bluuebunny/crossref_metadata_2025 huggingface dataset:
Impact ionization and band-to-band tunneling in InxGa1-xAs PIN ungated devices: A Monte Carlo analysis
Authors: Vasallo B. G. , González T. , Talbo V. , Lechaux Y. , Wichmann N. , Bollaert S. , Mateos J.
Published: January 2018

III-V Impact-ionization (II) metal-oxide-semiconductor FETs (I-MOSFETs) and tunnel FETs (TFETs) are being explored as promising devices for low-power digital applications. To assist the development of these devices from the physical point of view, a Monte Carlo (MC) model which includes impact ionization processes and band-to-band tunneling is presented. The MC simulator reproduces the I-V characteristics of experimental ungated In0.53Ga0.47As 100 nm PIN diodes, in which tunneling emerges for lower applied voltages than impact ionization events, thus being appropriate for TFETs. When the structure is enlarged up to 200 nm, the ON-state is achieved by means of impact ionization processes; however, the necessary applied voltage is higher, with the consequent drawback for low-power applications. In InAs PIN ungated structures, the onset of both impact ionization processes and band-to-band tunneling takes place for similar applied voltages, lower than 1 V; thus they are suitable for the design of low-power I-MOSFETs.
High-quality graphene flakes exfoliated on a flat hydrophobic polymer
Authors: Pedrinazzi Paolo , Caridad José M. , Mackenzie David M. A. , Pizzocchero Filippo , Gammelgaard Lene , Jessen Bjarke S. , Sordan Roman , Booth Timothy J. , Bøggild Peter
Published: January 2018

We show that graphene supported on a hydrophobic and flat polymer surface results in flakes with extremely low doping and strain as assessed by their Raman spectroscopic characteristics. We exemplify this technique by micromechanical exfoliation of graphene on flat poly(methylmethacrylate) layers and demonstrate Raman peak intensity ratios I(2D)/I(G) approaching 10, similar to pristine freestanding graphene. We verify that these features are not an artifact of optical interference effects occurring at the substrate: they are similarly observed when varying the substrate thickness and are maintained when the environment of the graphene flake is completely changed, by encapsulating preselected flakes between hexagonal boron nitride layers. The exfoliation of clean, pristine graphene layers directly on flat polymer substrates enables high performance, supported, and non-encapsulated graphene devices for flexible and transparent optoelectronic studies. We additionally show that the access to a clean and supported graphene source leads to high-quality van der Waals heterostructures and devices with reproducible carrier mobilities exceeding 50 000 cm2 V−1 s−1 at room temperature.
Ultra-fast relaxation, decoherence, and localization of photoexcited states in π-conjugated polymers
Authors: Mannouch Jonathan R. , Barford William , Al-Assam Sarah
Published: January 2018

The exciton relaxation dynamics of photoexcited electronic states in poly(p-phenylenevinylene) are theoretically investigated within a coarse-grained model, in which both the exciton and nuclear degrees of freedom are treated quantum mechanically. The Frenkel-Holstein Hamiltonian is used to describe the strong exciton-phonon coupling present in the system, while external damping of the internal nuclear degrees of freedom is accounted for by a Lindblad master equation. Numerically, the dynamics are computed using the time evolving block decimation and quantum jump trajectory techniques. The values of the model parameters physically relevant to polymer systems naturally lead to a separation of time scales, with the ultra-fast dynamics corresponding to energy transfer from the exciton to the internal phonon modes (i.e., the C–C bond oscillations), while the longer time dynamics correspond to damping of these phonon modes by the external dissipation. Associated with these time scales, we investigate the following processes that are indicative of the system relaxing onto the emissive chromophores of the polymer: (1) Exciton-polaron formation occurs on an ultra-fast time scale, with the associated exciton-phonon correlations present within half a vibrational time period of the C–C bond oscillations. (2) Exciton decoherence is driven by the decay in the vibrational overlaps associated with exciton-polaron formation, occurring on the same time scale. (3) Exciton density localization is driven by the external dissipation, arising from “wavefunction collapse” occurring as a result of the system-environment interactions. Finally, we show how fluorescence anisotropy measurements can be used to investigate the exciton decoherence process during the relaxation dynamics.
Piezoelectric effect on the thermal conductivity of monolayer gallium nitride
Authors: Zhang Jin
Published: January 2018

Using molecular dynamics and density functional theory simulations, in this work, we find that the heat transport property of the monolayer gallium nitride (GaN) can be efficiently tailored by external electric field due to its unique piezoelectric characteristic. As the monolayer GaN possesses different piezoelectric properties in armchair and zigzag directions, different effects of the external electric field on thermal conductivity are observed when it is applied in the armchair and zigzag directions. Our further study reveals that due to the elastoelectric effect in the monolayer GaN, the external electric field changes the Young's modulus and therefore changes the phonon group velocity. Also, due to the inverse piezoelectric effect, the applied electric field induces in-plane stress in the monolayer GaN subject to a length constraint, which results in the change in the lattice anharmonicity and therefore affects the phonon mean free path. Furthermore, for relatively long GaN monolayers, the in-plane stress may trigger the buckling instability, which can significantly reduce the phonon mean free path.
Tuning the interfacial charge, orbital, and spin polarization properties in La0.67Sr0.33MnO3/La1−xSrxMnO3 bilayers
Authors: Carreira Santiago J. , Aguirre Myriam H. , Briatico Javier , Weschke Eugen , Steren Laura B.
Published: January 2018

The possibility of controlling the interfacial properties of artificial oxide heterostructures is still attracting researchers in the field of materials engineering. Here, we used surface sensitive techniques and high-resolution transmission electron microscopy to investigate the evolution of the surface spin-polarization and lattice strains across the interfaces between La0.66Sr0.33MnO3 thin films and low-doped manganites as capping layers. We have been able to fine tune the interfacial spin-polarization by changing the capping layer thickness and composition. The spin-polarization was found to be the highest at a critical capping thickness that depends on the Sr doping. We explain the non-trivial magnetic profile by the combined effect of two mechanisms: On the one hand, the extra carriers supplied by the low-doped manganites that tend to compensate the overdoped interface, favouring locally a ferromagnetic double-exchange coupling. On the other hand, the evolution from a tensile-strained structure of the inner layers to a compressed structure at the surface that changes gradually the orbital occupation and hybridization of the 3d-Mn orbitals, being detrimental for the spin polarization. The finding of an intrinsic spin-polarization at the A-site cation observed in x-ray magnetic circular dichroism (XMCD) measurements also reveals the existence of a complex magnetic configuration at the interface, different from the magnetic phases observed at the inner layers.
Effect of superhydrophobicity on flashover characteristics of silicone rubber under wet conditions
Authors: Li Yufeng , Jin Haiyun , Nie Shichao , Tong Cheng , Gao Naikui
Published: January 2018

Superhydrophobic surface has aroused much interest among researchers due to the low adhesion between water and a substrate surface. This study focuses on the influence of the low adhesion of superhydrophobic surface on flashover characteristics under wet conditions. The flashover experiments were conducted under two different wet conditions. One was placing a constant volume droplet on the silicone rubber. The other one was that silicone rubber was wetted by salt fog. It was found that the adhesion between water droplets and a superhydrophobic surface was very low because of the presence of air cushion. Accordingly, water droplets were easy to slide on a superhydrophobic surface under the effect of electric filed. The sliding of droplets could provide a longer insulation path before flashover occurred. Results showed that flashover voltage could be improved greatly on a superhydrophobic silicone rubber surface.
Room temperature operation of quantum cascade lasers monolithically integrated onto a lattice-mismatched substrate
Authors: Go R. , Krysiak H. , Fetters M. , Figueiredo P. , Suttinger M. , Leshin J. , Fang X. M. , Fastenau J. M. , Lubyshev D. , Liu A. W. K. , Eisenbach A. , Furlong M. J. , Lyakh A.
Published: January 2018

Experimental data for an InP-based 40-stage quantum cascade laser structure grown on a 6-in. GaAs substrate with a metamorphic buffer are reported. The laser structure had an Al0.78In0.22As/In0.73Ga0.27As strain-balanced active region composition and an 8 μm-thick, all-InP waveguide. High reflection coated 3 mm × 30 μm devices processed from the wafer into a ridge-waveguide configuration with a lateral current injection scheme delivered over 200 mW of total peak power at 78 K with lasing observed up to 170 K. No signs of performance degradation were observed during a preliminary 200-min reliability testing. Temperature dependence for threshold current and slope efficiency in the range from 78 K to 230 K can be described with characteristic temperatures of T0 ≈ 460 K and T1 ≈ 210 K, respectively. Lasing was extended to 303 K by applying a partial high reflection coating to the front facet of the laser.
Ordering of rods near planar and curved surfaces
Authors: Izzo Dora , de Oliveira Mário J.
Published: January 2018

We study the orientational profile of a semi-infinite system of cylinders bounded in two different ways: by a flat and by a curved wall. The latter corresponds to the interior of a spherical shell, where the dimensions of the rods are comparable to the radius of curvature of the container: they have to accomodate to fill the available space, leading to a rich orientation profile. In order to study these problems, we make a mapping onto a three-state Potts model on a semi-infinite lattice, which is solved using a mean-field approach; we fix the boundary conditions on the surface and in the bulk. In the case of a curved surface, the increase in the effective volume interactions towards the bulk, due to compression, is obtained by increasing the nearest neighbor interactions. The mean-field equations are iterated numerically and we obtain various interesting results concerning the free energy and the orientation profile. We show that there is always a first order transition and the stability of the coexisting phases is strongly affected by the surface. When the surface is disordered and the bulk ordered, the profile may present a step that depends on the degree of disorder on the surface, on the rate of increase of the particle interactions and on the surface external potential. The existence of this step may be relevant to applications in nanotechnology.
Impact of wire metasurface eigenmode on the sensitivity enhancement of MRI system
Authors: Kretov Egor I. , Shchelokova Alena V. , Slobozhanyuk Alexey P.
Published: January 2018

The sensitivity of magnetic resonance imaging (MRI) is dictated by the signal-to-noise ratio. It was recently noted that the signal-to-noise ratio could be substantially increased via excitation of certain metasurface eigenmodes. Here, we provide a detailed discussion of the wire metasurface eigenmode impact on the sensitivity of MRI. We experimentally show that due to the spatial redistribution of the electromagnetic near field, mediated by the metasurface eigenmode, the received signal from the studied object becomes essentially dependent on its position on the metasurface. Moreover, we analyzed how the metasurface performance significantly depends on the dimensions of an examined object. Our work provides metasurface design guidelines for substantial enhancement of MRI sensitivity.
Femtosecond study of A1g phonons in the strong 3D topological insulators: From pump-probe to coherent control
Authors: Hu Jianbo , Igarashi Kyushiro , Sasagawa Takao , Nakamura Kazutaka G. , Misochko Oleg V.
Published: January 2018

Fully symmetric A1g phonons are expected to play a dominant role in electron scattering in strong topological insulators (TIs), thus limiting the ballistic transport of future electronic devices. Here, we report on femtosecond time-resolved observation of a pair of A1g coherent phonons and their optical control in two strong 3D TIs, Bi2Te3 and Bi2Se3, by using a second pump pulse in ultrafast spectroscopy measurements. Along with well-defined phonon properties such as frequency and lifetime, an obvious phonon chirp has been observed, implying a strong coupling between photo-carriers and lattices. The coherent phonon manipulation, on the other hand, allows us to change the phonon amplitude selectively but does not affect either the frequency or coherence lifetime of the chosen mode.
Thermal stability control system of photo-elastic interferometer in the PEM-FTs
Authors: Zhang M. J. , Jing N. , Li K. W. , Wang Z. B.
Published: January 2018

A drifting model for the resonant frequency and retardation amplitude of a photo-elastic modulator (PEM) in the photo-elastic modulated Fourier transform spectrometer (PEM-FTs) is presented. A multi-parameter broadband-matching driving control method is proposed to improve the thermal stability of the PEM interferometer. The automatically frequency-modulated technology of the driving signal based on digital phase-locked technology is used to track the PEM’s changing resonant frequency. Simultaneously the maximum optical-path-difference of a laser’s interferogram is measured to adjust the amplitude of the PEM’s driving signal so that the spectral resolution is stable. In the experiment, the multi-parameter broadband-matching control method is applied to the driving control system of the PEM-FTs. Control of resonant frequency and retardation amplitude stabilizes the maximum optical-path-difference to approximately 236 μm and results in a spectral resolution of 42 cm−1. This corresponds to a relative error smaller than 2.16% (4.28 standard deviation). The experiment shows that the method can effectively stabilize the spectral resolution of the PEM-FTs.
Effects of Pleistocene glaciation on the phylogeographic and demographic histories of chub mackerel Scomber japonicus in the north-western Pacific
Authors: Cheng Jiao , Han Zhiqiang , Song Na , Gao Tianxiang , Yanagimoto Takashi , Strüssmann Carlos A.
Published: January 2018

Pleistocene glacial cycles associated with geological and climatic changes have been suggested to affect the distribution and abundance of marine organisms in the north-western Pacific. In addition to historical processes, several contemporary forces are associated with spatial distributions and genetic structuring of marine species. Herein, we gathered partial mitochondrial control region sequences of chub mackerel Scomber japonicus from 14 localities over most of its geographical range in the north-western Pacific to infer the effect of Pleistocene climatic fluctuations on its historical demography, and to assess the role of historical process and contemporary factors in shaping present-day patterns of genetic differentiation within this species. Phylogeographic patterns revealed two distinct lineages that originated in vicariance during the Middle Pleistocene. However, there was no evidence of phylogeographic partitioning of haplotypes over the sampled range. Population structure analyses indicated a high degree of genetic homogeneity among chub mackerel populations. Demographic analyses indicated both lineages experienced Late Pleistocene population expansion. The observed genetic pattern of chub mackerel is consistent with a scenario of the survival of this species in at least two allopatric glacial refugia during the glacial maxima of the Pleistocene followed by massive dispersals throughout the north-western Pacific and species-specific ecological processes facilitating contemporary gene flow.
Molecular epidemiology reveals the role of war in the spread of HIV in Ukraine
Authors: Vasylyeva Tetyana I. , Liulchuk Mariia , Friedman Samuel R. , Sazonova Iana , Faria Nuno R. , Katzourakis Aris , Babii Nataliia , Scherbinska Alla , Thézé Julien , Pybus Oliver G. , Smyrnov Pavlo , Mbisa Jean L. , Paraskevis Dimitrios , Hatzakis Angelos , Magiorkinis Gkikas
Published: January 2018

Ukraine has one of the largest HIV epidemics in Europe, historically driven by people who inject drugs (PWID). The epidemic showed signs of stabilization in 2012, but the recent war in eastern Ukraine may be reigniting virus spread. We investigated the movement of HIV-infected people within Ukraine before and during the conflict. We analyzed HIV-1 subtype-A
pol
nucleotide sequences sampled during 2012–2015 from 427 patients of 24 regional AIDS centers and used phylogeographic analysis to reconstruct virus movement among different locations in Ukraine. We then tested for correlations between reported PWID behaviors and reconstructed patterns of virus spread. Our analyses suggest that Donetsk and Lugansk, two cities not controlled by the Ukrainian government in eastern Ukraine, were significant exporters of the virus to the rest of the country. Additional analyses showed that viral dissemination within the country changed after 2013. Spearman correlation analysis showed that incoming virus flow was correlated with the number of HIV-infected internally displaced people. Additionally, there was a correlation between more intensive virus movement and locations with a higher proportion of PWID practicing risky sexual behaviors. Our findings suggest that effective prevention responses should involve internally displaced people and people who frequently travel to war-affected regions. Scale-up of harm reduction services for PWID will be an important factor in preventing new local HIV outbreaks in Ukraine.
Immunogenetic novelty confers a selective advantage in host–pathogen coevolution
Authors: Phillips Karl P. , Cable Joanne , Mohammed Ryan S. , Herdegen-Radwan Magdalena , Raubic Jarosław , Przesmycka Karolina J. , van Oosterhout Cock , Radwan Jacek
Published: January 2018

The major histocompatibility complex (MHC) is crucial to the adaptive immune response of vertebrates and is among the most polymorphic gene families known. Its high diversity is usually attributed to selection imposed by fast-evolving pathogens. Pathogens are thought to evolve to escape recognition by common immune alleles, and, hence, novel MHC alleles, introduced through mutation, recombination, or gene flow, are predicted to give hosts superior resistance. Although this theoretical prediction underpins host–pathogen “Red Queen” coevolution, it has not been demonstrated in the context of natural MHC diversity. Here, we experimentally tested whether novel MHC variants (both alleles and functional “supertypes”) increased resistance of guppies (
Poecilia reticulata
) to a common ectoparasite (
Gyrodactylus turnbulli
). We used exposure-controlled infection trials with wild-sourced parasites, and
Gyrodactylus
-naïve host fish that were F
2
descendants of crossed wild populations. Hosts carrying MHC variants (alleles or supertypes) that were new to a given parasite population experienced a 35–37% reduction in infection intensity, but the number of MHC variants carried by an individual, analogous to heterozygosity in single-locus systems, was not a significant predictor. Our results provide direct evidence of novel MHC variant advantage, confirming a fundamental mechanism underpinning the exceptional polymorphism of this gene family and highlighting the role of immunogenetic novelty in host–pathogen coevolution.
The Bardet–Biedl syndrome protein complex is an adapter expanding the cargo range of intraflagellar transport trains for ciliary export
Authors: Liu Peiwei , Lechtreck Karl F.
Published: January 2018

Significance

Bardet–Biedl syndrome (BBS) is a rare disease caused by dysfunctional cilia. In
bbs
mutants, the composition of the ciliary membrane is altered due to defects in the BBSome, a conserved complex of BBS proteins. To determine the molecular function of the BBSome, we used single particle in vivo imaging. Transport of the ciliary membrane protein phospholipase D (PLD) is BBSome-dependent, and PLD comigrates with BBSomes on intraflagellar transport (IFT) trains. PLD accumulates inside cilia after removal of its ciliary export sequence (CES) or in the absence of BBSomes. In conclusion, the BBSome participates directly in ciliary protein transport by serving as an adapter allowing proteins that alone are unable to bind to IFT to be exported from cilia on IFT trains.
Electron mean-free-path filtering in Dirac material for improved thermoelectric performance
Authors: Liu Te-Huan , Zhou Jiawei , Li Mingda , Ding Zhiwei , Song Qichen , Liao Bolin , Fu Liang , Chen Gang
Published: January 2018

Significance

Using ab initio simulations, we uncover the electron mean-free-path (MFP) spectrum in Dirac material and specifically show how the thermoelectric efficiency can greatly benefit from a distinct, monotonically decreasing trend of electron MFPs arising from the linear energy-momentum dispersion implied by the Dirac band topology. In the past, it was generally assumed that for the nanostructuring approach to be effective, one should design nanostructures to have characteristic length larger than the electron MFP but smaller than the phonon MFP to reduce thermal conductivity. Our results show that enhancement in thermoelectric performance can be achieved in Dirac materials even when they are smaller than the electron MFP by selectively filtering out long-MFP electrons that are harmful to the Seebeck coefficient.
Evidence for convergent evolution of SINE-directed Staufen-mediated mRNA decay
Authors: Lucas Bronwyn A. , Lavi Eitan , Shiue Lily , Cho Hana , Katzman Sol , Miyoshi Keita , Siomi Mikiko C. , Carmel Liran , Ares Manuel , Maquat Lynne E.
Published: January 2018

Primate-specific
Alu
short interspersed elements (SINEs) as well as rodent-specific B and ID (B/ID) SINEs can promote Staufen-mediated decay (SMD) when present in mRNA 3′-untranslated regions (3′-UTRs). The transposable nature of SINEs, their presence in long noncoding RNAs, their interactions with Staufen, and their rapid divergence in different evolutionary lineages suggest they could have generated substantial modification of posttranscriptional gene-control networks during mammalian evolution. Some of the variation in SMD regulation produced by SINE insertion might have had a similar regulatory effect in separate mammalian lineages, leading to parallel evolution of the Staufen network by independent expansion of lineage-specific SINEs. To explore this possibility, we searched for orthologous gene pairs, each carrying a species-specific 3′-UTR SINE and each regulated by SMD, by measuring changes in mRNA abundance after individual depletion of two SMD factors, Staufen1 (STAU1) and UPF1, in both human and mouse myoblasts. We identified and confirmed orthologous gene pairs with 3′-UTR SINEs that independently function in SMD control of myoblast metabolism. Expanding to other species, we demonstrated that SINE-directed SMD likely emerged in both primate and rodent lineages >20–25 million years ago. Our work reveals a mechanism for the convergent evolution of posttranscriptional gene regulatory networks in mammals by species-specific SINE transposition and SMD.
Human ectoparasites and the spread of plague in Europe during the Second Pandemic
Authors: Dean Katharine R. , Krauer Fabienne , Walløe Lars , Lingjærde Ole Christian , Bramanti Barbara , Stenseth Nils Chr. , Schmid Boris V.
Published: January 2018

Significance

Plague is infamous as the cause of the Black Death (1347–1353) and later Second Pandemic (14th to 19th centuries CE), when devastating epidemics occurred throughout Europe, the Middle East, and North Africa. Despite the historical significance of the disease, the mechanisms underlying the spread of plague in Europe are poorly understood. While it is commonly assumed that rats and their fleas spread plague during the Second Pandemic, there is little historical and archaeological support for such a claim. Here, we show that human ectoparasites, like body lice and human fleas, might be more likely than rats to have caused the rapidly developing epidemics in pre-Industrial Europe. Such an alternative transmission route explains many of the notable epidemiological differences between historical and modern plague epidemics.
Identification of thioredoxin-interacting protein (TXNIP) as a downstream target for IGF1 action
Authors: Nagaraj Karthik , Lapkina-Gendler Lena , Sarfstein Rive , Gurwitz David , Pasmanik-Chor Metsada , Laron Zvi , Yakar Shoshana , Werner Haim
Published: January 2018

Significance

Insulin-like growth factor 1 (IGF1) plays an important role in the regulation of metabolism and growth. Epidemiological studies revealed that IGF1 deficiency is associated with cancer protection. Genomic analyses conducted on patients with Laron syndrome (LS), a rare form of dwarfism linked to mutation of the growth hormone receptor, identified thioredoxin-interacting protein (TXNIP) as a downstream target for IGF1 action.
TXNIP
is a metabolic gene involved in redox regulation that can also function as a tumor suppressor. Data identify a regulatory link between the IGF1 signaling pathway and TXNIP. Elevated TXNIP levels in patients with LS may account for cancer protection in this pathology. Furthermore, TXNIP may constitute a biomarker to predict and/or monitor responsiveness to anti-IGF1R therapy.
HELLS and CDCA7 comprise a bipartite nucleosome remodeling complex defective in ICF syndrome
Authors: Jenness Christopher , Giunta Simona , Müller Manuel M. , Kimura Hiroshi , Muir Tom W. , Funabiki Hironori
Published: January 2018

Significance

The molecular basis of immunodeficiency–centromeric instability–facial anomalies (ICF) syndrome is poorly understood. ICF is caused by mutations in HELLS, CDCA7, or the DNA methyltransferase DNMT3b. While these mutations all cause DNA methylation defects, little is known about the molecular function of CDCA7. It has been speculated that HELLS, which belongs to the SNF2 family ATPase, facilitates DNA methylation by DNMT3b through nucleosome remodeling, but HELLS on its own fails to exhibit such an activity. Here, starting from a comparative proteomic analysis of chromatin proteins in frog egg extracts, we demonstrated that CDCA7 is required for HELLS to associate with chromatin and exert nucleosome remodeling activity. Our finding delineates the molecular pathway involving CDCA7, HELLS, and DNMT3b.
miRNA-mediated targeting of human cytomegalovirus reveals biological host and viral targets of IE2
Authors: Møller Rasmus , Schwarz Toni M. , Noriega Vanessa M. , Panis Maryline , Sachs David , Tortorella Domenico , tenOever Benjamin R.
Published: January 2018

Human cytomegalovirus (HCMV) impacts more than one-half of the human population owing to its capacity to manipulate the cell and create latent reservoirs in the host. Despite an extensive understanding of HCMV biology during acute infection in fibroblasts, the molecular basis for latency in myeloid cells remains incomplete. This knowledge gap is due largely to the fact that the existing genetic systems require virus rescue in fibroblasts, precluding the study of genes that are essential during acute infection, yet likely play unique roles in myeloid cells or the establishment of latency. Here we present a solution to address this restriction. Through the exploitation of a hematopoietic-specific microRNA, we demonstrate a one-step recombineering approach that enables gene silencing only in cells associated with latency. As a proof of concept, here we describe a TB40/E variant that undergoes hematopoietic targeting of the Immediate Early-2 (IE2) gene to explore its function during infection of myeloid cells. While virus replication of the hematopoietic-targeted IE2 variant was unimpaired in fibroblasts, we observed a >100-fold increase in virus titers in myeloid cells. Virus replication in myeloid cells demonstrated that IE2 has a significant transcriptional footprint on both viral and host genes. These data implicate IE2 as an essential mediator of virus biology in myeloid cells and illustrate the utility of cell-specific microRNA-based targeting.
Structural basis of sterol recognition and nonvesicular transport by lipid transfer proteins anchored at membrane contact sites
Authors: Tong Junsen , Manik Mohammad Kawsar , Im Young Jun
Published: January 2018

Membrane contact sites (MCSs) in eukaryotic cells are hotspots for lipid exchange, which is essential for many biological functions, including regulation of membrane properties and protein trafficking. Lipid transfer proteins anchored at membrane contact sites (LAMs) contain sterol-specific lipid transfer domains [StARkin domain (SD)] and multiple targeting modules to specific membrane organelles. Elucidating the structural mechanisms of targeting and ligand recognition by LAMs is important for understanding the interorganelle communication and exchange at MCSs. Here, we determined the crystal structures of the yeast Lam6 pleckstrin homology (PH)-like domain and the SDs of Lam2 and Lam4 in the apo form and in complex with ergosterol. The Lam6 PH-like domain displays a unique PH domain fold with a conserved N-terminal α-helix. The Lam6 PH-like domain lacks the basic surface for phosphoinositide binding, but contains hydrophobic patches on its surface, which are critical for targeting to endoplasmic reticulum (ER)–mitochondrial contacts. Structures of the LAM SDs display a helix-grip fold with a hydrophobic cavity and a flexible Ω1-loop as a lid. Ergosterol is bound to the pocket in a head-down orientation, with its hydrophobic acyl group located in the tunnel entrance. The Ω1-loop in an open conformation is essential for ergosterol binding by direct hydrophobic interaction. Structural comparison suggested that the sterol binding mode of the Lam2 SD2 is likely conserved among the sterol transfer proteins of the StARkin superfamily. Structural models of full-length Lam2 correlated with the sterol transport function at the membrane contact sites.
Parental anxiety in cochlear implanted children’s family
Authors: Talebi Hossein , Habibi Zahra , Abtahi Hamid Reza , Tork Ladani Narges
Published: January 2018

Background and aim:

Early rehabilitation such as cochlear implantation is an effective way to reduce the negative effects of hearing impairment in children. Parents of hearing impaired children may feel anger, sorrow, guiltiness and anxiety. The aims of this study were measurement of anxiety level experienced by parents of children with CI and comparison between the level of experienced anxiety in parents of children with CI and parents of children with normal hearing.

Materials and methods:

This study was carried out on 25 parents whose child had cochlear implanted for six months and also 25 parents of normal children. Parents’ demographic data were collected. The Beck anxiety inventory was given to parents of both groups. The results were analyzed according to the questionnaire instructions.

Results:

Parents’ average age was 32.56 ± 4.4 and 31.76 ± 5.25 in the cochlear implant group and normal group respectively. No significant correlation between parents’ educational level and the score achieved by the Beck anxiety inventory was observed (p > .05). There was significant difference between the scores of the parents of cochlear implanted children and normal group (p < .05). Mild, moderate and severe anxiety levels were observed in 44% of the cochlear implanted children’s parents. On the other hand, 32% had mild and moderate anxiety levels and no severe anxiety was observed in normal hearing children’s parents.

Conclusion:

This study indicated significantly higher total average and also higher levels of anxiety in the parents of cochlear implanted children. Therefore, these parents’ anxiety levels affected their environment. Therefore, in order to prevent raising anxiety level in families with cochlear implanted child, controlling the environmental factors that affect families’ life should take place. In this way, a cochlear implanted child will have a smoother learning road ahead.
Feature specific quantile normalization enables cross-platform classification of molecular subtypes using gene expression data
Authors: Franks Jennifer M , Cai Guoshuai , Whitfield Michael L
Published: January 2018

Motivation

Molecular subtypes of cancers and autoimmune disease, defined by transcriptomic profiling, have provided insight into disease pathogenesis, molecular heterogeneity and therapeutic responses. However, technical biases inherent to different gene expression profiling platforms present a unique problem when analyzing data generated from different studies. Currently, there is a lack of effective methods designed to eliminate platform-based bias. We present a method to normalize and classify RNA-seq data using machine learning classifiers trained on DNA microarray data and molecular subtypes in two datasets: breast invasive carcinoma (BRCA) and colorectal cancer (CRC).

Results

Multiple analyses show that feature specific quantile normalization (FSQN) successfully removes platform-based bias from RNA-seq data, regardless of feature scaling or machine learning algorithm. We achieve up to 98% accuracy for BRCA data and 97% accuracy for CRC data in assigning molecular subtypes to RNA-seq data normalized using FSQN and a support vector machine trained exclusively on DNA microarray data. We find that maximum accuracy was achieved when normalizing RNA-seq datasets that contain at least 25 samples. FSQN allows comparison of RNA-seq data to existing DNA microarray datasets. Using these techniques, we can successfully leverage information from existing gene expression data in new analyses despite different platforms used for gene expression profiling.

Availability and implementation

FSQN has been submitted as an R package to CRAN. All code used for this study is available on Github (https://github.com/jenniferfranks/FSQN).

Supplementary information

Supplementary data are available at Bioinformatics online.
The effects of temporary exclusion of activity due to wind farm construction on a lobster (Homarus gammarus) fishery suggests a potential management approach
Authors: Roach Michael , Cohen Mike , Forster Rodney , Revill Andrew S , Johnson Magnus
Published: January 2018

Offshore wind farms (OWF) form an important part of many countries strategy for responding to the threat of climate change, their development can conflict with other offshore activities. Static gear fisheries targeting sedentary benthic species are particularly affected by spatial management that involves exclusion of fishers. Here we investigate the ecological effect of a short-term closure of a European lobster (Homarus gammarus (L.)) fishing ground, facilitated by the development of the Westermost Rough OWF located on the north-east coast of the United Kingdom. We also investigate the effects on the population when the site is reopened on completion of the construction. We find that temporary closure offers some respite for adult animals and leads to increases in abundance and size of the target species in that area. Reopening of the site to fishing exploitation saw a decrease in catch rates and size structure, this did not reach levels below that of the surrounding area. Opening the site to exploitation allows the fishery to recuperate some of the economic loss during the closure. We suggest that our results may indicate that temporary closures of selected areas may be beneficial and offer a management option for lobster fisheries.
A new mechanical stellar wind feedback model for the Rosette Nebula
Authors: Wareing C J , Pittard J M , Wright N J , Falle S A E G
Published: January 2018

The famous Rosette Nebula has an evacuated central cavity formed from the stellar winds ejected from the 2–6 Myr old codistant and comoving central star cluster NGC 2244. However, with upper age estimates of less than 110 000 yr, the central cavity is too young compared to NGC 2244 and existing models do not reproduce its properties. A new proper motion study herein using Gaia data reveals the ejection of the most massive star in the Rosette, HD 46223, from NGC 2244 occurred 1.73 (+0.34, −0.25) Myr (1σ uncertainty) in the past. Assuming this ejection was at the birth of the most massive stars in NGC 2244, including the dominant centrally positioned HD 46150, the age is set for the famous ionized region at more than 10 times that derived for the cavity. Here, we are able to reproduce the structure of the Rosette Nebula, through simulation of mechanical stellar feedback from a 40 M⊙ star in a thin sheet-like molecular cloud. We form the 135 000 M⊙ cloud from thermally unstable diffuse interstellar medium (ISM) under the influence of a realistic background magnetic field with thermal/magnetic pressure equilibrium. Properties derived from a snapshot of the simulation at 1.5 Myr, including cavity size, stellar age, magnetic field, and resulting inclination to the line of sight, match those derived from observations. An elegant explanation is thus provided for the stark contrast in age estimates based on realistic diffuse ISM properties, molecular cloud formation and stellar wind feedback.
Parity–time symmetric photonics
Authors: Zhao Han , Feng Liang
Published: January 2018

The establishment of non-Hermitian quantum mechanics (such as parity–time (PT) symmetry) stimulates a paradigmatic shift for studying symmetries of complex potentials. Owing to the convenient manipulation of optical gain and loss in analogy to complex quantum potentials, photonics provides an ideal platform for the visualization of many conceptually striking predictions from non-Hermitian quantum theory. A rapidly developing field has emerged, namely, PT-symmetric photonics, demonstrating intriguing optical phenomena including eigenstate coalescence and spontaneous PT-symmetry breaking. The advance of quantum physics, as the feedback, provides photonics with brand-new paradigms to explore the entire complex permittivity plane for novel optical functionalities. Here, we review recent exciting breakthroughs in PT-symmetric photonics while systematically presenting their underlying principles guided by non-Hermitian symmetries. The potential device applications for optical communication and computing, biochemical sensing and healthcare are also discussed.
Supporting Women’s Autonomy in Prenatal Testing
Authors: Johnston Josephine , Farrell Ruth M. , Parens Erik
Published: January 2018

(Abstracted from N Engl J Med 2017;377:505–507)

Informed consent is one of the central tenets of genetic counseling, because of the often difficult implications that come with prenatal sequencing results. Information from these results can call for pivotal decisions to be made by women that may include terminating a pregnancy.
Comparisons of Rigid Proctoscopy, Flexible Colonoscopy, and Digital Rectal Examination for Determining the Localization of Rectal Cancers
Authors: Tanaka Akira , Sadahiro Sotaro , Suzuki Toshiyuki , Okada Kazutake , Saito Gota
Published: January 2018

BACKGROUND:

Rigid proctoscopy is considered essential for rectal tumor localization, although the current gold standard for detection of colorectal cancers is colonoscopy. The European Society for Medical Oncology Guidelines indicate that rigid and flexible endoscopies afford essentially identical results, although little evidence is yet available to support this.

OBJECTIVE:

The purpose of this study was to determine the accuracy of colonoscopy in identifying the location of rectal cancer and to compare the results with those of rigid proctoscopy and digital rectal examination.

DESIGN:

This was a retrospective analysis of a prospective database.

SETTINGS:

The study was conducted at a single tertiary colorectal surgery referral center.

PATIENTS:

A total of 173 patients scheduled for curative surgery for histologically verified rectal adenocarcinoma between December 2009 and February 2015 were entered into the study, after having given informed consent.

MAIN OUTCOME MEASURES:

The main study measure was the mean difference and limits of agreement in assessment of the height of the distal edge of rectal cancer from the anal verge, using the Bland and Altman method.

RESULTS:

The mean difference between rigid proctoscopy and flexible colonoscopy was –0.2 cm (95% CI, –2.0 to 1.6 cm). The mean difference between rigid proctoscopy and digital rectal examination was 0.3 cm (95% CI, 1.9 to 2.4 cm). Intermethod variability larger than the 95% CI between rigid and flexible endoscopes was correlated to the tumor height (OR, 4.27 (95% CI, 1.84–3.10); p = 0.021).

LIMITATIONS:

This study was conducted in a single center.

CONCLUSIONS:

The limits of agreement (–2.0 and 1.6 cm) in identifying the height of rectal cancers from the anal verge are sufficiently small to support the view that flexible colonoscopy provides similar tumor locations to those measured by rigid proctoscopy, although the discrepancy occasionally exceeded 2 cm for tumors >5 cm above the anal verge. See Video Abstract at http://links.lww.com/DCR/A405.
Does Ventral Rectopexy Improve Pelvic Floor Function in the Long Term?
Authors: Mäkelä-Kaikkonen Johanna , Rautio Tero , Kairaluoma Matti , Carpelan-Holmström Monika , Kössi Jyrki , Rautio Anna , Ohtonen Pasi , Mäkelä Jyrki
Published: January 2018

BACKGROUND:

Information is needed on long-term functional results, sequelas, and outcome predictors for laparoscopic ventral mesh rectopexy.

OBJECTIVE:

The purpose of this study was to evaluate long-term function postventral rectopexy in patients with external rectal prolapse or internal rectal prolapse in a large cohort and to identify the possible effects of patient-related factors and operative technical details on patient-reported outcomes.

DESIGN:

This was a retrospective review with a cross-sectional questionnaire study.

SETTINGS:

Data were collated from prospectively collected registries in 2 university and 2 central hospitals in Finland.

PATIENTS:

All 508 consecutive patients treated with ventral rectopexy for external rectal prolapse or symptomatic internal rectal prolapse in 2005 to 2013 were included.

INTERVENTIONS:

A questionnaire concerning disease-related symptoms and effect on quality of life was used.

MAIN OUTCOME MEASURES:

Defecatory function measured by the Wexner score, the obstructive defecation score, and subjective symptom and quality-of-life evaluation using the visual analog scale were included. The effects of patient-related factors and operative technical details were assessed using multivariate analysis.

RESULTS:

The questionnaire response rate was 70.7% (330/467 living patients) with a median follow-up time of 44 months. The mean Wexner scores were 7.0 (SD = 6.1) and 6.9 (SD = 5.6), and the mean obstructive defecation scores were 9.7 (SD = 7.6) and 12.3 (SD = 8.0) for patients presenting with external rectal prolapse and internal rectal prolapse. Subjective symptom relief was experienced by 76% and reported more often by patients with external rectal prolapse than with internal rectal prolapse (86% vs 68%;p< 0.001). Complications occurred in 11.4% of patients, and the recurrence rate for rectal prolapse was 7.1%.

LIMITATIONS:

This study was limited by its lack of preoperative functional data and suboptimal questionnaire response rate.

CONCLUSIONS:

Ventral mesh rectopexy effectively treats posterior pelvic floor dysfunction with a low complication rate and an acceptable recurrence rate. Patients with external rectal prolapse benefit more from the operation than those with symptomatic internal rectal prolapse. SeeVideo Abstractat http://links.lww.com/DCR/A479.
Transition of Patients With Psoriasis From Office-Based Phototherapy to Nurse-Supported Home Phototherapy
Authors: Matthews Sarah W. , Simmer Michelle (Misha) , Williams Lisa , Fishman Paul , Shors Andrew R.
Published: January 2018

Background

Home phototherapy is a safe and effective treatment for psoriasis but is not commonly utilized as a treatment option in the United States. Recently, there has been renewed interest in home phototherapy. This pilot study describes the nursing support needed to facilitate effective transition of ongoing office-based phototherapy patients to home phototherapy.

Methods

Ten patients with a diagnosis of psoriasis receiving office-based phototherapy were identified as candidates for home phototherapy. They received group education on self-administration by specialized phototherapy nurses. Some patients required additional one-on-one training. Units were installed, and home phototherapy was initiated. Subsequent nursing care consisted of telephone support with the study nurse on a weekly basis for 4–8 weeks with follow-up telephone calls on an as-needed basis.

Results

Eleven patients initially participated in the 8-month trial. Ten were successfully transitioned to home treatments. One patient discontinued the study. The 10 patients were independently self-administering home phototherapy with minimal nursing support by Week 8 of the study.

Conclusion

Transition of patients with psoriasis receiving office-based phototherapy to home phototherapy can be done successfully while maintaining control of psoriasis. Considerable nursing resources are required for initial patient education, but they decrease significantly with time.
Cholesterol efflux in the transplant patient
Authors: Sudharshan Sangita , Javaheri Ali
Published: January 2018

Purpose of review

Cholesterol metabolism is increasingly recognized in inflammatory diseases including transplantation. This review discusses the mechanistic underpinnings that tie macrophage cholesterol efflux capacity (CEC) of high-density lipoprotein (HDL) to chronic rejection in transplanted patients.

Recent findings

Animal studies suggest that administration of apolipoprotein A-I, the main protein constituent of HDL, can prevent transplant arteriosclerosis. apoA-I administration increases CEC of HDL. In patients with cardiac allograft vasculopathy (CAV), decreased CEC has been associated with poorer survival. In addition, reduced CEC in recipients, pretransplant, has been associated with the development of CAV and renal allograft survival.

These recent findings raise the hypothesis that increasing cholesterol efflux may prevent chronic rejection and improve allograft survival after transplant. Reconstituted HDL significantly increases CEC and is currently in clinical development for traditional atherosclerosis. Clinical trials of reconstituted HDL administration in transplantation should be performed.
Chronic Hypertension and Adverse Pregnancy Outcome: A Cohort Study
Authors: Panaitescu A. M. , Syngelaki A. , Prodan N. , Akolekar R. , Nicolaides K. H.
Published: January 2018

(Abstracted from Ultrasound Obstet Gynecol 2017;50:228–235)

There is substantial evidence that chronic hypertension (CH) is associated with adverse pregnancy outcomes. Although meta-analyses of studies examining this issue have been previously conducted, confounding factors and heterogeneity between included studies weaken their impact.