bluuebunny/crossref_metadata_2025_split huggingface dataset:
On the Mechanical Effects of Poroelastic Crystal Mush in Classical Magma Chamber Models
Authors: Liao Yang , Soule S. Adam , Jones Max 
Published: October 2018

AbstractImproved constraints on the mechanical behavior of magma chambers is essential for understanding volcanic processes; however, the role of crystal mush on the mechanical evolution of magma chambers has not yet been systematically studied. Existing magma chamber models typically consider magma chambers to be isolated melt bodies surrounded by elastic crust. In this study, we develop a physical model to account for the presence and properties of crystal mush in magma chambers and investigate its impact on the mechanical processes during and after injection of new magma. Our model assumes the magma chamber to be a spherical body consisting of a liquid core of fluid magma within a shell of crystal mush that behaves primarily as a poroelastic material. We investigate the characteristics of time‐dependent evolution in the magma chamber, both during and after the injection, and find that quantities such as overpressure and tensile stress continue to evolve after the injection has stopped, a feature that is absent in elastic (mushless) models. The time scales relevant to the postinjection evolution vary from hours to thousands of years, depending on the micromechanical properties of the mush, the viscosity of magma, and chamber size. We compare our poroelastic results to the behavior of a magma chamber with an effectively viscoelastic shell and find that only the poroelastic model displays a time scale dependence on the size of the chamber for any fixed mush volume fraction. This study demonstrates that crystal mush can significantly influence the mechanical behaviors of crustal magmatic reservoirs.
Effect of Fault Roughness on Aftershock Distribution: Elastic Off‐Fault Material Properties
Authors: Aslam Khurram S. , Daub Eric G. 
Published: October 2018

AbstractWe perform physics‐based simulations of earthquake rupture propagation on geometrically complex strike‐slip faults to examine the off‐fault stress changes resulting from dynamic fault slip. We consider many different realizations of the fault profile and use the output of our simulations to calculate the Coulomb failure function (CFF) for each realization. We analyze the effects of fault maturity as well as the self‐affine character of the fault surface on the stress field. To quantify our results, we calculate the probability density function for the CFF as a function of distance and observe that the CFF values show a greater variability in the near‐fault region (distance <3 km away from fault), and this spread squeezes into a narrow negative range in the far‐field region. In the near‐fault region, we see many zones of positive CFF change, which are not observed in the far‐fault region. We consider these zones of CFF increase as locations of potential aftershocks and compare their size with rupture areas of aftershocks from relocated earthquake catalogs of Northern and Southern California. Our model results and observational data show a relatively high probability of occurrence of smaller potential aftershock areas compared to larger ones in the near‐fault region. Additionally, based on our comparison with aftershock and preshock data, we conclude that the stresses in the near‐fault region are dominated by fault roughness effects. Our results suggest that tectonic stresses are highly spatially heterogeneous, and this complexity persists throughout seismic cycle.
Attenuation artifacts in light sheet fluorescence microscopy corrected by OPTiSPIM
Authors: Mayer Jürgen , Robert-Moreno Alexandre , Sharpe James , Swoger Jim 
Published: October 2018

AbstractLight sheet fluorescence microscopy (LSFM) is rapidly becoming an essential technology for mesoscopic imaging of samples such as embryos and adult mouse organs. However, LSFM can suffer from optical artifacts for which there is no intrinsic solution. The attenuation of light due to absorbing material causes “shadow” artifacts along both the illumination and detection paths. Several approaches have been introduced to reduce this problem, including scanning illumination and multi-view imaging. However, neither of these approaches completely eliminates the problem. If the distribution of the absorbing material is complex, shadows cannot be avoided. We introduce a new approach that relies on multi-modal integration of two very different mesoscopic techniques. Unlike LSFM, optical projection tomography (OPT) can operate in transmission mode to create a voxel map of the 3D distribution of the sample’s optical attenuation. Here, we demonstrate a hybrid instrument (OPTiSPIM) that can quantify this attenuation and use the information to correct the shadow artifacts of LSFM.
Multimode optical fiber transmission with a deep learning network
Authors: Rahmani Babak , Loterie Damien , Konstantinou Georgia , Psaltis Demetri , Moser Christophe 
Published: October 2018

AbstractMultimode fibers (MMFs) are an example of a highly scattering medium, which scramble the coherent light propagating within them to produce seemingly random patterns. Thus, for applications such as imaging and image projection through an MMF, careful measurements of the relationship between the inputs and outputs of the fiber are required. We show, as a proof of concept, that a deep neural network can learn the input-output relationship in a 0.75 m long MMF. Specifically, we demonstrate that a deep convolutional neural network (CNN) can learn the nonlinear relationships between the amplitude of the speckle pattern (phase information lost) obtained at the output of the fiber and the phase or the amplitude at the input of the fiber. Effectively, the network performs a nonlinear inversion task. We obtained image fidelities (correlations) as high as ~98% for reconstruction and ~94% for image projection in the MMF compared with the image recovered using the full knowledge of the system transmission characterized with the complex measured matrix. We further show that the network can be trained for transfer learning, i.e., it can transmit images through the MMF, which belongs to another class not used for training/testing.
Genome mining of cyclodipeptide synthases unravels unusual tRNA-dependent diketopiperazine-terpene biosynthetic machinery
Authors: Yao Tingting , Liu Jing , Liu Zengzhi , Li Tong , Li Huayue , Che Qian , Zhu Tianjiao , Li Dehai , Gu Qianqun , Li Wenli 
Published: October 2018

AbstractCyclodipeptide synthases (CDPSs) can catalyze the formation of two successive peptide bonds by hijacking aminoacyl-tRNAs from the ribosomal machinery resulting in diketopiperazines (DKPs). Here, three CDPS-containing loci (dmt1–3) are discovered by genome mining and comparative genome analysis of Streptomyces strains. Among them, CDPS DmtB1, encoded by the gene of dmt1 locus, can synthesize cyclo(L-Trp-L-Xaa) (with Xaa being Val, Pro, Leu, Ile, or Ala). Systematic mutagenesis experiments demonstrate the importance of the residues constituting substrate-binding pocket P1 for the incorporation of the second aa-tRNA in DmtB1. Characterization of dmt1–3 unravels that CDPS-dependent machinery is involved in CDPS-synthesized DKP formation followed by tailoring steps of prenylation and cyclization to afford terpenylated DKP compounds drimentines. A phytoene-synthase-like family prenyltransferase (DmtC1) and a membrane terpene cyclase (DmtA1) are required for drimentines biosynthesis. These results set the foundation for further increasing the natural diversity of complex DKP derivatives.
A rapid rate of sex-chromosome turnover and non-random transitions in true frogs
Authors: Jeffries Daniel L. , Lavanchy Guillaume , Sermier Roberto , Sredl Michael J. , Miura Ikuo , Borzée Amaël , Barrow Lisa N. , Canestrelli Daniele , Crochet Pierre-André , Dufresnes Christophe , Fu Jinzhong , Ma Wen-Juan , Garcia Constantino Macías , Ghali Karim , Nicieza Alfredo G. , O’Donnell Ryan P. , Rodrigues Nicolas , Romano Antonio , Martínez-Solano Íñigo , Stepanyan Ilona , Zumbach Silvia , Brelsford Alan , Perrin Nicolas 
Published: October 2018

AbstractThe canonical model of sex-chromosome evolution predicts that, as recombination is suppressed along sex chromosomes, gametologs will progressively differentiate, eventually becoming heteromorphic. However, there are numerous examples of homomorphic sex chromosomes across the tree of life. This homomorphy has been suggested to result from frequent sex-chromosome turnovers, yet we know little about which forces drive them. Here, we describe an extremely fast rate of turnover among 28 species of Ranidae. Transitions are not random, but converge on several chromosomes, potentially due to genes they harbour. Transitions also preserve the ancestral pattern of male heterogamety, in line with the ‘hot-potato’ model of sex-chromosome transitions, suggesting a key role for mutation-load accumulation in non-recombining genomic regions. The importance of mutation-load selection in frogs might result from the extreme heterochiasmy they exhibit, making frog sex chromosomes differentiate immediately from emergence and across their entire length.
Electrophysiological mechanisms of human memory consolidation
Authors: Zhang Hui , Fell Juergen , Axmacher Nikolai 
Published: October 2018

AbstractConsolidation stabilizes memory traces after initial encoding. Rodent studies suggest that memory consolidation depends on replay of stimulus-specific activity patterns during fast hippocampal “ripple” oscillations. Here, we measured replay in intracranial electroencephalography recordings in human epilepsy patients, and related replay to ripples. Stimulus-specific activity was identified using representational similarity analysis and then tracked during waking rest and sleep after encoding. Stimulus-specific gamma (30–90 Hz) activity during early (100–500 ms) and late (500–1200 ms) encoding is spontaneously reactivated during waking state and sleep, independent of later memory. Ripples during nREM sleep, but not during waking state, trigger replay of activity from the late time window specifically for remembered items. Ripple-triggered replay of activity from the early time window during nREM sleep is enhanced for forgotten items. These results provide the first electrophysiological evidence for replay related to memory consolidation in humans, and point to a prominent role of nREM ripple-triggered replay in consolidation processes.
Suppressor mutations in Rpf2–Rrs1 or Rpl5 bypass the Cgr1 function for pre-ribosomal 5S RNP-rotation
Authors: Thoms Matthias , Mitterer Valentin , Kater Lukas , Falquet Laurent , Beckmann Roland , Kressler Dieter , Hurt Ed 
Published: October 2018

AbstractDuring eukaryotic 60S biogenesis, the 5S RNP requires a large rotational movement to achieve its mature position. Cryo-EM of the Rix1-Rea1 pre-60S particle has revealed the post-rotation stage, in which a gently undulating α-helix corresponding to Cgr1 becomes wedged between Rsa4 and the relocated 5S RNP, but the purpose of this insertion was unknown. Here, we show that cgr1 deletion in yeast causes a slow-growth phenotype and reversion of the pre-60S particle to the pre-rotation stage. However, spontaneous extragenic suppressors could be isolated, which restore growth and pre-60S biogenesis in the absence of Cgr1. Whole-genome sequencing reveals that the suppressor mutations map in the Rpf2–Rrs1 module and Rpl5, which together stabilize the unrotated stage of the 5S RNP. Thus, mutations in factors stabilizing the pre-rotation stage facilitate 5S RNP relocation upon deletion of Cgr1, but Cgr1 itself could stabilize the post-rotation stage.
2D organic molecular metallic soft material derived from BEDO-TTF with electrochromic and rectifying properties
Authors: Suarez Daniel , Steven Eden , Laukhina Elena , Gomez Andres , Crespi Anna , Mestres Narcis , Rovira Concepció , Choi Eun Sang , Veciana Jaume 
Published: October 2018

AbstractIn this article we demonstrate that a migration of iodine species and chemical transformation in a moist environment induced by a voltage-biased Pt electrode is able to alter the color and degree of charge transfer in a layer of the 2D organic molecular metal (BEDO-TTF)2.4I3 [BEDO = bis(ethylenedioxy)tetrathiafulvalene] self-assembled at the surface of a polycarbonate film. These effects produce a reversible electrochromic behavior of the layer with low operating voltages and fast operation times. Adjuvant with electrochromism, this flexible material exhibits rectifying behavior whose I-V curves are dependent on the voltage sweep directions. These results open new possibilities for the design and fabrication of organic flexible materials for soft electrochromic and rectifying components. The easy working principle ensures reliability, low power consumption, and versatility through its implementation into simple devices. Such working principle has been confirmed by temperature dependent resistance measurements, X-Ray, EDX-SEM, and conducting-AFM studies.
Mathematical Modeling and Analyses of Interspike-Intervals of Spontaneous Activity in Afferent Neurons of the Zebrafish Lateral Line
Authors: Song Sangmin , Lee Ji Ah , Kiselev Ilya , Iyengar Varun , Trapani Josef G. , Tania Nessy 
Published: October 2018

AbstractWithout stimuli, hair cells spontaneously release neurotransmitter leading to spontaneous generation of action potentials (spikes) in innervating afferent neurons. We analyzed spontaneous spike patterns recorded from the lateral line of zebrafish and found that distributions of interspike intervals (ISIs) either have an exponential shape or an “L” shape that is characterized by a sharp decay but wide tail. ISI data were fitted to renewal-process models that accounted for the neuron refractory periods and hair-cell synaptic release. Modeling the timing of synaptic release using a mixture of two exponential distributions yielded the best fit for our ISI data. Additionally, lateral line ISIs displayed positive serial correlation and appeared to exhibit switching between faster and slower modes of spike generation. This pattern contrasts with previous findings from the auditory system where ISIs tended to have negative serial correlation due to synaptic depletion. We propose that afferent neuron innervation with multiple and heterogenous hair-cells synapses, each influenced by changes in calcium domains, can serve as a mechanism for the random switching behavior. Overall, our analyses provide evidence of how physiological similarities and differences between synapses and innervation patterns in the auditory, vestibular, and lateral line systems can lead to variations in spontaneous activity.
Enhancement of PCR Sensitivity and Yield Using Thiol-modified Primers
Authors: Bai Yalong , Xiao Yi , Suo Yujuan , Shen Yuanyuan , Shao Yi , Zhang Donglai , Zhou Changyan 
Published: October 2018

AbstractVarious additives can enhance the quality of PCR amplification, but these generally require considerable optimization to achieve peak performance. Here, we demonstrate that the use of thiol-modified primers can enhance both PCR sensitivity and yield. In experiments with V. parahaemolyticus genomic DNA, this primer modification enhances PCR sensitivity by more than 100-fold, with accompanying improvements in amplicon yield. Then, an artificial plasmid with the same primer binding regions and different internal amplification sequence was designed. The result showed that the amplification also be improved by using the same thiol-modified primers. It indicated the enhancement was not caused by the effect of the thiol-modified primers on the second structure of amplification sequence. Subsequent experiments demonstrate that the effects of this modification are potentially due to altered interaction between the primers and proteins in the reaction mixture. Amplification with thiol-modified primers was strongly inhibited by the presence of extraneous proteins relative to standard DNA primers, which indicates that thiol-modified primers may be inhibited due to interaction with these proteins. In contaminant-free reactions, however, the thiol-modified primers might interact more strongly with DNA polymerase, which could in turn improve PCR amplification.
Phylogenetics of Mycoplasma hominis clinical strains associated with gynecological infections or infertility as disclosed by an expanded multilocus sequence typing scheme
Authors: Boujemaa Safa , Ben Allaya Amina , Mlik Béhija , Mardassi Helmi , Ben Abdelmoumen Mardassi Boutheina 
Published: October 2018

AbstractTo our knowledge, the phylodistribution of M. hominis clinical strains associated with various pathological conditions of the urogenital tract has not been explored hitherto. Here we analyzed the genetic diversity and phylogenetic relationships among 59 M. hominis Tunisian clinical isolates, categorized as gynecological infections- or infertility-associated pathotypes. For this purpose, we developed an expanded multilocus sequence typing (eMLST) scheme, combining the previously reported multilocus sequence typing (MLST) loci (gyrB, tuf, ftsY, uvrA, gap) with a new selected set of putative virulence genes (p120’, vaa, lmp1, lmp3, p60), referred herein to as multi-virulence-locus sequence typing (MVLST) loci. In doing so, M. hominis population was segregated into two distinct genetic lineages, which were differentially associated with each pathotype. Such a clear dichotomy was supported by several phylogenetic and population genetic analysis tools. Recombination was found to take place, but not sufficient enough to break down the overall clonal population structure of M. hominis, most likely as a result of purifying selection, which accommodated the most fit clones. In sum, and owing to the eMLST scheme described herein, we provide insightful data on the phylogenetics of M. hominis, arguing for the existence of genetically differentiable urogenital pathotypes.
An efficient code to solve the Kepler equation
Authors: Raposo-Pulido V. , Peláez J. 
Published: October 2018

Context. This paper introduces a new approach for solving the Kepler equation for hyperbolic orbits. We provide here the Hyperbolic Kepler Equation–Space Dynamics Group (HKE–SDG), a code to solve the equation.
Methods. Instead of looking for new algorithms, in this paper we have tried to substantially improve well-known classic schemes based on the excellent properties of the Newton–Raphson iterative methods. The key point is the seed from which the iteration of the Newton–Raphson methods begin. If this initial seed is close to the solution sought, the Newton–Raphson methods exhibit an excellent behavior. For each one of the resulting intervals of the discretized domain of the hyperbolic anomaly a fifth degree interpolating polynomial is introduced, with the exception of the last one where an asymptotic expansion is defined. This way the accuracy of initial seed is optimized. The polynomials have six coefficients which are obtained by imposing six conditions at both ends of the corresponding interval: the polynomial and the real function to be approximated have equal values at each of the two ends of the interval and identical relations are imposed for the two first derivatives. A different approach is used in the singular corner of the Kepler equation – |M| < 0.15 and 1 < e <  1.25 – where an asymptotic expansion is developed.
Results. In all simulations carried out to check the algorithm, the seed generated leads to reach machine error accuracy with a maximum of three iterations (∼99.8% of cases with one or two iterations) when using different Newton–Raphson methods in double and quadruple precision. The final algorithm is very reliable and slightly faster in double precision (∼0.3 s). The numerical results confirm the use of only one asymptotic expansion in the whole domain of the singular corner as well as the reliability and stability of the HKE–SDG. In double and quadruple precision it provides the most precise solution compared with other methods.
Zum Einfluss von Körpermaßen der Eltern auf das Geburtsgewicht von eutrophen Termingeborenen (TG) unter besonderer Berücksichtigung der Körperhöhe und des Körpergewichts des Vaters
Authors: Olbertz Dirk , Pippig Stanley , Hesse Volker , Schwab Karl , Wittwer-Backofen Ursula , Hentschel Roland , Voigt Manfred 
Published: October 2018

ZusammenfassungZur Bestimmung des quantitativen Einflusses der Körpermesswerte von Mutter und Vater auf das Geburtsgewicht Neugeborener wurden im Rahmen einer Multizenterstudie an 10 deutschen Geburtskliniken das Geburtsgewicht von 1312 eutrophen Termingeborenen sowie die Körperhöhe und das Körpergewicht ihrer Eltern erfasst. Auch wenn man die Körperhöhe der Väter von 176–184 cm mit einem Körpergewicht von 76–84 kg relativ konstant hält, liegen die Geburtsgewichte bei größeren Müttern höher als bei kleineren. Hinsichtlich Körpergewicht der Mutter und Geburtsgewicht zeigt sich ebenfalls ein deutlicher Anstieg des Geburtsgewichtes bei steigendem Körpergewicht der Mutter. Hält man hier Körperhöhe (164–172 cm) und Körpergewicht (56–64 kg) der Mutter konstant, so steigen auch hier die Geburtsgewichte deutlich mit der Körperhöhe des Vaters an. Ein signifikanter Beitrag des Körpergewichtes des Vaters zum Geburtsgewicht ist nicht zu erkennen. Aus der multivariablen Regressionsanalyse wurde folgende Rangfolge für die Einflussfaktoren Körperhöhe und Körpergewicht der Eltern auf das Geburtsgewicht ihrer Neugeborenen ermittelt: 1.: Körperhöhe der Mutter, 2.: Körpergewicht der Mutter, 3.: Körperhöhe des Vaters. Bei der Beurteilung des somatischen Entwicklungsstandes der Neugeborenen, sollten neben der Körperhöhe und Körpergewicht der Mutter auch die Körperhöhe des Vaters herangezogen werden.
Trochlear Nerve Repair during Retrosigmoid Suprameatal Approach for Petrotentorial Meningioma: Operative Video
Authors: Matsushima Ken , Kohno Michihiro , Nakajima Nobuyuki , Ichimasu Norio 
Published: October 2018

When operating on difficult skull base lesions, it is essential to be able to handle unexpected intraoperative findings or troubles, while achieving maximal lesion removal and minimal functional deficit. This video demonstrates a case of trochlear nerve repair that was performed during the retrosigmoid suprameatal approach for treatment of a petrotentorial meningioma, extending into the Meckel's cave. The patient is a 47-year-old woman with a right petrotentorial meningioma, extending into the Meckel's cave. The retrosigmoid suprameatal approach was performed with preservation of the superior petrosal vein. However, a divided trochlear nerve was incidentally found during tumor resection. We hence carefully dissected both nerve ends from the tumor without shortening their lengths, and repaired them by end-to-end anastomosis, using fibrin glue without any graft materials. The tumor was removed completely and the patient's preoperative facial sensory impairment disappeared after the surgery. The patient's facial sensory impairment disappeared completely, but she had transient diplopia after the surgery. However, the newly developed diplopia resolved completely, and she had no neurological deficits or tumor recurrence during the follow-up period of 1-year.The link to the video can be found at: https://youtu.be/g-B-w_zDudg.