bluuebunny/crossref_metadata_2025 huggingface dataset:
Visualising crystal packing interactions in solid-state NMR: Concepts and applications
Authors: Zilka Miri , Sturniolo Simone , Brown Steven P. , Yates Jonathan R.
Published: October 2017

In this article, we introduce and apply a methodology, based on density functional theory and the gauge-including projector augmented wave approach, to explore the effects of packing interactions on solid-state nuclear magnetic resonance (NMR) parameters. A visual map derived from a so-termed “magnetic shielding contribution field” can be made of the contributions to the magnetic shielding of a specific site—partitioning the chemical shift to specific interactions. The relation to the established approaches of examining the molecule to crystal change in the chemical shift and the nuclear independent chemical shift is established. The results are applied to a large sample of 71 molecular crystals and three further specific examples from supermolecular chemistry and pharmaceuticals. This approach extends the NMR crystallography toolkit and provides insight into the development of both cluster based approaches to the predictions of chemical shifts and for empirical predictions of chemical shifts in solids.
E-field controlled phase transformation in bismuth ferrite thin films, and effect of laser energy density
Authors: Gao Min , Viswan Ravindranath , Tang Xiao , Leung Chung Ming , Li Jiefang , Viehland D.
Published: October 2017

Heterostructures of BiFeO3/Pb(Mg1/3Nb2/3)O3-30%PbTiO3 (BFO/PMN-30PT) were fabricated by pulsed laser deposition. Electric fields (E) were applied on the PMN-30PT substrates along the in-plane and out-of-plane directions, and the induced strain of BFO was measured as a function of E by X-ray diffraction. Reciprocal space maps along the (110) zone axis evidenced that a monoclinic MA phase was induced in both PMN-PT and BFO, where the dominate domain structures could be switched between biaxial directions under application of in-plane E. Studies were done for films prepared under different laser energy densities (LED), in order to optimize the in-plane strain of BFO. A relatively low LED of 1 J/cm2 produced a better BFO thin film with larger in-plane strain.
Induction heating effect on the performance of flexible MoS2 field-effect transistors
Authors: Shin Jong Mok , Choi Jun hee , Kim Do-Hyun , Jang Ho-Kyun , Yun Jinyoung , Na Junhong , Kim Gyu-Tae
Published: October 2017

We investigated the induction heating effect on device characteristics of flexible molybdenum disulfide (MoS2) field-effect transistors (FETs). A polyimide film was employed as a flexible substrate, and poly(3,4-ethylenedioxythiophene):polystyrene sulfonate was coated on the flexible substrate as a bottom gate. After the annealing process on the flexible MoS2 FETs by induction heating, the field effect mobility was enhanced from 2.13 to 5.58 cm2/V·s with the slight increase of the on-off ratio from 5.17 × 102 to 1.98 × 103. Moreover, the low field mobility was almost unchanged from 7.75 to 7.33 cm2/V·s, indicating that the induction heating mainly contributed to the enhancement of the device performances by contact improvement between electrodes and MoS2. With the simple model of the diode and resistor connected in series, it was confirmed that the Schottky diode disappeared with contact enhancement. Our findings can contribute to the contact improvement with minimum damage when low dimensional nanomaterials are used as channel materials on flexible substrates.
Rotationally inelastic collisions of excited NaK and NaCs molecules with noble gas and alkali atom perturbers
Authors: Jones J. , Richter K. , Price T. J. , Ross A. J. , Crozet P. , Faust C. , Malenda R. F. , Carlus S. , Hickman A. P. , Huennekens J.
Published: October 2017

We report measurements of rate coefficients at T ≈ 600 K for rotationally inelastic collisions of NaK molecules in the 2(A)1Σ+ electronic state with helium, argon, and potassium atom perturbers. Several initial rotational levels J between 14 and 44 were investigated. Collisions involving molecules in low-lying vibrational levels (v = 0, 1, and 2) of the 2(A)1Σ+ state were studied using Fourier-transform spectroscopy. Collisions involving molecules in a higher vibrational level, v = 16, were studied using pump/probe, optical-optical double resonance spectroscopy. In addition, polarization spectroscopy measurements were carried out to study the transfer of orientation in these collisions. Many, but not all, of the measurements were carried out in the “single-collision regime” where more than one collision is unlikely to occur within the lifetime of the excited molecule. The analysis of the experimental data, which is described in detail, includes an estimate of effects of multiple collisions on the reported rate coefficients. The most significant result of these experiments is the observation of a strong propensity for ΔJ = even transitions in collisions involving either helium or argon atoms; the propensity is much stronger for helium than for argon. For the initial rotational levels studied experimentally, almost all initial orientation is preserved in collisions of NaK 2(A)1Σ+ molecules with helium. Roughly between 1/3 and 2/3 of the orientation is preserved in collisions with argon, and almost all orientation is destroyed in collisions with potassium atoms. Complementary measurements on rotationally inelastic collisions of NaCs 2(A)1Σ+ with argon do not show a ΔJ = even propensity. The experimental results are compared with new theoretical calculations of collisions of NaK 2(A)1Σ+ with helium and argon. The calculations are in good agreement with the absolute magnitudes of the experimentally determined rate coefficients and accurately reproduce the very strong propensity for ΔJ = even transitions in helium collisions and the less strong propensity for ΔJ = even transitions in argon collisions. The calculations also show that collisions with helium are less likely to destroy orientation than collisions with argon, in agreement with the experimental results.
Weak antilocalization effect due to topological surface states in Bi2Se2.1Te0.9
Authors: Shrestha K. , Graf D. , Marinova V. , Lorenz B. , Chu C. W.
Published: October 2017

We have investigated the weak antilocalization (WAL) effect in the p-type Bi2Se2.1Te0.9 topological system. The magnetoconductance shows a cusp-like feature at low magnetic fields, indicating the presence of the WAL effect. The WAL curves measured at different tilt angles merge together when they are plotted as a function of the normal field components, showing that surface states dominate the magnetoconductance in the Bi2Se2.1Te0.9 crystal. We have calculated magnetoconductance per conduction channel and applied the Hikami-Larkin-Nagaoka formula to determine the physical parameters that characterize the WAL effect. The number of conduction channels and the phase coherence length do not change with temperature up to T = 5 K. In addition, the sample shows a large positive magnetoresistance that reaches 1900% under a magnetic field of 35 T at T = 0.33 K with no sign of saturation. The magnetoresistance value decreases with both increasing temperature and tilt angle of the sample surface with respect to the magnetic field. The large magnetoresistance of topological insulators can be utilized in future technology such as sensors and memory devices.
Enhanced breakdown strength of polymer composites by low filler loading and its mechanisms
Authors: Ding Shanjun , Yu Shuhui , Zhu Xiaodong , Xie Shenghui , Sun Rong , Liao Wei-Hsin , Wong Ching-Ping
Published: October 2017

Dielectric polymer materials with high energy density and low dielectric loss are highly desired for applications in advanced electronic devices and electric power systems. Here, we report on flexible dielectric composites using semiconductor nanoparticles as fillers and polyvinylidene fluoride (PVDF) as a matrix. The introduction of a small amount of ZnO filler results in significantly enhanced voltage breakdown strength and energy density in comparison with pure PVDF. Based on the multi-core model, combining the electric double layer theory and the interface contact theory, we investigate mechanisms and come out with that transportation of carriers under applied voltage is regulated by the charged interface, which delays the formation of the conduction path. Besides, the electric field imposed on the composites is alleviated by the internal micro-electric field.
Oxygen deficiency and cooling field driven vertical hysteretic shift in epitaxial SrRuO3/SrTiO3 heterostructures
Authors: Zheng Ming , Li Xueyan , Xiao Wen , Wang Wei , Ni Hao
Published: October 2017

SrRuO3 thin films have been epitaxially grown on SrTiO3 substrates using a pulsed laser deposition technique. By adjusting the oxygen partial pressure during deposition, a sharp drop in the Curie temperature (TC) of 95 K and vertical magnetization shift (MShift) of 82.7% in the hysteresis loop was observed due to the oxygen deficiency induced lattice distortion that modifies the strong hybridization of p-d orbitals and perpendicular uniaxial magnetic anisotropy. In particular, the vertical hysteretic shift can also be effectively tuned by the applied cooling field, and thus, we obtained a giant and complete MShift of 106% with a large volume of pinned Ru4+ moments. These findings reveal the critical role played by intrinsic oxygen defects and extrinsic cooling field in controlling magnetic couplings in this perovskite-type complex oxide system.
Investigation of the effects of misfit strain on barium strontium titanate thin films deposited on base metal substrates by a modified phenomenological model
Authors: Dong Hanting , Li Hongfang , Chen Jianguo , Jin Dengren , Cheng Jinrong
Published: October 2017

The Landau-Devonshire phenomenological model, which has been utilized to investigate epitaxial barium strontium titanate (BST) thin films, was modified to investigate the effects of misfit strain on the dielectric properties of polycrystalline BST thin films deposited on base metal substrates. The modification considers the relaxation of lattice misfit stress resulting from the formation of in-plane misfit dislocations. The modified lattice misfit strain was calculated by referring to the ferroelectric critical grain size. Moreover, the misfit strain and dielectric properties of BST thin films with different structures and substrates were investigated by the models. It was found that the measured dielectric constant and tunability of BST thin films on different metal substrates overall agreed with the computed data. In addition, the good agreement was also observed for sandwich-like structural BST thin films deposited on LNO buffered stainless steel plates. Our results indicated that the modified L-D models might be utilized to predict dielectric properties of polycrystalline BST thin films for varied substrates and multilayer structures.
A new algorithm for computing branching rules and Clebsch–Gordan coefficients of unitary representations of compact groups
Authors: Ibort A. , López Yela A. , Moro J.
Published: October 2017

A numerical algorithm that computes the decomposition of any finite-dimensional unitary reducible representation of a compact Lie group is presented. The algorithm, which does not rely on an algebraic insight into the group structure, is inspired by quantum mechanical notions. After generating two adapted states (these objects will be conveniently defined in Definition II.1) and after appropriate algebraic manipulations, the algorithm returns the block matrix structure of the representation in terms of its irreducible components. It also provides an adapted orthonormal basis. The algorithm can be used to compute the Clebsch–Gordan coefficients of the tensor product of irreducible representations of a given compact Lie group. The performance of the algorithm is tested on various examples: the decomposition of the regular representation of two finite groups and the computation of Clebsch–Gordan coefficients of two examples of tensor products of representations of SU(2).
Entropic uncertainty measures for large dimensional hydrogenic systems
Authors: Puertas-Centeno D. , Temme N. M. , Toranzo I. V. , Dehesa J. S.
Published: October 2017

The entropic moments of the probability density of a quantum system in position and momentum spaces describe not only some fundamental and/or experimentally accessible quantities of the system but also the entropic uncertainty measures of Rényi type, which allow one to find the most relevant mathematical formalizations of the position-momentum Heisenberg’s uncertainty principle, the entropic uncertainty relations. It is known that the solution of difficult three-dimensional problems can be very well approximated by a series development in 1/D in similar systems with a non-standard dimensionality D; moreover, several physical quantities of numerous atomic and molecular systems have been numerically shown to have values in the large-D limit comparable to the corresponding ones provided by the three-dimensional numerical self-consistent field methods. The D-dimensional hydrogenic atom is the main prototype of the physics of multidimensional many-electron systems. In this work, we rigorously determine the leading term of the Rényi entropies of the D-dimensional hydrogenic atom at the limit of large D. As a byproduct, we show that our results saturate the known position-momentum Rényi-entropy-based uncertainty relations.
Fabrication of microchannels in polycrystalline diamond using pre-fabricated Si substrates
Authors: Chandran Maneesh , Elfimchev Sergey , Michaelson Shaul , Akhvlediani Rozalia , Ternyak Orna , Hoffman Alon
Published: October 2017

In this paper, we report on a simple, feasible method to fabricate microchannels in diamond. Polycrystalline diamond microchannels were produced by fabricating trenches in a Si wafer and subsequently depositing a thin layer of diamond onto this substrate using the hot filament vapor deposition technique. Fabrication of trenches in the Si substrate at different depths was carried out by standard photolithography, and the subsequent deposition of the diamond layer was performed by the hot filament chemical vapor deposition technique. The growth mechanism of diamond that leads to the formation of closed diamond microchannels is discussed in detail based on the Knudsen number and growth chemistry of diamond. Variations in the crystallite size, crystalline quality, and thickness of the diamond layer along the trench depths were systematically analyzed using cross-sectional scanning electron microscopy and Raman spectroscopy. Defect density and formation of non-diamond forms of carbon in the diamond layer were found to increase with the trench depth, which sets a limit of 5–45 μm trench depth (or an aspect ratio of 1–9) for the fabrication of diamond microchannels using this method under the present conditions.
A method to control and analyze vortex ring collisions in the laminar regime
Authors: Hendricks-Sturrup Rachele
Published: October 2017

Experimental physicists describe how complex laminar vortex ring collisions distribute their energy to produce diverse secondary rings.
Delayed feedback control of self-mobile cavity solitons in a wide-aperture laser with a saturable absorber
Authors: Schemmelmann T. , Tabbert F. , Pimenov A. , Vladimirov A. G. , Gurevich S. V.
Published: October 2017

We investigate the spatiotemporal dynamics of cavity solitons in a broad area vertical-cavity surface-emitting laser with saturable absorption subjected to time-delayed optical feedback. Using a combination of analytical, numerical, and path continuation methods, we analyze the bifurcation structure of stationary and moving cavity solitons and identify two different types of traveling localized solutions, corresponding to slow and fast motion. We show that the delay impacts both stationary and moving solutions either causing drifting and wiggling dynamics of initially stationary cavity solitons or leading to stabilization of intrinsically moving solutions. Finally, we demonstrate that the fast cavity solitons can be associated with a lateral mode-locking regime in a broad-area laser with a single longitudinal mode.
A Novel Strategy to Introduce 18F, a Positron Emitting Radionuclide, into a Gallium Nitrate Complex: Synthesis, NMR, X-Ray Crystal Structure, and Preliminary Studies on Radiolabelling with 18F
Authors: Venkatachalam Taracad K. , Bernhardt Paul V. , Stimson Damion H. R. , Pierens Gregory K. , Bhalla Rajiv , Reutens David C.
Published: October 2017

A hexan-3,4-dione bis(4N-phenylthiosemicarbazone) gallium nitrate complex was synthesised and the structure was confirmed by NMR studies. The complex was prepared using an appropriately substituted dithiosemicarbazone and sodium methoxide in anhydrous methanol. The structure was further confirmed using single crystal X-ray crystallography. The crystal structure of gallium nitrate complex of diphenylthiosemicarbazone comprise a planar configuration of the tetradentate coordinated thiosemicarbazone with the Ga3+ ion, with the nitrate ligand occupying the apical coordination site. The X-ray structure of the gallium fluoride complex of pentan-2,3-dione bis(4N-phenylthiosemicarbazone) has been determined and confirms exchange of the nitrate can be achieved with fluoride. We show facile exchange of 18F, a positron emitter, to form the 18F-gallium complex under mild conditions, thus providing confirmation that such a transformation can be used to introduce 18F directly into nitrate-coordinated complexes of gallium-thiosemicarbozone complexes, a new labelling strategy for the preparation of imaging agents.
Corrigendum to: Boron deficiency in pasture based on subterranean clover (Trifolium subterraneum L.) is linked to symbiotic malfunction
Authors: Hamilton Leo J. , Reed Kevin F. M. , Leach Elainne M. A. , Brockwell John
Published: October 2017

Field and glasshouse experiments confirmed the occurrence of boron (B) deficiency in subterranean clover (Trifolium subterraneum L.) pasture in eastern Victoria. Diminished productivity was linked to the small-seededness of clover and the poor effectiveness of clover root-nodule bacteria (rhizobia, Rhizobium leguminosarum bv. trifolii). Productivity, especially of clover and clover seed, increased following applications of up to 6 kg B ha–1 (P
B deficiency in the nodulated legume induced conditions within the plant and or its rhizobia that led to impaired nitrogen (N2) fixation. Glasshouse research indicated that populations of soil-borne rhizobia taken from B-deficient soils were poorly effective in N2 fixation and that rhizobia from soils growing subterranean clover cv. Leura were significantly less effective (P
Additionally, subterranean clover seed generated in B-deficient soils was at least one-third smaller than the seed of commercial seed but responded to inoculation with effective rhizobia. This indicated that any symbiotic malfunction of clover from B-deficient soils was not due to an inability to respond to nitrogen per se. On the other hand, cv. Leura from B-deficient soils fixed significantly less N2 than commercial cv. Leura when each was inoculated with rhizobia from B-deficient soils.
The sharks and rays of the Solomon Islands: a synthesis of their biological diversity, values and conservation status
Authors: Hylton S. , White W. T. , Chin A.
Published: October 2017

Sharks and rays are facing increasing anthropogenic pressure globally, including in the Pacific. However, data on their status and biodiversity are lacking for many Pacific Large Ocean Island States. This study aimed to construct a species checklist for the sharks and rays occurring in the Solomon Islands, review the human interactions with these species, and present a synthesis of their conservation status. Given the paucity of available data, a wide range of data sources were used including fisheries data, citizen science, and ethnobiological studies. Results were validated through a review process involving expert informants. Fifty sharks and rays were identified from the Solomon Islands, of which 20 are assessed as Vulnerable or Endangered on the IUCN Red List, 10 in the Convention on International Trade in Endangered Species, and 11 in the Convention for Migratory Species. The checklist also presents an eastwards range extension for the Endangered dwarf sawfish Pristis clavata. Fishing appears to be the main impact, though impacts from habitat loss and degradation are possible. This study provides a systematic synthesis and review of the biological diversity, uses, and cultural significance of Solomon Islands sharks and rays, and describes a process for assembling species checklists and reviews in data-poor contexts. However, this synthesis is based on limited information and a complete assessment of shark and ray status in the Solomon Islands will require primary fieldwork.
Self-association of a highly charged arginine-rich cell-penetrating peptide
Authors: Tesei Giulio , Vazdar Mario , Jensen Malene Ringkjøbing , Cragnell Carolina , Mason Phil E. , Heyda Jan , Skepö Marie , Jungwirth Pavel , Lund Mikael
Published: October 2017

Significance

Arginine-rich cell-penetrating peptides are promising candidates for intracellular drug delivery. These cationic peptides spontaneously traverse biological membranes via a direct mode of entry which is not yet fully understood. In this study, we report the complex solution behavior of the cell-penetrating peptide deca-arginine. Despite its large net positive charge, deca-arginine self-associates at low-to-intermediate ionic strengths, owing to an interaction mode which is present in the structure of a significant number of proteins. Self-association may thus enhance the bioavailability of deca-arginine. Our findings provide the key to the understanding of the self-association mechanism in deca-arginine with implications for the potential biological roles of this unusual binding motif.
Diel cycling and long-term persistence of viruses in the ocean’s euphotic zone
Authors: Aylward Frank O. , Boeuf Dominique , Mende Daniel R. , Wood-Charlson Elisha M. , Vislova Alice , Eppley John M. , Romano Anna E. , DeLong Edward F.
Published: October 2017

Significance

Marine microbial communities exert a large influence on ocean ecosystem processes, and viruses in these communities play key roles in controlling microbial abundances, nutrient cycling, and productivity. We show here that dominant viruses in the open ocean persist for long time periods and that many appear tightly locked in coordinated diel oscillations with their bacterial hosts. The persistent structure of viral assemblages, as well as synchronized daily oscillations of viruses and hosts, are in part the result of the regular diurnal coupling of viral and host replication cycles. Collectively, our results suggest that viruses, as key components of marine ecosystems, are intrinsically synchronized with the daily rhythms of microbial community processes in the ocean’s photic zone.
Expression, purification, and characterization of a novel acid phosphatase that displays protein tyrosine phosphatases activity from Metarhizium anisopliae strain CQMa102
Authors: Zhang Xue , Yang Shuiying , Li Xinqiang , Zhu Pei , Xie Enyu , Li Zhenlun
Published: October 2017

The protein tyrosine phosphatase (PTPase) plays an important role in insect immune system. Our group has purified a type of acid phosphatase that could specifically dephosphorylate trans-Golgi p230 in vitro. In order to study this phosphatase further, we have identified and cloned the phosphatase gene from a locust specific Metarhizium anisopliae Strain CQMa102. The CQMa102 phosphatase was expressed in Pichia pastoris to verify its protease activity. The molecular weight (MW) and the isoelectric point (pI) of the phosphatase were about 85 kDa and 6.15, respectively. Substrate specificity evaluation showed that the purified enzyme exhibited high activity on O-phospho-L-tyrosine. At its optimal pH of 6.5 and optimum temperature of 70 °C, the protein showed the highest activity respectively. It can be activated by Ca2+, Mg2+, Mn2+, Ba2+, Co2+ and phosphate analogs, but inhibited by Zn2+, Cu2+, fluoride, dithiothreitol, β-mercaptoethanol and N-ethylmaleimide.
A preliminary study of gut dysbiosis in children with food allergy
Authors: Inoue Ryo , Sawai Toshihiro , Sawai Chihiro , Nakatani Masako , Romero-Pérez Gustavo A , Ozeki Motoyuki , Nonomura Kazuo , Tsukahara Takamitsu
Published: October 2017

Gut microbiota of food allergic children was analyzed by high throughput 16S rRNA gene sequencing. Signs of gut dysbiosis, which is likely associated with gut inflammation, was observed in children with food allergies. For example, decreased abundance of genus Akkermansia but increased abundance of Veillonella was found in children with food allergy in comparison with healthy control children.
The voltage sensor of excitation–contraction coupling in mammals: Inactivation and interaction with Ca2+
Authors: Ferreira Gregorio Juan , Pequera Germán , Manno Carlo , Ríos Eduardo , Brum Gustavo
Published: October 2017

In skeletal muscle, the four-helix voltage-sensing modules (VSMs) of CaV1.1 calcium channels simultaneously gate two Ca2+ pathways: the CaV1.1 pore itself and the RyR1 calcium release channel in the sarcoplasmic reticulum. Here, to gain insight into the mechanism by which VSMs gate RyR1, we quantify intramembrane charge movement associated with VSM activation (sensing current) and gated Ca2+ release flux in single muscle cells of mice and rats. As found for most four-helix VSMs, upon sustained depolarization, rodent VSMs lose the ability to activate Ca2+ release channels opening; their properties change from a functionally capable mode, in which the mobile sensor charge is called charge 1, to an inactivated mode, charge 2, with a voltage dependence shifted toward more negative voltages. We find that charge 2 is promoted and Ca2+ release inactivated when resting, well-polarized muscle cells are exposed to low extracellular [Ca2+] and that the opposite occurs in high [Ca2+]. It follows that murine VSMs are partly inactivated at rest, which establishes the reduced availability of voltage sensing as a pathogenic mechanism in disorders of calcemia. We additionally find that the degree of resting inactivation is significantly different in two mouse strains, which underscores the variability of voltage sensor properties and their vulnerability to environmental conditions. Our studies reveal that the resting and activated states of VSMs are equally favored by extracellular Ca2+. Promotion by an extracellular species of two states of the VSM that differ in the conformation of the activation gate requires the existence of a second gate, inactivation, topologically extracellular and therefore accessible from outside regardless of the activation state.
Quasispheres and metric doubling measures
Authors: Lohvansuu Atte , Rajala Kai , Rasimus Martti
Published: October 2017

Applying the Bonk-Kleiner characterization of Ahlfors22-regular quasispheres, we show that a metric two-sphereXXis a quasisphere if and only ifXXis linearly locally connected and carries aweak metric doubling measure, i.e., a measure that deforms the metric onXXwithout much shrinking.
Direct evidence of amyloid precursor–like protein 1 trans interactions in cell–cell adhesion platforms investigated via fluorescence fluctuation spectroscopy
Authors: Dunsing Valentin , Mayer Magnus , Liebsch Filip , Multhaup Gerhard , Chiantia Salvatore
Published: October 2017

The amyloid precursor–like protein 1 (APLP1) is a type I transmembrane protein that plays a role in synaptic adhesion and synaptogenesis. Past investigations indicated that APLP1 is involved in the formation of protein–protein complexes that bridge the junctions between neighboring cells. Nevertheless, APLP1–APLP1 trans interactions have never been directly observed in higher eukaryotic cells. Here, we investigated APLP1 interactions and dynamics directly in living human embryonic kidney cells using fluorescence fluctuation spectroscopy techniques, namely cross-correlation scanning fluorescence correlation spectroscopy and number and brightness analysis. Our results show that APLP1 forms homotypic trans complexes at cell–cell contacts. In the presence of zinc ions, the protein forms macroscopic clusters, exhibiting an even higher degree of trans binding and strongly reduced dynamics. Further evidence from giant plasma membrane vesicles suggests that the presence of an intact cortical cytoskeleton is required for zinc-induced cis multimerization. Subsequently, large adhesion platforms bridging interacting cells are formed through APLP1–APLP1 trans interactions. Taken together, our results provide direct evidence that APLP1 functions as a neuronal zinc-dependent adhesion protein and allow a more detailed understanding of the molecular mechanisms driving the formation of APLP1 adhesion platforms.
UC2 search: using unique connectivity of uncharged compounds for metabolite annotation by database searching in mass spectrometry-based metabolomics
Authors: Sakurai Nozomu , Narise Takafumi , Sim Joon-Soo , Lee Chang-Muk , Ikeda Chiaki , Akimoto Nayumi , Kanaya Shigehiko
Published: October 2017

For metabolite annotation in metabolomics, variations in the registered states of compounds (charged molecules and multiple components, such as salts) and their redundancy among compound databases could be the cause of misannotations and hamper immediate recognition of the uniqueness of metabolites while searching by mass values measured using mass spectrometry. We developed a search system named UC2 (Unique Connectivity of Uncharged Compounds), where compounds are tentatively neutralized into uncharged states and stored on the basis of their unique connectivity of atoms after removing their stereochemical information using the first block in the hash of the IUPAC International Chemical Identifier, by which false-positive hits are remarkably reduced, both charged and uncharged compounds are properly searched in a single query and records having a unique connectivity are compiled in a single search result.

Availability and implementation

The UC2 search tool is available free of charge as a REST web service (http://webs2.kazusa.or.jp/mfsearcher) and a Java-based GUI tool.

Supplementary information

Supplementary data are available at Bioinformatics online.
The role of communicative acts in the Dream process: engaging Moroccan migrants in a community development initiative in urban Spain
Authors: Carrillo Anna , Girbés-Peco Sandra , De Botton Lena , Valls-Carol Rosa
Published: October 2017

The present article offers relevant insights into how the evidence-based community development initiative known as the Dream process has had a positive impact on the inclusion, participation and leadership of a marginalized community of Moroccan immigrants in urban Spain. More specifically, we analyse how the commitment to promote dialogic communicative acts and to reduce power communicative acts during the process has attenuated some of the race, gender and class barriers that hindered the community’s involvement in dialogic and decision-making spaces aimed at improving their living conditions. In this article, we first introduce the state of the art using studies that have examined the role of interaction and deliberation in community development processes in disadvantaged contexts. Then, we briefly refer to the deterioration of the living conditions of the Moroccan immigrant population in Spain. Finally, we present the main results obtained from the qualitative case study research carried out through the implementation of the communicative methodology. This case study provides both theoretical claims and practical orientations to examine how dialogic approaches can contribute to community development processes in contexts severely affected by racial segregation and poverty.
Assessing causal links in fish stock–recruitment relationships
Authors: Pierre Maud , Rouyer Tristan , Bonhommeau Sylvain , Fromentin J M
Published: October 2017

Understanding whether recruitment fluctuations in fish stock arise from stochastic forcing (e.g. environmental variations) rather than deterministic forces (e.g. intrinsic dynamics) is a long standing question with important applied consequences for fisheries ecology. In particular, the relationship between recruitment, spawning stock biomass and environmental factors is still poorly understood, even though this aspect is crucial for fisheries management. Fisheries data are often short, but arise from complex dynamical systems with a high degree of stochastic forcing, which are difficult to capture through classic modelling approaches. In the present study, recent statistical approaches based on the approximation of the attractors of dynamical systems are applied on a large dataset of time series to assess (i) the directionality of potential causal relationships between recruitment and spawning stock biomass and potential influence of sea-surface temperature on recruitment and (ii) their performance to forecast recruitment. Our study shows that (i) whereas spawning stock biomass and sea surface temperature influence the recruitment to a lesser extent, recruitment causes also parental stock size and (ii) that non-linear forecasting methods performed well for the short-term predictions of recruitment time series. Our results underline that the complex and stochastic nature of the processes characterizing recruitment are unlikely to be captured by classical stock–recruitment relationships, but that non-linear forecasting methods provide interesting perspectives in that respect.
Stability and performance analysis of Compound TCP with the Exponential-RED and the Drop-Tail queue policies
Authors: Prasad Sai , Raina Gaurav
Published: October 2017

The analysis of transport protocols, along with queue management policies, forms an important aspect of performance evaluation for the Internet. In this article, we study Compound TCP (C-TCP), the default TCP in the Windows operating system, along with the Exponential-RED (E-RED) queue policy and the widely used Drop-Tail queue policy. We consider queuing delay, link utilization and the stability of the queue size as the performance metrics. We first analyse the stability properties of a nonlinear model for C-TCP coupled with the E-RED queue policy. We observe that this system, in its current form, may be difficult to stabilize as the feedback delay gets large. Further, using an exogenous and non-dimensional parameter, we show that the system loses local stability via a Hopf bifurcation, which gives rise to limit cycles. Employing Poincaré normal forms and the center manifold theory, we outline an analytical framework to characterize the type of the Hopf bifurcation and to determine the orbital stability of the emerging limit cycles. Numerical examples, stability charts and bifurcation diagrams complement our analysis. We also conduct packet-level simulations, with E-RED and Drop-Tail, in small and large buffer-sizing regimes. With large buffers, E-RED can achieve small queue sizes compared with Drop-Tail. However, it is difficult to maintain the stability of the E-RED policy as the feedback delay gets large. On the other hand, with small buffers, E-RED offers no clear advantage over the simple Drop-Tail queue policy. Our work can offer insights for the design of queue policies that can ensure low latency and stability.
LoCuSS: pre-processing in galaxy groups falling into massive galaxy clusters at z = 0.2
Authors: Bianconi M , Smith G P , Haines C P , McGee S L , Finoguenov A , Egami E
Published: October 2017

We report direct evidence of pre-processing of the galaxies residing in galaxy groups falling into galaxy clusters drawn from the Local Cluster Substructure Survey (LoCuSS). 34 groups have been identified via their X-ray emission in the infall regions of 23 massive (〈M200〉 = 1015 M⊙) clusters at 0.15 < z < 0.3. Highly complete spectroscopic coverage combined with 24 μm imaging from Spitzer allows us to make a consistent and robust selection of cluster and group members including star-forming galaxies down to a stellar mass limit of M⋆ = 2 × 1010 M⊙. The fraction fSF of star-forming galaxies in infalling groups is lower and with a flatter trend with respect to clustercentric radius when compared to the rest of the cluster galaxy population. At R ≈ 1.3 r200, the fraction of star-forming galaxies in infalling groups is half that in the cluster galaxy population. This is direct evidence that star-formation quenching is effective in galaxies already prior to them settling in the cluster potential, and that groups are favourable locations for this process.
Development of a Tandem Repeat-Based Polymerase Chain Displacement Reaction Method for Highly Sensitive Detection of ‘Candidatus Liberibacter asiaticus’
Authors: Lou Binghai , Song Yaqin , RoyChowdhury Moytri , Deng Chongling , Niu Ying , Fan Qijun , Tang Yan , Zhou Changyong
Published: October 2017

Huanglongbing (HLB) is one of the most destructive diseases in citrus production worldwide. Early detection of HLB pathogens can facilitate timely removal of infected citrus trees in the field. However, low titer and uneven distribution of HLB pathogens in host plants make reliable detection challenging. Therefore, the development of effective detection methods with high sensitivity is imperative. This study reports the development of a novel method, tandem repeat-based polymerase chain displacement reaction (TR-PCDR), for the detection of ‘Candidatus Liberibacter asiaticus’, a widely distributed HLB-associated bacterium. A uniquely designed primer set (TR2-PCDR-F/TR2-PCDR-1R) and a thermostable Taq DNA polymerase mutant with strand displacement activity were used for TR-PCDR amplification. Performed in a regular thermal cycler, TR-PCDR could produce more than two amplicons after each amplification cycle. Sensitivity of the developed TR-PCDR was 10 copies of target DNA fragment. The sensitive level was proven to be 100× higher than conventional PCR and similar to real-time PCR. Data from the detection of ‘Ca. L. asiaticus’ with filed samples using the above three methods also showed similar results. No false-positive TR-PCDR amplification was observed from healthy citrus samples and water controls. These results thereby illustrated that the developed TR-PCDR method can be applied to the reliable, highly sensitive, and cost-effective detection of ‘Ca. L. asiaticus’.
Pediatric Auditory Brainstem Implantation: Surgical, Electrophysiologic, and Behavioral Outcomes
Authors: Teagle Holly F. B. , Henderson Lillian , He Shuman , Ewend Matthew G. , Buchman Craig A.
Published: October 2017

Objectives:

The objectives of this study were to demonstrate the safety of auditory brainstem implant (ABI) surgery and document the subsequent development of auditory and spoken language skills in children without neurofibromatosis type II (NFII).

Design:

A prospective, single-subject observational study of ABI in children without NFII was undertaken at the University of North Carolina at Chapel Hill. Five children were enrolled under an investigational device exemption sponsored by the investigators. Over 3 years, patient demographics, medical/surgical findings, complications, device mapping, electrophysiologic measures, audiologic outcomes, and speech and language measures were collected.

Results:

Five children without NFII have received ABIs to date without permanent medical sequelae, although 2 children required treatment after surgery for temporary complications. All children wear their device daily, and the benefits of sound awareness have developed slowly. Intra-and postoperative electrophysiologic measures augmented surgical placement and device programming. The slow development of audition skills precipitated limited changes in speech production but had little impact on growth in spoken language.

Conclusions:

ABI surgery is safe in young children without NFII. Benefits from device use develop slowly and include sound awareness and the use of pattern and timing aspects of sound. These skills may augment progress in speech production but progress in language development is dependent upon visual communication. Further monitoring of this cohort is needed to better delineate the benefits of this intervention in this patient population.
Prevention of Ventilator-Associated Pneumonia: The Multimodal Approach of the Spanish ICU “Pneumonia Zero” Program*
Authors: Álvarez-Lerma Francisco , Palomar-Martínez Mercedes , Sánchez-García Miguel , Martínez-Alonso Montserrat , Álvarez-Rodríguez Joaquín , Lorente Leonardo , Arias-Rivera Susana , García Rosa , Gordo Federico , Añón José M. , Jam-Gatell Rosa , Vázquez-Calatayud Mónica , Agra Yolanda
Published: October 2017

Objectives:

The “Pneumonia Zero” project is a nationwide multimodal intervention based on the simultaneous implementation of a comprehensive evidence-based bundle measures to prevent ventilator-associated pneumonia in critically ill patients admitted to the ICU.

Design:

Prospective, interventional, and multicenter study.

Setting:

A total of 181 ICUs throughout Spain.

Patients:

All patients admitted for more than 24 hours to the participating ICUs between April 1, 2011, and December 31, 2012.

Intervention:

Ten ventilator-associated pneumonia prevention measures were implemented (seven were mandatory and three highly recommended). The database of the National ICU-Acquired Infections Surveillance Study (Estudio Nacional de Vigilancia de Infecciones Nosocomiales [ENVIN]) was used for data collection. Ventilator-associated pneumonia rate was expressed as incidence density per 1,000 ventilator days. Ventilator-associated pneumonia rates from the incorporation of the ICUs to the project, every 3 months, were compared with data of the ENVIN registry (April–June 2010) as the baseline period. Ventilator-associated pneumonia rates were adjusted by characteristics of the hospital, including size, type (public or private), and teaching (postgraduate) or university-affiliated (undergraduate) status.

Measurements and Main Results:

The 181 participating ICUs accounted for 75% of all ICUs in Spain. In a total of 171,237 ICU admissions, an artificial airway was present on 505,802 days (50.0% of days of stay in the ICU). A total of 3,474 ventilator-associated pneumonia episodes were diagnosed in 3,186 patients. The adjusted ventilator-associated pneumonia incidence density rate decreased from 9.83 (95% CI, 8.42–11.48) per 1,000 ventilator days in the baseline period to 4.34 (95% CI, 3.22–5.84) after 19–21 months of participation.

Conclusions:

Implementation of the bundle measures included in the “Pneumonia Zero” project resulted in a significant reduction of more than 50% of the incidence of ventilator-associated pneumonia in Spanish ICUs. This reduction was sustained 21 months after implementation.
MULTIMODAL IMAGING ADDS NEW INSIGHTS INTO ACUTE SYPHILITIC POSTERIOR PLACOID CHORIORETINITIS
Authors: Tsui Edmund , Gal-Or Orly , Ghadiali Quraish , Freund K. Bailey
Published: October 2017

Purpose:

Acute syphilitic posterior placoid chorioretinitis (ASPPC) is an uncommon manifestation of ocular syphilis with distinct clinical features. We describe new multimodal imaging findings in a patient with ASPPC.

Methods:

Observational case report with multimodal imaging.

Results:

A 44-year-old woman presented with 5 days of decreased vision in her right eye. Visual acuity was counting fingers in her right eye and 20/20 in her left eye. Funduscopic examination of the right eye showed a yellow placoid macular lesion with extension beyond the equator, which was encircled by an annular ring of outer retinal whitening. Ultra-widefield fundus autofluorescence demonstrated hyperautofluorescence corresponding to the placoid lesion. Examination of the left eye appeared unremarkable, but ultra-widefield fundus autofluorescence showed an area of hyperautofluorescence located superonasal to the optic nerve. Optical coherence tomography of the right eye demonstrated subretinal fluid and overlying disruption of the ellipsoid zone. Fluorescein angiography demonstrated early hypofluorescent and hyperfluorescent spots and late staining within the placoid lesion. Optical coherence tomography angiography showed several areas of decreased flow signal within the placoid lesion at the level of the choriocapillaris. Laboratory testing revealed a rapid plasma reagin titer of 1:1,024. Two months after treatment with intravenous penicillin G, visual acuity had improved to 20/25 in her right eye, and optical coherence tomography showed partial restoration of the ellipsoid zone. The annular ring resolved with near normalization of fundus autofluorescence and optical coherence tomography angiography demonstrated resolution of flow.

Conclusion:

Multimodal imaging provides further insight into the pathogenesis of ASPPC. Ultra-widefield fundus autofluorescence may show evidence of ellipsoid zone disruption in areas that clinically appear normal. Flow voids within the choriocapillaris in ASPPC appear to resolve with appropriate treatment, a finding that suggests a transient disruption of choriocapillaris flow in ASPPC.
Effects of physical exercise in older adults with reduced physical capacity: meta-analysis of resistance exercise and multimodal exercise
Authors: Liu Chiung-ju , Chang Wen-Pin , Araujo de Carvalho Islene , Savage Katie E.L. , Radford Lori W. , Amuthavalli Thiyagarajan Jotheeswaran
Published: October 2017

Older adults with reduced physical capacity are at greater risk of progression to care dependency. Progressive resistance strength exercise and multimodal exercise have been studied to restore reduced physical capacity. To summarize the best evidence of the two exercise regimes, this meta-analysis study appraised randomized-controlled trials from published systematic reviews. Medline, Embase, and the Cochrane Database of Systematic Review and Cochrane Central Register of Controlled Clinical Trials were searched for relevant systematic reviews. Two reviewers independently screened the relevant systematic reviews to identify eligible trials, assessed trial methodological quality, and extracted data. RevMan 5.3 software was used to analyze data on muscle strength, physical functioning, activities of daily living, and falls. Twenty-three eligible trials were identified from 22 systematic reviews. The mean age of the trial participants was 75 years or older. Almost all multimodal exercise trials included muscle strengthening exercise and balance exercise. Progressive resistance exercise is effective in improving muscle strength of the lower extremity and static standing balance. Multimodal exercise is effective in improving muscle strength of the lower extremity, dynamic standing balance, gait speed, and chair stand. In addition, multimodal exercise is effective in reducing falls. Neither type of exercise was effective in improving activities of daily living. For older adults with reduced physical capacity, multimodal exercise appears to have a broad effect on improving muscle strength, balance, and physical functioning of the lower extremity, and reducing falls relative to progressive resistance exercise alone.