bluuebunny/crossref_metadata_2025 huggingface dataset:
Force probe simulations of a reversibly rebinding system: Impact of pulling device stiffness
Authors: Jaschonek Stefan , Diezemann Gregor
Published: March 2017

We present a detailed study of the parameter dependence of force probe molecular dynamics (FPMD) simulations. Using a well studied calix[4]arene catenane dimer as a model system, we systematically vary the pulling velocity and the stiffness of the applied external potential. This allows us to investigate how the results of pulling simulations operating in the constant velocity mode (force-ramp mode) depend on the details of the simulation setup. The system studied has the further advantage of showing reversible rebinding meaning that we can monitor the opening and the rebinding transition. Many models designed to extract kinetic information from rupture force distributions work in the limit of soft springs and all quantities are found to depend solely on the so-called loading rate, the product of spring stiffness and pulling velocity. This approximation is known to break down when stiff springs are used, a situation often encountered in molecular simulations. We find that while some quantities only depend on the loading rate, others show an explicit dependence on the spring constant used in the FPMD simulation. In particular, the force versus extension curves show an almost stiffness independent rupture force but the force jump after the rupture transition does depend roughly linearly on the value of the stiffness. The kinetic rates determined from the rupture force distributions show a dependence on the stiffness that can be understood in terms of the corresponding dependence of the characteristic forces alone. These dependencies can be understood qualitatively in terms of a harmonic model for the molecular free energy landscape. It appears that the pulling velocities employed are so large that the crossover from activated dynamics to diffusive dynamics takes place on the time scale of our simulations. We determine the effective distance of the free energy minima of the closed and the open configurations of the system from the barrier via an analysis of the hydrogen-bond network with results in accord with earlier simulations. We find that the system is quite brittle in the force regime monitored in the sense that the barrier is located near to the closed state.
Effects of the matrix and intramolecular interactions on the stability of the higher-energy conformers of 2-fluorobenzoic acid
Authors: Kuş Nihal , Fausto Rui
Published: March 2017

DFT(B3LYP)/6-311++G(d,p) calculations on 2-fluorobenzoic acid (2FBA) show that the molecule has four conformers: two low energy conformers (forms I and II) with the carboxylic acid group assuming the cis configuration (O=C—O—H dihedral equal to 0°) and two higher-energy conformers (III, IV) with a trans carboxylic group configuration. Isolation of 2FBA monomers in argon or nitrogen matrices allows for the efficient trapping of both low-energy conformers. Narrowband selective near-IR (NIR) excitation of the 2νOH mode of I in both argon and N2 matrices leads to its efficient conversion into conformer III, which is stabilized by an intramolecular O—H···F interaction. On the other hand, upon identical selective vibrational excitation of II no changes could be noticed in the argon matrix spectra, while experiments carried out on N2 matrices showed conversion of II into III. In conformer IV (the expected direct product resulting from NIR excitation of II), the stabilizing O—H···F interaction existing in III is replaced by an O—H···H repulsive interaction, which leads to a barrier separating this form from II that is about one third of that separating III from I. Under these circumstances, once formed by vibrational excitation of II, conformer IV can easily convert to the reactant species by fast tunneling, justifying the apparent inefficiency of the II → IV conversion upon vibrational excitation of II in an argon matrix. On the other hand, the stabilization of the initially formed conformer IV by the N2 matrix (due to OH···N2 interactions) allows this species to survive long enough to allow the IV → III over-the-barrier conversion to be competitive with the IV → II tunneling, justifying the observed net conversion of the NIR excited conformer II into form III in N2 matrix. These results demonstrate as the intramolecular local topology may decisively influence the intrinsic kinetic stability of different conformers of the same molecule. They are also a clear additional evidence of the stabilization of higher-energy trans conformers of carboxylic acids by the N2 matrix medium that has been found before for other molecules of the same family.
Novel experimental technique for 3D investigation of high-speed cavitating diesel fuel flows by X-ray micro computed tomography
Authors: Lorenzi M. , Mitroglou N. , Santini M. , Gavaises M.
Published: March 2017

An experimental technique for the estimation of the temporal-averaged vapour volume fraction within high-speed cavitating flow orifices is presented. The scientific instrument is designed to employ X-ray micro computed tomography (microCT) as a quantitative 3D measuring technique applied to custom designed, large-scale, orifice-type flow channels made from Polyether-ether-ketone (PEEK). The attenuation of the ionising electromagnetic radiation by the fluid under examination depends on its local density; the transmitted radiation through the cavitation volume is compared to the incident radiation, and combination of radiographies from sufficient number of angles leads to the reconstruction of attenuation coefficients versus the spatial position. This results to a 3D volume fraction distribution measurement of the developing multiphase flow. The experimental results obtained are compared against the high speed shadowgraph visualisation images obtained in an optically transparent nozzle with identical injection geometry; comparison between the temporal mean image and the microCT reconstruction shows excellent agreement. At the same time, the real 3D internal channel geometry (possibly eroded) has been measured and compared to the nominal manufacturing CAD drawing of the test nozzle.
Electric field induced reversible spreading of droplets into films on lubricant impregnated surfaces
Authors: Brabcova Zuzana , McHale Glen , Wells Gary G. , Brown Carl V. , Newton Michael I.
Published: March 2017

Electric fields can be used to force a droplet to wet a solid surface using an applied voltage. However, significant hysteresis usually occurs associated with pinning forces at the contact line. Here, we report the forced spreading and subsequent retraction of droplets into liquid films in air on lubricant impregnated surfaces (also known as slippery liquid infused porous surfaces) where the contact line is completely mobile. We first confirm that we achieve a complete removal of hysteresis for the electrowetting of droplets above the saturation voltage. We then show that contact angle hysteresis can be reduced to less than 4° whilst retaining the ability to fully spread a droplet into a liquid film using an interface localized from liquid dielectrophoresis (dielectrowetting). In both cases, we find that the cosine of the contact angle has a quadratic dependence on applied voltage, consistent with previous theoretical expectations. Thus, our work demonstrates that fully reversible spreading encompassing a wide range of partial wetting droplet states and a film state can be achieved in air in a controllable manner with very low levels of hysteresis.
Electric-field-driven domain wall dynamics in perpendicularly magnetized multilayers
Authors: López González Diego , Shirahata Yasuhiro , Van de Wiele Ben , Franke Kévin J. A. , Casiraghi Arianna , Taniyama Tomoyasu , van Dijken Sebastiaan
Published: March 2017

We report on reversible electric-field-driven magnetic domain wall motion in a Cu/Ni multilayer on a ferroelectric BaTiO3 substrate. In our heterostructure, strain-coupling to ferroelastic domains with in-plane and perpendicular polarization in the BaTiO3 substrate causes the formation of domains with perpendicular and in-plane magnetic anisotropy, respectively, in the Cu/Ni multilayer. Walls that separate magnetic domains are elastically pinned onto ferroelectric domain walls. Using magneto-optical Kerr effect microscopy, we demonstrate that out-of-plane electric field pulses across the BaTiO3 substrate move the magnetic and ferroelectric domain walls in unison. Our experiments indicate an exponential increase of domain wall velocity with electric field strength and opposite domain wall motion for positive and negative field pulses. The application of a magnetic field does not affect the velocity of magnetic domain walls, but independently tailors their internal spin structure, causing a change in domain wall dynamics at high velocities.
Molecular mechanisms accompanying nitric oxide signalling through tyrosine nitration and S-nitrosylation of proteins in plants
Authors: Jain Prachi , Bhatla Satish C.
Published: March 2017

Nitric oxide (NO) signalling in plants is responsible for modulation of a variety of plant developmental processes. Depending on the tissue system, the signalling of NO-modulated biochemical responses majorly involves the processes of tyrosine nitration or S-nitrosylation of specific proteins/enzymes. It has further been observed that there is a significant impact of various biotic/abiotic stress conditions on the extent of tyrosine nitration and S-nitrosylation of various metabolic enzymes, which may act as a positive or negative modulator of the specific routes associated with adaptive mechanisms employed by plants under the said stress conditions. In addition to recent findings on the modulation of enzymes of primary metabolism by NO through these two biochemical mechanisms, a major mechanism for regulating the levels of reactive oxygen species (ROS) under stress conditions has also been found to be through tyrosine nitration or S-nitrosylation of ROS-scavenging enzymes. Recent investigations have further highlighted the differential manner in which the ROS-scavenging enzymes may be S-nitrosylated and tyrosine nitrated, with reference to their tissue distribution. Keeping in mind the very recent findings on these aspects, the present review has been prepared to provide an analytical view on the significance of protein tyrosine nitration and S-nitrosylation in plant development.
Effect of FLOWERING LOCUS C on seed germination depends on dormancy
Authors: Blair Logan , Auge Gabriela , Donohue Kathleen
Published: March 2017

FLOWERING LOCUS C (FLC) has a major regulatory role in the timing of flowering in Arabidopsis thaliana (L.) Heynh. and has more recently been shown to influence germination. Here, we investigated the conditions under which FLC influences germination, and demonstrated that its effect depends on the level of primary and secondary dormancy and the temperature of seed imbibition. We tested the germination response of genotypes with different degrees of FLC activity over the course of after-ripening and after secondary dormancy induction by hot stratification. Genotypes with high FLC-activity showed higher germination; this response was greatest when seeds exhibited primary dormancy or were induced into secondary dormancy by hot stratification. In this study, which used less dormant seeds, the effect of FLC was more evident at 22°C, the less permissive germination temperature, than at 10°C, in contrast to prior published results that used more dormant seeds. Thus, because effects of FLC variation depend on dormancy, and because the range of temperature that permits germination also depends on dormancy, the temperature at which FLC affects germination can also vary with dormancy. Finally, we document that the effect of FLC can depend on FRIGIDA and that FRIGIDA itself appears to influence germination. Thus, pleiotropy between germination and flowering pathways in A. thaliana extends beyond FLC and involves other genes in the FLC genetic pathway.
Melatonin in plant signalling and behaviour
Authors: Erland Lauren A. E. , Saxena Praveen K. , Murch Susan J.
Published: March 2017

Melatonin is an indoleamine neurotransmitter that has recently become well established as an important multi-functional signalling molecule in plants. These signals have been found to induce several important physiological responses that may be interpreted as behaviours. The diverse processes in which melatonin has been implicated in plants have expanded far beyond the traditional roles for which it has been implicated in mammals, which include sleep, tropisms and reproduction. These functions, however, appear to also be important melatonin mediated processes in plants, though the mechanisms underlying these functions have yet to be fully elucidated. Mediation or redirection of plant physiological processes induced by melatonin can be summarised as a series of behaviours including, among others: herbivore defence, avoidance of undesirable circumstances or attraction to opportune conditions, problem solving and response to environmental stimulus. As the mechanisms of melatonin action are elucidated, its involvement in plant growth, development and behaviour is likely to expand beyond the aspects discussed in this review and hold promise for applications in diverse fundamental and applied plant sciences including conservation, cryopreservation, morphogenesis, industrial agriculture and natural health products.
Inositol phosphates and phosphoinositides activate insulin-degrading enzyme, while phosphoinositides also mediate binding to endosomes
Authors: Song Eun Suk , Jang HyeIn , Guo Hou-Fu , Juliano Maria A. , Juliano Luiz , Morris Andrew J. , Galperin Emilia , Rodgers David W. , Hersh Louis B.
Published: March 2017

Significance

A diverse collection of peptides mediates cell–cell communication. Enzymes that cleave these peptides modulate their signals and thus play an important role in the physiology of multicellular organisms. Insulin-degrading enzyme (IDE) is one such enzyme that cleaves a number of bioactive peptides. IDE is activated by polyanions, but physiological activators remain unidentified. Here we show that inositol-containing molecules, known to modulate various cellular functions, activate IDE, identifying them as potential physiological regulators. Inositol phosphates are potent soluble activators of IDE. Phosphatidylinositol phosphates, lipid components of cell membranes, also activate but in addition facilitate the localization of IDE to intracellular compartments, where the enzyme gains access to substrates, such as insulin, internalized by cells.
Using chiral tactoids as optical probes to study the aggregation behavior of chromonics
Authors: Nayani Karthik , Fu Jinxin , Chang Rui , Park Jung Ok , Srinivasarao Mohan
Published: March 2017

Significance

Confined liquid crystals occupy a sweet spot in their continued relevance to a host of fundamental studies as well as being exploited for many technological applications. We report on interesting phenomenology in a particularly exciting class of liquid crystals called chromonics by observing the director configurations in tactoids as the phase boundary is traversed. Unique chiral structures in chromonic tactoids are rationalized by appealing to the variation of the aggregate lengths as the concentration and temperature change. We arrive at an interesting conclusion that higher concentrations have shorter aggregates at the nematic–biphasic transition temperature. Our study opens up pathways to exploit this unique class of water-soluble liquid crystals for a host of potential applications while tuning their concentration and temperature.
Probabilistic models of species discovery and biodiversity comparisons
Authors: Edie Stewart M. , Smits Peter D. , Jablonski David
Published: March 2017

Significance

Estimates of species numbers are central to many analyses in fields ranging from conservation biology to macroecology and macroevolution. However, new species continue to be discovered and described at an uneven rate among regions and taxonomic groups, raising questions about the robustness of currently observed biodiversity patterns. We present a statistical approach to the rate of species description that incorporates uncertainty in species numbers across space and among clades. This approach identifies regions or clades where taxonomic knowledge is most complete, and provides estimates of stability in large-scale patterns given continued species discoveries through probabilistic forecasts of diversity levels.
Priming GPCR signaling through the synergistic effect of two G proteins
Authors: Gupte Tejas M. , Malik Rabia U. , Sommese Ruth F. , Ritt Michael , Sivaramakrishnan Sivaraj
Published: March 2017

Significance

In this study, we uncover a G-protein–coupled receptor (GPCR) priming mechanism that results from the synergistic effects of two distinct G proteins. Although recent structural and spectroscopic studies of GPCR structure reveal a broad receptor conformational landscape, G-protein activation and downstream signaling are still viewed through the lens of individual ternary complexes between ligand, receptor, and individual effectors. Instead, our findings suggest positive interference between otherwise-disparate signaling pathways that can impact both the potency of GPCR ligands and their cell type-specific responses.
Small RNA-mediated repair of UV-induced DNA lesions by the DNA DAMAGE-BINDING PROTEIN 2 and ARGONAUTE 1
Authors: Schalk Catherine , Cognat Valérie , Graindorge Stéfanie , Vincent Timothée , Voinnet Olivier , Molinier Jean
Published: March 2017

Significance

As obligate photosynthetic and sessile organisms, plants are particularly exposed to the damaging effects of excess light and UV wavelengths, which can impact genome integrity by inducing DNA sequence alterations. As a response, plants have evolved efficient genome surveillance processes, some of which appear to also overlap with mechanisms of gene expression control. Our study extends this emerging notion by uncovering complex interconnections linking DNA repair and RNA silencing in
Arabidopsis
, illustrating the ever-expanding array of biological functions mediated by silencing small RNAs in plants.
Balancing selection maintains polymorphisms at neurogenetic loci in field experiments
Authors: Lonn Eija , Koskela Esa , Mappes Tapio , Mokkonen Mikael , Sims Angela M. , Watts Phillip C.
Published: March 2017

Significance

Arginine vasopressin receptor 1a (
Avpr1a
) and oxytocin receptor (
Oxtr
) are evolutionarily conserved loci that affect socio-reproductive behavior in many animals. That these loci affect fitness and exhibit substantial genetic variation in wild populations raises questions about the processes that maintain genetic variation at these loci. We show that the length of microsatellites located in the 5′ regulatory regions of
Avpr1a
and
Oxtr
are associated with reproductive success and gene expression in the brain. Crucially, balancing selection through sexually antagonistic fitness effects and density-related social influences is capable of maintaining microsatellite length polymorphisms at both genes. The action of sex and population density operating at two loci indicates that balancing selection may maintain diversity at many other behavioral loci.
La métamorphose des Minéides en chauves-souris dans l’Ovide moralisé
Authors: Calenda Angela
Published: March 2017

La présente étude s’occupe de l’épisode de la transformation des filles de Minyas en chauves-souris, tel qu’il est décrit dans le quatrième livre de l’Ovide moralisé. Cette œuvre est la première traduction intégrale en langue romane des Métamorphoses et comprend quelques 72000 octosyllabes dans les manuscrits complets. L’ouvrage, probablement rédigé par un franciscain, a une valeur hautement didactique, qui ressort surtout dans les moralisations, que le clerc a ajoutées à la traduction des Métamorphoses. Dans un premier temps, nous analyserons la description de l’animal, qui mérite attention du fait que la chauve-souris est considérée, dans la tradition naturaliste antique, comme une bête hybride, entre oiseau et souris, ce qui donne lieu à un traitement original de la part de l’auteur de l’Ovide moralisé. De là, nous essayerons d’expliquer les multiples facettes de la chauve-souris à l’intérieur du mythe des Minéides, en étudiant les multiples sens qui en découlent dans le texte français, et leur utilisation pour illustrer le comportement du chrétien exemplaire.
Antigone, “cigoigne orde et vilz”
Authors: Endress Laura
Published: March 2017

Le mythe d’Antigone transformée en cigogne a trouvé son chemin de l’Antiquité gréco-romaine vers le Moyen Âge occidental à travers les Métamorphoses ovidiennes, adaptés au XIVe siècle dans l’immense poème qu’est l’Ovide Moralisé. En retravaillant la matière mythologique dans le contexte chrétien, l’auteur de cette œuvre médiévale a fait de l’évocation succincte et anecdotique de la cigogne chez Ovide un discours moralisateur étendu qui multiplie les traits dépréciatifs attribués à l’oiseau blanc, en lui conférant une image foncièrement négative. La présente contribution tentera de mettre en lumière le cheminement et les possibles raisons de cette évolution, en examinant les différentes sources qui ont fourni des matériaux pour la composition du portrait tardo-médiévale de la cigogne moralisée.
Comparison of Selected Nonlethal Samples from Adult Steelhead for Detection of Infectious Hematopoietic Necrosis Virus Using Cell Culture
Authors: Burbank David R. , Fehringer Tyson R. , Chiaramonte Luciano V.
Published: March 2017

Nonlethal sampling techniques have previously been evaluated for detection of a variety of viral salmonid pathogens. However, many of these studies have used molecular assays in lieu of widely accepted cell culture techniques to evaluate the sampled tissues. Samples were collected from female steelhead Oncorhynchus mykiss broodstock using three potential nonlethal sampling methods (mucus/skin scrape, pectoral fin clip, and gill tissue biopsy) and evaluated for the presence of infectious hematopoietic necrosis virus (IHNV) via cell culture techniques. The results were compared with those from samples collected using a standard lethal sampling method (pooled anterior kidney and spleen tissues) applied to the same fish. Of the three nonlethal sampling techniques that were evaluated, fin clipping was the easiest and least invasive method. Furthermore, fin tissue was as sensitive as or more sensitive than kidney/spleen tissue for detecting IHNV in this population of fish. However, with the exception of gill tissue, the nonlethal samples did not appear to be appropriate surrogates for lethally collected tissues with regard to identifying an active infection in a particular fish. Nevertheless, nonlethal sampling coupled with cell culture appears to be suitable for helping to define the IHNV status of a steelhead population.

Received July 27, 2016; accepted December 11, 2016 Published online March 21, 2017
MultiPic: A standardized set of 750 drawings with norms for six European languages
Authors: Duñabeitia Jon Andoni , Crepaldi Davide , Meyer Antje S. , New Boris , Pliatsikas Christos , Smolka Eva , Brysbaert Marc
Published: March 2017

Numerous studies in psychology, cognitive neuroscience and psycholinguistics have used pictures of objects as stimulus materials. Currently, authors engaged in cross-linguistic work or wishing to run parallel studies at multiple sites where different languages are spoken must rely on rather small sets of black-and-white or colored line drawings. These sets are increasingly experienced as being too limited. Therefore, we constructed a new set of 750 colored pictures of concrete concepts. This set, MultiPic, constitutes a new valuable tool for cognitive scientists investigating language, visual perception, memory and/or attention in monolingual or multilingual populations. Importantly, the MultiPic databank has been normed in six different European languages (British English, Spanish, French, Dutch, Italian and German). All stimuli and norms are freely available at http://www.bcbl.eu/databases/multipic .
Cognitive load during route selection increases reliance on spatial heuristics
Authors: Brunyé Tad T , Martis Shaina B , Taylor Holly A
Published: March 2017

Planning routes from maps involves perceiving the symbolic environment, identifying alternate routes and applying explicit strategies and implicit heuristics to select an option. Two implicit heuristics have received considerable attention, the southern route preference and initial segment strategy. This study tested a prediction from decision-making theory that increasing cognitive load during route planning will increase reliance on these heuristics. In two experiments, participants planned routes while under conditions of minimal (0-back) or high (2-back) working memory load. In Experiment 1, we examined how memory load impacts the southern route heuristic. In Experiment 2, we examined how memory load impacts the initial segment heuristic. Results replicated earlier results demonstrating a southern route preference (Experiment 1) and initial segment strategy (Experiment 2) and further demonstrated that evidence for heuristic reliance is more likely under conditions of concurrent working memory load. Furthermore, the extent to which participants maintained efficient route selection latencies in the 2-back condition predicted the magnitude of this effect. Together, results demonstrate that working memory load increases the application of heuristics during spatial decision making, particularly when participants attempt to maintain quick decisions while managing concurrent task demands.
Raft-based sphingomyelin interactions revealed by new fluorescent sphingomyelin analogs
Authors: Kinoshita Masanao , Suzuki Kenichi G.N. , Matsumori Nobuaki , Takada Misa , Ano Hikaru , Morigaki Kenichi , Abe Mitsuhiro , Makino Asami , Kobayashi Toshihide , Hirosawa Koichiro M. , Fujiwara Takahiro K. , Kusumi Akihiro , Murata Michio
Published: March 2017

Sphingomyelin (SM) has been proposed to form cholesterol-dependent raft domains and sphingolipid domains in the plasma membrane (PM). How SM contributes to the formation and function of these domains remains unknown, primarily because of the scarcity of suitable fluorescent SM analogs. We developed new fluorescent SM analogs by conjugating a hydrophilic fluorophore to the SM choline headgroup without eliminating its positive charge, via a hydrophilic nonaethylene glycol linker. The new analogs behaved similarly to the native SM in terms of their partitioning behaviors in artificial liquid order-disorder phase-separated membranes and detergent-resistant PM preparations. Single fluorescent molecule tracking in the live-cell PM revealed that they indirectly interact with each other in cholesterol- and sphingosine backbone–dependent manners, and that, for ∼10–50 ms, they undergo transient colocalization-codiffusion with a glycosylphosphatidylinositol (GPI)-anchored protein, CD59 (in monomers, transient-dimer rafts, and clusters), in CD59-oligomer size–, cholesterol-, and GPI anchoring–dependent manners. These results suggest that SM continually and rapidly exchanges between CD59-associated raft domains and the bulk PM.
Secretogranin III as a disease-associated ligand for antiangiogenic therapy of diabetic retinopathy
Authors: LeBlanc Michelle E. , Wang Weiwen , Chen Xiuping , Caberoy Nora B. , Guo Feiye , Shen Chen , Ji Yanli , Tian Hong , Wang Hui , Chen Rui , Li Wei
Published: March 2017

Diabetic retinopathy (DR) is a leading cause of vision loss with retinal vascular leakage and/or neovascularization. Current antiangiogenic therapy against vascular endothelial growth factor (VEGF) has limited efficacy. In this study, we applied a new technology of comparative ligandomics to diabetic and control mice for the differential mapping of disease-related endothelial ligands. Secretogranin III (Scg3) was discovered as a novel disease-associated ligand with selective binding and angiogenic activity in diabetic but not healthy vessels. In contrast, VEGF bound to and induced angiogenesis in both diabetic and normal vasculature. Scg3 and VEGF signal through distinct receptor pathways. Importantly, Scg3-neutralizing antibodies alleviated retinal vascular leakage in diabetic mice with high efficacy. Furthermore, anti-Scg3 prevented retinal neovascularization in oxygen-induced retinopathy mice, a surrogate model for retinopathy of prematurity (ROP). ROP is the most common cause of vision impairment in children, with no approved drug therapy. These results suggest that Scg3 is a promising target for novel antiangiogenic therapy of DR and ROP.
Evolutionary insights into T-type Ca2+ channel structure, function, and ion selectivity from the Trichoplax adhaerens homologue
Authors: Smith Carolyn L. , Abdallah Salsabil , Wong Yuen Yan , Le Phuong , Harracksingh Alicia N. , Artinian Liana , Tamvacakis Arianna N. , Rehder Vincent , Reese Thomas S. , Senatore Adriano
Published: March 2017

Four-domain voltage-gated Ca2+ (Cav) channels play fundamental roles in the nervous system, but little is known about when or how their unique properties and cellular roles evolved. Of the three types of metazoan Cav channels, Cav1 (L-type), Cav2 (P/Q-, N- and R-type) and Cav3 (T-type), Cav3 channels are optimized for regulating cellular excitability because of their fast kinetics and low activation voltages. These same properties permit Cav3 channels to drive low-threshold exocytosis in select neurons and neurosecretory cells. Here, we characterize the single T-type calcium channel from Trichoplax adhaerens (TCav3), an early diverging animal that lacks muscle, neurons, and synapses. Co-immunolocalization using antibodies against TCav3 and neurosecretory cell marker complexin labeled gland cells, which are hypothesized to play roles in paracrine signaling. Cloning and in vitro expression of TCav3 reveals that, despite roughly 600 million years of divergence from other T-type channels, it bears the defining structural and biophysical features of the Cav3 family. We also characterize the channel’s cation permeation properties and find that its pore is less selective for Ca2+ over Na+ compared with the human homologue Cav3.1, yet it exhibits a similar potent block of inward Na+ current by low external Ca2+ concentrations (i.e., the Ca2+ block effect). A comparison of the permeability features of TCav3 with other cloned channels suggests that Ca2+ block is a locus of evolutionary change in T-type channel cation permeation properties and that mammalian channels distinguish themselves from invertebrate ones by bearing both stronger Ca2+ block and higher Ca2+ selectivity. TCav3 is the most divergent metazoan T-type calcium channel and thus provides an evolutionary perspective on Cav3 channel structure–function properties, ion selectivity, and cellular physiology.
Computing geometric Lorenz attractors with arbitrary precision
Authors: Graça D. , Rojas C. , Zhong N.
Published: March 2017

The Lorenz attractor was introduced in 1963 by E. N. Lorenz as one of the first examples of strange attractors. However, Lorenz’ research was mainly based on (non-rigorous) numerical simulations, and, until recently, the proof of the existence of the Lorenz attractor remained elusive. To address that problem some authors introduced geometric Lorenz models and proved that geometric Lorenz models have a strange attractor. In 2002 it was shown that the original Lorenz model behaves like a geometric Lorenz model and thus has a strange attractor.

In this paper we show that geometric Lorenz attractors are computable, as well as show their physical measures.
Weighted floating bodies and polytopal approximation
Authors: Besau Florian , Ludwig Monika , Werner Elisabeth
Published: March 2017

Asymptotic results for weighted floating bodies are established and used to obtain new proofs for the existence of floating areas on the sphere and in hyperbolic space and to establish the existence of floating areas in Hilbert geometries. Results on weighted best and random approximation and the new approach to floating areas are combined to derive new asymptotic approximation results on the sphere, in hyperbolic space, and in Hilbert geometries.
NeBcon: protein contact map prediction using neural network training coupled with naïve Bayes classifiers
Authors: He Baoji , Mortuza S M , Wang Yanting , Shen Hong-Bin , Zhang Yang
Published: March 2017

Motivation

Recent CASP experiments have witnessed exciting progress on folding large-size non-humongous proteins with the assistance of co-evolution based contact predictions. The success is however anecdotal due to the requirement of the contact prediction methods for the high volume of sequence homologs that are not available to most of the non-humongous protein targets. Development of efficient methods that can generate balanced and reliable contact maps for different type of protein targets is essential to enhance the success rate of the ab initio protein structure prediction.

Results

We developed a new pipeline, NeBcon, which uses the naïve Bayes classifier (NBC) theorem to combine eight state of the art contact methods that are built from co-evolution and machine learning approaches. The posterior probabilities of the NBC model are then trained with intrinsic structural features through neural network learning for the final contact map prediction. NeBcon was tested on 98 non-redundant proteins, which improves the accuracy of the best co-evolution based meta-server predictor by 22%; the magnitude of the improvement increases to 45% for the hard targets that lack sequence and structural homologs in the databases. Detailed data analysis showed that the major contribution to the improvement is due to the optimized NBC combination of the complementary information from both co-evolution and machine learning predictions. The neural network training also helps to improve the coupling of the NBC posterior probability and the intrinsic structural features, which were found particularly important for the proteins that do not have sufficient number of homologous sequences to derive reliable co-evolution profiles.

Availiablity and Implementation

On-line server and standalone package of the program are available at http://zhanglab.ccmb.med.umich.edu/NeBcon/.

Supplementary information

Supplementary data are available at Bioinformatics online.
Preoperative Magnetic Resonance and Intraoperative Computed Tomography Fusion for Real-Time Neuronavigation in Intramedullary Lesion Surgery
Authors: Costa Francesco , Ortolina Alessandro , Cardia Andrea , Riva Marco , Revay Martina , Pecchioli Guido , Anania Carla Daniela , Asteggiano Francesco , Fornari Maurizio
Published: March 2017

BACKGROUND: Image-guided surgery techniques in spinal surgery are usually based upon fluoroscopy or computed tomography (CT) scan, which allow for a real-time navigation of bony structures, though not of neural structures and soft tissue remains.

OBJECTIVE: To verify the effectiveness and efficacy of a novel technique of imaging merging between preoperative magnetic resonance imaging (MRI) and intraoperative CT scan during removal of intramedullary lesions.

METHODS: Ten consecutive patients were treated for intramedullary lesions using a navigation system aid. Preoperative contrast-enhanced MRI was merged in the navigation software, with an intraoperative CT acquisition, performed using the O-armTM system (Medtronic Sofamor Danek, Minneapolis, Minnesota). Dosimetric and timing data were also acquired for each patient.

RESULTS: The fusion process was achieved in all cases and was uneventful. The merged imaging information was useful in all cases for defining the exact area of laminectomy, dural opening, and the eventual extension of cordotomy, without requiring exposition corrections. The radiation dose for the patients was 0.78 mSv. Using the authors’ protocol, it was possible to merge a preoperative MRI with navigation based on intraoperative CT scanning in all cases. Information gained with this technique was useful during the different surgical steps. However, there were some drawbacks, such as the merging process, which still remains partially manual.

CONCLUSION: In this initial experience, MRI and CT merging and its feasibility were tested, and we appreciated its safety, precision, and ease.
Navigation and Image Injection for Control of Bone Removal and Osteotomy Planes in Spine Surgery
Authors: Kosterhon Michael , Gutenberg Angelika , Kantelhardt Sven Rainer , Archavlis Elefterios , Giese Alf
Published: March 2017

BACKGROUND AND IMPORTANCE: In contrast to cranial interventions, neuronavigation in spinal surgery is used in few applications, not tapping into its full technological potential. We have developed a method to preoperatively create virtual resection planes and volumes for spinal osteotomies and export 3-D operation plans to a navigation system controlling intraoperative visualization using a surgical microscope's head-up display. The method was developed using a Sawbone® model of the lumbar spine, demonstrating feasibility with high precision. Computer tomographic and magnetic resonance image data were imported into Amira®, a 3-D visualization software. Resection planes were positioned, and resection volumes representing intraoperative bone removal were defined. Fused to the original Digital Imaging and Communications in Medicine data, the osteotomy planes were exported to the cranial version of a Brainlab® navigation system. A navigated surgical microscope with video connection to the navigation system allowed intraoperative image injection to visualize the preplanned resection planes.

CLINICAL PRESENTATION: The workflow was applied to a patient presenting with a congenital hemivertebra of the thoracolumbar spine. Dorsal instrumentation with pedicle screws and rods was followed by resection of the deformed vertebra guided by the in-view image injection of the preplanned resection planes into the optical path of a surgical microscope. Postoperatively, the patient showed no neurological deficits, and the spine was found to be restored in near physiological posture.

CONCLUSION: The intraoperative visualization of resection planes in a microscope's head-up display was found to assist the surgeon during the resection of a complex-shaped bone wedge and may help to further increase accuracy and patient safety.
Supraorbital Keyhole Craniotomy for Basilar Artery Aneurysms: Accounting for the “Cliff” Effect
Authors: Stamates Melissa M. , Wong Andrew K. , Bhansali Anita , Wong Ricky H.
Published: March 2017

BACKGROUND: Treatment of basilar artery aneurysms is challenging. While endovascular techniques have dominated, there still remain circumstances where open surgical clipping is required or preferred. Minimally invasive “keyhole” approaches are being used more frequently to provide the durability of surgical clipping with a lower morbidity profile; however, careful patient selection is required. The supraorbital “keyhole” approach has been described for the treatment of basilar artery aneurysms, but careful assessment of the basilar exposure is necessary to ensure proper visualization of the aneurysm and ability to obtain proximal vascular control. Various methods of estimating the basilar artery exposure in this approach have been described, including the anterior skull base line and the posterior clinoid line, but both are unreliable and inaccurate.

OBJECTIVE: To propose a new method, the orbital roof-dorsum line, to simply and accurately predict the basilar artery exposure.

METHODS: CT angiograms for 20 consecutive unique patients were analyzed to obtain the anterior skull base line, posterior clinoid line, and the orbital roof-dorsum line. CT angiograms were then loaded onto a Stealth neuronavigation system (Medtronic, Minneapolis, Minnesota) to obtain “true” visualization lengths. A case illustration is presented.

RESULTS: Pairwise comparison tests demonstrated that both the anterior skull base and the posterior clinoid estimation lines differed significantly from the “true”  value (P < .0001). Our orbital roof-dorsum estimation provided results that accurately predicted the “true” value (P = .71).

CONCLUSION: The orbital roof-dorsum line provides a simple and reliable method of estimating basilar artery exposure and should be used whenever considering patients for surgical clipping by this approach.
A search for Ly α emitters around a concentrated region of strong Ly α absorbers at z = 2.3
Authors: Ogura Kazuyuki , Nagao Tohru , Imanishi Masatoshi , Kashikawa Nobunari , Taniguchi Yoshiaki , Kajisawa Masaru , Kobayashi Masakazu A. R. , Toba Yoshiki , Nobuhara Kodai
Published: March 2017

In order to investigate the physical relationship between strong Ly α absorbers ($\log N_{{\rm H}\,{{\small I}}} \ge 20.0\:$cm−2) such as damped Ly α absorption systems (DLAs) and young star-forming galaxies at high redshift, we have conducted narrow-band observations of Ly α emitters (LAEs) in a concentrated region of strong Ly α absorbers at z = 2.3, the J1230+34 field. Using a catalog of Ly α absorbers with $\log N_{\rm H\,{{\small I}}} \ge 20.0\:$cm−2 based on the Baryon Oscillation Spectroscopic Survey, we found six fields where three or more absorbers are concentrated within a (50 Mpc)3 cubic box in the comoving scale. Among them, we focus on the J1230+34 field, where two DLAs and two sub-DLAs are present. Our narrow-band imaging observations with Subaru/Suprime-Cam using a custom-made filter, NB400 (λc = 4003 Å and FWHM = 92 Å) yield a sample of 149 LAEs in this field. In the large scale (∼50 Mpc), we have found no differences between the obtained Ly α luminosity function and those in the blank fields at similar redshifts. We also compare the frequency distribution of the Ly α rest-frame equivalent width ($\mathit {EW}_{0}$) in the target field and other fields including both overdensity region and blank field, but find no differences. On the other hand, in the small scale (∼10 Mpc), we have found a possible overdensity of LAEs around a DLA with the highest ${\rm H}\,{\small I}$ column density ($N_{\rm H\,{{\small I}}} = 21.08\:$cm−2) in the target field while there are no density excesses around the other absorbers with a lower $N_{\rm H\,{{\small I}}}$.
Outstanding animal studies in allergy I. From asthma to food allergy and anaphylaxis
Authors: Jensen-Jarolim Erika , Pali-Schöll Isabella , Roth-Walter Franziska
Published: March 2017

Purpose of review

Animal models published within the past 18 months on asthma, food allergy and anaphylaxis, all conditions of rising public health concern, were reviewed.

Recent findings

While domestic animals spontaneously develop asthma, food allergy and anaphylaxis, in animal models, divergent sensitization and challenge routes, dosages, intervals and antigens are used to induce asthmatic, food allergic or anaphylactic phenotypes. This must be considered in the interpretation of results. Instead of model antigens, gradually relevant allergens such as house dust mite in asthma, and food allergens like peanut, apple and peach in food allergy research were used. Novel engineered mouse models such as a mouse with a T-cell receptor for house dust mite allergen Der p 1, or with transgenic human hFcγR genes, facilitated the investigation of single molecules of interest. Whole-body plethysmography has become a state-of-the-art in-vivo readout in asthma research. In food allergy and anaphylaxis research, novel techniques were developed allowing real-time monitoring of in-vivo effects following allergen challenge. Networks to share tissues were established as an effort to reduce animal experiments in allergy which cannot be replaced by in-vitro measures.

Natural and artificial animal models were used to explore the pathophysiology of asthma, food allergy and anaphylaxis and to improve prophylactic and therapeutic measures. Especially the novel mouse models mimicking molecular aspects of the complex immune network in asthma, food allergy and anaphylaxis will facilitate proof-of-concept studies under controlled conditions.
A Mindfulness Program Adapted for Adolescents With Chronic Pain
Authors: Ruskin Danielle A. , Gagnon Michelle M. , Kohut Sara A. , Stinson Jennifer N. , Walker Kathryn S.
Published: March 2017

Objectives:

Pediatric chronic pain is a major health issue that can lead to significant interference in daily functioning. Mindfulness-based interventions (MBI’s), which emphasize acceptance rather than control of pain, have gained increasing attention as a viable treatment option among adults with chronic pain. The effectiveness of MBIs for chronic pain in pediatric populations remains largely unknown. This prospective pre-post interventional study was conducted to examine the feasibility, acceptability, and initial effectiveness of an 8-week group MBI adapted for adolescents (MBI-A) with chronic pain.

Materials and Methods:

Self-report measures assessing pain characteristics, anxiety, depression, disability, pain catastrophizing, perceived social support, mindfulness, and pain acceptance were administered at baseline, postintervention, and at a 3-month follow-up. In addition, session data were collected to assess each session’s impact on patients’ coping with pain and stress, body awareness, and sense of feeling less alone.

Results:

In total, 42 consecutive patients in a tertiary care chronic pain clinic met eligibility criteria to participate in the MBI-A group. Of these, 21 participated. A treatment completion rate of 90.5% was observed. Between session mindfulness practice was reported by 77% of participants. Participants were highly satisfied with the MBI-A and all participants reported they would recommend the group to a friend. Improvements in pain acceptance were observed between baseline and the 3-month follow-up, in domains of Pain Willingness and Activity Engagement. Session data revealed improved body awareness and improved ability to cope with stress across sessions.

Discussion:

The MBI-A is a feasible, well-received intervention for adolescents with chronic pain conditions. Findings support the need for further investigation of the efficacy of MBI-A through randomized-controlled trials.
Prevalence and Impact on Weaning of Pleural Effusion at the Time of Liberation from Mechanical Ventilation
Authors: Dres Martin , Roux Damien , Pham Tài , Beurton Alexandra , Ricard Jean-Damien , Fartoukh Muriel , Demoule Alexandre
Published: March 2017

Background

Pleural effusion is frequent in intensive care unit patients, but its impact on the outcome of weaning remains unknown.

Methods

In a prospective study performed in three intensive care units, pleural ultrasound was performed at the first spontaneous breathing trial to detect and quantify pleural effusion (small, moderate, and large). Weaning failure was defined by a failed spontaneous breathing trial and/or extubation requiring any form of ventilatory support within 48 h. The primary endpoint was the prevalence of pleural effusion according to weaning outcome.

Results

Pleural effusion was detected in 51 of 136 (37%) patients and was quantified as moderate to large in 18 (13%) patients. As compared to patients with no or small pleural effusion, their counterparts were more likely to have chronic renal failure (39 vs. 7%; P = 0.01), shock as the primary reason for admission (44 vs. 19%; P = 0.02), and a greater weight gain (+4 [0 to 7] kg vs. 0 [−1 to 5] kg; P = 0.02). The prevalence of pleural effusion was similar in weaning success and weaning failure patients (odds ratio, 1.23; 95% CI, 0.61 to 2.49; P = 0.56), as was the prevalence of moderate to large pleural effusion (odds ratio, 0.89; 95% CI, 0.33 to 2.41; P = 1.00). Duration of mechanical ventilation and intensive care unit length of stay were similar between patients with no or small pleural effusion and those with moderate to large pleural effusion.

Conclusions

Significant pleural effusion was observed in 13% of patients at the time of liberation from mechanical ventilation and was not associated with an alteration of weaning outcome. (Anesthesiology 2017; 126:1107–15)