bluuebunny/crossref_metadata_2025 huggingface dataset:
New data-driven method of simulating coronal mass ejections
Authors: Liu Cheng’ao , Chen Tao , Zhao Xinhua
Published: May 2019

Context. Coronal mass ejections (CMEs) are large eruptions of plasma and magnetic field from the Sun’s corona. Understanding the evolution of the CME is important to evaluate its impact on space weather. Using numerical simulation, we are able to reproduce the occurrence and evolution process of the CME.

Aims. The aim of this paper is to provide a new data-driven method to mimic the coronal mass ejections. By using this method, we can investigate the phsical mechanisms of the flux rope formation and the cause of the CME eruption near the real background.

Methods. Starting from a potential magnetic field extrapolation, we have solved a full set of magnetohydrodynamic (MHD) equations by using the conservation element and solution element (CESE) numerical method. The bottom boundary is driven by the vector magnetograms obtained from SDO/HMI and vector velocity maps derived from DAVE4VM method.

Results. We present a three-dimensional numerical MHD data-driven model for the simulation of the CME that occurred on 2015 June 22 in the active region NOAA 12371. The numerical results show two elbow-shaped loops formed above the polarity inversion line (PIL), which is similar to the tether-cutting picture previously proposed. The temporal evolutions of magnetic flux show that the sunspots underwent cancellation and flux emergence. The signature of velocity field derived from the tracked magnetograms indicates the persistent shear and converging motions along the PIL. The simulation shows that two elbow-shaped loops were reconnected and formed an inverse S-shaped sigmoid, suggesting the occurrence of the tether-cutting reconnection, which was supported by observations of the Atmospheric Imaging Assembly (AIA) telescope. Analysis of the decline rate of the magnetic field indicates that the flux rope reached a region where the torus instability was triggered.

Conclusions. We conclude that the eruption of this CME was caused by multiple factors, such as photosphere motions, reconnection, and torus instability. Moreover, our simulation successfully reproduced the three-component structures of typical CMEs.
Convergence of the finite volume method on a Schwarzschild background
Authors: Dong Shijie , LeFloch Philippe G.
Published: May 2019

We introduce a class of nonlinear hyperbolic conservation laws on a Schwarzschild black hole background and derive several properties satisfied by (possibly weak) solutions. Next, we formulate a numerical approximation scheme which is based on the finite volume methodology and takes the curved geometry into account. An interesting feature of our model is that no boundary conditions is required at the black hole horizon boundary. We establish that this scheme converges to an entropy weak solution to the initial value problem and, in turn, our analysis also provides us with a theory of existence and stability for a new class of conservation laws.
Role of RF-amid Related Peptide-3 (RFRP-3) in Inhibitory Effect of Orexin A on Reproductive Function in the Animal Model of Male Wistar Rats
Authors: Hefshejanni Jafar Alipoor , Khazali Homayoun
Published: May 2019

Aims The aim of the present study is to examine the orexin A (OXA) signaling can leave any impact on the hypothalamic-pituitary-gonadal (HPG) axis and this impact can be relayed through the pathway of RF amide-related peptide-3 (RFRP-3, the mammalian ortholog of the avian gonadotropin-inhibitory hormone)/G-protein coupled receptor (GPR)-147 (RFRP-3 receptor) as a novel target for controlling of HPG axis in the male rats.

Materials and Methods Male rats were categorized randomly into experimental groups including control vehicle, OXA, and its antagonists’ group and went through to surgical cannulation into the third ventricle. After the intracerebroventricular injection of each solution, blood samples were collected for measurements of the LH and testosterone using radioimmunoassay method. Hypothalamus of the animals were isolated for analysis of the relative expression of Rfrp-3/Gpr-147 along with Gnrh gene by Real time-PCR. Also, in the different cohort of animal sexual behavior test was done.

Results It was shown that OXA significantly decreases the mean serum level of the LH and testosterone and, at the same time, its antagonists neutralize this impact. Moreover, we demonstrated that OXA has reduced the hypothalamic gene expression of Gnrh and increased the expression of Rfrp-3 and Gpr-147 genes. While OXA antagonists neutralize this impact.

Conclusions The results of this study are related to the impact of orexin on the HPG axis. It is recommended that RFRP-3/GPR-147 system as the interneural pathway relay the data of orexin to the neurons of GnRH.
Stellenwert der Digitalisierung im urologischen Alltag
Authors: Salem Johannes , Struck Julian Peter
Published: May 2019

Kaum eine andere digitale Technologie hat die Gesellschaft so geprägt und verändert wie das Internet. Kulturell wird die Bedeutung mit der Einführung des Buchdruckes verglichen. Im Jahr 2018 hatten über 4 Milliarden Menschen Zugang zum Internet. Etwa 80 % der Internetnutzer suchen nach Gesundheitsinformationen, am häufigsten über Krebserkrankungen. Patienten schätzen das Internet als hilfreiche Informationsmöglichkeit ein. Es existieren über 2,6 Milliarden aktive Nutzer von Sozialen Medien. Unter deutschen urologischen Weiterbildungsassistenten nutzen 97 % Soziale Medien privat oder beruflich. Insbesondere für uroonkologische Themen besteht ein großes Potential, mittels Digitalisierung die Gesundheitskompetenz der Patienten zu fördern und zur Optimierung der Patientenversorgung beizutragen. Zusammenfassend birgt die Digitalisierung ein immenses Potential für die Urologie.
Ag(I)-Mediated Oxidative Radical Triﬂuoromethylthiolation of Alkenes
Authors: Zheng Changge , Liu Yang , Hong Jianquan , Huang Shuai , Zhang Wei , Yang Yupeng , Fang Ge
Published: May 2019

A simple, mild, and efficient method for an oxidative radical triﬂuoromethylthiolation of alkenes through AgSCF3/K2S2O8 system has been developed. This reaction provides a straightforward way to synthesize a variety of useful α-SCF3-substituted ketone compounds from a wide range of alkenes in moderate to good yields.
The Catalytic Asymmetric Construction of Trifluoromethylated Quaternary Carbon-Containing Thiochromans
Authors: Chen Hui , Wang Cui , Wen Dongwa , Deng Yabo , Liu Xin , Liu Xueting , Zhang Jiang , Yan Wenjin
Published: May 2019

Trifluoromethylated chiral quaternary stereogenic carbon center at 2-position of thiochromans has been constructed through organocatalyzed Michael-aldol reaction. With quinine squaramide as catalyst, the reaction of 2-mercaptobenzaldehyde with β-aryl-β-CF3 enones or β-alkyl-β-CF3 enones gave 2-CF3-thiochromans bearing three contiguous stereogenic centers in good to excellent diastereoselectivities, enantioselectivities, and yields.
A Simple Method for the Preparation of Stainless and Highly Pure Trichloroacetimidates
Authors: Ikeuchi Kazutada , Murasawa Kentaro , Yamada Hidetoshi
Published: May 2019

We describe a method for obtaining various allylic, benzylic, and glucosyl 2,2,2-trichloroacetimidates (TCAIs) as stainless liquids or solids at the crude stage. The general synthetic method for the preparation of TCAIs often leads to stained products, and further purification of crude TCAIs causes decomposition due to their instability. In the described method, we use a solvent that barely dissolves the reactant, providing stainless and sufficiently pure TCAIs without requiring a purification step. Furthermore, the reaction mixture is turbid at the beginning and clear at the end, allowing us to monitor the progress of the reaction visually.
Synthesis of N-Pyridyl Hydroxylamines via Copper-Catalyzed Cross-Coupling
Authors: Torruellas Carilyn , Hsu Fu-Lian , Walz Andrew J.
Published: May 2019

N-Pyridyl hydroxylamine derivatives were prepared via copper-catalyzed cross-coupling of orthogonally functionalized hydroxylamines with iodopyridines. Various amino- and hydroxyl-protecting groups were tolerated. A total of 20 examples were synthesized in 28–90% yield.
Impact of Intermittent Functional Internal Iliac Artery Occlusion on Spinal Cord Blood Supply during TEVAR
Authors: Maier Sven , Morlock Julia , Benk Christoph , Kari Fabian Alexander , Siepe Matthias , Beyersdorf Friedhelm , Czerny Martin , Rylski Bartosz
Published: May 2019

Background Measuring transcranial motor evoked potentials (EPs) and somatosensory EPs is a well-established method to assess spinal cord function during thoracic endovascular aortic repair (TEVAR). Functional occlusion of one or both internal iliac arteries by large bore sheaths during TEVAR can cause unilateral intermittently EP loss.

Methods Between 2006 and 2016, 194 patients underwent TEVAR entailing EP monitoring. The ISIS IOM System (Inomed Medizintechnik GmbH, Emmendingen, Germany) was employed in all patients. EPs were recorded after inducing anesthesia, during the procedure, and before discontinuing anesthesia.

Results We observed a unilateral intermittently EP decrease or loss in 12 (6.2%) patients. Most events were ipsilateral (9 of 12). The underlying pathologies were descending aortic aneurysm in six patients and type B dissection in six patients. An evoked-potential decrease or loss was always associated with the insertion of large bore stent-graft-introducing sheaths. The median duration of the unilaterally EP decrease or loss was 16 (10; 31) minutes (range, 2–77 minutes) with baseline values re-established at the end of the procedure after sheath removal in all cases. No patient developed irreversible symptomatic spinal cord ischemia.

Conclusion A functional occlusion of internal iliac arteries via large bore TEVAR-introducing sheaths is associated with a unilateral intermittent decrease in or loss of EPs returning to baseline after sheath removal. This observation highlights the importance of the internal iliac arteries as one of the major spinal cord's blood supply territories, and may serve as a stimulus to reduce the duration of sheath indwelling to a minimum.
The v2 = 1, 2 and v4 = 1 bending states of 15NH3 and their analysis at experimental accuracy
Authors: Canè E. , Di Lonardo G. , Fusina L. , Tamassia F. , Predoi-Cross A.
Published: May 2019

15NH3 is the object of extensive investigation due to the central role of ammonia in astronomical sciences and to the complexity of modeling its interacting vibrationally excited states. Of major interest in astrochemistry is the determination of the 14N/15N ratio in space, characterized by unexpected variability among different solar system objects and reservoirs. Recently, the spectroscopic analysis of ground and v2 = 1 a, s states of 15NH3 has been completed at experimental accuracy. Here, the characterization of the a, s inversion symmetry levels of v2 = 1, 2 and v4 = 1 states is presented. New spectra of 15NH3 have been recorded from 325 to 2000 cm−1 at a resolution ranging from 0.00096 cm−1 to 0.003 cm−1, using the Canadian Light Source synchrotron at CLS. 7518 transitions covering nine bands, ν2, 2ν2, ν4, 2ν2 ← ν2, ν4 ← ν2, 2ν2 ↔ ν4 and the inversion-rotation transitions in the excited states, have been fitted simultaneously. The effective Hamiltonian adopted includes all symmetry allowed interactions between and within the studied excited states, according to the most recent results on ammonia. The transitions have been reproduced at experimental accuracy using 185 spectroscopic parameters, determined with high precision. The leading diagonal parameters, Gv, B, C, D’s, compare well with those of 14NH3. The wavenumbers of the assigned transitions are compared with their theoretically predicted values. An improved set of ground state parameters is also derived. These results noticeably improve the wavenumber line list in the high-resolution transmission molecular absorption (HITRAN) database.
Whole genome amplification of single epithelial cells dissociated from snap-frozen tissue samples in microfluidic platform
Authors: Liu Yuguang , Yao Janet , Walther-Antonio Marina
Published: May 2019

Single cell sequencing is a technology capable of analyzing the genome of a single cell within a population. This technology is mostly integrated with microfluidics for precise cell manipulation and fluid handling. So far, most of the microfluidic-based single cell genomic studies have been focused on lab-cultured species or cell lines that are relatively easy to handle following standard microfluidic-based protocols without additional adjustments. The major challenges for performing single cell sequencing on clinical samples is the complex nature of the samples which requires additional sample processing steps to obtain intact single cells of interest without using amplification-inhibitive agents. Fluorescent-activated cell sorting is a common option to obtain single cells from clinical samples for single cell applications but requires >100 000 viable cells in suspension and the need for specialized laboratory and personnel. In this work, we present a protocol that can be used to obtain intact epithelial cells from snap-frozen postsurgical human endometrial tissues for single cell whole genome amplification. Our protocol includes sample thawing, cell dissociation, and labeling for genome amplification of targeted cells. Between 80% and 100% of single cell replicates lead to >25 ng of DNA after amplification with no measurable contamination, sufficient for downstream sequencing.
Ions’ motion in water
Authors: Banerjee Puja , Bagchi Biman
Published: May 2019

Over the decades, a great deal of attention has been focused on the solvation and transport properties of small rigid monatomic ions such as Na+, K+, Li+, Cl−, and Br− due to their importance in physical chemistry. Much less attention has been devoted to polyatomic ions although many polyatomic ions (such as nitrate, acetate, sulfate, and ammonium) are of great importance in biological and chemical processes. While the translational diffusion of smaller rigid ions shows the remarkable nonmonotonic dependence on inverse ion size (known as the “breakdown of Walden product”), the intermediate- to large-sized polyatomic ions (such as nitrate, acetate, and sulfate) exhibit different anomalies pointed out only recently. In this Perspective article, we provide an overview of how rotational diffusion and translational diffusion of these ions themselves are coupled to translational and rotational motions of water molecules. We discuss how diffusion of polyatomic ions is different from that of monatomic ions due to the rotational self-motion of the former that enhances diffusion in specific cases because of symmetry. While a continuum hydrodynamic model fails to describe the motion of polyatomic ions, we discuss how a mode-coupling theory approach can capture many aspects of this coupling between the solute ion and solvent water. We discuss how ionic mobility in water and other dipolar solvents are intimately connected to the dipolar solvation dynamics, in particular to its ultrafast component. We point out how the usual thinking on the relation between the diffusion and entropy needs to be modified in the case of ion diffusion.
Terahertz quantum cascade laser with non-resonant extraction
Authors: Baranov A. N. , Nguyen-Van H. , Loghmari Z. , Bahriz M. , Teissier R.
Published: May 2019

In order to improve the maximum operating temperature of THz quantum cascade lasers (QCLs) we propose to modify the three well resonant phonon design by increasing the energy of the separation between the bottom transition levels and the ground states, which is usually adjusted to the LO-phonon energy in GaAs. The fabricated devices based on this design with non-resonant depopulation of the bottom transition level operated in pulsed mode up to 190K, which is the best-reported performance for THz QCLs with Al0.15Ga0.85As barriers based on an Au-Au double-metal waveguide. The performed analysis showed that the achieved improvement could be explained by the proposed design modification.
Generation of field-emitting surface dielectric barrier discharges in Ar and N2
Authors: Kanno Moriyuki , Tanaka Ryo , Stauss Sven , Ito Tsuyohito , Terashima Kazuo
Published: May 2019

Field-emitting modes of surface dielectric barrier discharges (DBDs) have been generated thus far only in high-pressure CO2, including its liquid and supercritical phases, and in silicone oil. In this study, a generalized discussion with a one-dimensional Townsend-based theory is proposed to predict the accessibility of the field-emitting mode in various media. The field-emitting modes of surface DBDs are demonstrated experimentally in high-density Ar and N2 using Fowler–Nordheim coordinates and image observations.
Blocker escape kinetics from a membrane channel analyzed by mapping blocker diffusive dynamics onto a two-site model
Authors: Berezhkovskii Alexander M. , Bezrukov Sergey M.
Published: May 2019

When a large solute molecule enters a membrane channel from the membrane-bathing electrolyte solution, it blocks the small-ion current flowing through the channel. If the molecule spends in the channel sufficiently long time, individual blockades can be resolved in single-channel experiments. In this paper, we develop an analytical theory of the blocker escape kinetics from the channel, assuming that a charged blocking molecule cannot pass through a constriction region (bottleneck). We focus on the effect of the external voltage bias on the blocker survival probability in the channel. The bias creates a potential well for the charged blocker in the channel with the minimum located near the bottleneck. When the bias is strong, the well is deep, and escape from the channel is a slow process that allows for time-resolved observation of individual blocking events. Our analysis is performed in the framework of a two-site model of the blocker dynamics in the channel. Importantly, the rate constants, fully determining this model, are derived from a more realistic continuum diffusion model. This is done by mapping the latter onto its two-site counterpart which, while being much simpler, captures the main features of the blocker escape kinetics at high biases.
Layered structure around an extended gliding discharge column in a methane-nitrogen mixture at high pressure
Authors: Kong Chengdong , Gao Jinlong , Li Zhongshan , Aldén Marcus , Ehn Andreas
Published: May 2019

The current work aims at investigating the detailed spatial structure of the thin plasma column of a gliding arc (GA) discharge extended in N2-CH4 gas mixtures, using visualization techniques. The GA discharge was operated at up to 5 atm in a high-pressure vessel with extensive optical access. The results show that the emission intensity from the plasma column increased tenfold with the addition of 0.1% CH4 in nitrogen, compared to that in pure N2. Furthermore, an additional layer located around the GA discharge column is detected. Imaging through spectral filters and spectral analysis of the emitted signal indicate that the emissions of this outer layer are mostly from the CN A-X and CH A-X transitions. This outer layer can propagate and extinguish dynamically, similar to the flame front in combustion. Besides, the separation of this outer layer to the plasma core decreases with pressure. The layered structure and its dynamical behaviors can be explained by a plasma-sustained radical propagation mechanism. The high-power plasma column can produce a high-temperature zone with rich atomic species, surrounded by the relatively cold N2-CH4 mixture. At the mixing layer between the high-temperature zone and the N2-CH4 mixture, some highly exothermic reactions occur to produce excited CN and CH species, which emit their specific spectra. As the high-temperature zone expands with time, the outer layer propagates outward. However, with the propagation continuing, the radical species involved in the outer layer formation are rapidly consumed, and thus, this layer disappears when it propagates too far away from the plasma column.
Effect of non-hydrostatic stress on the structure and elasticity of NaCl by first-principles calculation
Authors: Liu Lei , Yang Longxing , Yi Li , Liu Hong
Published: May 2019

Non-hydrostatic stresses have a unique influence on materials. To understand the effect of non-hydrostatic stress on NaCl, one of the most widely used pressure calibrant in high-pressure experiments, the lattice constants, density, elastic modulus, Young’s modulus, and phase transitions of the B1 and B2 phases of NaCl were calculated under hydrostatic and non-hydrostatic stresses. The effects of non-hydrostatic stresses on the lattice constants and Young’s modulus show the Poisson effect. The effect of non-hydrostatic stresses on lattice constants increases linearly with increasing differential stress, however, these effects decrease with increasing pressure. Non-hydrostatic stresses explored in this study have no effect on the density (the equation of state), elastic modulus, and phase-equilibrium pressure of the B1 and B2 phases of NaCl). Therefore, non-hydrostatic stresses do not affect the NaCl acting as a pressure scale to indicate pressure values in high-pressure experiments, but it may not accurately reflect the state of stress. The state of non-hydrostatic stress is complex in high-pressure experiments, but we only considered one non-hydrostatic state in this study; thus, more work is needed to clarify the effect of non-hydrostatic stress.
Immersed in the source text
Authors: Naranjo Sánchez Beatriz
Published: May 2019

This study aims at exploring the phenomenon of psychological transportation in translation from an experimental approach. Firstly, we investigate whether the emotions depicted in source texts may influence the level of transportation experienced by translators. Secondly, we try to determine whether different levels of transportation in the texts can make a difference in terms of translation performance. Based on previous work about narrative transportation in products of fiction, as well as the phenomenon known as the “paradox of pleasurable sadness”, we depart from the hypothesis that sad texts lead to a higher degree of psychological transportation than happy texts (H1). Taking into account previous theories and empirical results about the benefits of visualization and emotional engagement in translation, we also predict that highly-transported participants will render higher-quality (H2) and more creative translations (H3) than low-transported participants. For this purpose, a pilot study was conducted consisting of two literary translation tasks with opposing-valence texts (happy vs. sad). Lack of statistically significant differences for our hypothesis suggests that some adjustments in the methodology would be needed to achieve conclusive results; however, we believe that further research on the impact of transportation in translation quality and creativity is still worthwhile.
Rab46 integrates Ca2+ and histamine signaling to regulate selective cargo release from Weibel-Palade bodies
Authors: Miteva Katarina T. , Pedicini Lucia , Wilson Lesley A. , Jayasinghe Izzy , Slip Raphael G. , Marszalek Katarzyna , Gaunt Hannah J. , Bartoli Fiona , Deivasigamani Shruthi , Sobradillo Diego , Beech David J. , McKeown Lynn
Published: May 2019

Endothelial cells selectively release cargo stored in Weibel-Palade bodies (WPBs) to regulate vascular function, but the underlying mechanisms are poorly understood. Here we show that histamine evokes the release of the proinflammatory ligand, P-selectin, while diverting WPBs carrying non-inflammatory cargo away from the plasma membrane to the microtubule organizing center. This differential trafficking is dependent on Rab46 (CRACR2A), a newly identified Ca2+-sensing GTPase, which localizes to a subset of P-selectin–negative WPBs. After acute stimulation of the H1 receptor, GTP-bound Rab46 evokes dynein-dependent retrograde transport of a subset of WPBs along microtubules. Upon continued histamine stimulation, Rab46 senses localized elevations of intracellular calcium and evokes dispersal of microtubule organizing center–clustered WPBs. These data demonstrate for the first time that a Rab GTPase, Rab46, integrates G protein and Ca2+ signals to couple on-demand histamine signals to selective WPB trafficking.
A balancing act: PHLPP2 fine tunes AKT activity and MYC stability in prostate cancer
Authors: Toivanen Roxanne , Furic Luc
Published: May 2019

PTEN loss stimulates prostate tumor progression by sustaining AKT activation. Nowak et al. (2019. J. Cell Biol. https://doi.org/10.1083/jcb.201902048) surprisingly show that the AKT-suppressing phosphatase PHLPP2 promotes disease progression in the context of dual PTEN and p53 loss by increasing MYC stability.
Diarrhea Among Residents of Long-Term Care Facilities
Authors: Bennett Richard G.
Published: May 2019

Both sporadic cases of diarrhea and outbreaks of infectious gastroenteritis occur commonly in long-term care facilities. There are no national statistics on the prevalence or incidence of diarrhea among residents of nursing homes, but recent studies from the Centers for Disease Control and Prevention have described the increased morbidity and mortality associated with gastrointestinal illnesses among the elderly. Although deaths related to diarrheal illnesses have long been considered a problem of infants and young children in the developed world, 51% of the 28,538 diarrhea-related deaths in the United States from 1979 through 1987 occurred in adults older than 74 years, and 27% occurred in adults between 55 and 74 years old. In contrast, only 11% of these deaths occurred in children <5 years old (ie, the vast majority of deaths occurred in older Americans rather than in children). For both the very young and the very old, there were winter peaks in the mortality rates consistent with the presumption that infectious illnesses led to death, and one of the major risk factors for dying from diarrhea was being a resident of a nursing home. In a subsequent study in which 87,181 hospitalizations were analyzed, 85% of 514 diarrhea-related deaths occurred in adults over 65 years old. The odds ratio of dying during a hospitalization involving gastroenteritis was 52.6 (CI95, 37.0 to 76.9) for adults ≥70 years old as compared with children <5 years old.
Beltrami-net: domain-independent deep D-bar learning for absolute imaging with electrical impedance tomography (a-EIT)
Authors: Hamilton S J , Hänninen A , Hauptmann A , Kolehmainen V
Published: May 2019

Objective: To develop, and demonstrate the feasibility of, a novel image reconstruction method for absolute electrical impedance tomography (a-EIT) that pairs deep learning techniques with real-time robust D-bar methods and examine the influence of prior information on the reconstruction.Approach: A D-bar method is paired with a trained convolutional neural network (CNN) as a post-processing step. Training data is simulated for the network using no knowledge of the boundary shape by using an associated nonphysical Beltrami equation rather than simulating the traditional current and voltage data specific to a given domain. This allows the training data to be boundary shape independent. The method is tested on experimental data from two EIT systems (ACT4 and KIT4) with separate training sets of varying prior information.Main results: Post-processing the D-bar images with a CNN produces significant improvements in image quality measured by structural SIMilarity indices (SSIMs) as well as relativeandimage errors.Significance: This work demonstrates that more general networks can be trained without being specific about boundary shape, a key challenge in EIT image reconstruction. The work is promising for future studies involving databases of anatomical atlases.
SYZ transforms for immersed Lagrangian multisections
Authors: Chan Kwokwai , Suen Yat-Hin
Published: May 2019

In this paper, we study the geometry of the SYZ transform on a semiflat Lagrangian torus fibration. Our starting point is an investigation on the relation between Lagrangian surgery of a pair of straight lines in a symplectic 2-torus and the extension of holomorphic vector bundles over the mirror elliptic curve, via the SYZ transform for immersed Lagrangian multisections defined by Arinkin and Joyce [Fukaya category and Fourier transform, AMS/IP Stud. Adv. Math., Amer. Math. Soc., Providence, RI, 2001] and Leung, Yau, and Zaslow [Adv. Theor. Math. Phys. 4 (2000), no. 6, 1319–1341]. This study leads us to a new notion of equivalence between objects in the immersed Fukaya category of a general compact symplectic manifold

(
M
,
ω
)

(M, \omega )

, under which the immersed Floer cohomology is invariant; in particular, this provides an answer to a question of Akaho and Joyce [J. Differential Geom. 86 (2010), no. 3, 831–500, Question 13.15]. Furthermore, if

M
M

admits a Lagrangian torus fibration over an integral affine manifold, we prove, under some additional assumptions, that this new equivalence is mirror to an isomorphism between holomorphic vector bundles over the dual torus fibration via the SYZ transform.
Clathrin and clathrin adaptor AP-1 control apical trafficking of megalin in the biosynthetic and recycling routes
Authors: Gravotta Diego , Perez Bay Andres , Jonker Caspar T. H. , Zager Patrick J. , Benedicto Ignacio , Schreiner Ryan , Caceres Paulo S. , Rodriguez-Boulan Enrique
Published: May 2019

Megalin (gp330, LRP-2) is a protein structurally related to the low-density lipoprotein receptor family that displays a large luminal domain with multiligand binding properties. Megalin localizes to the apical surface of multiple epithelia, where it participates in endocytosis of a variety of ligands performing roles important for development or homeostasis. We recently described the apical recycling pathway of megalin in Madin–Darby canine kidney (MDCK) cells and found that it is a long-lived, fast recycling receptor with a recycling turnover of 15 min and a half-life of 4.8 h. Previous work implicated clathrin and clathrin adaptors in the polarized trafficking of fast recycling basolateral receptors. Hence, here we study the role of clathrin and clathrin adaptors in megalin’s apical localization and trafficking. Targeted silencing of clathrin or the γ1 subunit of clathrin adaptor AP-1 by RNA interference in MDCK cells disrupted apical localization of megalin, causing its redistribution to the basolateral membrane. In contrast, silencing of the γ2 subunit of AP-1 had no effect on megalin polarity. Trafficking assays we developed using FM4-HA-miniMegalin-GFP, a reversible conditional endoplasmic reticulum–retained chimera, revealed that clathrin and AP-1 silencing disrupted apical sorting of megalin in both biosynthetic and recycling routes. Our experiments demonstrate that clathrin and AP-1 control the sorting of an apical transmembrane protein.
Closing the gap between formats for storing layout information in systems biology
Authors: Hoksza David , Gawron Piotr , Ostaszewski Marek , Hasenauer Jan , Schneider Reinhard
Published: May 2019

The understanding of complex biological networks often relies on both a dedicated layout and a topology. Currently, there are three major competing layout-aware systems biology formats, but there are no software tools or software libraries supporting all of them. This complicates the management of molecular network layouts and hinders their reuse and extension. In this paper, we present a high-level overview of the layout formats in systems biology, focusing on their commonalities and differences, review their support in existing software tools, libraries and repositories and finally introduce a new conversion module within the MINERVA platform. The module is available via a REST API and offers, besides the ability to convert between layout-aware systems biology formats, the possibility to export layouts into several graphical formats. The module enables conversion of very large networks with thousands of elements, such as disease maps or metabolic reconstructions, rendering it widely applicable in systems biology.
AlphaFold at CASP13
Authors: AlQuraishi Mohammed
Published: May 2019

Summary: Computational prediction of protein structure from sequence is broadly viewed as a foundational problem of biochemistry and one of the most difficult challenges in bioinformatics. Once every two years the Critical Assessment of protein Structure Prediction (CASP) experiments are held to assess the state of the art in the field in a blind fashion, by presenting predictor groups with protein sequences whose structures have been solved but have not yet been made publicly available. The first CASP was organized in 1994, and the latest, CASP13, took place last December, when for the first time the industrial laboratory DeepMind entered the competition. DeepMind's entry, AlphaFold, placed first in the Free Modeling (FM) category, which assesses methods on their ability to predict novel protein folds (the Zhang group placed first in the Template-Based Modeling (TBM) category, which assess methods on predicting proteins whose folds are related to ones already in the Protein Data Bank.) DeepMind's success generated significant public interest. Their approach builds on two ideas developed in the academic community during the preceding decade: (i) the use of co-evolutionary analysis to map residue co-variation in protein sequence to physical contact in protein structure, and (ii) the application of deep neural networks to robustly identify patterns in protein sequence and co-evolutionary couplings and convert them into contact maps. In this Letter, we contextualize the significance of DeepMind's entry within the broader history of CASP, relate AlphaFold's methodological advances to prior work, and speculate on the future of this important problem.
Disordered Punishment: Workaround Technologies of Criminal Records Disclosure and the Rise of a New Penal Entrepreneurialism
Authors: Corda Alessandro , Lageson Sarah E
Published: May 2019

The privatization of punishment is a well-established phenomenon in modern criminal justice operations. Less understood are the market and technological forces that have dramatically reshaped the creation and sharing of criminal record data in recent years. Analysing trends in both the United States and Europe, we argue that this massive shift is cause to reconceptualize theories of penal entrepreneurialism to more directly address the role of technology and commercial interests. Criminal records, or proxies for them, are now actively produced and managed by third parties via corporate decision-making processes, rather than government dictating boundaries or outsourcing duties to private actors. This has led to what we term ‘disordered punishment’, imposed unevenly and inconsistently across multiple platforms, increasingly difficult for both government and individuals to control.
Putting Coercive Control into Practice: Problems and Possibilities
Authors: Barlow Charlotte , Johnson Kelly , Walklate Sandra , Humphreys Les
Published: May 2019

There is growing international interest in translating Stark’s concept of coercive control into criminal justice policy and practice. In December 2015 an offence of coercive control was introduced in England and Wales. This paper offers an empirical investigation of the problems and possibilities associated with the translation of this offence into practice in one police force area in England. The findings offer some scope for optimism in response to patterns of abuse, but they also support the view that the current gender-neutral version of the legislation requires revision; there is a need for greater resourcing and training to improve understandings of the nature and impact of coercive control at all points of contact within the criminal justice process and finally, it remains the case that effective responses to domestic abuse need to be genuinely holistic.
Inter-Individual Differences in Striatal Connectivity Is Related to Executive Function Through Fronto-Parietal Connectivity
Authors: Darki Fahimeh , Sauce Bruno , Klingberg Torkel ,   for the Pediatric Imaging, Neurocognition, and Genetics Study
Published: May 2019

The striatum has long been associated with cognitive functions, but the mechanisms behind this are still unclear. Here we tested a new hypothesis that the striatum contributes to executive function (EF) by strengthening cortico-cortical connections. Striatal connectivity was evaluated by measuring the resting-state functional connectivity between ventral and dorsal striatum in 570 individuals, aged 3–20 years. Using structural equation modeling, we found that inter-individual differences in striatal connectivity had an indirect effect (via fronto-parietal functional connectivity) and a direct effect on a compound EF measure of working memory, inhibition, and set-shifting/flexibility. The effect of fronto-parietal connectivity on cognition did not depend on age: the influence was as strong in older as younger children. In contrast, striatal connectivity was closely related to changes in cognitive ability during childhood development, suggesting a specific role of the striatum in cognitive plasticity. These results support a new principle for striatal functioning, according to which striatum promotes cognitive development by strengthening of cortico-cortical connectivity.
Antibiotic Prescribing and Respiratory Viral Testing for Acute Upper Respiratory Infections Among Adult Patients at an Ambulatory Cancer Center
Authors: Krantz Elizabeth M , Zier Jacqlynn , Stohs Erica , Ogimi Chikara , Sweet Ania , Marquis Sara , Klaassen John , Pergam Steven A , Liu Catherine
Published: May 2019

Background

Outpatient antibiotic prescribing for acute upper respiratory infections (URIs) is a high-priority target for antimicrobial stewardship that has not been described for cancer patients.

Methods

We conducted a retrospective cohort study of adult patients at an ambulatory cancer center with URI diagnoses from 1 October 2015 to 30 September 2016. We obtained antimicrobial prescribing, respiratory viral testing, and other clinical data at first encounter for the URI through day 14. We used generalized estimating equations to test associations of baseline factors with antibiotic prescribing.

Results

Of 341 charts reviewed, 251 (74%) patients were eligible for analysis. Nearly one-third (32%) of patients were prescribed antibiotics for URIs. Respiratory viruses were detected among 85 (75%) of 113 patients tested. Antibiotic prescribing (P = .001) and viral testing (P < .001) varied by clinical service. Sputum production or chest congestion was associated with higher risk of antibiotic prescribing (relative risk [RR], 2.3; 95% confidence interval [CI], 1.4–3.8; P < .001). Viral testing on day 0 was associated with lower risk of antibiotic prescribing (RR, 0.4; 95% CI 0.2–0.8; P = .01), though collinearity between viral testing and clinical service limited our ability to separate these effects on prescribing.

Conclusions

Nearly one-third of hematology–oncology outpatients were prescribed antibiotics for URIs, despite viral etiologies identified among 75% of those tested. Antibiotic prescribing was significantly lower among patients who received an initial respiratory viral test. The role of viral testing in antibiotic prescribing for URIs in outpatient oncology settings merits further study.
Targeting the highly abundant circular RNA circSlc8a1 in cardiomyocytes attenuates pressure overload induced hypertrophy
Authors: Lim Tingsen Benson , Aliwarga Edita , Luu Tuan Danh Anh , Li Yiqing Peter , Ng Shi Ling , Annadoray Lavenniah , Sian Stephanie , Ackers-Johnson Matthew Andrew , Foo Roger Sik-Yin
Published: May 2019

Aims

We and others have previously described the expression landscape of circular RNA (circRNA) in mouse and human hearts. However, the functional relevance of many of these abundantly expressed cardiomyocyte circRNA remains to be fully explored. Among the most abundant circRNA, one stems from the sodium-calcium exchanger gene, Slc8a1, exon 2 locus. Because of its very high abundance in cardiomyocytes we investigated the possible role of circSlc8a1 in the heart.

Methods and results

We performed a miRNA screen using an array of 752 miRNAs with RNA recovered from a pull-down of endogenous cardiomyocyte circSlc8a1. MicroRNA-133a (miR-133a), with a prior well-recognized role in cardiac hypertrophy, was highly enriched in the fraction of circSlc8a1 pull-down (adjusted P-value < 0.001). We, therefore, followed-up validation of the functional interaction between circSlc8a1 and miR-133 using luciferase assays and reciprocal pull-down assays. In vivo, AAV9-mediated RNAi knockdown of circSlc8a1 attenuates cardiac hypertrophy from pressure-overload, whereas forced cardiomyocyte specific overexpression of circSlc8a1 resulted in heart failure. Molecular analyses showed targets of miR-133a including serum response factor (Srf), connective tissue growth factor (Ctgf), adrenoceptor beta 1 (Adrb1), and adenylate cyclase 6 (Adcy6) to be regulated by circSlc8a1-directed intervention of knockdown and overexpression.

Conclusion

In summary, circSlc8a1 can function as an endogenous sponge for miR-133a in cardiomyocytes. We propose that circSlc8a1 may serve as a novel therapeutic target for cardiac hypertrophy.
Phenology, Distribution, and Diversity of Dung Beetles (Coleoptera: Scarabaeidae) in North Florida’s Pastures and Forests
Authors: Conover Derrick , Dubeux Jose , Martini Xavier
Published: May 2019

Dung beetles are important to ecosystems as they aid in nutrient recycling and waste removal. In North Florida, there is a high diversity of dung beetles due to the intentional and accidental introduction of non-native species. Understanding patterns and processes on local scales is important for conservational planning. The aim of this study was to evaluate how dung beetle communities respond to different dung sources, forage composition, and habitat types. We surveyed for the presence and distribution of dung beetles in an open field and forest as well as in three types of pasture forage designs. In the first experiment, four transects with pitfall traps from forest to open field were established with either horse, pig, or cow feces bait. In the second experiment, three cattle grazing systems with different forage species were tested with only cow feces. In the first experiment, 16 species were identified between the field and forest sites including native and exotic species. Although the dung type had little effect on beetle distribution, a significantly different distribution of dung beetles between the field and forest was observed. Only one species, Onthophagus hecate Panzer (Coleoptera: Scarabaeidae) showed no preference between open field and forest habitat. During this second experiment, no difference in dung beetle distribution was found between the three types of pasture assemblages. This study supports habitat type as a driver of interspecies distribution and diversity of dung beetles in North Florida.
A new model of literary competences and the revised CEFR descriptors
Authors: Alter Grit , Ratheiser Ulla
Published: May 2019

This article presents a new theoretical model of literary competences for use in the language classroom. The work has been both triggered by an unintended consequence of the introduction of the original CEFR in 2001, namely the marginalization of literature teaching, and inspired by the inclusion of literature in the 2018 Companion. It proposes ways to move away from a pure language-based approach to using literature by providing a model for developing literary literacy in the learner. It outlines four basic literary competences, defines each, and illustrates how they can be both used in class and related to the new CEFR descriptors and existing levels.
Impact of preoperative fractional flow reserve on arterial bypass graft anastomotic function: the IMPAG trial
Authors: Glineur David , Grau Juan B , Etienne Pierre-Yves , Benedetto Umberto , Fortier Jacqueline H , Papadatos Spiridon , Laruelle Christophe , Pieters Denis , El Khoury Elie , Blouard Philippe , Timmermans Patrick , Ruel Marc , Chong Aun-Yeong , So Derek , Chan Vincent , Rubens Fraser , Gaudino Mario Fl
Published: May 2019

Aims

Visual estimation is the most commonly used method to evaluate the degree of coronary artery stenosis prior to coronary artery bypass grafting. In interventional cardiology, the use of fractional flow reserve (FFR) to guide revascularization decisions has become routine. We investigated whether the preoperative FFR measurement of coronary lesions is associated with anastomosis function 6 months after surgical revascularization using a multiarterial grafting strategy.

Methods and results

In this prospective double-blind study, 67 patients were enrolled from two institutions in Europe and Canada. From these patients, 199 coronary lesions were assessed visually and with FFR at the time of the preoperative angiogram. All patients received coronary revascularization using multiple arterial grafts. A post-operative 6-month angiogram was performed to assess anastomosis functionality using a described angiographic method. The primary outcome was the association between preoperative FFR values and anastomosis function 6 months after surgery. Preoperative FFR was significantly associated with 6-months anastomotic function for all conduits and for all targets (P  <  0.001). An FFR value of ≤0.78 was associated with an anastomotic occlusion rate of 3%.

Conclusion

We found a significant association between the preoperative FFR measurement of the target vessel and the anastomotic functionality at 6 months, with a cut-off of 0.78. Integration of FFR measurement into the preoperative diagnostic workup before multiarterial coronary surgical revascularization leads to improved anastomotic graft function.

Clinical Trials. gov Identifier

NCT02527044.
Natural disasters and infectious disease in Europe: a literature review to identify cascading risk pathways
Authors: Suk Jonathan E , Vaughan Eleanor C , Cook Robert G , Semenza Jan C
Published: May 2019

Background

Natural disasters are increasing in their frequency and complexity. Understanding how their cascading effects can lead to infectious disease outbreaks is important for developing cross-sectoral preparedness strategies. The review focussed on earthquakes and floods because of their importance in Europe and their potential to elucidate the pathways through which natural disasters can lead to infectious disease outbreaks.

Methods

A systematic literature review complemented by a call for evidence was conducted to identify earthquake or flooding events in Europe associated with potential infectious disease events.

Results

This review included 17 peer-reviewed papers that reported on suspected and confirmed infectious disease outbreaks following earthquakes (4 reports) or flooding (13 reports) in Europe. The majority of reports related to food- and water-borne disease. Eleven studies described the cascading effect of post-disaster outbreaks. The most reported driver of disease outbreaks was heavy rainfall, which led to cross-connections between water and other environmental systems, leading to the contamination of rivers, lakes, springs and water supplies. Exposure to contaminated surface water or floodwater following flooding, exposure to animal excreta and post-disaster living conditions were among other reported drivers of outbreaks.

Conclusions

The cascade effects of natural disasters, such as earthquakes and floods, include outbreaks of infectious disease. The projection that climate change-related extreme weather events will increase in Europe in the coming century highlights the importance of strengthening preparedness planning and measures to mitigate and control outbreaks in post-disaster settings.