bluuebunny/crossref_metadata_2025 huggingface dataset:
Transjugular portal vein recanalization with creation of intrahepatic portosystemic shunt (PVR-TIPS) in patients with chronic non-cirrhotic, non-malignant portal vein thrombosis
Authors: Klinger Christoph , Riecken Bettina , Schmidt Arthur , De Gottardi Andrea , Meier Benjamin , Bosch Jaime , Caca Karel
Published: November 2017

Purpose To determine safety and efficacy of transjugular portal vein recanalization with creation of intrahepatic portosystemic shunt (PVR-TIPS) in patients with chronic non-cirrhotic, non-malignant portal vein thrombosis (PVT).

Methods This retrospective study includes 17 consecutive patients with chronic non-cirrhotic PVT (cavernous transformation n = 15). PVR-TIPS was indicated because of variceal bleeding (n = 13), refractory ascites (n = 2), portal biliopathy with recurrent cholangitis (n = 1), or abdominal pain (n = 1). Treatment consisted of a combination of transjugular balloon angioplasty, mechanical thrombectomy, and—depending on extent of residual thrombosis—transjugular intrahepatic portosystemic shunt and additional stenting of the portal venous system.

Results Recanalization was successful in 76.5 % of patients despite cavernous transformation in 88.2 %. Both 1- and 2-year secondary PV and TIPS patency rates were 69.5 %. Procedure-related bleeding complications occurred in 2 patients (intraperitoneal bleeding due to capsule perforation, n = 1; liver hematoma, n = 1) and resolved spontaneously. However, 1 patient died due to subsequent nosocomial pneumonia. During follow-up, 3 patients with TIPS occlusion and PVT recurrence experienced portal hypertensive complications.

Conclusions PVR-TIPS is safe and effective in selected patients with chronic non-cirrhotic PVT. Due to technical complexity and possible complications, it should be performed only in specialized centers with high experience in TIPS procedures.
Improved accuracy of capacitive sensor-based micro-angle measurement with angular-to-linear displacement conversion
Authors: Tan Xinran , Zhu Fan , Wang Chao , Shi Jian , Qi Xue , Yu Yang , Yuan Feng , Tan Jiubin
Published: November 2017

This paper presents a capacitive sensor-based micro-angle measurement (CSMAM) method that uses an angular-to-linear displacement conversion to achieve high accuracy. The principal and secondary error components of CSMAMs are modeled and analyzed to reveal their impacts on the measurement accuracy. The theoretical accuracies of six types of commonly used CSMAMs are analyzed to determine the optimum configuration of capacitive sensors for 1D and 2D micro-angle measurements. An angular-to-linear displacement conversion method with a linear motional stage and a hemisphere decoupler is used to eliminate the principal error of CSMAM. Experimental results indicate that the optimized CSMAM can achieve accuracies of 0.157 arc sec and 0.052 arc sec in the ranges of ±900 arc sec and ±300 arc sec, respectively, in the case that the effective length of the rotation arm is 100 mm and the linear displacement measurement accuracy of the capacitive sensor is 2 nm. These results can be used as a reference to further improve CSMAM designs and achieve high accuracy in a large measurement range, for use in a wide range of precision engineering applications including angle metrology, micro- and nano-radian angle generators, beam steering mechanisms, and high-performance precision stages.
Frictional shear thickening in suspensions: The effect of rigid asperities
Authors: Townsend Adam K. , Wilson Helen J.
Published: November 2017

We study non-Brownian suspensions under steady shear flow. In concentrated suspensions, we are trying to reproduce the shear thickening phenomenon seen in, for example, cornstarch. We investigate the effect of different frictional contact models. When contact acts to impose a fixed minimum separation between particles, there is a strict upper bound to the viscosity predicted by simulations. We deduce that soft or compressible contacts are a critical component of the strong shear thickening seen in experiments.
Microwave evaluation of electromigration susceptibility in advanced interconnects
Authors: Sunday Christopher E. , Veksler Dmitry , Cheung Kin C. , Obeng Yaw S.
Published: November 2017

Traditional metrology has been unable to adequately address the needs of the emerging integrated circuits (ICs) at the nano scale; thus, new metrology and techniques are needed. For example, the reliability challenges in fabrication need to be well understood and controlled to facilitate mass production of through-substrate-via (TSV) enabled three-dimensional integrated circuits (3D-ICs). This requires new approaches to the metrology. In this paper, we use the microwave propagation characteristics to study the reliability issues that precede the physical damage caused by electromigration in the Cu-filled TSVs. The pre-failure microwave insertion losses and group delay are dependent on both the device temperature and the amount of current forced through the devices-under-test. The microwave insertion losses increase with the increase in the test temperature, while the group delay increases with the increase in the forced direct current magnitude. The microwave insertion losses are attributed to the defect mobility at the Cu-TiN interface, and the group delay changes are due to resistive heating in the interconnects, which perturbs the dielectric properties of the cladding dielectrics of the copper fill in the TSVs.
The effect of conductor permeability on electric current transducers
Authors: Mirzaei M. , Ripka P. , Chirtsov A. , Kaspar P. , Vyhnanek J.
Published: November 2017

In this paper, experimental works and theoretical analysis are presented to analyze the influence of the conductor permeability on the precision of yokeless current sensors. The results of finite-element method (FEM) fit well the measured field values around the conductor. Finally we evaluate the difference in magnetic fields distribution around non-magnetic and magnetic conductor. The calculated values show that the permeability of the ferromagnetic conductor significally affects the reading of the electric current sensors even at DC.
Driving higher magnetic field sensitivity of the martensitic transformation in MnCoGe ferromagnet
Authors: Ma S. C. , Ge Q. , Hu Y. F. , Wang L. , Liu K. , Jiang Q. Z. , Wang D. H. , Hu C. C. , Huang H. B. , Cao G. P. , Zhong Z. C. , Du Y. W.
Published: November 2017

The sharp metamagnetic martensitic transformation (MMT) triggered by a low critical field plays a pivotal role in magnetoresponsive effects for ferromagnetic shape memory alloys (FSMAs). Here, a sharper magnetic-field-induced metamagnetic martensitic transformation (MFIMMT) is realized in Mn1−xCo1+xGe systems with a giant magnetocaloric effect around room temperature, which represents the lowest magnetic driving and completion fields as well as the largest magnetization difference around MFIMMT reported heretofore in MnCoGe-based FSMAs. More interestingly, a reversible MFIMMT with field cycling is observed in the Mn0.965Co0.035Ge compound. These results indicate that the consensus would be broken that the magnetic field is difficult to trigger the MMT for MnCoGe-based systems. The origin of a higher degree of sensitivity of martensitic transformation to the magnetic field is discussed based on the X-ray absorption spectroscopic results.
Delayed Slater determinant update algorithms for high efficiency quantum Monte Carlo
Authors: McDaniel T. , D’Azevedo E. F. , Li Y. W. , Wong K. , Kent P. R. C.
Published: November 2017

Within ab initio Quantum Monte Carlo simulations, the leading numerical cost for large systems is the computation of the values of the Slater determinants in the trial wavefunction. Each Monte Carlo step requires finding the determinant of a dense matrix. This is most commonly iteratively evaluated using a rank-1 Sherman-Morrison updating scheme to avoid repeated explicit calculation of the inverse. The overall computational cost is, therefore, formally cubic in the number of electrons or matrix size. To improve the numerical efficiency of this procedure, we propose a novel multiple rank delayed update scheme. This strategy enables probability evaluation with an application of accepted moves to the matrices delayed until after a predetermined number of moves, K. The accepted events are then applied to the matrices en bloc with enhanced arithmetic intensity and computational efficiency via matrix-matrix operations instead of matrix-vector operations. This procedure does not change the underlying Monte Carlo sampling or its statistical efficiency. For calculations on large systems and algorithms such as diffusion Monte Carlo, where the acceptance ratio is high, order of magnitude improvements in the update time can be obtained on both multi-core central processing units and graphical processing units.
Understanding the interface between silicon-based materials and water: Molecular-dynamics exploration of infrared spectra
Authors: Martinez-Gonzalez José A. , English Niall J. , Gowen Aoife A.
Published: November 2017

Molecular-dynamics simulations for silicon, hydrogen- and hydroxyl-terminated silicon in contact with liquid water, at 220 and 300 K, display water-density ‘ordering’ along the laboratory z-axis, emphasising the hydrophobicity of the different systems and the position of this first adsorbed layer. Density of states (DOS) of the oxygen and proton velocity correlation functions (VACFs) and infrared (IR) spectra of the first monolayer of adsorbed water, calculated via Fourier transformation, indicate similarities to more confined, ice-like dynamical behaviour (redolent of ice). It was observed that good qualitative agreement is obtained between the DOS for this first layer in all systems. The DOS for the lower-frequency zone indicates that for the interface studied (i.e., the first layer near the surface), the water molecules try to organise in a similar form, and that this form is intermediate between liquid water and ice. For IR spectra, scrutiny of the position of the highest-intensity peaks for the stretching and bending bands indicate that such water molecules in the first solvating layer are organised in an intermediate fashion between ice and liquid water.
Spin-orbit-torque driven magnetoimpedance in Pt-layer/magnetic-ribbon heterostructures
Authors: Hajiali M. R. , Mohseni S. Morteza , Jamilpanah L. , Hamdi M. , Roozmeh S. E. , Mohseni S. Majid
Published: November 2017

When a flow of electrons passes through a paramagnetic layer with strong spin-orbit-coupling such as platinum (Pt), a net spin current is produced via the spin Hall effect (SHE). This spin current can exert a torque on the magnetization of an adjacent ferromagnetic layer which can be probed via magnetization dynamic responses, e.g., spin-torque ferromagnetic resonance. Nevertheless, that effect in the lower frequency magnetization dynamic regime where the skin effect occurs in high permeability ferromagnetic conductors, namely, the magneto-impedance (MI) effect, can be fundamentally important, and has not been studied so far. Here, by utilizing the MI effect in the magnetic-ribbon/Pt heterostructure with high transvers magnetic permeability that allows the ac current effectively confined at the skin depth of ∼100 nm thickness, the effect of spin-orbit-torque (SOT) induced by the SHE probed via the MI measurement is investigated. We observed a systematic MI frequency shift that increases by increasing the applied current amplitude and thickness of the Pt layer (varying from 0 nm to 20 nm). In addition, the role of the Pt layer in the ribbon/Pt heterostructure is evaluated with the ferromagnetic resonance effect representing a standard Gilbert damping increase as a result of the presence of the SHE. Our results unveil the role of SOT in dynamic control of the transverse magnetic permeability probed by impedance spectroscopy as a useful and valuable technique for detection of future SHE devices.
Avalanches driven by pressure gradients in a magnetized plasma
Authors: Van Compernolle B. , Morales G. J.
Published: November 2017

The results are presented for a basic heat transport experiment involving an off-axis heat source in which avalanche events occur. The configuration consists of a long, hollow, cylindrical region of elevated electron temperature embedded in a colder plasma, and far from the device walls [Van Compernolle et al. Phys. Rev. E 91, 031102(R) (2015)]. The avalanche events are identified as sudden rearrangements of the pressure profile following the growth of fluctuations from ambient noise. The intermittent collapses of the plasma pressure profile are associated with unstable drift-Alfvén waves and exhibit both radial and poloidal dynamics. After each collapse, the plasma enters a quiescent phase in which the pressure profile slowly recovers and steepens until a threshold is exceeded, and the process repeats. The use of reference probes as time markers allows for the visualization of the 2D spatio-temporal evolution of the avalanche events. Avalanches are observed only for a limited combination of heating powers and magnetic fields. At higher heating powers, the system transits from the avalanche regime into a regime dominated by sustained drift-Alfvén wave activity. This manuscript focuses on new results that illustrate the individual contributions to the avalanche process from density and temperature gradients in the presence of zero-order, sheared flows.
Comparison of optimized ion acceleration from thin foils and low-density targets for linearly and circularly polarized laser pulses
Authors: Brantov A. V. , Ksenofontov P. A. , Bychenkov V. Yu.
Published: November 2017

A multiparameter comparative analysis of ion acceleration with linearly and circularly polarized relativistically intense laser pulses for solid-density thin foils and low-density planar targets was performed using 3D particle-in-cell (PIC) simulations. Ion acceleration optimization was studied with 3D PIC MANDOR over the laser energy range of three orders of magnitude from three hundred millijoules to three hundred joules in a femtosecond pulse. The optimum target thickness and density was found for a given energy of the laser pulse corresponding to the maximum energy of the accelerated ions. This allows deriving a dependence of the maximum ion energy on laser energy for the optimized solid or low-density targets. The advantage of a circularly polarized laser pulse for generating the most energetic ions was demonstrated, which happens for the regimes of volumetrically heated semitransparent solid foils (directed Coulomb explosion) and of synchronized ion acceleration by slow light from low-density targets. The dependence of the maximum ion energy on laser energy for the optimized targets and both linearly and circularly polarized femtosecond pulses demonstrates a sharper-than-square-root increase.
Improved performance of inkjet-printed Ag source/drain electrodes for organic thin-film transistors by overcoming the coffee ring effects
Authors: Liu Cheng-Fang , Lin Yan , Lai Wen-Yong , Huang Wei
Published: November 2017

Inkjet printing is a promising technology for the scalable fabrication of organic electronics because of the material conservation and facile patterning as compared with other solution processing techniques. In this study, we have systematically investigated the cross-sectional profile control of silver (Ag) electrode via inkjet printing. A facile methodology for achieving inkjet-printed Ag source/drain with improved profiles is developed. It is demonstrated that the printing conditions such as substrate temperature, drop spacing and printing layers affect the magnitude of the droplet deposition and the rate of evaporation, which can be optimized to greatly reduce the coffee ring effects for improving the inkjet-printed electrode profiles. Ag source/drain electrodes with uniform profiles were successfully inkjet-printed and incorporated into organic thin-film transistors (OTFTs). The resulting devices showed superior electrical performance than those without special treatments. It is noted to mention that the strategy for modulating the inkjet-printed Ag electrodes in this work does not demand the ink formulation or complicated steps, which is beneficial for scaling up the printing techniques for potential large-area/mass manufacturing.
Magnetic coupling in nonmagnetic metal adsorption on arsenene monolayer: Ab initio study
Authors: Min Luo , Xu Yu E. , Song Xi Yu
Published: November 2017

The structural, electronic and magnetic properties of adsorbed arsenene monolayer with a series of nonmagnetic metal atoms, including Al, Ga, Li, Mg, and Na, are systematically investigated using first-principles calculations. From our calculations, nonmagnetic states appear in the cases of Li, Mg, and Na. The magnetism has been observed for Al and Ga adatoms. Then, we study the magnetic interaction between the moments induced by Al and Ga adatoms. It is found that a p–d exchange-like p-p hybridization results in the ferromagnetic (FM) state. However, when the distance of Ga-Ga or Al-Al is increased, it is found out that the FM interaction has been extremely depressed. This phenomenon can be explained by a simple Heisenberg model. The X-adsorbed (X= Al and Ga) arsenene systems are promising candidates for spintronic devices in the future.
Signal processing and analysis for copper layer thickness measurement within a large variation range in the CMP process
Authors: Li Hongkai , Zhao Qian , Lu Xinchun , Luo Jianbin
Published: November 2017

In the copper (Cu) chemical mechanical planarization (CMP) process, accurate determination of a process reaching the end point is of great importance. Based on the eddy current technology, the in situ thickness measurement of the Cu layer is feasible. Previous research studies focus on the application of the eddy current method to the metal layer thickness measurement or endpoint detection. In this paper, an in situ measurement system, which is independently developed by using the eddy current method, is applied to the actual Cu CMP process. A series of experiments are done for further analyzing the dynamic response characteristic of the output signal within different thickness variation ranges. In this study, the voltage difference of the output signal is used to represent the thickness of the Cu layer, and we can extract the voltage difference variations from the output signal fast by using the proposed data processing algorithm. The results show that the voltage difference decreases as thickness decreases in the conventional measurement range and the sensitivity increases at the same time. However, it is also found that there exists a thickness threshold, and the correlation is negative, when the thickness is more than the threshold. Furthermore, it is possible that the in situ measurement system can be used within a larger Cu layer thickness variation range by creating two calibration tables.
In situ ultraviolet shock radiance measurements using GaN-on-sapphire photodetectors
Authors: Miller Ruth A. , Cruden Brett A. , Martinez Ramon , Senesky Debbie G.
Published: November 2017

Gallium nitride (GaN)-on-sapphire photodetectors are used to measure the ultraviolet (UV) radiance behind a shock wave in support of atmospheric entry sensing technologies. DC spectral response characterization of the GaN-based photodetectors shows a peak response around 365 nm with an UV/visible rejection of an order of magnitude. To conduct in situ measurements of UV shock-layer radiation, the GaN-based photodetectors were installed, without protective packaging, in the test section of a shock tube. The measured UV radiation, in terms of incident optical power on the photodetectors, is in excellent agreement with average UV radiation measured by the shock tube facility spectrometers. Furthermore, the device response after being subjected to the shock wave is unaltered, suggesting that the GaN-based material platform is suitable for implementation in aerospace and other harsh environment sensing applications.
Emergent kink stability of a magnetized plasma jet injected into a transverse background magnetic field
Authors: Zhang Yue , Gilmore Mark , Hsu Scott C. , Fisher Dustin M. , Lynn Alan G.
Published: November 2017

We report experimental results on the injection of a magnetized plasma jet into a transverse background magnetic field in the HelCat linear plasma device at the University of New Mexico [M. Gilmore et al., J. Plasma Phys. 81(1), 345810104 (2015)]. After the plasma jet leaves the plasma-gun muzzle, a tension force arising from an increasing curvature of the background magnetic field induces in the jet a sheared axial-flow gradient above the theoretical kink-stabilization threshold. We observe that this emergent sheared axial flow stabilizes the n = 1 kink mode in the jet, whereas a kink instability is observed in the jet when there is no background magnetic field present.
Spatial-temporal evolution of self-organized loop-patterns on a water surface and a diffuse discharge in the gap
Authors: Li Xuechen , Geng Jinling , Jia Pengying , Zhang Panpan , Zhang Qi , Li Yaru
Published: November 2017

Excited by an alternating current voltage, a patterned discharge and a diffuse discharge are generated in a needle to liquid configuration. Using an intensified charge-coupled device (ICCD), temporal evolution of the discharge between the two electrodes is investigated for the diffuse mode and the patterned mode, respectively. For the diffuse mode, the positive discharge is in a glow regime, and the negative discharge is in a Townsend discharge regime. For the patterned mode, the discharge always belongs to the Townsend discharge regime. Moreover, in the patterned mode, various patterns including the single loop, single loop with the surrounding corona, triple loops, and concentric loops with a central spot are observed on the water surface with the increasing positive peak-value of the applied voltage (Upp). Temporally resolved images of the loop-patterns are captured on the water surface. From the electrical measurements and the ICCD imaging, it is found that the loop pattern emerges after the discharge bridges the two electrodes. Then, it begins to evolve and finally degenerates with the decrease in the discharge current. The pattern does not disappear until the discharge quenches. Formation of the loop-patterns is attributed to the role of negative ions.
Updated approach improves quantum Monte Carlo simulation performance
Authors: Cockbill Louisa
Published: November 2017

Researchers propose an improved matrix update algorithm that increases the computational calculation speed of quantum Monte Carlo simulations.
Bright, near-IR photon emission from nanodiamonds is sharp enough for quantum communication
Authors: Majors J. H.
Published: November 2017

Nanodiamond defects demonstrate sharp, bright emission deeper in the near-IR than common alternatives, and are a new candidate in the search for scalable quantum communication components.
Immature HIV-1 lattice assembly dynamics are regulated by scaffolding from nucleic acid and the plasma membrane
Authors: Pak Alexander J. , Grime John M. A. , Sengupta Prabuddha , Chen Antony K. , Durumeric Aleksander E. P. , Srivastava Anand , Yeager Mark , Briggs John A. G. , Lippincott-Schwartz Jennifer , Voth Gregory A.
Published: November 2017

Significance

In order for HIV to proliferate, viral proteins and genomic dimers are assembled at host cell membranes and released as immature virions. Disrupting this key intermediate step in viral replication is a potential target for treatment. However, a detailed molecular view of this process remains lacking. Here, we elucidate a network of constitutive interactions that regulate viral assembly dynamics through a combined computational and experimental approach. Specifically, our analysis reveals the active roles of nucleic acid and the membrane as scaffolds that promote the multimerization of Gag polyprotein, which proceeds through multistep and self-correcting nucleation. Our findings also illustrate the functional importance of the N-terminal, C-terminal, and spacer peptide 1 protein domains.
High-temperature charge density wave correlations in La
1.875
Ba
0.125
CuO
4
without spin–charge locking
Authors: Miao H. , Lorenzana J. , Seibold G. , Peng Y. Y. , Amorese A. , Yakhou-Harris F. , Kummer K. , Brookes N. B. , Konik R. M. , Thampy V. , Gu G. D. , Ghiringhelli G. , Braicovich L. , Dean M. P. M.
Published: November 2017

Significance

Charge correlations have now been identified in the low-temperature phase of essentially all families of underdoped cuprates, but in two apparently distinct types. The first hosts locked charge and spin stripes of which the material La
1.875
Ba
0.125
CuO
4
(LBCO

1
/
8

) is a paradigmatic example. In the second type, a charge density wave (CDW) exists without any obviously related spin correlations. Here we report the discovery of high-temperature CDW correlations that exist at temperatures above the CDW transition in the canonical striped cuprate LBCO

1
/
8

. We find that the high-temperature CDW is decoupled from the fluctuating spin density wave, lessening apparent differences in behavior among different materials and setting important constraints for how we understand their electronic states.
Filament rigidity and connectivity tune the deformation modes of active biopolymer networks
Authors: Stam Samantha , Freedman Simon L. , Banerjee Shiladitya , Weirich Kimberly L. , Dinner Aaron R. , Gardel Margaret L.
Published: November 2017

Significance

Living cells spontaneously change their shape in physiological processes like cell migration and division. Forces generated by molecular motors on biopolymers must underlie these dynamics, but how molecular-scale forces give rise to cellular-scale shape changes is unknown. We use experimental measurements on reconstituted actomyosin networks and computer simulations to show that polymer stiffness and connectivity regulate motor-generated stresses and, in turn, longer-length-scale shape deformations. Importantly, we find that filament rigidity controls whether stresses transmitted are uniaxial or biaxial and that, for rigid filaments, the connectivity can control a transition between extensile and contractile deformations. These results have implications for how conserved molecular mechanisms give rise to diverse morphogenic events in cells.
Directed evolution of SecB chaperones toward toxin-antitoxin systems
Authors: Sala Ambre Julie , Bordes Patricia , Ayala Sara , Slama Nawel , Tranier Samuel , Coddeville Michèle , Cirinesi Anne-Marie , Castanié-Cornet Marie-Pierre , Mourey Lionel , Genevaux Pierre
Published: November 2017

Significance

Toxin-antitoxin (TA) systems are small genetic modules known to modulate bacterial growth in response to stress. Their major contribution to the formation of persister cells and to the virulence of several important pathogens has highlighted them as promising new targets for therapy. TA-chaperone (TAC) modules are atypical TA systems tightly controlled by a third partner: a molecular chaperone that directly assists the antitoxin. Remarkably, TAC chaperones belong to the family of the canonical SecB chaperone known to facilitate protein secretion in bacteria, thus potentially connecting toxin activation and protein export. Herein, we have used the TAC system of the major human pathogen
Mycobacterium tuberculosis
to reveal how generic chaperones can rapidly evolve to become specialized for TA systems.
Pulsed evolution shaped modern vertebrate body sizes
Authors: Landis Michael J. , Schraiber Joshua G.
Published: November 2017

Significance

The diversity of forms found among animals on Earth is striking. Despite decades of study, it has been difficult to reconcile the patterns of diversity seen between closely related species with those observed when studying single species on ecological timescales. We propose a set of models, called Lévy processes, to attempt to reconcile rapid evolution between species with the relatively stable distributions of phenotypes seen within species. These models, which have been successfully used to model stock market data, allow for long periods of stasis followed by bursts of rapid change. We find that many vertebrate groups are well fitted by Lévy models compared with models for which traits evolve toward a stationary optimum or evolve in an incremental and wandering manner.
Three-dimensional visualization and a deep-learning model reveal complex fungal parasite networks in behaviorally manipulated ants
Authors: Fredericksen Maridel A. , Zhang Yizhe , Hazen Missy L. , Loreto Raquel G. , Mangold Colleen A. , Chen Danny Z. , Hughes David P.
Published: November 2017

Significance

Microbial parasites may behave collectively to manipulate their host’s behavior. We examine adaptations of a microbial parasite in its natural environment: the body of its coevolved and manipulated host. Electron microscopy and 3D reconstructions of host and parasite tissues reveal that this fungus invades muscle fibers throughout the ant’s body but leaves the brain intact, and that the fungal cells connect to form extensive networks. The connections are likened to structures that aid in transporting nutrients and organelles in several plant-associated fungi. These findings alter the current view of parasite-extended phenotypes by demonstrating that behavior control does not require the parasite to physically invade the host brain and that parasite cells may coordinate to change host behavior.
Cell-to-cell variation sets a tissue-rheology–dependent bound on collective gradient sensing
Authors: Camley Brian A. , Rappel Wouter-Jan
Published: November 2017

Significance

Cells cooperate to sense the direction of a chemical gradient by communicating with each other, which may be important when clumps of cancer cells metastasize or embryos develop. However, because each cell is distinct, we find these clumps are biased toward cells that are “loud”—sending inappropriately large signals. Cell clusters can reduce this bias by rearranging themselves so loud cells change their locations. This means the mechanical dynamics of the cluster matter—fluid, squishy clumps of cells are better at sensing than solid ones. If a single cell’s motion gets noisier, it will make the cluster more fluid—so adding noise can actually make a cluster of cells a better sensor.
DNA damage response protein TOPBP1 regulates X chromosome silencing in the mammalian germ line
Authors: ElInati Elias , Russell Helen R. , Ojarikre Obah A. , Sangrithi Mahesh , Hirota Takayuki , de Rooij Dirk G. , McKinnon Peter J. , Turner James M. A.
Published: November 2017

Significance

A fundamental step of meiosis is prophase I, when homologous chromosomes synapse and recombine to generate cross-overs that are accurate for chromosome segregation. In male mammals, chromosomes that are asynapsed undergo meiotic silencing, a process that may serve as a surveillance mechanism to prevent aneuploidy in offspring. We identify TOPBP1 as a factor involved in meiotic silencing. Deletion of TOPBP1 in male germ cells results in germ cell loss and failure to silence asynapsed chromosomes. We find that TOPBP1 acts at multiple stages in the silencing pathway. Our study highlights that TOPBP1 regulates sex chromosome expression in mammalian germ cells.
Effect of naturally occurring
Wolbachia
in
Anopheles gambiae s.l.
mosquitoes from Mali on
Plasmodium falciparum
malaria transmission
Authors: Gomes Fabio M. , Hixson Bretta L. , Tyner Miles D. W. , Ramirez Jose Luis , Canepa Gaspar E. , Alves e Silva Thiago Luiz , Molina-Cruz Alvaro , Keita Moussa , Kane Fouseyni , Traoré Boïssé , Sogoba Nafomon , Barillas-Mury Carolina
Published: November 2017

Significance

The introduction of
Wolbachia
(an intracellular bacterium that does not infect higher organisms) into culicine mosquito populations from endemic areas is a promising strategy to prevent arboviral transmission. Anopheline mosquitoes were thought to be naturally refractory to
Wolbachia
, but a population of
Anopheles gambiae
from Burkina Faso infected with
Wolbachia
was recently reported. We identified a
Wolbachia
strain in
A. gambiae
mosquitoes from Mali (
w
Anga-Mali).
w
Anga-Mali infection was associated with reduced prevalence and intensity of sporozoite infection in field-collected females. Experimental infections indicate that
w
Anga-Mali infection reduces malaria transmission by a mechanism that affects sporozoites and opens the possibility of exploring the introduction of
Wolbachia
into natural populations of anophelines as a strategy to reduce disease transmission.
Regulation and dysregulation of axon infrastructure by myelinating glia
Authors: Pan Simon , Chan Jonah R.
Published: November 2017

Axon loss and neurodegeneration constitute clinically debilitating sequelae in demyelinating diseases such as multiple sclerosis, but the underlying mechanisms of secondary degeneration are not well understood. Myelinating glia play a fundamental role in promoting the maturation of the axon cytoskeleton, regulating axon trafficking parameters, and imposing architectural rearrangements such as the nodes of Ranvier and their associated molecular domains. In the setting of demyelination, these changes may be reversed or persist as maladaptive features, leading to axon degeneration. In this review, we consider recent insights into axon–glial interactions during development and disease to propose that disruption of the cytoskeleton, nodal architecture, and other components of axon infrastructure is a potential mediator of pathophysiological damage after demyelination.
4. Alienation and reification
Authors: Bronner Stephen Eric
Published: November 2017

‘Alienation and reification’ explores the concepts of alienation and reification in Karl Marx's Economic and Philosophic Manuscripts of 1844, and how this affected 20th century Western Marxism. Alienation is not a uniquely Marxist concept, but Marx defined it as an inability to grasp the workings of history and subject them to human control. In the capitalist system, alienation occurs through the lack of working class consciousness, and their transformation from people into objects—their reification. The Frankfurt School saw alienation and reification as philosophical and experiential problems, but believed that trying to remedy them in the current system was pointless, and a new framework was needed to cultivate autonomy.
5. Enlightened illusions
Authors: Bronner Stephen Eric
Published: November 2017

‘Enlightened illusions’ examines Horkheimer and Adorno's Dialectic of Enlightenment. The work shows how scientific (or instrumental) rationality expels freedom from historical process and enables reification to permeate society. The work connects the growth of instrumental rationality with a totally administered society, and calls for resistance against it. Scientific reason was originally intended to destroy superstitions, but it turned on all non-scientific precepts. This perversion of autonomy has been blamed for the rise of anti–Semitism and fascism. However, these phenomena were due to the conflict of real organizations, and to ignore that is to engage in the very reification processes that the Frankfurt School sought to combat.
Projects: A Very Short Introduction
Authors: Davies Andrew
Published: November 2017

What is a project? How is it organized? Projects: A Very Short Introduction looks at how projects have developed since the industrial revolution to create the human-built world in which we live, work, and play. Considering some of our greatest endeavours—such as the Erie Canal, Apollo Moon landing, and Chinese eco-city projects—it identifies how projects are organized and managed to design and produce large and complex systems, cope with fast changing conditions, and deal with the immense uncertainties required to create breakthrough innovations in products and services. It concludes by considering how projects could be organized to address the challenges facing the post-industrial society of the 21st century.
From Manhattan to the Moon
Authors: Davies Andrew
Published: November 2017

The real breakthrough in the management and organization of large, complex projects can be traced back to the Second World War Manhattan Project, which developed the atom bomb, and the early post-war Atlas Project, which produced the intercontinental ballistic missile. ‘From Manhattan to the Moon’ considers these projects and explains how with few precedents to guide them, new structures, processes, and tools had to be created to coordinate, schedule, and integrate the vast networks of people, resources, and organizations involved in these projects. Systems-based project management spread quickly in the 1970s, but while this approach may work well on routine and simple projects, it ignores the need for adaptability in truly novel and complex projects.
Back to the future
Authors: Davies Andrew
Published: November 2017

‘Back to the future’ considers whether the new and emerging forms of project organization are equipped to deal with the major challenges individuals, organizations, and societies are facing in the 21st century, such as rapid urbanization, climate change, an ageing population, poverty, terrorism, and the migration and refugee crisis. A flexible and adaptive model of project management supported by digital technologies is required for these dynamic and unpredictable projects that are difficult to define with no clear solutions. How will projects of the future be able to respond to these societal challenges and the relentless pressure to innovate and compete in global markets? What can we learn from the past?
What is perception?
Authors: Rogers Brian
Published: November 2017

The word ‘perception’ can be used in two different ways. It can refer to our experience of seeing, hearing, touching, tasting, and smelling objects and individuals around us. It can also refer to the processes that allow us to extract information from the patterns of energy that impinge on our sense organs. Thinking about perception as a set of processes has the advantage that it includes situations where there is no subjective experience. ‘What is perception?’ explains that sometimes our perceptual systems can be fooled and we experience illusions. Is this because of past experience and our knowledge of the world, or is it that we are not extracting the information in the patterns of energy reaching our senses?
Motion perception
Authors: Rogers Brian
Published: November 2017

The ability to detect motion is one of the most important properties of our visual system and the visual systems of nearly every other species. Motion perception is not just important for detecting the movement of objects—both for catching prey and for avoiding predators—but it is also important for providing information about the 3-D structure of the world, for maintaining balance, determining our direction of heading, segregating the scene and breaking camouflage, and judging time-to-contact with other objects in the world. ‘Motion perception’ describes the spatio-temporal process of motion perception and the perceptual effects that tell us something about the characteristics of the motion system: apparent motion, the motion after-effect, and induced motion.
Delusions about illusions
Authors: Rogers Brian
Published: November 2017

The term illusion is used to describe situations where we make mistakes and perceive the surrounding world incorrectly. But what is an illusion? Richard Gregory described illusions as ‘departures from reality’ and this fits with our everyday idea that illusions represent situations where what we perceive does not correspond to some physical characteristic of the particular scene. ‘Delusions about illusions’ considers illusions that have a physiological basis and those with a cognitive basis. It seems very likely that our perceptual systems have evolved to extract the invariant characteristics of the world—the things that don’t change—rather than requiring mechanisms to ‘correct’ for things that do change.
The physiology and anatomy of the visual system
Authors: Rogers Brian
Published: November 2017

‘The physiology and anatomy of the visual system’ describes what we have learned from neurophysiology and anatomy over the past eighty years and what this tells us about the meaning of the circuits involved in visual information processing. It explains how psychologists and physiologists use the terms ‘mechanism’ and ‘process’. For physiologists, a mechanism is linked to the actions of individual neurons, neural pathways, and the ways in which the neurons are connected up. For psychologists, the term is typically used to describe the processes the neural circuits may carry out. The human retina is described with explanations of lateral inhibition, receptive fields, and feature detectors as well as the visual cortex and different visual pathways.
8. Ensuring the effectiveness of environmental law
Authors: Fisher Elizabeth
Published: November 2017

Much of the stretching of the legal imagination of environmental lawyers has been trying to make environmental law more effective. Enforcement practices have evolved, innovative regulatory strategies have been developed, and courts have been entrusted with a role in enforcement. ‘Ensuring the effectiveness of environmental law’ looks at how the success of environmental laws is assessed. For some laws, success is obvious, but for others it is less so; the effective management of environmental problems is often an ongoing process. The challenges of enforcement are also discussed, along with public engagement that can improve the effectiveness of environmental laws through vesting in the public a range of different rights to participate and enforce environmental laws.
Self-reference: what is this chapter about?
Authors: Priest Graham
Published: November 2017

Sometimes things seem deceptively easy when we consider normal cases. With more unusual cases, the simplicity can disappear—as with self-reference. ‘Self-Reference: what is this chapter about?’ examines the concept of self-reference in various examples like: ‘This very sentence that I am now uttering is false’. It is possible for a name to refer to something of which it, itself, is part. Some of the most ancient paradoxes fall into this area of logic, such as the liar paradox. They challenge the assumption that every sentence is either true or false, but not both. What does this tell us about validity? Sentences can be true, false, both, but never neither.
Vagueness: how do you stop sliding down a slippery slope?
Authors: Priest Graham
Published: November 2017

The idea of identity is beset with problems. Everything wears out in time. Parts get replaced. Do such changes affect the identity of the object? How about if we eventually change all the parts of the original object? ‘Vagueness: how do you stop sliding down a slippery slope?’ considers identity and time. Another good example is of a child, who is still a child a second later, and again another second later. Eventually he or she isn’t a child anymore. How can logic explain that? Such sorites paradoxes provide some of the most annoying paradoxes in logic. The issue here is one of vagueness, where nothing is straightforward.
Probability: the strange case of the missing reference class
Authors: Priest Graham
Published: November 2017

A probability is a number assigned to a sentence, measuring how likely it is that the sentence might turn out to be true. It is measured on a scale of 0 to 10. ‘Probability: the strange case of the missing reference class’ examines probability in terms of the question of inductive validity: the validity of those inferences where the premisses give some ground for the conclusion; yet where, even if the premisses are true, the conclusion could still be false. An inference is inductively valid if the conditional probability of the conclusion given the (conjunction of the) premiss or premisses is greater than that of its negation given the premisses.
Maybe it is true—but you can’t prove it!
Authors: Priest Graham
Published: November 2017

‘Maybe it is true—but you can’t prove it!’ first considers David Hilbert’s Program in the Foundations of Mathematics, which was to prove that mathematics was consistent. Hilbert’s ambitious proposal required all of mathematics to be axiomatized. The existence of such an axiom-system was disproved by the Austrian mathematician Kurt Gödel (1906–78). What Gödel showed was that such an axiom system cannot be provided even for the fragment of mathematics that concerns natural numbers, let alone the rest of it. Gödel’s result has been held to have many other philosophical consequences, concerning the nature of numbers, our knowledge of them, and even the nature of the human mind.
Colony personality and plant health in the Azteca-Cecropia mutualism
Authors: Marting Peter R , Wcislo William T , Pratt Stephen C
Published: November 2017

For interspecific mutualisms, the behavior of one partner can influence the fitness of the other, especially in the case of symbiotic mutualisms where partners live in close physical association for much of their lives. Behavioral effects on fitness may be particularly important if either species in these long-term relationships displays personality. We conducted a field study on collective personality in Azteca constructor colonies that live in Cecropia trees, one of the most successful and prominent mutualisms of the neotropics. These pioneer plants provide hollow internodes for nesting and nutrient-rich food bodies; in return, the ants provide protection from herbivores and encroaching vines. We tested the consistency and correlation of 5 colony-level behavioral traits, censused colonies, and measured the amount of leaf damage for each plant. Four of five traits were both consistent within colonies and correlated among colonies. This reveals a behavioral syndrome along a docile-aggressive axis, with higher-scoring colonies showing greater activity, aggression, and responsiveness. Scores varied substantially between colonies and were independent of colony size and age. Host plants of more active, aggressive colonies had less leaf damage, suggesting a link between a colony’s personality and effective defense of its host, though the directionality of this link remains uncertain. Our field study shows that colony personality is an ecologically relevant phenomenon and sheds light on the importance of behavioral differences within mutualism dynamics.
Deep learning for tumor classification in imaging mass spectrometry
Authors: Behrmann Jens , Etmann Christian , Boskamp Tobias , Casadonte Rita , Kriegsmann Jörg , Maaβ Peter
Published: November 2017

Motivation

Tumor classification using imaging mass spectrometry (IMS) data has a high potential for future applications in pathology. Due to the complexity and size of the data, automated feature extraction and classification steps are required to fully process the data. Since mass spectra exhibit certain structural similarities to image data, deep learning may offer a promising strategy for classification of IMS data as it has been successfully applied to image classification.

Results

Methodologically, we propose an adapted architecture based on deep convolutional networks to handle the characteristics of mass spectrometry data, as well as a strategy to interpret the learned model in the spectral domain based on a sensitivity analysis. The proposed methods are evaluated on two algorithmically challenging tumor classification tasks and compared to a baseline approach. Competitiveness of the proposed methods is shown on both tasks by studying the performance via cross-validation. Moreover, the learned models are analyzed by the proposed sensitivity analysis revealing biologically plausible effects as well as confounding factors of the considered tasks. Thus, this study may serve as a starting point for further development of deep learning approaches in IMS classification tasks.

Availability and implementation

https://gitlab.informatik.uni-bremen.de/digipath/Deep_Learning_for_Tumor_Classification_in_IMS.

Supplementary information

Supplementary data are available at Bioinformatics online.