight intervention participation by individuals with SMI, one direction may be to improve weight loss SE.
Obstetric Phenotypes in the Heterogeneity of Schizophrenia
Authors: Mezquida Gisela , Fernandez-Egea Emilio , Treen Devi , Mané Anna , Bergé Daniel , Savulich George , Garcia-Alvarez Leticia , García-Portilla Paz , Bobes Julio , Bernardo Miguel , Garcia-Rizo Clemente
Published: October 2018

Schizophrenia is a complex mental disorder with genetic and environmental components. Obstetric complications (OCs) are one of the most common environmental risk factors described. However, despite being different in timing and outcome, OCs are usually described as a homogeneous entity. In the present study, we evaluate the presence of different patterns of OCs evaluated with the Lewis-Murray Scale in chronic schizophrenia patients (n = 101) and their association with a crude marker of the intrauterine environment such as weight at birth.

OCs related with abnormal fetal growth (p < 0.001) and OCs during gestation (p = 0.003) were associated with lower birth weight. However, difficulties in delivery, complications in pregnancy, and OCs all together (as a set) were not associated with weight at birth.

Our results infer that OCs cannot be taken as a homogeneous group. Different patterns of OCs result in different birth weights, which is associated with specific metabolic, cognitive, and brain structure outcomes.