bluuebunny/crossref_metadata_2025 huggingface dataset:
New insight on improving electrical strength and toughness of polyethylene blends: Turning point of supramolecular structure
Authors: Li Lunzhi , Zhong Lisheng , Zhang Kai , Gao Jinghui , Xu Man , Wang Yu
Published: December 2018

We report an effective approach on improving the electrical strength and mechanical impact toughness in polyethylene blends by locating the composition on a submicroscopic supramolecular structure turning point. The designed linear low density polyethylene (LLDPE)-high density polyethylene (HDPE) blends exhibit the enhanced electrical breakdown strength and toughness with the optimal value of E0=95.48kV/mm and G=54.67 kJ·m-2 respectively, which is around 6% and 18% higher than pure LLDPE. The scanning electron microscopic (SEM) investigation and X-ray diffraction (XRD) study show no obvious variation in mesoscopic and microscopic structure with the change of HDPE content. Further differential scanning calorimetric (DSC) study using successive self-nucleation/annealing (SSA) method reveals that the turning point with optimal performance corresponds with a peculiar supramolecular structure with a high density of tie molecules, which enhances the toughness and the electromechanical breakdown strength. Our work provides a new insight on improving electrical strength and toughness for dielectric polymers, and may aid to enhance the electric insulation performance for dielectric materials in power equipment.
Coefficients of thermal expansion of single crystalline β-Ga2O3 and in-plane thermal strain calculations of various materials combinations with β-Ga2O3
Authors: Liao Michael E. , Li Chao , Yu Hsuan Ming , Rosker Eva , Tadjer Marko J. , Hobart Karl D. , Goorsky Mark S.
Published: December 2018

The coefficients of thermal expansion (CTEs) of single crystalline, monoclinic β-Ga2O3 were determined by employing high-resolution X-ray diffraction measurements. This work reports the CTE measurements on a single crystalline β-Ga2O3 substrate. The CTE values along the “a,” “b,” and “c” axes are 3.77 × 10−6 °C−1, 7.80 × 10−6 °C−1, and 6.34 × 10−6 °C−1, respectively, and the CTE of the angle β (the angle between the “a” and “c” axes) is determined to be 1.31 × 10−4 ° K−1. All CTE values reported here are linear under the temperature regime between room temperature and 1000 °C. All measurements were performed in a controlled nitrogen gas environment, and no surface degradation was observed after these measurements. Thermal strain calculations with different material combinations involving β-Ga2O3 are also presented relevant to both epitaxial and wafer bonding applications for Si, InP, 3C–SiC, 6H–SiC, GaN, and sapphire.
Linearization and Krein-like functionals of hypergeometric orthogonal polynomials
Authors: Dehesa J. S. , Moreno-Balcázar J. J. , Toranzo I. V.
Published: December 2018

The Krein-like r-functionals of the hypergeometric orthogonal polynomials {pn(x)}, with the kernel of the form xs[ω(x)]βpm1(x)…pmr(x) being ω(x) the weight function on the interval Δ∈R, are determined by means of the Srivastava linearization method. The particular 2-functionals, which are particularly relevant in quantum physics, are explicitly given in terms of the degrees and the characteristic parameters of the polynomials. They include the well-known power moments and the novel Krein-like moments. Moreover, various related types of exponential and logarithmic functionals are also investigated.
A two-axis tilt control system on a turntable for rotating-optical-cavity experiments
Authors: Zhang Tao , Bi Jin , Zhi Yunlin , Peng Jiankang , Chen Lisheng , Li Liufeng
Published: December 2018

Many precision measurements using rotating optical cavities have tight requirement on the level of a rotating platform on which the cavities are installed. We develop a single-stage tilt control system as one part of the experimental setup for testing Lorentz invariance using two optical cavities that are perpendicular to each other. Home built voice-coil actuators, together with a tilt sensor and control electronics, are adopted to simultaneously suppress the tilt of the rotating platform in two orthogonal directions. The large cross coupling between two orthogonal axes is observed, and its mechanism is examined. By adding a compensating weight, the loop instability resulting from the cross coupling is effectively removed. With the active control, the variation of the tilt around each of the two axes is reduced from the free-running value of ±30 µrad to within ±0.2 µrad, independently measured by using a second tilt sensor. This residual tilt has a component at the rotational frequency with an amplitude of 0.1 µrad, which contributes a systematical offset of 1.8 × 10−17 to the Lorentz violating parameter κe−ZZ, estimated by assuming that the tilt sensitivity of the optical cavity is 1 × 10−16/μrad. Further improvement is still possible by using piezo-electric actuators that exhibit higher resonant frequencies, a different approach that will suppress the residual variation of the tilt to within ±0.01 µrad and allow a reduced systematical offset of 1.8 × 10−18 for κe−ZZ.
Dislocation bending and stress evolution in Mg-doped GaN films on Si substrates
Authors: Soman Rohith , Mohan Nagaboopathy , Chandrasekar Hareesh , Bhat Navakanta , Raghavan Srinivasan
Published: December 2018

P-type doping using Mg is essential for realizing a variety of electronic and optoelectronic III-nitride devices involving hetero-epitaxial thin films that also contain a significant number of dislocations. We report on the effect of Mg incorporation on dislocation and stress evolution during the growth of GaN thin films by using in situ curvature measurements and ex situ transmission electron microscopy. A complete picture involving the interplay between three effects—dopant size effect, dislocation bending, and polarity inversion—is presented. Mg aids dislocation bending, which in turn generates tensile stresses in Mg-doped GaN films. As a result, the compressive stress expected due to the dopant size difference effect can only be discerned clearly in films with dislocation densities below 5 × 109 cm−2. Polarity inversion at doping exceeding 1019 cm−3 is associated with a sharp drop in screw dislocation density. A kinetic stress evolution model has been developed to capture dislocation bending and size difference effects, and a match between calculated bending angle from the model and that measured from TEM images is obtained.
Metallic conduction and ferromagnetism in MAl2O4/SrTiO3 spinel/perovskite heterostructures (M = Fe, Co, Ni)
Authors: Zhang Yu , Gan Yulin , Zhang Hongrui , Zhang Hui , Norby Poul , Shen Baogen , Sun Jirong , Chen Yunzhong
Published: December 2018

Recently, a high mobility quasi-two-dimensional electron gas has been reported for the heterointerface between two insulating and nonmagnetic oxides of spinel γ-Al2O3 and perovskite SrTiO3 (STO). Herein, we fabricated the epitaxial heterostructure with Al-based magnetic spinel oxide MAl2O4 (M = Fe, Co, Ni) on perovskite STO. Remarkably, all the MAl2O4 (M = Fe, Co, Ni) films exhibit ferromagnetic behavior up to room temperature. Although FeAl2O4/STO is insulating, the NiAl2O4/STO and CoAl2O4/STO heterointerfaces are found to be highly metallic and exhibit the anomalous Hall effect (AHE) at temperatures below 30 K. Their Hall mobility is as high as 3 × 104 cm2 V−1 s−1, comparable to that of the γ-Al2O3/STO interface. There has been evidence of oxygen-vacancy-related magnetism in γ-Al2O3/STO at temperatures below 5 K, while the enhanced AHE in NiAl2O4/STO and CoAl2O4/STO likely comes from the magnetic proximity effect induced by the top ferromagnetic MAl2O4 spinel films.
High-resolution inductive measurement of electrical resistivity and density of electromagnetically levitated liquid metal droplets
Authors: Lohöfer Georg
Published: December 2018

A new device for the inductive measurement of electrical resistivity and density of liquid metals and semiconductors is presented. It is integrated in two electromagnetic levitation facilities operating under microgravity. As a result, the completely noninvasive handling and measuring of the metallic melt enables the extension of the accessible sample temperature range far into the undercooled liquid state below the melting point. The microgravity environment permits the undisturbed joining of the containerless inductive sample handling method by the electromagnetic levitation with the inductive sample measurement technique. The following sections explain in detail the basic principles and the technical realization of the whole measurement apparatus and present experimental data showing its high resolution resulting from the combination of microgravity, electromagnetic levitation, and inductive measurement technique.
Charge-spin current conversion in high quality epitaxial Fe/Pt systems: Isotropic spin Hall angle along different in-plane crystalline directions
Authors: Guillemard C. , Petit-Watelot S. , Andrieu S. , Rojas-Sánchez J.-C.
Published: December 2018

We report the growth of MgO[001]//Fe(6 nm)/MgO(7 nm) and MgO[001]//Fe(6 nm)/Pt(6 nm) by molecular beam epitaxy and show that the full characterization by spin-orbit ferromagnetic resonance (SO-FMR) allows the determination of magnetic anisotropies by classical FMR-only studies. The spin mixing conductance of the epitaxial Fe/Pt interface was measured to be geffect↑↓=2.6±0.5×1019 m2, and the effective spin Hall angle (SHA) θSHEeffect was estimated at different in-plane crystalline directions. It was found that θSHEeffect is the same in all directions. When taking into account high enough excitation frequencies to achieve uniform precession of magnetization, the effective SHA for epitaxial Pt in Fe/Pt is θSHEeffect=0.051±0.005. We address about the proper conditions to determine those relevant spintronic parameters.
Note: Low sliding friction piezoelectric motor using motion of hula hoop
Authors: Zhong Jinfeng , Ma Yuting , Yan Xintao , Song Feifei , Wang Ce
Published: December 2018

A piezoelectric motor that imitates the motion of a hula hoop was developed. It has the advantage of low sliding wear as static friction force is used to drive the rotor. The rotation speed of the rotor can be regulated by changing the exciting frequency of piezoelectric transducers. The stator is composed of four piezoelectric plates attached to a steel rod. Two orthogonal bending modes were excited by driving two pairs of piezoelectric plates, and circular motion was formed on the rod. The reversed motion of the rotor can be obtained by adjusting the phase of two bending modes. The prototype stator working at 39.1 Hz produced a rotation speed of 1142 rpm and a torque of 0.23 mN m.
A passive isolator realized by magnetoelectric laminate composites
Authors: Tu Cheng , Dong Cunzheng , Chu Zhaoqiang , Chen Huaihao , Liang Xianfeng , Sun Nian Xiang
Published: December 2018

This work demonstrates a passive isolator realized by magnetoelectric laminate composites. The proposed isolator consists of a magnetoelectric gyrator, two impedance matching networks, and a load impedance. The equivalent circuit model of the isolator is developed. Good agreement has been obtained between the measured and computed results based on the proposed equivalent circuit model. The measured forward insertion loss and reverse isolation of the proposed isolator are 4.7 dB and 19 dB, respectively. A figure-of-merit which determines the performance of the isolator is proposed, which can be used to guide the design of such isolators.
Probing spin-orbit interaction via Fano interference
Authors: Rajesh Desapogu , Nechayev Sergey , Cheskis Dima , Sternklar Shmuel , Gorodetski Yuri
Published: December 2018

We experimentally investigate the behavior of the Fano-like plasmonic resonance lineshape in a simple plasmonic system comprising a subwavelength hole or a particle illuminated by a tightly focused Gaussian beam. We observe that for a small lateral displacement of the scatterer, the k-space distribution of the plasmonic wave exhibits a strong spin-dependent azimuthal variation. We attribute this phenomenon to the sensitive light-plasmon coupling conditions arising due to the specific phase matching requirements. This effect is qualitatively described by a Fano-like interference with a complex coupling factor.
High-mobility InAs heterostructure meets criteria for topological superconductivity regime
Authors: Patrick Chris
Published: December 2018

Measuring magnetotransport properties of InAs heterostructure reveals characteristics compatible with superconducting quantum computing.
Switch between critical percolation modes in city traffic dynamics
Authors: Zeng Guanwen , Li Daqing , Guo Shengmin , Gao Liang , Gao Ziyou , Stanley H. Eugene , Havlin Shlomo
Published: December 2018

Significance

With the same static road network, it is essentially unknown for urban traffic if traffic flows have the same spatial organization properties for different hours. Based on real-time high-resolution GPS data on the city scale, our results indicate two distinct modes characterized by different percolation critical exponents. The mode during rush hours on working days behaves like a 2D lattice with mainly short-range links, while the mode for other instants behaves like a small world (i.e., a lattice with long-range links). The difference between these two modes is explained here by the free flow on urban highways during nonrush hours, which is like adding long-range links in a 2D lattice. In contrast, during rush hours, such links almost disappear.
Blacklisting variants common in private cohorts but not in public databases optimizes human exome analysis
Authors: Maffucci Patrick , Bigio Benedetta , Rapaport Franck , Cobat Aurélie , Borghesi Alessandro , Lopez Marie , Patin Etienne , Bolze Alexandre , Shang Lei , Bendavid Matthieu , Scott Eric M. , Stenson Peter D. , Cunningham-Rundles Charlotte , Cooper David N. , Gleeson Joseph G. , Fellay Jacques , Quintana-Murci Lluis , Casanova Jean-Laurent , Abel Laurent , Boisson Bertrand , Itan Yuval
Published: December 2018

Computational analyses of human patient exomes aim to filter out as many nonpathogenic genetic variants (NPVs) as possible, without removing the true disease-causing mutations. This involves comparing the patient’s exome with public databases to remove reported variants inconsistent with disease prevalence, mode of inheritance, or clinical penetrance. However, variants frequent in a given exome cohort, but absent or rare in public databases, have also been reported and treated as NPVs, without rigorous exploration. We report the generation of a blacklist of variants frequent within an in-house cohort of 3,104 exomes. This blacklist did not remove known pathogenic mutations from the exomes of 129 patients and decreased the number of NPVs remaining in the 3,104 individual exomes by a median of 62%. We validated this approach by testing three other independent cohorts of 400, 902, and 3,869 exomes. The blacklist generated from any given cohort removed a substantial proportion of NPVs (11–65%). We analyzed the blacklisted variants computationally and experimentally. Most of the blacklisted variants corresponded to false signals generated by incomplete reference genome assembly, location in low-complexity regions, bioinformatic misprocessing, or limitations inherent to cohort-specific private alleles (e.g., due to sequencing kits, and genetic ancestries). Finally, we provide our precalculated blacklists, together with ReFiNE, a program for generating customized blacklists from any medium-sized or large in-house cohort of exome (or other next-generation sequencing) data via a user-friendly public web server. This work demonstrates the power of extracting variant blacklists from private databases as a specific in-house but broadly applicable tool for optimizing exome analysis.
Bioactive cell-like hybrids from dendrimersomes with a human cell membrane and its components
Authors: Yadavalli Srujana S. , Xiao Qi , Sherman Samuel E. , Hasley William D. , Klein Michael L. , Goulian Mark , Percec Virgil
Published: December 2018

Significance

Gram-negative bacterial cells such as
Escherichia coli
contain a relatively rigid outer membrane, and cross-linked peptidoglycan in their periplasm, giving them the rigidity and stability to survive independently in harsh environments. To dismantle these strong bacterial cell envelopes, enzymatic processes need to be used. In contrast, human cell membranes are much more fragile, making it possible to dismantle them more easily by relatively mild mechanical disruption. Once these membranes are dismantled, they can be coassembled with synthetic phospholipid mimics, named Janus dendrimers, into cell-like hybrids. This method stabilizes the delicate human cell membranes, introducing the potential for the study of human cell membranes and of their constituents in vitro in a more robust environment.
RNA-binding protein YTHDF3 suppresses interferon-dependent antiviral responses by promoting FOXO3 translation
Authors: Zhang Yuan , Wang Xin , Zhang Xiao , Wang Jiaming , Ma Yuanwu , Zhang Lianfeng , Cao Xuetao
Published: December 2018

Significance

Type I IFN signaling is maintained under homeostatic conditions, which plays a crucial role in antiviral immunity. Epigenetic regulation of innate immunity and inflammation attracts much attention now. However, the underlying mechanisms need further investigation. Here, we demonstrate that
N
6
-methyladenosine (m
6
A) “reader” YT521-B homology domain-containing family 3 (YTHDF3) selectively inhibits IFN-stimulated gene expression under basal conditions by binding to the translation initiation region of the transcription corepressor forkhead box protein O3 (FOXO3) mRNA and promoting its translation. Unexpectedly, the capacity of YTHDF3 for binding FOXO3 mRNA is independent of METTL3-mediated m
6
A modification. Our paper adds a view of YTHDF family proteins in the control of IFN antiviral responses. Overall, the roles of RNA-binding proteins and their RNA targets with certain modifications in inflammation and autoimmune diseases need further identification.
Regulation of acetate metabolism and coordination with the TCA cycle via a processed small RNA
Authors: De Mets François , Van Melderen Laurence , Gottesman Susan
Published: December 2018

Significance

In bacteria, small RNAs pair with target mRNAs to rapidly adjust gene expression in response to environmental and physiological changes. In this study, we identified a small RNA, SdhX, in
Escherichia coli
, whose expression is dependent on expression of tricarboxylic acid cycle genes. SdhX adjusts carbon flux by negatively regulating acetate kinase levels, improving growth on acetate. SdhX also leads to increased resistance to hydroxyurea, as do deletions of acetate kinase. Balancing metabolic flux is important for all bacterial cells, and SdhX plays a major role in this process by linking expression of tricarboxylic acid cycle genes to regulation of acetate metabolism, thus playing a role in gating overflow metabolism.
Mapping Occupational Hazards with a Multi-sensor Network in a Heavy-Vehicle Manufacturing Facility
Authors: Zuidema Christopher , Sousan Sinan , Stebounova Larissa V , Gray Alyson , Liu Xiaoxing , Tatum Marcus , Stroh Oliver , Thomas Geb , Peters Thomas , Koehler Kirsten
Published: December 2018

Due to their small size, low-power demands, and customizability, low-cost sensors can be deployed in collections that are spatially distributed in the environment, known as sensor networks. The literature contains examples of such networks in the ambient environment; this article describes the development and deployment of a 40-node multi-hazard network, constructed with low-cost sensors for particulate matter (SHARP GP2Y1010AU0F), carbon monoxide (Alphasense CO-B4), oxidizing gases (Alphasense OX-B421), and noise (developed in-house) in a heavy-vehicle manufacturing facility. Network nodes communicated wirelessly with a central database in order to record hazard measurements at 5-min intervals. Here, we report on the temporal and spatial measurements from the network, precision of network measurements, and accuracy of network measurements with respect to field reference instruments through 8 months of continuous deployment. During typical production periods, 1-h mean hazard levels ± standard deviation across all monitors for particulate matter (PM), carbon monoxide (CO), oxidizing gases (OX), and noise were 0.62 ± 0.2 mg m−3, 7 ± 2 ppm, 155 ± 58 ppb, and 82 ± 1 dBA, respectively. We observed clear diurnal and weekly temporal patterns for all hazards and daily, hazard-specific spatial patterns attributable to general manufacturing processes in the facility. Processes associated with the highest hazard levels were machining and welding (PM and noise), staging (CO), and manual and robotic welding (OX). Network sensors exhibited varying degrees of precision with 95% of measurements among three collocated nodes within 0.21 mg m−3 for PM, 0.4 ppm for CO, 9 ppb for OX, and 1 dBA for noise of each other. The median percent bias with reference to direct-reading instruments was 27%, 11%, 45%, and 1%, for PM, CO, OX, and noise, respectively. This study demonstrates the successful long-term deployment of a multi-hazard sensor network in an industrial manufacturing setting and illustrates the high temporal and spatial resolution of hazard data that sensor and monitor networks are capable of. We show that network-derived hazard measurements offer rich datasets to comprehensively assess occupational hazards. Our network sets the stage for the characterization of occupational exposures on the individual level with wireless sensor networks.
DeepPhos: prediction of protein phosphorylation sites with deep learning
Authors: Luo Fenglin , Wang Minghui , Liu Yu , Zhao Xing-Ming , Li Ao
Published: December 2018

Motivation

Phosphorylation is the most studied post-translational modification, which is crucial for multiple biological processes. Recently, many efforts have been taken to develop computational predictors for phosphorylation site prediction, but most of them are based on feature selection and discriminative classification. Thus, it is useful to develop a novel and highly accurate predictor that can unveil intricate patterns automatically for protein phosphorylation sites.

Results

In this study we present DeepPhos, a novel deep learning architecture for prediction of protein phosphorylation. Unlike multi-layer convolutional neural networks, DeepPhos consists of densely connected convolutional neuron network blocks which can capture multiple representations of sequences to make final phosphorylation prediction by intra block concatenation layers and inter block concatenation layers. DeepPhos can also be used for kinase-specific prediction varying from group, family, subfamily and individual kinase level. The experimental results demonstrated that DeepPhos outperforms competitive predictors in general and kinase-specific phosphorylation site prediction.

Availability and implementation

The source code of DeepPhos is publicly deposited at https://github.com/USTCHIlab/DeepPhos.

Supplementary information

Supplementary data are available at Bioinformatics online.
UbiHub: a data hub for the explorers of ubiquitination pathways
Authors: Liu Lihua , Damerell David R , Koukouflis Leonidas , Tong Yufeng , Marsden Brian D , Schapira Matthieu
Published: December 2018

Motivation

Protein ubiquitination plays a central role in important cellular machineries such as protein degradation or chromatin-mediated signaling. With the recent discovery of the first potent ubiquitin-specific protease inhibitors, and the maturation of proteolysis targeting chimeras as promising chemical tools to exploit the ubiquitin-proteasome system, protein target classes associated with ubiquitination pathways are becoming the focus of intense drug-discovery efforts.

Results

We have developed UbiHub, an online resource that can be used to visualize a diverse array of biological, structural and chemical data on phylogenetic trees of human protein families involved in ubiquitination signaling, including E3 ligases and deubiquitinases. This interface can inform target prioritization and drug design, and serves as a navigation tool for medicinal chemists, structural and cell biologists exploring ubiquitination pathways.

Availability and implementation

https://ubihub.thesgc.org.
SIAN: software for structural identifiability analysis of ODE models
Authors: Hong Hoon , Ovchinnikov Alexey , Pogudin Gleb , Yap Chee
Published: December 2018

Biological processes are often modeled by ordinary differential equations with unknown parameters. The unknown parameters are usually estimated from experimental data. In some cases, due to the structure of the model, this estimation problem does not have a unique solution even in the case of continuous noise-free data. It is therefore desirable to check the uniqueness a priori before carrying out actual experiments. We present a new software SIAN (Structural Identifiability ANalyser) that does this. Our software can tackle problems that could not be tackled by previously developed packages.

Availability and implementation

SIAN is open-source software written in Maple and is available at https://github.com/pogudingleb/SIAN.

Supplementary information

Supplementary data are available at Bioinformatics online.
Galaxy mothur Toolset (GmT): a user-friendly application for 16S rRNA gene sequencing analysis using mothur
Authors: Hiltemann Saskia D , Boers Stefan A , van der Spek Peter J , Jansen Ruud , Hays John P , Stubbs Andrew P
Published: December 2018

Background

The determination of microbial communities using the mothur tool suite (https://www.mothur.org) is well established. However, mothur requires bioinformatics-based proficiency in order to perform calculations via the command-line. Galaxy is a project dedicated to providing a user-friendly web interface for such command-line tools (https://galaxyproject.org/).

Results

We have integrated the full set of 125+ mothur tools into Galaxy as the Galaxy mothur Toolset (GmT) and provided a set of workflows to perform end-to-end 16S rRNA gene analyses and integrate with third-party visualization and reporting tools. We demonstrate the utility of GmT by analyzing the mothur MiSeq standard operating procedure (SOP) dataset (https://www.mothur.org/wiki/MiSeq_SOP).

Conclusions

GmT is available from the Galaxy Tool Shed, and a workflow definition file and full Galaxy training manual for the mothur SOP have been created. A Docker image with a fully configured GmT Galaxy is also available.
Postoperative Steroid Taper Is Associated With Pelvic Sepsis After Ileal Pouch-anal Anastomosis
Authors: Ritter Kaitlin A , Burke John P , Stocchi Luca , Aiello Alexandra , Holubar Stefan , Ashburn Jean H , Lipman Jeremy M , Shawki Sherief , Hull Tracy
Published: December 2018

Objective

We hypothesized that postoperative oral steroid taper after ileal pouch-anal anastomosis for inflammatory bowel disease would not be associated with pelvic septic complications.

Background

Recent data has emphasized the possible association between biologic medication use and pelvic sepsis following ileal pouch-anal anastomosis. Limited contemporary data exist examining the effects of steroid use on these complications.

Methods

Consecutive patients undergoing ileal pouch-anal anastomosis for inflammatory bowel disease at a single institution from January 2009 to December 2013 were included. Factors associated with anastomotic leak and pelvic sepsis were assessed using univariate and multivariate analysis.

Results

A total of 686 patients were included (mean age 39.5 years, 59% males). Postoperative oral steroid taper was associated with both anastomotic leak and pelvic sepsis on univariate analysis. Stress dose intravenous steroid use was not associated with complications. Multivariate analysis indicated total proctocolectomy (odds ratio [OR] 2.2; confidence interval [CI] 1.01–4.7, P = 0.047), and postoperative oral steroid taper (OR 2.3; CI 1.06–5.1; P = 0.035) as independent factors significantly associated with pelvic sepsis.

Conclusions

Prolonged postoperative oral steroid taper after ileal pouch-anal anastomosis should be avoided. If preoperative steroid weaning is not possible before a planned total proctocolectomy and ileal pouch-anal anastomosis, patients should undergo an initial total abdominal colectomy.
Results of Phrenic Nerve Transfer to the Musculocutaneous Nerve Using Video-Assisted Thoracoscopy in Patients with Traumatic Brachial Plexus Injury: Series of 28 Cases
Authors: Cardoso Marcio de Mendonça , Gepp Ricardo de Amoreira , Mamare Eduardo , Guedes-Correa José Fernando
Published: December 2018

BACKGROUND

The phrenic nerve can be transferred to the musculocutaneous nerve using video-assisted thoracoscopy, aiming at the recovery of elbow flexion in patients with traumatic brachial plexus injuries. There are few scientific papers in the literature that evaluate the results of this operative technique.

OBJECTIVE

To evaluate biceps strength and pulmonary function after the transfer of the phrenic nerve to the musculocutaneous nerve using video-assisted thoracoscopy.

METHODS

A retrospective study was carried out in a sample composed of 28 patients who were victims of traumatic injury to the brachial plexus from 2008 to 2013. Muscle strength was graded using the British Medical Research Council (BMRC) scale and pulmonary function through spirometry. Statistical tests, with significance level of 5%, were used.

RESULTS

In total, 74.1% of the patients had biceps strength greater than or equal to M3. All patients had a decrease in forced vital capacity and forced expiratory volume in 1 s, with no evidence of recovery over time.

CONCLUSION

Transferring the phrenic nerve to the musculocutaneous nerve using video-assisted thoracoscopy may lead to an increase in biceps strength to BMRC M3 or greater in most patients. Considering the deterioration in the parameters of spirometry observed in our patients and the future effects of aging in the respiratory system, it is not possible at the moment to guarantee the safety of this operative technique in the long term.
Differential expression of microRNAs in Alzheimer's disease brain, blood and cerebrospinal fluid: a systematic review and meta-analysis
Authors: Takousis Petros , Sadlon Angélique , Schulz Jessica , Wohlers Inken , Dobricic Valerija , Middleton Lefkos , Lill Christina M. , Perneczky Robert , Bertram Lars
Published: December 2018

INTRODUCTION: Several microRNAs (miRNAs) have been implicated in Alzheimer's disease (AD) pathogenesis but the evidence from individual case control studies remains inconclusive. METHODS: A systematic literature review was performed, followed by standardised multi-stage data extraction, quality control, and meta-analyses on eligible data for brain, blood, and cerebrospinal fluid (CSF) specimens. Results were compared with miRNAs reported in the abstracts of eligible studies or recent qualitative reviews to assess novelty. RESULTS: Data from 147 independent datasets across 107 publications were quantitatively assessed in 461 meta-analyses. Twenty-five, five, and 32 miRNAs showed study-wide significant differential expression (α<1.08x10-4) in brain, CSF, and blood-derived specimens, respectively, with 5 miRNAs showing differential expression in both brain and blood. Of these 57 miRNAs, 13 had not been reported in the abstracts of previous original or review articles. DISCUSSION: Our systematic assessment of differential miRNA expression is the first of its kind in AD and highlights miRNAs of relevance.
An efficient analytical reduction of detailed nonlinear neuron models
Authors: Amsalem Oren , Eyal Guy , Rogozinski Noa , Schürmann Felix , Gevaert Michael , Kumbhar Pramod , Segev Idan
Published: December 2018

Detailed conductance-based nonlinear neuron models consisting of thousands of synapses are key for understanding of the computational properties of single neurons and large neuronal networks, and for interpreting experimental results. Simulations of these models are computationally expensive, considerably curtailing their utility.Neuron_Reduceis a new analytical approach to reduce the morphological complexity and computational time of nonlinear neuron models. Synapses and active membrane channels are mapped to the reduced model preserving their transfer impedance to the soma; synapses with identical transfer impedance are merged into one NEURON process still retaining their individual activation times.Neuron_Reduceaccelerates the simulations by 40-250 folds for a variety of cell types and realistic number (10,000-100,000) of synapses while closely replicating voltage dynamics and specific dendritic computations. The reduced neuron-models will enable realistic simulations of neural networks at unprecedented scale, including networks emerging from micro-connectomics efforts and biologically-inspired “deep networks”.Neuron_Reduceis publicly available and is straightforward to implement.
Altered resting state functional connectivity in a thalamo-cortico-cerebellar network in patients with schizophrenia
Authors: Forlim Caroline Garcia , Klock Leonie , Baechle Johanna , Stoll Laura , Giemsa Patrick , Fuchs Marie , Schoofs Nikola , Montag Christiane , Gallinat Juergen , Kuehn Simone
Published: December 2018

Schizophrenia is described as a disease in which complex psychopathology together with cognitive and behavioral impairments are related to widely disrupted brain circuitry causing a failure in coordinating information across multiple brain sites. This led to the hypothesis of schizophrenia as a network disease e.g. in the cognitive dysmetria model and the dysconnectivity theory. Nevertheless, there is no consensus regarding localized mechanisms, namely dysfunction of certain networks underlying the multifaceted symptomatology. In this study, we investigated potential functional disruptions in 35 schizophrenic patients and 41 controls using complex cerebral network analysis, namely network-based statistic (NBS) and graph theory in resting state fMRI. NBS can reveal locally impaired subnetworks whereas graph analysis characterizes whole brain network topology. Using NBS we observed a local hyperconnected thalamo-cortico-cerebellar subnetwork in the schizophrenia group. Furthermore, nodal graph measures retrieved from the thalamo-cortico-cerebellar subnetwork revealed that the total number of connections from/to (degree) of the thalamus is higher in patients with schizophrenia. Interestingly, graph analysis on the whole brain functional networks did not reveal group differences. Together, our results suggest that disruptions in the brain networks of schizophrenia patients are situated at the local level of the hyperconnected thalamo-cortico-cerebellar rather than globally spread in brain. Our results provide further evidence for the importance of the thalamus and cerebellum in schizophrenia and to the notion that schizophrenia is a network disease in line with the dysconnectivity theory and cognitive dysmetria model.
Genomic Prediction of Complex Disease Risk
Authors: Lello Louis , Raben Timothy G. , Yong Soke Yuen , Tellier Laurent CAM , Hsu Stephen D.H.
Published: December 2018

We construct risk predictors using polygenic scores (PGS) computed from common Single Nucleotide Polymorphisms (SNPs) for a number of complex disease conditions, using L1-penalized regression (also known as LASSO) on case-control data from UK Biobank. Among the disease conditions studied are Hypothyroidism, (Resistant) Hypertension, Type 1 and 2 Diabetes, Breast Cancer, Prostate Cancer, Testicular Cancer, Gallstones, Glaucoma, Gout, Atrial Fibrillation, High Cholesterol, Asthma, Basal Cell Carcinoma, Malignant Melanoma, and Heart Attack. We obtain values for the area under the receiver operating characteristic curves (AUC) in the range ~ 0.58 – 0.71 using SNP data alone. Substantially higher predictor AUCs are obtained when incorporating additional variables such as age and sex. Some SNP predictors alone are sufficient to identify outliers (e.g., in the 99th percentile of PGS) with 3 – 8 times higher risk than typical individuals. We validate predictors out-of-sample using the eMERGE dataset, and also with different ancestry subgroups within the UK Biobank population. Our results indicate that substantial improvements in predictive power are attainable using training sets with larger case populations. We anticipate rapid improvement in genomic prediction as more case-control data become available for analysis.
ChIA-PIPE: A fully automated pipeline for ChIA-PET data analysis and visualization
Authors: Capurso Daniel , Wang Jiahui , Tian Simon Zhongyuan , Cai Liuyang , Namburi Sandeep , Lee Byoungkoo , Tjong Harianto , Tang Zhonghui , Wang Ping , Wei Chia-Lin , Ruan Yijun , Li Sheng
Published: December 2018

ChIA-PET enables the genome-wide discovery of chromatin interactions involving specific protein factors, with base-pair resolution. Interpreting ChIA-PET data depends on having a robust analytic pipeline. Here, we introduce ChIA-PIPE, a fully automated pipeline for ChIA-PET data processing, quality assessment, analysis, and visualization. ChIA-PIPE performs linker filtering, read mapping, peak calling, loop calling, chromatin-contact-domain calling, and can resolve allele-specific peaks and loops. ChIA-PIPE also automates quality-control assessment for each dataset. Furthermore, ChIA-PIPE generates input files for visualizing 2D contact maps with Juicebox and HiGlass, and provides a new dockerized visualization tool for high-resolution, browser-based exploration of peaks and loops. With minimal adjusting, ChIA-PIPE can also be suited for the analysis of other related chromatin-mapping data.
Functional imaging of microbial interactions with tree roots using a microfluidics setup
Authors: Noirot-Gros Marie-Francoise , Shinde Shalaka V. , Akins Chase , Johnson Jessica L. , Zerbs Sarah , Wilton Rosemarie , Kemner Ken , Noirot Philippe , Babnigg Gyorgy
Published: December 2018

Coupling microfludics with microscopy has emerged as a powerful approach to study at cellular resolution the dynamics in plant physiology and root-microbe interactions. Most devices have been designed to study the model plant Arabidopsis thaliana at higher throughput than conventional methods. However, there is a need for microfluidic devices which enable in vivo studies of root development and root-microbe interactions in woody plants. Here, we developed the RMI-chip, a simple microfluidic setup in which Populus tremuloides (aspen tree) seedlings can grow for over a month, allowing continuous microscopic observation of interactions between live roots and rhizobacteria. We find that the colonization of growing aspen roots by Pseudomonas fluorescens in the RMI-chip involves dynamic biofilm formation and dispersal, in keeping with previous observations in a different experimental set-up. Also, we find that whole-cell biosensors based on the rhizobacterium Bacillus subtilis can be used to monitor compositional changes in the rhizosphere but that the application of these biosensors is limited by their efficiency at colonizing aspen roots and persisting. These results indicate that functional imaging of dynamic root-bacteria interactions in the RMI-chip requires careful matching between the host plant and the bacterial root colonizer.
Energy Optimization is a Major Objective in the Real-Time Control of Step Width in Human Walking
Authors: Abram Sabrina J. , Selinger Jessica C. , Donelan J. Maxwell
Published: December 2018

People prefer to move in energetically optimal ways during walking. We have recently found that this preference arises not just through evolution and development, but that the nervous system will continuously optimize step frequency in response to new energetic cost landscapes. Here we test whether energy optimization is also a major objective in the nervous system's real-time control of step width. To accomplish this, we use a device that can reshape the relationship between step width and energetic cost, shifting the energy optimal width wider than that initially preferred. We find that the nervous system doesn't spontaneously initiate energy optimization, but instead requires experience with a lower energetic cost step width. After initiating optimization, people converge towards their new energy optimal width within hundreds of steps and update this as their new preferred width, rapidly returning to it when perturbed away. However, energy optimization was incomplete as this new preferred width was slightly narrower than the energetically optimal width. This suggests that the nervous system may determine its preferred width by optimizing energy simultaneously with other objectives such as stability or maneuverability. Collectively, these findings indicate that the nervous systems of able-bodied people continuously optimize energetic cost to determine preferred step width.
Elucidating genomic patterns and recombination events in plant cybrid mitochondria
Authors: Garcia Laura E. , Zubko Mikhajlo K. , Zubko Elena I. , Sanchez-Puerta M. Virginia
Published: December 2018

The maintenance of a dynamic equilibrium between the mitochondrial and nuclear genomes requires continuous communication and a high level of compatibility between them, so that alterations in one genetic compartment need adjustments in the other. The co-evolution of nuclear and mitochondrial genomes has been poorly studied, even though the consequences and effects of this interaction are highly relevant for human health, as well as for crop improvement programs and for genetic engineering. The mitochondria of plants represent an excellent system to understand the mechanisms of genomic rearrangements, chimeric gene formation, incompatibility between nucleus and cytoplasm, and horizontal gene transfer. We carried out detailed analyses of the mitochondrial genome (mtDNA) of a repeated cybrid between the solanaceaeNicotiana tabacumandHyoscyamus niger. The mtDNA of the cybrid was intermediate between the size of parental mtDNAs and the sum of them. Noticeably, most of the homologous sequences inherited from both parents were lost. In contrast, the majority of the sequences exclusive of a single parent were maintained. The mitochondrial gene content included a majority ofN. tabacumderived genes, but also chimeric, two-parent derived, andH. niger-derivedgenes in a tobacco nuclear background. Any of these alterations in the gene content could be the cause of CMS in the cybrid. The parental mtDNAs interacted through 28 homologous recombination events and a single case of illegitimate recombination. Three main homologous recombination mechanisms were recognized in the cybrid mitochondria. Break induced replication (BIR) pathway was the most frequent. We propose that BIR could be one of the mechanisms responsible for the loss of the majority of the repeated regions derived fromH. niger.
A thorough RNA-seq characterization of the porcine sperm transcriptome and its seasonal changes
Authors: Gòdia M. , Estill M. , Castelló A. , Balasch S. , Rodríguez-Gil J.E. , Krawetz S.A. , Sánchez A. , Clop A.
Published: December 2018

Understanding the molecular basis of cell function and ultimate phenotypes is crucial for the development of biological markers. With this aim, several RNA-seq studies have been devoted to characterize the transcriptome of ejaculated spermatozoa in relation to sperm quality and fertility. Semen quality follows a seasonal pattern and decays in the summer months in several animal species. The aim of this study was to deeply profile the transcriptome of the boar sperm and to evaluate its seasonal changes. We sequenced the total and the short fractions of the sperm RNA from 10 Pietrain boars, 5 collected in summer and 5 five sampled in winter, and identified a complex and rich transcriptome with 4,436 coding genes of moderate to high abundance. Transcript fragmentation was high but less obvious in genes related to spermatogenesis, chromatin compaction and fertility. Short non-coding RNAs mostly included piwi-interacting RNAs, transfer RNAs and micro-RNAs. We also compared the transcriptome of the summer and the winter ejaculates and identified 34 coding genes and 7 micro-RNAs with a significantly distinct distribution. These genes were mostly related to oxidative stress, DNA damage and autophagy. This is the deepest characterization of the boar sperm transcriptome and the first study linking the transcriptome and the seasonal variability of semen quality in animals. The annotation described here can be used as a reference for the identification of markers of sperm quality in pigs.
Mantoniella Beaufortii and Mantoniella Baffinensis sp. nov. (Mamiellales, Mamiellophyceae), Two New Green Algal Species from the High Arctic
Authors: Yau Sheree , dos Santos Adriana Lopes , Eikrem Wenche , Ribero Catherine Gérikas , Gourvil Priscilla , Balzano Sergio , Escande Marie-Line , Moreau Hervé , Vaulot Daniel
Published: December 2018

Members of the class Mamiellophyceae comprise species that can dominate picophytoplankton diversity in polar waters. Yet polar species are often morphologically indistinguishable from temperate species, although clearly separated by molecular features. Here we examine four Mamiellophyceae strains from the Canadian Arctic. The 18S rRNA and Internal Transcribed Spacer 2 (ITS2) gene phylogeny place these strains within the family Mamiellaceae (Mamiellales, Mamiellophyceae) in two separate clades of the genus Mantoniella. ITS2 synapomorphies support their placement as two new species, Mantoniella beaufortii and Mantoniella baffinensis. Both species have round green cells with diameter between 3–5 μm, one long flagellum and a short reduced flagellum (~1 μm) and are covered by spiderweb-like scales, making both species similar to other Mantoniella species. Morphologically, M. beaufortii and M. baffinensis are most similar to the cosmopolitan M. squamata with only minor differences in scale structure distinguishing them. Screening of global marine metabarcoding datasets indicates M. beaufortii has only been recorded in seawater and sea ice samples from the Arctic while no environmental barcode matches M. baffinensis. Like other Mamiellophyceae genera that have distinct polar and temperate species, the polar distribution of these new species suggests they are cold or ice-adapted Mantoniella species.
Wnt signalling is a major determinant of neuroblastoma cell lineages
Authors: Szemes Marianna , Greenhough Alexander , Malik Karim
Published: December 2018

The neural crest, which has been referred to as the fourth germ layer, comprises a multipotent cell population which will specify diverse cells and tissues, including craniofacial cartilage and bones, melanocytes, the adrenal medulla and the peripheral nervous system. These cell fates are known to be determined by gene regulatory networks (GRNs) acting at various stages of neural crest development, such as induction, specification, and migration. Although transcription factor hierarchies and some of their interplay with morphogenetic signalling pathways have been characterised, the full complexity of activities required for regulated development remains uncharted. Deregulation of these pathways may contribute to tumourigenesis, as in the case of neuroblastoma, a frequently lethal embryonic cancer thought to arise from the sympathoadrenal lineage of the neural crest.

In this conceptual analysis, we utilise next generation sequencing data from neuroblastoma cells and tumours to evaluate the possible influences of Wnt signalling on neural crest GRNs and on neuroblastoma cell lineages. We provide evidence that Wnt signalling is a major determinant of regulatory networks that underlie mesenchymal/NCC-like cell identities through PRRX1 and YAP/TAZ transcription factors. Furthermore, Wnt may also co-operate with Hedgehog signalling in driving proneural differentiation programmes along the adrenergic lineage. We propose that elucidation of Signalling Regulatory Networks can augment and complement GRNs in characterising cell identities, which will in turn contribute to the design of improved therapeutics tailored to primary and relapsing neuroblastoma.