bluuebunny/crossref_metadata_2025_split huggingface dataset:
Distinct functional roles for hopanoid composition in the chemical tolerance ofZymomonas mobilis
Authors: Brenac Léa , Baidoo Edward E.K. , Keasling Jay D. , Budin Itay 
Published: October 2018

SummaryHopanoids are abundant membrane lipids found in diverse bacterial lineages, but their physiological roles are not well understood. The ethanol fermenterZymomonas mobilisfeatures the highest measured concentration of hopanoids, leading to the hypothesis that these lipids can protect against bacterial solvent toxicity. However, the lack of genetic tools for manipulating hopanoid compositionin vivohas limited their further functional analysis. Because of polyploidy (> 50 genome copies per cell), we found that disruptions of essential hopanoid biosynthesis (hpn) genes inZ. mobilisact as genetic knockdowns, reliably modulating the abundance of different hopanoid species. Using a set ofhpntransposon mutants, we demonstrate that both reduced hopanoid content and modified hopanoid head group composition mediate growth and survival in ethanol. In contrast, the amount of hopanoids, but not their polar group composition, contributes to fitness at low pH. Spectroscopic analysis of model membranes showed that hopanoids protect against several ethanol-driven phase transitions in membrane structure, including lipid interdigitation and bilayer dissolution. We propose that hopanoids act through a combination of hydrophobic and inter-lipid hydrogen bonding interactions to stabilize bacterial membranes against solvent stress.Graphical abstract
Dissection of protonation sites for antibacterial recognition and transport in QacA, a multi-drug efflux transporter
Authors: Majumder Puja , Khare Shashank , Athreya Arunabh , Hussain Nazia , Gulati Ashutosh , Penmatsa Aravind 
Published: October 2018

AbstractQacA is a drug:H+ antiporter (DHA2) with 14 transmembrane helices, that renders antibacterial resistance to methicillin-resistant Staphylococcus aureus (MRSA) strains, with homologues in other pathogenic organisms. It is a highly promiscuous antiporter, capable of H+- driven efflux of a wide array of cationic antibacterial compounds and dyes. Our study, using a homology model of QacA, reveals a group of six protonatable residues in its vestibule. Systematic mutagenesis resulted in identification of D34 (TM1), and a cluster of acidic residues in TM13 including E407 and D411 and D323 in TM10, as being crucial for substrate recognition and transport of monovalent and divalent cationic antibacterial compounds. The transport and binding properties of QacA and its mutants were explored using whole cells, inside-out vesicles, substrate-induced H+ release and microscale thermophoresis. We identify two sites, D34 and D411 as vital players in substrate recognition while E407 facilitates substrate efflux as a protonation site. We also observe that E407 plays a moonlighting role as a substrate recognition site for dequalinium transport. These observations rationalize the promiscuity of QacA for diverse substrates. The study unravels the role of acidic residues in QacA with implications for substrate recognition, promiscuity and processive transport in multidrug efflux transporters, related to QacA.HighlightsA homology model of QacA with 14 TM helices was used to test the importance of acidic residues within the vestibule.Mono and Divalent cationic substrate recognition requires two sites D34 (TM1) and D411 (TM13).E407 (TM13) is important for protonation driven efflux.Substrate recognition of a divalent substrate, dequalinium occurs at E407 instead of D411 providing glimpses into the promiscuity of substrate recognition in QacA.
Adaptive disinhibitory gating by VIP interneurons permits associative learning
Authors: Krabbe Sabine , Paradiso Enrica , D’Aquin Simon , Bitterman Yael , Xu Chun , Yonehara Keisuke , Markovic Milica , Gründemann Jan , Ferraguti Francesco , Lüthi Andreas 
Published: October 2018

AbstractLearning drives behavioral adaptations necessary for survival. While plasticity of excitatory projection neurons during associative learning is studied extensively, little is known about the contributions of local interneurons. Using fear conditioning as a model for associative learning, we find that behaviorally relevant, salient stimuli cause learning by tapping into a local microcircuit consisting of precisely connected subtypes of inhibitory interneurons. By employing calcium imaging and optogenetics, we demonstrate that vasoactive intestinal peptide (VIP)-expressing interneurons in the basolateral amygdala are activated by aversive events and provide an instructive disinhibitory signal for associative learning. Notably, VIP interneuron responses are plastic and shift from the instructive to the predictive cue upon memory formation. We describe a novel form of adaptive disinhibitory gating by VIP interneurons that allows to discriminate unexpected, important from irrelevant information, and might be a general dynamic circuit motif to trigger stimulus-specific learning, thereby ensuring appropriate behavioral adaptations to salient events.
Bud13 Promotes a Type I Interferon Response by Countering Intron Retention in Irf7
Authors: Frankiw Luke S. , Majumdar Devdoot , Burns Christian , Moradian Annie , Sweredoski Michael J. , Baltimore David 
Published: October 2018

SUMMARYIntron retention (IR) has emerged as an important mechanism of gene expression control. Despite this, the factors that control IR events remain poorly understood. We observed consistent IR in one intron of the Irf7 gene and identified Bud13 as an RNA-binding protein that acts at this intron to increase the amount of successful splicing. Deficiency in Bud13 led to increased IR, decreased mature Irf7 transcript and protein levels, and consequently to a dampened type I interferon response. This impairment of Irf7 production in Bud13-deficient cells compromised their ability to withstand VSV infection. Global analysis of Bud13 knockdown and BUD13 cross-linking to RNA revealed a subset of introns that share many characteristics with the one found in Irf7 and are spliced in a Bud13-dependent manner. Deficiency of Bud13 led to decreased mature transcript from genes containing such introns. Thus, by acting as an antagonist to IR, Bud13 facilitates the expression of genes at which IR occurs.
Diversity and population genetic structure of the wax palmCeroxylon quindiuensein the Colombian Coffee Region
Authors: González-Rivillas Natalia , Bohórquez Adriana , Patricia Gutierrez Janeth , García-Merchán Víctor Hugo 
Published: October 2018

AbstractThe wax palm from Quindío (Ceroxylon quindiuense) is an icon of the cultural identity of the coffee growing eco-region and of all Colombia. Processes of urbanization, expansion of the agricultural and livestock area, among others, have increased its level of threat. Protecting this palm from extinction is important at an ecological level, given its function as a key species in Andean ecosystems. This work evaluated the diversity and population genetic structure of the wax palm from Quindío in five populations of the Colombian coffee region eco-region (Andean zone) by using ten microsatellite molecular markers. Two groups were identified at genetic diversity level, along with a heterozygote deficiency in all the populations possibly due to cryptic population structure effects mediated by loss of habitat. The five sampling units considered presented a total significant genetic structure, revealing a high degree of reproductive isolation. The results presented here add to the Conservation Plan for this species existing in Colombia.
The effect of butyrate-supplemented parenteral nutrition on intestinal defence mechanisms and the parenteral nutrition-induced shift in the gut microbiota
Authors: Jirsova Z , Heczkova M , Dankova H , Malinska H , Videnska P , Vespalcova H , Micenkova L , Bartonova L , Sticova E , Lodererova A , Prefertusová L. , Sekerkova A , Cahova M 
Published: October 2018

AbstractButyrate produced by the intestinal microbiota is essential for proper functioning of the intestinal immune system. Total dependence on parenteral nutrition (PN) is associated with numerous adverse effects, including severe microbial dysbiosis and loss of important butyrate producers. We hypothesised that a lack of butyrate produced by the gut microbiota may be compensated by its supplementation in PN mixtures. We tested whetheri.v.butyrate administration would (a) positively modulate intestinal defence mechanisms and (b) counteract PN-induced dysbiosis. Male Wistar rats were randomised to chow, PN, and PN supplemented with 9 mM butyrate (PN+But) for 12 days. Antimicrobial peptides, mucins, tight junction proteins and cytokine expression were assessed by RT-qPCR. T-cell subpopulations in mesenteric lymph nodes (MLN) were analysed by flow cytometry. Microbiota composition was assessed in caecum content. Butyrate supplementation resulted in increased expression of tight junction proteins (ZO-1, claudin-7, E-cadherin), antimicrobial peptides (Defa 8, Rd5, RegIIIγ) and lysozyme in the ileal mucosa. Butyrate partially alleviated PN-induced intestinal barrier impairment and normalised IL-4, IL-10 and IgA mRNA expression. PN administration was associated with an increase in Tregs in MLN, which was normalised by butyrate. Butyrate increased the total number of CD4+ and decreased a relative amount of CD8+ memory T cells in MLN. Lack of enteral nutrition and PN administration led to a shift in caecal microbiota composition. Butyrate did not reverse the altered expression of most taxa but did influence the abundance of some potentially beneficial/ pathogenic genera, which might contribute to its overall beneficial effect.
Bidirectional action of nitric oxide on mitochondrial respiration and permeability transition pore induced by calcium and palmitoylcarnitine
Authors: Dynnik Vladimir V. , Grishina Elena V. , Fedotcheva Nadezhda I 
Published: October 2018

AbstractThe role of mitochondrial calcium-dependent NO synthase in the control of respiration and mitochondrial permeability transition pore (MPTP) opening, as well as possible involvement of mitochondrial NO synthase/guanylate cyclase/kinase G-signaling system (mtNOS-SS) in the regulation of these processes are not sufficiently studied. In this work, using rat liver mitochondria, we applied specific inhibitors of the enzymes of this signaling system to evaluate its role in the control of respiration and MPTP. The respiration was supported by pyruvate and glutamate or succinate in the presence of hexokinase, glucose and ADP. The results indicate that L-arginine and NO donors SNP and SNAP produce bidirectional concentration-dependent effects on the respiration and MPTP opening evoked by calcium ions or D,L-palmitoylcarnitine. Maximal activation of respiration was observed at 20 µM of L-arginine or SNP. At low concentrations, L-arginine (to 500 µM) and NO donors (to 50 µM) increased the threshold concentrations of calcium and D,L-palmitoylcarnitine required for the dissipation of the mitochondrial membrane potential and pore opening. The application of the inhibitors of NO synthase, guanylate cyclase, and kinase G eliminated both effects. These data indicate the involvement of mtNOS-SS in the activation of respiration and deceleration of MPTP opening. At high concentrations, L-arginine and NO donors inhibited the respiration and promoted pore opening, indicating that the inhibition induced by NO excess dominates over the protection caused by mtNOS-SS. These results demonstrate that the functioning of mtNOS-SS might provide a feedforward activation of respiration and a lowering of MPTP sensitivity to calcium and palmitoylcarnitine overload.
Using pan RNA-seq analysis to reveal the ubiquitous existence of 5’ end and 3’ end small RNAs
Authors: Xu Xiaofeng , Ji Haishuo , Cheng Zhi , Jin Xiufeng , Yao Xue , Liu Yanqiang , Zhao Qiang , Zhang Tao , Ruan Jishou , Bu Wenjun , Chen Ze , Gao Shan 
Published: October 2018

AbstractIn this study, we used pan RNA-seq analysis to reveal the ubiquitous existence of 5’ end and 3’ end small RNAs. 5’ and 3’ sRNAs alone can be used to annotate mitochondrial with 1-bp resolution and nuclear non-coding genes and identify new steady-state RNAs, which are usually from functional genes. Using 5’, 3’ and intronic sRNAs, we revealed that the enzymatic dsRNA cleavage and RNAi could involve in the RNA degradation and gene expression regulation of U1 snRNA in human. The further study of 5’, 3’ and intronic sRNAs help rediscover double-stranded RNA (dsRNA) cleavage, RNA interference (RNAi) and the regulation of gene expression, which challenges the classical theories. In this study, we provided a simple and cost effective way for the annotation of mitochondrial and nuclear non-coding genes and the identification of new steady-state RNAs, particularly long non-coding RNAs (lncRNAs). We also provided a different point of view for cancer and virus, based on the new discoveries of dsRNA cleavage, RNAi and the regulation of gene expression.
RBF network based adaptive sliding mode control for solar sails
Authors: Lian Xiaobin , Liu Jiafu , Wang Chuang , Yuan Tiger , Cui Naigang 
Published: October 2018

Purpose
The purpose of this paper is to resolve complex nonlinear dynamical problems of the pitching axis of solar sail in body coordinate system compared with inertial coordinate system. And saturation condition of controlled torque of vane in the orbit with big eccentricity ration, uncertainty and external disturbance under complex space background are considered.

Design/methodology/approach
The pitch dynamics of the sailcraft in the prescribed elliptic earth orbits is established considering the torques by the control vanes, gravity gradient and offset between the center-of-mass (cm) and center-of-pressure (cp). The maximal torques afforded by the control vanes are numerically determined for the sailcraft at any position with any pitch angle, which will be used as the restriction of the attitude control torques. The finite/infinite time adaptive sliding mode saturation controller and Bang–Bang–Radial Basis Function (RBF) controller are designed for the sailcraft with restricted attitude control torques. The model uncertainty and the input error (the error between real input and ideal control law input) are solved using the RBF network.

Findings
The finite true anomaly adaptive sliding mode saturation controller performed better than the other two controllers by comparing the numerical results in the paper. The control torque saturation, the model uncertainty and the external disturbance were also effectively solved using the infinite and finite time adaptive sliding mode saturation controllers by analyzing the numerical simulations. The stabilization of the pitch motion was accomplished within half orbit period.

Practical implications
The complex accurate dynamics can be approximated using the RBF network. The controllers can be applied to stabilization of spacecraft attitude dynamics with uncertainties in complex space environment.

Originality/value
Advanced control method is used in this paper; saturation of controlled torque of vane is resolved when the orbit with big eccentricity ration is considered and uncertainty and external disturbance under complex space background are settled. Moreover, complex and accurate nonlinear dynamical model of pitching axis of solar sail in body coordinate system compared with inertial coordinate system is provided.
Hardware-in-the-loop flight motion simulation of flexible variable sweep aircraft
Authors: Inayat Irum , Amin Rooh ul , Ali Malik Mazhar 
Published: October 2018

Purpose
This paper aims to propose an improved and computationally efficient motion simulation of a flexible variable sweep aircraft.

Design/methodology/approach
The motion simulation is performed on hardware-in-the-loop simulation setup using 6 degree-of-freedom motion platform. The dynamic model of a flexible variable sweep aircraft, Rockwell B-1 Lancer is presented using equations of motions for combined rigid and flexible motions. The peak filter is introduced as a new method to separate flexible motion from aircraft motion data. Standard adaptive washout filter is modified and redesigned for an accurate flexible aircraft flight simulation. The flight data are generated using FlightGear software. Another motion profile with significant oscillations is also tested. The peak filter and the modified adaptive washout filter both are used to process the data according to the motion envelop of motion platform.

Findings
The performance of the modified adaptive washout filter is evaluated using hardware-in-the-loop simulation setup and results are compared with the standard adaptive washout filter. Results exhibit that the proposed method is computationally cost-effective and improves the motion simulation of flexible aircraft with close to realistic motion cues.

Originality/value
The proposed work presents motion simulation of a flexible aircraft by introducing a peak filter to extract flexible motion in contrast to the traditional motion separation methods. Also, a modified adaptive washout filter is designed and implemented in place of the traditional washout filters for improved flexible aircraft flight motion simulation.
A dynamic simplified Lund model for large-eddy simulation and its application to a centrifugal pump
Authors: Huang Xianbei , Qiu Baoyun , Guo Qiang , Liu Zhuqing , Yang Wei , Li Yaojun 
Published: October 2018

Purpose
Construct a new sub-grid scale (SGS) model which can improve the efficiency and maintain comparative accuracy comparing to the existing dynamic cubic non-linear SGS model (DCNM).

Design/methodology/approach
The polynomial constitutive relation between the SGS stress tensor and both strain and rotation rate is selected as a basement. Simplification is achieved by eliminating the solid-body rotation term and adopting the assumption proposed by Kosovic. A dynamic procedure is applied to calculate three model coefficients in the new model. The new model (named dynamic simplified Lund model) and DCNM are applied to the rotating channel flow and the internal flow in a centrifugal pump impeller to examine the performance.

Findings
The new model is as accurate as DCNM but decreases 25 per cent computational resources. The ability of capturing rotation effect and reflecting backscatter is verified through cases. In addition, good numerical stability is shown during the calculation.

Research limitations/implications
More benchmark and engineering cases should be used to get further confidence on the new model.

Practical implications
The new model is promising in industrial application with the advantage of both accuracy and efficiency. For the flow with large-scale separation or more complicate phenomenon, the model is thought to give accurate flow structure.

Originality/value
A new non-linear SGS model is proposed in this paper. The accuracy, numerical stability and efficiency are validated for this model. Therefore, it is promising in the prediction of the flow structure in centrifugal pumps.
Numerical analysis for interphase forces of gas-liquid flow in a multiphase pump
Authors: Liu Ming , Cao Shan , Cao Shuliang 
Published: October 2018

Purpose
The modeling of interphase forces plays a significant role in the numerical simulation of gas–liquid flow in a rotodynamic multiphase pump, which deserves detailed study.

Design/methodology/approach
Numerical analysis is conducted to estimate the influence of interphase forces, including drag force, lift force, virtual mass force, wall lubrication force and turbulent dispersion force.

Findings
The results show that the magnitude of the interphase forces can be sorted by: drag force > virtual mass force > lift force > turbulent dispersion force > wall lubrication force. The relations between interphase forces and velocity difference of gas–liquid flow and also the interphase forces and gas volume fraction are revealed. The distribution characteristics of interphase forces in the passages from impeller inlet to diffuser outlet are illustrated and analyzed. According to the results, apart from the drag force, the virtual mass force, lift force and turbulent dispersion force are required, whereas wall lubrication force can be neglected for numerical simulation of gas–liquid flow in a rotodynamic multiphase pump. Compared with the conventional numerical method which considers drag force only, the relative errors of predicted pressure rise and efficiency based on the proposed numerical method in account of four major forces can be reduced by 4.95 per cent and 3.00 per cent, respectively.

Originality value
The numerical analysis reveals the magnitude and distribution of interphase forces inside multiphase pump, which is meaningful for the simulation and design of multiphase pump.
Evidential uncertainty quantification of the Park–Ang damage model in performance based design
Authors: Tang Hesheng , Li Dawei , Deng Lixin , Xue Songtao 
Published: October 2018

Purpose
This paper aims to develop a comprehensive uncertainty quantification method using evidence theory for Park–Ang damage index-based performance design in which epistemic uncertainties are considered. Various sources of uncertainty emanating from the database of the cyclic test results of RC members provided by the Pacific Earthquake Engineering Research Center are taken into account.

Design/methodology/approach
In this paper, an uncertainty quantification methodology based on evidence theory is presented for the whole process of performance-based seismic design (PBSD), while considering uncertainty in the Park–Ang damage model. To alleviate the burden of high computational cost in propagating uncertainty, the differential evolution interval optimization strategy is used for efficiently finding the propagated belief structure throughout the whole design process.

Findings
The investigation results of this paper demonstrate that the uncertainty rooted in Park–Ang damage model have a significant influence on PBSD design and evaluation. It might be worth noting that the epistemic uncertainty present in the Park–Ang damage model needs to be considered to avoid underestimating the true uncertainty.

Originality/value
This paper presents an evidence theory-based uncertainty quantification framework for the whole process of PBSD.
Waste identification diagram and value stream mapping
Authors: Dinis-Carvalho Jose , Guimaraes Levi , Sousa Rui M. , Leao Celina Pinto 
Published: October 2018

PurposeThe purpose of this paper is to compare the well-known value stream mapping (VSM) with a recent tool named waste identification diagram (WID), regarding the capacity of information representation and easiness of interpretation.Design/methodology/approachThe work begins with a brief literature review comparing the main tools for representation of production units, with special emphasis on VSM and WID, in terms of ability to identify several types of waste. Then, the authors developed the VSM and the WID of a specific production unit and after that several groups composed by students of Industrial Engineering (IE) and/or professionals from industry were asked to analyse/interpret only one of these diagrams. Finally, a questionnaire with closed and open questions was applied to the groups to evaluate the analysed tool.FindingsIn general, the results revealed that WID is more effective than VSM and participants recognized that most of the WID elements are relevant. Specifically, a measure coined overall effectiveness was applied (based on the response time and percentage of correct interpretations), indicating a clear advantage of WID (22 per cent of correct interpretations per minute) compared to VSM (9 per cent of correct interpretations per minute). The main drawback pointed to the WID is the lack of representation of the information flow.Originality/valueThis work contributes to the IE field by revealing WID as a new promising graphical tool for representation of production units, especially in terms of identification/quantification of wastes. The tool was quantitative and qualitatively evaluated by persons both from academia and industry.