bluuebunny/crossref_metadata_2025 huggingface dataset:
Stress-induced magnetic properties of PLD-grown high-quality ultrathin YIG films
Authors: Bhoi Biswanath , Kim Bosung , Kim Yongsub , Kim Min-Kwan , Lee Jae-Hyeok , Kim Sang-Koog
Published: May 2018

Yttrium iron garnet (YIG:Y3Fe5O12) thin films were grown on (111) gadolinium gallium garnet (Gd3Ga5O12, GGG) substrates using pulsed-laser deposition under several different deposition and annealing conditions. X-ray diffraction measurements revealed that the crystallographical orientation of the YIG films is pseudomorphic to and the same as that of the GGG substrate, with a slight rhombohedral distortion along the surface normal. Furthermore, X-ray reciprocal space mapping evidenced that in-situ annealed YIG films during film growth are under compressive strain, whereas ex-situ annealed films have two different regions under compressive and tensile strain. The saturation magnetization (4πMS) of the films was found to vary, according to the deposition conditions, within the range of 1350 to 1740 G, with a very low coercivity of HC < 5 Oe. From ferromagnetic resonance (FMR) measurements, we estimated the effective saturation magnetization (4πMeff) to be 1810 to 2530 G, which are larger than that of single crystalline bulk YIG (∼1750 G). Such high values of 4πMeff are attributable to the negative anisotropy field (HU) that increases in size with increasing compressive in-plane strain induced in YIG films. The damping constant (αG) of the grown YIG films was found to be quite sensitive to the strain employed. The lowest value of αG obtained was 2.8 × 10−4 for the case of negligible strain. These results suggest a means of tailoring HU and αG in the grown YIG films by the engineering of strain for applications in spintronics and magneto-optical devices.
The nature of the Pt(111)/α-Fe2O3(0001) interfaces revealed by DFT calculations
Authors: Mahmoud Agnes , Deleuze Pierre-Marie , Dupont Céline
Published: May 2018

Density functional theory calculations are performed to give a thorough description of structural, energetic, and electronic properties of Pt(111)/α-Fe2O3(0001) systems by spin-polarized calculations, accounting for the on-site Coulomb interaction. Toward the better understanding of Pt(111)/α-Fe2O3(0001) interfaces, two terminations of α-Fe2O3(0001) surface, namely, the single Fe- and the O3-termination, are considered and coupled with the four possible (top, hcp, fcc, and bridge) sites on Pt(111). The effect of the strain on clean hematite surfaces due to the lattice mismatch between the substrate and the overlayer is included in the analysis. Among the possible adsorption configurations, bridge sites are unstable, while the most favorable configurations are the ones at hollow sites. The stability of the interfaces is not only influenced by the termination of the overlayer but also influenced by the degree of its structural relaxation and the relative position of the first layer of O atoms in hematite with respect to Pt. To elucidate the different nature of the two terminations of the overlayer on Pt, projected density of states and 3D charge density difference plots are also discussed.
Microchannel plate cross-talk mitigation for spatial autocorrelation measurements
Authors: Lipka Michał , Parniak Michał , Wasilewski Wojciech
Published: May 2018

Microchannel plates (MCP) are the basis for many spatially resolved single-particle detectors such as ICCD or I-sCMOS cameras employing image intensifiers (II), MCPs with delay-line anodes for the detection of cold gas particles or Cherenkov radiation detectors. However, the spatial characterization provided by an MCP is severely limited by cross-talk between its microchannels, rendering MCP and II ill-suited for autocorrelation measurements. Here, we present a cross-talk subtraction method experimentally exemplified for an I-sCMOS based measurement of pseudo-thermal light second-order intensity autocorrelation function at the single-photon level. The method merely requires a dark counts measurement for calibration. A reference cross-correlation measurement certifies the cross-talk subtraction. While remaining universal for MCP applications, the presented cross-talk subtraction, in particular, simplifies quantum optical setups. With the possibility of autocorrelation measurements, the signal needs no longer to be divided into two camera regions for a cross-correlation measurement, reducing the experimental setup complexity and increasing at least twofold the simultaneously employable camera sensor region.
Superhydrophobic, carbon-infiltrated carbon nanotubes on Si and 316L stainless steel with tunable geometry
Authors: Stevens Kimberly A. , Esplin Christian D. , Davis Taylor M. , Butterfield D. Jacob , Ng Philip S. , Bowden Anton E. , Jensen Brian D. , Iverson Brian D.
Published: May 2018

The use of carbon nanotubes to create superhydrophobic coatings has been considered due to their ability to offer a relatively uniform nanostructure. However, carbon nanotubes (CNTs) may be considered delicate with a typical diameter of tens of nanometers for a multi-walled CNT; as-grown carbon nanotubes often require the addition of a thin-film hydrophobic coating to render them superhydrophobic. Furthermore, fine control over the diameter of the as-grown CNTs or the overall nanostructure is difficult. This work demonstrates the utility of using carbon infiltration to layer amorphous carbon on multi-walled nanotubes to improve structural integrity and achieve superhydrophobic behavior with tunable geometry. These carbon-infiltrated carbon nanotube (CICNT) surfaces exhibit an increased number of contact points between neighboring tubes, resulting in a composite structure with improved mechanical stability. Additionally, the native surface can be rendered superhydrophobic with a vacuum pyrolysis treatment, with contact angles as high as 160° and contact angle hysteresis on the order of 1°. The CICNT diameter, static contact angle, sliding angle, and contact angle hysteresis were examined for varying levels of carbon-infiltration to determine the effect of infiltration on superhydrophobicity. The same superhydrophobic behavior and tunable geometry were also observed with CICNTs grown directly on stainless steel without an additional catalyst layer. The ability to tune the geometry while maintaining superhydrophobic behavior offers significant potential in condensation heat transfer, anti-icing, microfluidics, anti-microbial surfaces, and other bio-applications where control over the nanostructure is beneficial.
Optimising fishery characteristics through control of an invasive species: strategies for redfin perch control in Lake Purrumbete, Australia
Authors: Gwinn Daniel C. , Ingram Brett A.
Published: May 2018

Invasive fish species can present difficult management problems, particularly when the species has recreational value. One such case is redfin perch in Lake Purrumbete, Australia, which have recreational value but have become invasive in the lake. In this study we evaluated removal strategies for redfin perch in Lake Purrumbete with the aim of improving the quality of the recreational fishery. We evaluated removal scenarios for redfin perch with a population model and conducted a sensitivity analysis to determine the robustness of our general results. The results suggest that removal scenarios that direct exploitation, on an annual time scale, at fish ≤150-mm total length, with high levels of exploitation, will result in the greatest reduction in small undesirable fish and the greatest increase in large desirable fish in the lake. This was consistent across most assumptions about life-history characteristics, density-dependent processes and population dynamics rates, suggesting that this management strategy is robust to most relevant biological uncertainties. Furthermore, exploiting redfin perch on an annual time scale would result in the lowest annual variation in the population because of disruption of the age and size structure. These results can help managers choose strategies to manipulate the fishery of Lake Purrumbete to achieve more desirable characteristics.
Assessing the value of rural community health services
Authors: Farmer Jane , Davis Hilary , Blackberry Irene , de Cotta Tracy
Published: May 2018

Rural health services are challenging to manage, a situation perhaps exacerbated by necessity to comply with one-size-fits-all performance frameworks designed for larger services. This raises the questions: do we know what rural health services are doing that is valuable and how should that be evaluated? Twenty-eight qualitative interviews with CEOs and staff of seven Victorian rural health services were conducted, exploring what they value about their ‘best practice’. Themes emergent from analysis were compared with 19 government-produced health planning and performance documents. It was found that most dimensions of rural services value aligned with current performance frameworks, but a significant theme about ‘community’ was missing. Highlighting the relevance of this theme, achieving community-oriented goals accounted for one-third of best practice case studies identified by health services personnel. It is concluded that generating community outcomes is a significant area of value aimed for by rural health services that is missing from current performance measurement frameworks applied to Victorian health services. In this study, a new Evaluative Framework is outlined and further steps needed are suggested.
Defective phagosome motility and degradation in cell nonautonomous RPE pathogenesis of a dominant macular degeneration
Authors: Esteve-Rudd Julian , Hazim Roni A. , Diemer Tanja , Paniagua Antonio E. , Volland Stefanie , Umapathy Ankita , Williams David S.
Published: May 2018

Significance

Cell nonautonomous toxicity is involved in various neurodegenerations, but mechanistic understanding is limited. Here, we provide insight into cellular mechanisms underlying a dominant macular degeneration, which results from mutant
ELOVL4
, and represents an unusual case of two separate cell nonautonomous events. We demonstrate that the first event involves RPE phagocytosis of photoreceptor disc membranes that contain mislocalized mutant ELOVL4 protein. We show that the mutant phagosomes are degraded inefficiently, thus introducing toxicity to the RPE. This leads to the second event involving perturbed retinal homeostasis of the neural retina and photoreceptor degeneration. In addition, our results provide a unique demonstration that phagosome content affects phagosome motility and that the motility of the phagosome, specifically, may be critical for its timely degradation.
Dopamine receptors mediate strategy abandoning via modulation of a specific prelimbic cortex–nucleus accumbens pathway in mice
Authors: Cui Qiaoling , Li Qian , Geng Hongyan , Chen Lei , Ip Nancy Y. , Ke Ya , Yung Wing-Ho
Published: May 2018

Significance

Strategy-switching flexibility is a critical executive function necessary for living in an ever-evolving environment, and this ability is often impaired in attentional deficit and hyperactivity disorder, schizophrenia, and early Parkinson’s disease. To date, the underlying brain circuitry and receptor mechanisms are not entirely clear. The results of the present study suggest the essential role of a specific projection from prelimbic cortex to nucleus accumbens (NAc) D2 medium spiny neurons as well as NAc dopamine and presynaptic dopamine receptors of this projection in controlling the strategy-switching flexibility. These findings promote a better understanding of circuitry and neurobiology of strategy-switching flexibility and could contribute to identifying novel therapeutic targets for patients suffering from strategy-switching inflexibility.
LRRK2 phosphorylation of auxilin mediates synaptic defects in dopaminergic neurons from patients with Parkinson’s disease
Authors: Nguyen Maria , Krainc Dimitri
Published: May 2018

Significance

Identifying dysfunctional cellular mechanisms in sporadic neurodegenerative diseases has been challenging. Therefore, in-depth investigation of genetic forms of disease can provide valuable insight into pathogenic disease mechanisms. Here, we demonstrate the novel interaction between two Parkinson’s disease-linked genes, LRRK2 and auxilin. Additionally, as both genes have described roles at the synapse, we identify synaptic dysfunction as a contributor of dopamine-mediated toxic effects in human dopaminergic neurons. Together, these results highlight the importance of the mechanistic dissection of genetic forms of Parkinson’s disease to identify converging pathways and targets for therapeutic intervention.
Importing food damages domestic environment: Evidence from global soybean trade
Authors: Sun Jing , Mooney Harold , Wu Wenbin , Tang Huajun , Tong Yuxin , Xu Zhenci , Huang Baorong , Cheng Yeqing , Yang Xinjun , Wei Dan , Zhang Fusuo , Liu Jianguo
Published: May 2018

Significance

Achieving global environmental sustainability and food security is among the world’s biggest challenges. International food trade plays an important role in global food security. It is widely believed that importing countries benefit environmentally from international food trade at the environmental cost of exporting countries. Contrary to the conventional wisdom, our study reveals a major environmental problem in importing countries. The unexpected findings suggest the need to reevaluate environmental consequences of international trade in all importing countries through discussions regarding environmental responsibilities among consumers and producers. There is an urgent need for innovative solutions for reducing environmental pollution and enhancing food security to offset the negative impacts of international trade globally.
Pan-cancer transcriptional signatures predictive of oncogenic mutations reveal that Fbw7 regulates cancer cell oxidative metabolism
Authors: Davis Ryan J. , Gönen Mehmet , Margineantu Daciana H. , Handeli Shlomo , Swanger Jherek , Hoellerbauer Pia , Paddison Patrick J. , Gu Haiwei , Raftery Daniel , Grim Jonathan E. , Hockenbery David M. , Margolin Adam A. , Clurman Bruce E.
Published: May 2018

Significance

Tumor suppression by the Fbw7 ubiquitin ligase remains poorly understood. Here, we used informatics and engineered cancer cells to show that Fbw7 mutations cause metabolic reprogramming by increasing oxidative phosphorylation and metabolic vulnerabilities that may represent therapeutic targets. Our approach may be applied to study other complex cancer genes.
Critical vaporization of MgSiO
3
Authors: Xiao Bing , Stixrude Lars
Published: May 2018

Significance

During accretion, giant impacts may partially vaporize planets, with profound consequences for energy and mass transfer between the growing planet and its satellites. We find that giant impacts produce much more supercritical fluid than previously thought, with a much lower liquid–vapor critical temperature. The vapor is depleted in Mg with respect to coexisting liquid and has very different chemical bonding, being dominated by covalent molecules (O
2
and SiO) up to the critical point. These molecules also appear in significant fractions within the near-critical liquid phase, making the liquid structure fundamentally different from that near the melting point.
Osmotic stabilization prevents cochlear synaptopathy after blast trauma
Authors: Kim Jinkyung , Xia Anping , Grillet Nicolas , Applegate Brian E. , Oghalai John S.
Published: May 2018

Significance

Trauma due to roadside bombs is an unfortunate consequence of modern warfare and terrorist attacks. Hearing loss often occurs because the cochlea is the body’s most sensitive pressure transducer. Here, we used in vivo imaging of the mouse cochlea using optical coherence tomography to show that increased endolymph volume correlates with damage to the auditory synapse. Reducing endolymph volume by increasing perilymph tonicity treated the synaptic loss. Therefore, this study identifies a treatment for noise-induced hearing loss. Furthermore, it suggests that this treatment may help patients with Meniere’s disease, a disabling syndrome of vertigo and hearing loss due to increased endolymph volume.
Fully gapped
d
-wave superconductivity in CeCu
2
Si
2
Authors: Pang Guiming , Smidman Michael , Zhang Jinglei , Jiao Lin , Weng Zongfa , Nica Emilian M. , Chen Ye , Jiang Wenbing , Zhang Yongjun , Xie Wu , Jeevan Hirale S. , Lee Hanoh , Gegenwart Philipp , Steglich Frank , Si Qimiao , Yuan Huiqiu
Published: May 2018

Significance

Identifying the gap structure of superconductors is vital for understanding the underlying pairing mechanism of the Cooper pairs. The first heavy fermion superconductor to be discovered, CeCu
2
Si
2
, was thought to be a

d

-wave superconductor with gap nodes, until recent specific heat measurements provided evidence that the gap is fully open across the Fermi surface. We propose a resolution to this puzzle from measurements of the London penetration depth, which give further evidence for fully gapped superconductivity. We analyze the data using a

d

-wave band-mixing pairing model, which leads to a fully open superconducting gap. Our model accounts well for the penetration depth and specific heat data, while reconciling the nodeless and sign-changing nature of the gap function.
Artificial selection reveals sex differences in the genetic basis of sexual attractiveness
Authors: Gosden Thomas P. , Reddiex Adam J. , Chenoweth Stephen F.
Published: May 2018

Significance

Using artificial selection on fruit fly pheromones, we tested how mate choice by both sexes can cause evolutionary change. Results show that although both sexes choose mates, the evolutionary outcomes are fundamentally different for each sex. Specifically, experimental results show that the evolution of pheromones can only be driven through female choice of males because genetic relationships exist between pheromones, mating success, and fitness. Male choice of females, however, cannot drive evolutionary change by itself because the correlation between pheromones and mating success is generated by environmental rather than genetic variation. Therefore, the traits targeted in females by male choice are likely to evolve through correlated responses to selection on males.
Simulated night shift work induces circadian misalignment of the human peripheral blood mononuclear cell transcriptome
Authors: Kervezee Laura , Cuesta Marc , Cermakian Nicolas , Boivin Diane B.
Published: May 2018

Significance

Night shift work is associated with adverse health effects, including diabetes, cardiovascular disease, and cancer. Understanding the molecular mechanisms that underlie this association is instrumental in advancing the diagnosis, prevention, and treatment of shift work-related health concerns. We characterized the effect on genome-wide gene expression levels of a 4-day protocol simulating night shifts in healthy human subjects under highly controlled laboratory conditions. We demonstrate that this night shift protocol leads to a dampening of gene expression rhythms and a desynchrony between rhythmic transcripts and the shifted sleep/wake cycle. Moreover, we uncovered key biological processes and regulatory molecules that are altered during this night shift protocol and that may contribute to the development of health problems on the long term.
Anomalous density fluctuations in a strange metal
Authors: Mitrano M. , Husain A. A. , Vig S. , Kogar A. , Rak M. S. , Rubeck S. I. , Schmalian J. , Uchoa B. , Schneeloch J. , Zhong R. , Gu G. D. , Abbamonte P.
Published: May 2018

Significance

The strange metal is a poorly understood state of matter found in a variety of quantum materials, notably both Cu- and Fe-based high-temperature superconductors. Strange metals exhibit a nonsaturating, T-linear electrical resistivity, seemingly indicating the absence of electron quasiparticles. Using inelastic electron scattering, we report a momentum-resolved measurement of the dynamic charge susceptibility of a strange metal, optimally doped Bi
2.1
Sr
1.9
CaCu
2
O
8+x
. We find that it does not exhibit propagating collective modes, such as the plasmon excitation of normal metals, but instead exhibits a featureless continuum lacking either temperature or momentum dependence. Our study suggests the defining characteristic of the strange metal is a singular type of charge dynamics of a new kind for which there is no generally accepted theory.
Interferometric imaging of nonlocal electromechanical power transduction in ferroelectric domains
Authors: Zheng Lu , Dong Hui , Wu Xiaoyu , Huang Yen-Lin , Wang Wenbo , Wu Weida , Wang Zheng , Lai Keji
Published: May 2018

Significance

The conversion between electrical and acoustic signals in piezoelectric materials is of fundamental importance for their applications. Because of the much slower speed of sound than speed of light in solids, mesoscopic imaging is imperative for the study of electroacoustic behaviors at microwave frequencies. In this paper, the electromechanical power transduction in lithium niobate domains is spatially resolved by microwave impedance microscopy. Because of the sign reversal of piezoelectric tensor in opposite domains, the interaction between electric fields and elastic waves leads to fringe patterns that are fundamentally different from the acoustic displacement fields. This approach uncovers hidden information in the piezoelectric transduction process and opens a frontier to explore various elastic phenomena in materials and devices.
Robustness and universality of surface states in Dirac materials
Authors: Shtanko Oles , Levitov Leonid
Published: May 2018

Significance

We predict that generic Dirac materials host ballistically propagating surface states. Despite being nontopological, these states are robust and insensitive to surface disorder, occurring in a universal manner at generic boundaries, both atomically smooth and disordered. These properties originate from the multicomponent character of the Dirac–Bloch wavefunction, which results in strong coupling to generic boundaries. Dispersion of the surface states can be tuned by external gates to exhibit a variety of different regimes, including flat bands and linear crossings within the bulk bandgap. These surface states provide a natural explanation for anomalous long-range edge transport observed recently in a variety of Dirac materials in both topological and nontopological phases.
Laboratory evolution of virus-like nucleocapsids from nonviral protein cages
Authors: Terasaka Naohiro , Azuma Yusuke , Hilvert Donald
Published: May 2018

Significance

Viruses consist of a protective proteinaceous shell that packages a DNA or RNA genome. The critical step in the evolution of primitive viruses was presumably the emergence of protein cages that could load, protect, and transfer their own genetic information. Here, we show that a nonviral protein cage formed by
Aquifex aeolicus
lumazine synthase and its encoding mRNA can be engineered and evolved into virus-like nucleocapsids. The optimized proteins specifically recognize designed motifs on cognate mRNAs, and these RNA tags can also be employed for the encapsulation of other RNA molecules. These model systems have great potential for the investigation of nucleocapsid assembly and evolution and as tailored protein compartments for protective packaging and delivery of nucleic acids.
IonStar enables high-precision, low-missing-data proteomics quantification in large biological cohorts
Authors: Shen Xiaomeng , Shen Shichen , Li Jun , Hu Qiang , Nie Lei , Tu Chengjian , Wang Xue , Poulsen David J. , Orsburn Benjamin C. , Wang Jianmin , Qu Jun
Published: May 2018

Significance

Reliable proteome-wide quantification in large biological cohorts is highly valuable for clinical and pharmaceutical research yet remains extremely challenging despite recent technical advancements. Specifically, elevated missing data levels and compromised quantitative quality are common issues for prevalent methods. Here, we describe an IonStar technique taking advantage of sensitive and selective MS1 ion current-base quantification via innovations in effective and reproducible quantitative feature generation. Compared with several label-free strategies, IonStar showed superior performance in large-cohort analysis, manifested by excellent accuracy/precision, extremely low missing data, and confident discovery of subtle protein changes. In a proof-of-concept study, we demonstrated that IonStar quantified >7,000 unique proteins in 100 brain samples with no missing data and excellent quantitative quality, which has not been achievable by existing methods.
Inverted allosteric coupling between activation and inactivation gates in K
+
channels
Authors: Labro Alain J. , Cortes D. Marien , Tilegenova Cholpon , Cuello Luis G.
Published: May 2018

Significance

In K
+
channels, an allosteric coupling between their activation gate and selectivity filter underlies C-type inactivation coupled to activation gating. We have found that the second Threonine within the TTVGYGD signature sequence of K
+
channels is a crucial player for this allosteric communication. Interestingly, an Alanine substitution at this position in K
+
channels from bacteria to humans removed C-type inactivation gating and strikingly inverted the allosteric coupling (i.e., closing of the activation gate collapses the channel’s selectivity filter, closed-state inactivation gating). Finally, we provide a crystallographic demonstration that closed-state inactivation can be achieved by the structural collapse of the channel’s selectivity filter.
Polypentagonal ice-like water networks emerge solely in an activity-improved variant of ice-binding protein
Authors: Mahatabuddin Sheikh , Fukami Daichi , Arai Tatsuya , Nishimiya Yoshiyuki , Shimizu Rumi , Shibazaki Chie , Kondo Hidemasa , Adachi Motoyasu , Tsuda Sakae
Published: May 2018

Significance

This study expands our knowledge of protein hydration, which is highly related to the macromolecular antifreeze property of proteins. We examined a polypentagonal network formation of waters for a series of artificial variants of a 65-residue ice-binding protein. The polypentagonal waters were created solely on the surface of an activity-improved variant, which appeared to contain two sets of water clusters exhibiting a perfect position match to the waters constructing the first prism and pyramidal ice planes. These data suggest that a minute structural change in a protein organizes the surface waters into a polypentagonal arrangement, which merges with the intrinsically disordered ice surface and freezes to specific ice crystal planes.
ZNRF3 functions in mammalian sex determination by inhibiting canonical WNT signaling
Authors: Harris Abigail , Siggers Pam , Corrochano Silvia , Warr Nick , Sagar Danielle , Grimes Daniel T. , Suzuki Makoto , Burdine Rebecca D. , Cong Feng , Koo Bon-Kyoung , Clevers Hans , Stévant Isabelle , Nef Serge , Wells Sara , Brauner Raja , Ben Rhouma Bochra , Belguith Neïla , Eozenou Caroline , Bignon-Topalovic Joelle , Bashamboo Anu , McElreavey Ken , Greenfield Andy
Published: May 2018

Significance

Sex determination involves antagonistic interactions between the testis-determining (SRY-SOX9-FGF9) and ovary-promoting (RSPO1-WNT/β-catenin-FOXL2) pathways, but the underlying molecular mechanisms remain unclear. We show that ZNRF3, an E3 ubiquitin ligase that inhibits WNT signaling and is a direct target of RSPO1-mediated membrane clearance, is testis-determining in mice. Testis determination defects in the absence of ZNRF3 arise due to ectopic canonical WNT signaling in XY gonads at the sex-determining stage. We identify human
ZNRF3
sequence variants in cases of 46,XY disorders of sex development with XY female presentation. In vitro functional assays show that these variants disrupt ZNRF3 function. Our data reveal a sex-determining role for ZNRF3 and indicate that interactions between ZNRF3 and RSPO1 regulate mammalian sex determination.
Periplasmic depolymerase provides insight into ABC transporter-dependent secretion of bacterial capsular polysaccharides
Authors: Liston Sean D. , McMahon Stephen A. , Le Bas Audrey , Suits Michael D. L. , Naismith James H. , Whitfield Chris
Published: May 2018

Significance

Capsules are critical virulence determinants for bacterial pathogens. They are composed of capsular polysaccharides (CPSs) with diverse structures, whose assembly on the cell surface is often powered by a conserved ABC transporter. Current capsule-assembly models include a contiguous trans-envelope channel directing nascent CPSs from the transporter to the cell surface. This conserved apparatus is an attractive target for antivirulence antimicrobial development. This work describes a CPS depolymerizing lyase enzyme found in the
Burkholderiales
and unique structural features that define its mechanism, CPS specificity, and evolution to function in the periplasm in a noncatabolic role. The activity of this enzyme provides evidence that CPS assembled in an ABC transporter-dependent system is exposed to periplasm during translocation to the cell surface.
Mutations in
EID1
and
LNK2
caused light-conditional clock deceleration during tomato domestication
Authors: Müller Niels A. , Zhang Lei , Koornneef Maarten , Jiménez-Gómez José M.
Published: May 2018

Significance

Internal timekeepers, called circadian clocks, are prevalent in all domains of life. Variation in circadian rhythms allows fine-tuning of an organism to its specific environment. Here we show that a mutation in
LNK2
, in addition to the already described mutation in
EID1
, was responsible for the deceleration of circadian rhythms in cultivated tomatoes. We show that the mutant alleles of both genes arose in the earliest cultivated types and were selected during the domestication process. Notably, both mutant alleles specifically affect light input to the clock, leading to a light-conditional clock deceleration. Such light-conditionality may be a widespread means to enhance resonance with changed day–night cycles at higher latitudes, despite the fixed 24-h period of the Earth.
Recurrent bridgehead effects accelerate global alien ant spread
Authors: Bertelsmeier Cleo , Ollier Sébastien , Liebhold Andrew M. , Brockerhoff Eckehard G. , Ward Darren , Keller Laurent
Published: May 2018

Significance

Because of the globalization of trade and travel, worldwide invasion rates are high. A potential driver of the global acceleration of new invasions is the so-called bridgehead effect, in which initial invasive populations serve as the source of additional invasions via secondary introductions. However, the frequency and overall importance of secondary introductions remain largely unknown. Using a remarkable dataset, spanning nearly 100 years (1914–2013), of ant interceptions at air and maritime ports in the United States and New Zealand, we found that most ant introductions arise via secondary transport via intermediate regions. Our analyses also reveal positive feedback between the introduction and establishment stages of the invasion process via secondary introductions acting as a critical driver of increasing global invasion rates.
Phase-transition temperature suppression to achieve cubic GeTe and high thermoelectric performance by Bi and Mn codoping
Authors: Liu Zihang , Sun Jifeng , Mao Jun , Zhu Hangtian , Ren Wuyang , Zhou Jingchao , Wang Zhiming , Singh David J. , Sui Jiehe , Chu Ching-Wu , Ren Zhifeng
Published: May 2018

Significance

Phase-transition behavior in thermoelectric materials is detrimental for their application in thermoelectric devices. Here we designed, and experimentally realized the high thermoelectric performance of cubic GeTe-based material by suppressing the phase transition from a cubic to a rhombohedral structure to below room temperature through a simple Bi and Mn codoping on the Ge site. Bi doping reduced the hole concentration while Mn alloying largely suppressed the phase-transition temperature and also induced modification of the valence bands. Our work provides the basis for studying phase transitions in other thermoelectric materials to optimize these materials for applications.
Ca
2+
-activated Cl current predominates in threshold response of mouse olfactory receptor neurons
Authors: Li Rong-Chang , Lin Chih-Chun , Ren Xiaozhi , Wu Jingjing Sherry , Molday Laurie L. , Molday Robert S. , Yau King-Wai
Published: May 2018

Significance

Odorants activate in mammalian olfactory receptor neurons (ORNs) an inward cyclic nucleotide-gated (CNG), nonselective cation current and, importantly, a follower inward Ca
2+
-activated Cl current serving to amplify the olfactory signal. This concept is nonetheless refuted by a report describing no increase in behavioral olfactory threshold for a mouse line engineered to harbor an ablated gene for the Cl current. Two other reports on the same mouse line, however, did observe some subtle olfactory defects. We take a different approach here by dissecting the normal mouse ORN receptor current into its CNG- and Cl-current components, and showing that, at signaling threshold to the brain, the Cl current indeed accounts for most of the olfactory response, and thus should contribute importantly to olfactory signaling.
Autophagosomal YKT6 is required for fusion with lysosomes independently of syntaxin 17
Authors: Matsui Takahide , Jiang Peidu , Nakano Saori , Sakamaki Yuriko , Yamamoto Hayashi , Mizushima Noboru
Published: May 2018

Macroautophagy is an evolutionarily conserved catabolic mechanism that delivers intracellular constituents to lysosomes using autophagosomes. To achieve degradation, lysosomes must fuse with closed autophagosomes. We previously reported that the soluble N-ethylmaleimide–sensitive factor attachment protein receptor (SNARE) protein syntaxin (STX) 17 translocates to autophagosomes to mediate fusion with lysosomes. In this study, we report an additional mechanism. We found that autophagosome–lysosome fusion is retained to some extent even in STX17 knockout (KO) HeLa cells. By screening other human SNAREs, we identified YKT6 as a novel autophagosomal SNARE protein. Depletion of YKT6 inhibited autophagosome–lysosome fusion partially in wild-type and completely in STX17 KO cells, suggesting that YKT6 and STX17 are independently required for fusion. YKT6 formed a SNARE complex with SNAP29 and lysosomal STX7, both of which are required for autophagosomal fusion. Recruitment of YKT6 to autophagosomes depends on its N-terminal longin domain but not on the C-terminal palmitoylation and farnesylation that are essential for its Golgi localization. These findings suggest that two independent SNARE complexes mediate autophagosome–lysosome fusion.
Dynamics of RecA-mediated repair of replication-dependent DNA breaks
Authors: Amarh Vincent , White Martin A. , Leach David R.F.
Published: May 2018

Chromosomal replication is the major source of spontaneous DNA double-strand breaks (DSBs) in living cells. Repair of these DSBs is essential for cell viability, and accuracy of repair is critical to avoid chromosomal rearrangements. Repair of replication-dependent DSBs occurs primarily by homologous recombination with a sister chromosome. However, this reaction has never been visualized at a defined chromosomal locus, so little is known about its spatial or temporal dynamics. Repair of a replication-independent DSB generated in Escherichia coli by a rare-cutting endonuclease leads to the formation of a bundle of RecA filaments. In this study, we show that in contrast, repair of a replication-dependent DSB involves a transient RecA focus localized in the central region of the cell in which the DNA is replicated. The recombining loci remain centrally located with restricted movement before segregating with little extension to the period of postreplicative sister-chromosome cohesion. The spatial and temporal efficiency of this reaction is remarkable.
Tissue-resident macrophages in the intestine are long lived and defined by Tim-4 and CD4 expression
Authors: Shaw Tovah N. , Houston Stephanie A. , Wemyss Kelly , Bridgeman Hayley M. , Barbera Thomas A. , Zangerle-Murray Tamsin , Strangward Patrick , Ridley Amanda J.L. , Wang Ping , Tamoutounour Samira , Allen Judith E. , Konkel Joanne E. , Grainger John R.
Published: May 2018

A defining feature of resident gut macrophages is their high replenishment rate from blood monocytes attributed to tonic commensal stimulation of this site. In contrast, almost all other tissues contain locally maintained macrophage populations, which coexist with monocyte-replenished cells at homeostasis. In this study, we identified three transcriptionally distinct mouse gut macrophage subsets that segregate based on expression of Tim-4 and CD4. Challenging current understanding, Tim-4+CD4+ gut macrophages were found to be locally maintained, while Tim-4–CD4+ macrophages had a slow turnover from blood monocytes; indeed, Tim-4–CD4– macrophages were the only subset with the high monocyte-replenishment rate currently attributed to gut macrophages. Moreover, all macrophage subpopulations required live microbiota to sustain their numbers, not only those derived from blood monocytes. These findings oppose the prevailing paradigm that all macrophages in the adult mouse gut rapidly turn over from monocytes in a microbiome-dependent manner; instead, these findings supplant it with a model of ontogenetic diversity where locally maintained subsets coexist with rapidly replaced monocyte-derived populations.
Exhaustive Classification of the Invariant Solutions for a Specific Nonlinear Model Describing Near Planar and Marginally Long-Wave Unstable Interfaces for Phase Transition
Authors: Ahangari Fatemeh
Published: May 2018

Problems of thermodynamic phase transition originate inherently in solidification, combustion and various other significant fields. If the transition region among two locally stable phases is adequately narrow, the dynamics can be modeled by an interface motion. This paper is devoted to exhaustive analysis of the invariant solutions for a modified Kuramoto-Sivashinsky equation in two spatial and one temporal dimensions is presented. This nonlinear partial differential equation asymptotically characterizes near planar interfaces, which are marginally long-wave unstable. For this purpose, by applying the classical symmetry method for this model the classical symmetry operators are attained. Moreover, the structure of the Lie algebra of symmetries is discussed and the optimal system of subalgebras, which yields the preliminary classification of group invariant solutions is constructed. Mainly, the Lie invariants corresponding to the infinitesimal symmetry generators as well as associated similarity reduced equations are also pointed out. Furthermore, the nonclassical symmetries of this nonlinear PDE are also comprehensively investigated.
Impact of the Cotton–Mouton effect on Faraday polarimetry measurements using circular polarization
Authors: Chen J , Ding W X , Brower D L
Published: May 2018

A comprehensive understanding of the impact of the Cotton–Mouton effect on Faraday polarimetry measurements using counter-rotating circular polarization (CP) probe beams has been developed. By using the Jones theory, an analytic study shows that the Cotton–Mouton effect cancels to first order with coupling into the Faraday measurement only at higher orders. A Jones-based numerical study shows the coupling effect strongly depends on the Cotton–Mouton effect, Faraday effect, and wavelength chosen for the measurement. For realistic DIII-D plasma conditions and far-infrared wavelength, numerical calculation suggests the measurement is dominated by the Faraday effect while the coupling effect leads to a small but finite correction. By statistical comparison between the experimental measurement and the Jones-based numerical calculation under various plasma parameters, the impact of the Cotton–Mouton effect has been verified. Proper treatment of the coupling effect is essential in the data analysis under certain conditions for polarimetric measurement using CP in present devices and beyond.
Evidence of evolutionary history and selective sweeps in the genome of Meishan pig reveals its genetic and phenotypic characterization
Authors: Zhao Pengju , Yu Ying , Feng Wen , Du Heng , Yu Jian , Kang Huimin , Zheng Xianrui , Wang Zhiquan , Liu George E , Ernst Catherine W , Ran Xueqin , Wang Jiafu , Liu Jian-Feng
Published: May 2018

Background

Meishan is a pig breed indigenous to China and famous for its high fecundity. The traits of Meishan are strongly associated with its distinct evolutionary history and domestication. However, the genomic evidence linking the domestication of Meishan pigs with its unique features is still poorly understood. The goal of this study is to investigate the genomic signatures and evolutionary evidence related to the phenotypic traits of Meishan via large-scale sequencing.

Results

We found that the unique domestication of Meishan pigs occurred in the Taihu Basin area between the Majiabang and Liangzhu Cultures, during which 300 protein-coding genes have underwent positive selection. Notably, enrichment of the FoxO signaling pathway with significant enrichment signal and the harbored gene IGF1R were likely associated with the high fertility of Meishan pigs. Moreover, NFKB1 exhibited strong selective sweep signals and positively participated in hyaluronan biosynthesis as the key gene of NF-kB signaling, which may have resulted in the wrinkled skin and face of Meishan pigs. Particularly, three population-specific synonymous single-nucleotide variants occurred in PYROXD1, MC1R, and FAM83G genes; the T305C substitution in the MCIR gene explained the black coat of the Meishan pigs well. In addition, the shared haplotypes between Meishan and Duroc breeds confirmed the previous Asian-derived introgression and demonstrated the specific contribution of Meishan pigs.

Conclusions

These findings will help us explain the unique genetic and phenotypic characteristics of Meishan pigs and offer a plausible method for their utilization of Meishan pigs as valuable genetic resources in pig breeding and as an animal model for human wrinkled skin disease research.
The research data management platform (RDMP): A novel, process driven, open-source tool for the management of longitudinal cohorts of clinical data
Authors: Nind Thomas , Galloway James , McAllister Gordon , Scobbie Donald , Bonney Wilfred , Hall Christopher , Tramma Leandro , Reel Parminder , Groves Martin , Appleby Philip , Doney Alex , Guthrie Bruce , Jefferson Emily
Published: May 2018

Background

The Health Informatics Centre at the University of Dundee provides a service to securely host clinical datasets and extract relevant data for anonymized cohorts to researchers to enable them to answer key research questions. As is common in research using routine healthcare data, the service was historically delivered using ad-hoc processes resulting in the slow provision of data whose provenance was often hidden to the researchers using it. This paper describes the development and evaluation of the Research Data Management Platform (RDMP): an open source tool to load, manage, clean, and curate longitudinal healthcare data for research and provide reproducible and updateable datasets for defined cohorts to researchers.

Results

Between 2013 and 2017, RDMP tool implementation tripled the productivity of data analysts producing data releases for researchers from 7.1 to 25.3 per month and reduced the error rate from 12.7% to 3.1%. The effort on data management reduced from a mean of 24.6 to 3.0 hours per data release. The waiting time for researchers to receive data after agreeing a specification reduced from approximately 6 months to less than 1 week. The software is scalable and currently manages 163 datasets. A total 1,321 data extracts for research have been produced, with the largest extract linking data from 70 different datasets.

Conclusions

The tools and processes that encompass the RDMP not only fulfil the research data management requirements of researchers but also support the seamless collaboration of data cleaning, data transformation, data summarization and data quality assessment activities by different research groups.
On Integrable Field Theories as Dihedral Affine Gaudin Models
Authors: Vicedo Benoît
Published: May 2018

We introduce the notion of a classical dihedral affine Gaudin model, associated with an untwisted affine Kac–Moody algebra $\widetilde{\mathfrak{g}}$ equipped with an action of the dihedral group $D_{2T}$, $T \geq 1$ through (anti-)linear automorphisms. We show that a very broad family of classical integrable field theories can be recast as examples of such classical dihedral affine Gaudin models. Among these are the principal chiral model on an arbitrary real Lie group $G_0$ and the $\mathbb{Z}_T$-graded coset $\sigma $-model on any coset of $G_0$ defined in terms of an order $T$ automorphism of its complexification. Most of the multi-parameter integrable deformations of these $\sigma $-models recently constructed in the literature provide further examples. The common feature shared by all these integrable field theories, which makes it possible to reformulate them as classical dihedral affine Gaudin models, is the fact that they are non-ultralocal. In particular, we also obtain affine Toda field theory in its lesser-known non-ultralocal formulation as another example of this construction. We propose that the interpretation of a given classical non-ultralocal integrable field theory as a classical dihedral affine Gaudin model provides a natural setting within which to address its quantisation. At the same time, it may also furnish a general framework for understanding the massive ordinary differential equations (ODE)/integrals of motion (IM) correspondence since the known examples of integrable field theories for which such a correspondence has been formulated can all be viewed as dihedral affine Gaudin models.
Identifying surgical site infections in electronic health data using predictive models
Authors: Grundmeier Robert W , Xiao Rui , Ross Rachael K , Ramos Mark J , Karavite Dean J , Michel Jeremy J , Gerber Jeffrey S , Coffin Susan E
Published: May 2018

Objective

The objective was to prospectively derive and validate a prediction rule for detecting cases warranting investigation for surgical site infections (SSI) after ambulatory surgery.

Methods

We analysed electronic health record (EHR) data for children who underwent ambulatory surgery at one of 4 ambulatory surgical facilities. Using regularized logistic regression and random forests, we derived SSI prediction rules using 30 months of data (derivation set) and evaluated performance with data from the subsequent 10 months (validation set). Models were developed both with and without data extracted from free text. We also evaluated the presence of an antibiotic prescription within 60 days after surgery as an independent indicator of SSI evidence. Our goal was to exceed 80% sensitivity and 10% positive predictive value (PPV).

Results

We identified 234 surgeries with evidence of SSI among the 7910 surgeries available for analysis. We derived and validated an optimal prediction rule that included free text data using a random forest model (sensitivity = 0.9, PPV = 0.28). Presence of an antibiotic prescription had poor sensitivity (0.65) when applied to the derivation data but performed better when applied to the validation data (sensitivity = 0.84, PPV = 0.28).

Conclusions

EHR data can facilitate SSI surveillance with adequate sensitivity and PPV.