bluuebunny/crossref_metadata_2025 huggingface dataset:
Extending coherent state transforms to Clifford analysis
Authors: Kirwin William D. , Mourão José , Nunes João P. , Qian Tao
Published: October 2016

Segal-Bargmann coherent state transforms can be viewed as unitary maps from L2 spaces of functions (or sections of an appropriate line bundle) on a manifold X to spaces of square integrable holomorphic functions (or sections) on Xℂ. It is natural to consider higher dimensional extensions of X based on Clifford algebras as they could be useful in studying quantum systems with internal, discrete, degrees of freedom corresponding to nonzero spins. Notice that the extensions of X based on the Grassmann algebra appear naturally in the study of supersymmetric quantum mechanics. In Clifford analysis, the zero mass Dirac equation provides a natural generalization of the Cauchy-Riemann conditions of complex analysis and leads to monogenic functions. For the simplest but already quite interesting case of X = ℝ, we introduce two extensions of the Segal-Bargmann coherent state transform from L2(ℝ, dx) ⊗ ℝm to Hilbert spaces of slice monogenic and axial monogenic functions and study their properties. These two transforms are related by the dual Radon transform. Representation theoretic and quantum mechanical aspects of the new representations are studied.
Dynamics of H2 dissociation on the close-packed (111) surface of the noblest metal: H2 + Au(111)
Authors: Wijzenbroek Mark , Helstone Darcey , Meyer Jörg , Kroes Geert-Jan
Published: October 2016

We have performed calculations on the dissociative chemisorption of H2 on un-reconstructed and reconstructed Au(111) with density functional theory, and dynamics calculations on this process on un-reconstructed Au(111). Due to a very late barrier for dissociation, H2 + Au(111) is a candidate H2-metal system for which the dissociative chemisorption could be considerably affected by the energy transfer to electron-hole pairs. Minimum barrier geometries and potential energy surfaces were computed for six density functionals. The functionals tested yield minimum barrier heights in the range of 1.15-1.6 eV, and barriers that are even later than found for the similar H2 + Cu(111) system. The potential energy surfaces have been used in quasi-classical trajectory calculations of the initial (v,J) state resolved reaction probability for several vibrational states v and rotational states J of H2 and D2. Our calculations may serve as predictions for state-resolved associative desorption experiments, from which initial state-resolved dissociative chemisorption probabilities can be extracted by invoking detailed balance. The vibrational efficacy ηv=0→1 reported for D2 dissociating on un-reconstructed Au(111) (about 0.9) is similar to that found in earlier quantum dynamics calculations on H2 + Ag(111), but larger than found for D2 + Cu(111). With the two functionals tested most extensively, the reactivity of H2 and D2 exhibits an almost monotonic increase with increasing rotational quantum number J. Test calculations suggest that, for chemical accuracy (1 kcal/mol), the herringbone reconstruction of Au(111) should be modeled.
Temperature dependence of an AlInP 63Ni betavoltaic cell
Authors: Butera S. , Lioliou G. , Krysa A. B. , Barnett A. M.
Published: October 2016

In this paper, the performance of an Al0.52In0.48P 63Ni radioisotope cell is reported over the temperature range of −20 °C to 140 °C. A 400 μm diameter p+-i-n+ (2 μm i-layer) Al0.52In0.48P mesa photodiode was used as a conversion device in a novel betavoltaic cell. Dark current measurements on the Al0.52In0.48P detector showed that the saturation current increased increasing the temperature, while the ideality factor decreased. The effects of the temperature on the key cell parameters were studied in detail showing that the open circuit voltage, the maximum output power, and the internal conversion efficiency decreased when the temperature was increased. At −20 °C, an open circuit voltage and a maximum output power of 0.52 V and 0.28 pW, respectively, were measured.
Optical sites in Eu- and Mg-codoped GaN grown by NH3-source molecular beam epitaxy
Authors: Sekiguchi Hiroto , Sakai Masaru , Kamada Takuho , Tateishi Hiroki , Syouji Atsushi , Wakahara Akihiro
Published: October 2016

Mg codoping can improve the luminescence properties of Eu-doped GaN. However, the enhanced optical sites differ depending on the fabrication method. In this study, the optical sites in Eu- and Mg-codoped GaN [GaN:(Eu, Mg)] grown by NH3-source molecular beam epitaxy (MBE) were evaluated. The optical properties of an Eu–Mg-related site grown by NH3-MBE were highly stable against thermal annealing. Although the luminescence at sites A (622.3 and 633.8 nm) and B (621.9 and 622.8 nm) was dominant under indirect excitation of Eu ions through GaN, four different optical site groups in addition to sites A and B were observed under resonant excitation. These optical sites are inconsistent with the Eu–Mg-related sites reportedly observed in GaN:(Eu, Mg) fabricated by organometallic vapor phase epitaxy, indicating that the optical site constitution strongly depends on the growth method. Furthermore, site A, with a high cross section, contributed to as much as 22% of the total photoluminescence (PL) integrated intensity for GaN:(Eu, Mg) grown by NH3-MBE, which resulted in a high PL intensity.
Features of the non-contact carotid pressure waveform: Cardiac and vascular dynamics during rebreathing
Authors: Casaccia S. , Sirevaag E. J. , Richter E. J. , O’Sullivan J. A. , Scalise L. , Rohrbaugh J. W.
Published: October 2016

This report amplifies and extends prior descriptions of the use of laser Doppler vibrometry (LDV) as a method for assessing cardiovascular activity, on a non-contact basis. A rebreathing task (n = 35 healthy individuals) was used to elicit multiple effects associated with changes in autonomic drive as well as blood gases including hypercapnia. The LDV pulse was obtained from two sites overlying the carotid artery, separated by 40 mm. A robust pulse signal was obtained from both sites, in accord with the well-described changes in carotid diameter over the blood pressure cycle. Emphasis was placed on extracting timing measures from the LDV pulse, which could serve as surrogate measures of pulse wave velocity (PWV) and the associated arterial stiffness. For validation purposes, a standard measure of pulse transit time (PTT) to the radial artery was obtained using a tonometric sensor. Two key measures of timing were extracted from the LDV pulse. One involved the transit time along the 40 mm distance separating the two LDV measurement sites. A second measure involved the timing of a late feature of the LDV pulse contour, which was interpreted as reflection wave latency and thus a measure of round-trip travel time. Both LDV measures agreed with the conventional PTT measure, in disclosing increased PWV during periods of active rebreathing. These results thus provide additional evidence that measures based on the non-contact LDV technique might provide surrogate measures for those obtained using conventional, more obtrusive assessment methods that require attached sensors.
Fully nonlinear δf gyrokinetics for scrape-off layer parallel transport
Authors: Pan Q. , Told D. , Jenko F.
Published: October 2016

Edge plasmas present a few challenges for gyrokinetic simulations that are absent in tokamak cores. Among them are large fluctuation amplitudes and plasma-wall interactions in the open field line region. In this paper, the widely used core turbulence code GENE, which employs a δf-splitting technique, is extended to simulate open systems with large electrostatic fluctuations. With inclusion and proper discretization of the parallel nonlinear term, it becomes equivalent to a full-f code and the δf-splitting causes no fundamental difficulty in handling large fluctuations. The loss of particles to the wall is accounted for by using a logical sheath boundary, which is implemented in the context of a finite-volume method. The extended GENE code is benchmarked for the well-established one-dimensional parallel transport problem in the scrape-off layer during edge-localized modes. The parallel heat flux deposited onto the divertor target is compared with previous simulation results and shows good agreement.
Interplay between relaxation and Sn segregation during thermal annealing of GeSn strained layers
Authors: Comrie C. M. , Mtshali C. B. , Sechogela P. T. , Santos N. M. , van Stiphout K. , Loo R. , Vandervorst W. , Vantomme A.
Published: October 2016

The effect of thermal annealing on epitaxial GeSn (6.5% Sn) strained layers grown on Ge-buffered Si(100) wafers has been investigated using Rutherford backscattering spectrometry and X-ray diffraction to unambiguously determine the Sn substitutional content as well as the elastic strain in the layers. Vacuum annealing at temperatures below 400 °C for 20 min has no noticeable effect on the strain in the epitaxial layers. Once the temperature was raised above 400 °C, however, relaxation of the layer sets in and the GeSn layer has essentially completely relaxed following a 20 min anneal at 650 °C. Using Rutherford backscattering and channelling spectrometry to provide compositional information as a function of depth enables one to monitor the effect of the thermal anneal on the Sn distribution throughout the layer, and also to directly extract their substitutional fraction (i.e., their solubility in the lattice). The results obtained show that when the relaxation initially sets in both the Ge and the Sn remain firmly bound in substitutional lattice sites and it is only around 600 °C, and after substantial relaxation has taken place, that Sn is finally expelled from lattice sites and diffuses to the surface of the sample.
Suprathermal electron energy spectrum and nonlocally affected plasma-wall interaction in helium/air micro-plasma at atmospheric pressure
Authors: Demidov V. I. , Adams S. F. , Miles J. A. , Koepke M. E. , Kurlyandskaya I. P.
Published: October 2016

Details of ground-state and excited-state neutral atoms and molecules in an atmospheric-pressure micro-discharge plasma may be obtained by plasma electron spectroscopy (PLES), based on a wall probe. The presence and transport of energetic (suprathermal) electrons, having a nonlocal origin, are responsible for electrostatic charging of the plasma boundary surfaces to potentials many times that associated with the ambient electron kinetic energy. The energy-flux distribution function is shown to be controllable for applications involving analysis of composition and processes taking place in a multiphase (plasma-gas-solid), chemically reactive, interaction region.
Ion streaming instability of dust-acoustic surface waves in a semi-infinite Lorentzian complex plasma
Authors: Lee Myoung-Jae , Jung Young-Dae
Published: October 2016

The growth rate of the dust-acoustic surface wave in the semi-infinite complex plasma with an ion streaming passing through the plasma at rest is analytically derived. We have adopted the Lorentzian distribution for electrons to investigate the nonthermal property of a plasma on the growth rate. We find that the growth rate of the surface wave increases as the wave number increases, and it is always larger than that of the bulk wave, especially in the realm of large wave numbers. The nonthermal effect of Lorentzian electrons in the high-energy tail is found to enhance the growth rate. It is also found that the density and speed of streaming ion would increase the growth rate. The growth rate of the surface wave is compared to that of the bulk wave for various physical parameters.
Metastable coupled-growth kinetics between primary and peritectic phases of undercooled hypoperitectic Fe54.5Ti45.5 alloy
Authors: Wu Y. H. , Chang J. , Wang W. L. , Wei B.
Published: October 2016

The metastable coupled-growth kinetics between the primary Fe2Ti and peritectic FeTi phases of undercooled Fe54.5Ti45.5 alloy was systematically investigated by both electromagnetic levitation and drop tube techniques. Employing a high-speed camera, the rapid crystallization processes of levitated bulk alloy were recorded in the undercooling range of 34–187 K. In small undercooling regime below 143 K, peritectic solidification proceeded and the dependence of primary Fe2Ti dendritic growth velocity V on the bulk undercooling ΔT satisfied a power relation of V = 2.43 × 10−14 × ΔT7.72 (mm s−1). Once liquid undercooling increased beyond 143 K, the metastable coupled-growth was induced and the microstructure was characterized by the Fe2Ti rods embedded in FeTi phase. Furthermore, the coupled-growth velocity decreased linearly with the rise in undercooling according to V = 1.47 × 103-7.44ΔT (mm s−1). In drop tube experiment, peritectic solidification characteristics of small alloy droplets disappeared and the primary and peritectic phases directly nucleated from undercooled liquid and grew cooperatively to form spherical coupled-growth cells if droplet diameter decreased below 481 μm.
Characterisation of active dopants in boron-doped self-assembled silicon nanostructures
Authors: Puthen Veettil Binesh , Zhang Tian , Chin Robert Lee , Jia Xuguang , Nomoto Keita , Yang Terry Chien-Jen , Lin Ziyun , Wu Lingfeng , Rexiati Reyifate , Gutsch Sebastian , Conibeer Gavin , Perez-Würfl Ivan
Published: October 2016

Doping of silicon nanocrystals has become an important topic due to its potential to enable the fabrication of environmentally friendly and cost-effective optoelectronic and photovoltaic devices. However, doping of silicon nanocrystals has been proven difficult and most of the structural and electronic properties are still not well understood. In this work, the intrinsic and boron-doped self-assembled silicon nanocrystals were prepared and mainly characterised by the transient current method to study the behaviour of charge carriers in these materials. Our experiments quantified the amount of electrically active boron dopants that contributed to charge transport. From this, the boron doping efficiency in the nanocrystal superlattice was estimated.
Stable discrete representation of relativistically drifting plasmas
Authors: Kirchen M. , Lehe R. , Godfrey B. B. , Dornmair I. , Jalas S. , Peters K. , Vay J.-L. , Maier A. R.
Published: October 2016

Representing the electrodynamics of relativistically drifting particle ensembles in discrete, co-propagating Galilean coordinates enables the derivation of a Particle-In-Cell algorithm that is intrinsically free of the numerical Cherenkov instability for plasmas flowing at a uniform velocity. Application of the method is shown by modeling plasma accelerators in a Lorentz-transformed optimal frame of reference.
Discharge effects on gas flow dynamics in a plasma jet
Authors: Xian Yu Bin , Hasnain Qaisrani M. , Yue Yuan Fu , Lu Xin Pei
Published: October 2016

Plasma is used as a flow visualization method to display the gas flow of a plasma jet. Using this method, it is found that a discharge in a plasma jet promotes the transition of the gas flow to turbulence. A discharge at intermediate frequency (∼6 kHz in this paper) has a stronger influence on the gas flow than that at lower or higher frequencies. Also, a higher discharge voltage enhances the transition of the gas flow to turbulence. Analysis reveals that pressure modulation induced both by the periodically directed movement of ionized helium and Ohmic heating on the gas flow plays an important role in inducing the transition of the helium flow regime. In addition, since the modulations induced by the high- and low-frequency discharges are determined by the frequency-selective effect, only intermediate-frequency (∼6 kHz) discharges effectively cause the helium flow transition from the laminar to the turbulent flow. Moreover, a discharge with a higher applied voltage makes a stronger impact on the helium flow because it generates stronger modulations. These conclusions are useful in designing cold plasma jets and plasma torches. Moreover, the relationship between the discharge parameters and the gas flow dynamics is a useful reference on active flow control with plasma actuators.
Shape engineering for electronic and optoelectronic properties of Si nanostructure solar cells
Authors: He Yan , Zhao Yipeng , Quan Jun , Ouyang Gang
Published: October 2016

An analytical model is developed to explore the shape-dependent electronic and optoelectronic properties of silicon nanostructure solar cells, including nanocones (NCs), nanowires (NWs), and truncated-nanocones (TNCs), on the basis of atomic-bond-relaxation consideration and detailed balance principle. It is found that the inhomogeneous NCs can not only make the band gap shrink gradually from the top to the bottom, but also suppress the surface recombination and enhance light absorption. Moreover, the optimal performance of silicon nanostructures can be achieved through modulating the geometrical parameters. Strikingly, the SiNCs show the highest solar conversion efficiency compared with that of NWs and TNCs under identical conditions, which suggest that this kind of nanostructures could be expected to be applicable for the new-typed and friendly alternative solar cell unit.
Cavity-based high-efficiency and wideband 90° polarization rotator
Authors: Wang Jiang , Shen Zhongxiang , Wu Wen
Published: October 2016

We present a high-efficiency wideband 90° polarization rotator based on 2D array of substrate integrated waveguide cavities etched with three twisted slots, which can rotate a horizontally polarized incident wave into an outgoing vertically polarized wave. The twisted slots etched on the surface of the cavity are utilized to couple the wave into and out of the cavity with the polarization direction rotated. As a proof-of-concept, a prototype of the proposed rotator is fabricated and measured in the microwave regime. The proposed 90° polarization rotator features a low insertion loss of about 0.5 dB in the pass band with a factional bandwidth of 28.6%, as well as high polarization rotation efficiency of over 90%.
Data-driven identification of prognostic tumor subpopulations using spatially mapped t-SNE of mass spectrometry imaging data
Authors: Abdelmoula Walid M. , Balluff Benjamin , Englert Sonja , Dijkstra Jouke , Reinders Marcel J. T. , Walch Axel , McDonnell Liam A. , Lelieveldt Boudewijn P. F.
Published: October 2016

Significance

Mass spectrometry imaging provides untargeted spatiomolecular information necessary to uncover molecular intratumor heterogeneity. The challenge has been to identify those tumor subpopulations that drive patient outcomes within the highly complex datasets (hyperdimensional data, intratumor heterogeneity, and patient variation). Here we report an automatic, unbiased pipeline to nonlinearly map the hyperdimensional data into a 3D space, and identify molecularly distinct, clinically relevant tumor subpopulations. We demonstrate this pipeline’s ability to uncover subpopulations statistically associated with patient survival in primary tumors of gastric cancer and with metastasis in primary tumors of breast cancer.
Notch3 drives development and progression of cholangiocarcinoma
Authors: Guest Rachel V. , Boulter Luke , Dwyer Benjamin J. , Kendall Timothy J. , Man Tak-Yung , Minnis-Lyons Sarah E. , Lu Wei-Yu , Robson Andrew J. , Gonzalez Sofia Ferreira , Raven Alexander , Wojtacha Davina , Morton Jennifer P. , Komuta Mina , Roskams Tania , Wigmore Stephen J. , Sansom Owen J. , Forbes Stuart J.
Published: October 2016

Significance

Clinical outcomes in cholangiocarcinoma (CC) are poor; few patients are candidates for curative resection, and palliative chemotherapy produces only modest effects on survival. With an increasing incidence, new targets are urgently needed. Notch has been identified as having potential to induce CC when transgenically overexpressed, and this study aimed to characterize how endogenous Notch might drive tumorigenesis. We identify the atypical receptor Notch3 as differentially overactivated in CCs in humans, rats, and mice, with genetic deletion significantly reducing CC growth. Notch3 sustains tumor cell survival through PI3k/Akt activation via a noncanonical mechanism independent of Recombinant Signal Binding Protein for Immunoglobulin Kappa J Region (RBPJ), presenting an opportunity to target the pathway without disrupting classical Notch and bypassing toxicities associated with γ-secretase inhibitors.
Hurricane Sandy’s flood frequency increasing from year 1800 to 2100
Authors: Lin Ning , Kopp Robert E. , Horton Benjamin P. , Donnelly Jeffrey P.
Published: October 2016

Significance

This study demonstrates quantitatively that the frequency of Hurricane Sandy-like extreme flood events has increased significantly over the past two centuries and is very likely to increase more sharply over the 21st century, due to the compound effects of sea level rise and storm climatology change.
Essential protective role of tumor necrosis factor receptor 2 in neurodegeneration
Authors: Dong Yun , Fischer Roman , Naudé Petrus J. W. , Maier Olaf , Nyakas Csaba , Duffey Maëlle , Van der Zee Eddy A. , Dekens Doortje , Douwenga Wanda , Herrmann Andreas , Guenzi Eric , Kontermann Roland E. , Pfizenmaier Klaus , Eisel Ulrich L. M.
Published: October 2016

Significance

TNF is known to play an important role in various neurodegenerative diseases. However, anti-TNF therapeutics failed in clinical trials of neurodegenerative diseases. This failure is most likely due to antithetic effects of the TNF receptors in the central nervous system, whereby TNFR1 promotes inflammatory degeneration and TNFR2 neuroprotection. Here we show that novel TNFR-selective therapeutics, i.e., a TNFR1 antagonist and a TNFR2 agonist, block neuroinflammation and promote neuronal survival in a mouse model of neurodegeneration related to Alzheimer disease as well as other neurodegenerative diseases. Most important, neuroprotection mediated by the TNFR1 antagonist is abrogated by simultaneous blockade of TNFR2 activation, revealing that neuroprotection requires TNFR2 signaling and uncover why anti-TNF drugs failed in treatment of neurodegenerative diseases.
A Population of planetary systems characterized by short-period, Earth-sized planets
Authors: Steffen Jason H. , Coughlin Jeffrey L.
Published: October 2016

Significance

Characterizing the variety of planets and planetary systems orbiting distant stars (exoplanets) is a key ingredient to improving our understanding of the Solar System and of planet formation in general. One important observable property of a planetary system is its architecture—the sizes and orbital periods of the planets in a system and how they are related to each other. From a statistical analysis of the planet candidate catalog from NASA’sKeplermission, we identify a population of planetary systems characterized by a unique system architecture. Differences in system architecture indicate different paths in the formation or dynamical history of a planetary system—giving clues to the physical conditions or processes that drive systems along those paths.
Flavodiiron proteins act as safety valve for electrons in
Physcomitrella patens
Authors: Gerotto Caterina , Alboresi Alessandro , Meneghesso Andrea , Jokel Martina , Suorsa Marjaana , Aro Eva-Mari , Morosinotto Tomas
Published: October 2016

Significance

Photosynthesis regulation is fundamental to responding to environmental dynamic changes and avoiding oxidative damage. These regulatory mechanisms were shaped during evolution from cyanobacteria to plants, as well as after the colonization of new habitats. Land colonization was a key phase in evolution with plants capable of adapting to drastically different conditions with respect to their aquatic ancestors. Valuable information on this adaptation can be obtained studying nonvascular plants, such as the moss
Physcomitrella patens
, that diverged from flowering plants early after land colonization. Here we show that in
P. patens
, Flavodiiron (FLV) proteins are acting as an electron sink to avoid photosynthetic electron transport chain over-reduction after any increase in illumination and are fundamental for protection under fluctuating light conditions.
Proteolytic processing of Middle East respiratory syndrome coronavirus spikes expands virus tropism
Authors: Park Jung-Eun , Li Kun , Barlan Arlene , Fehr Anthony R. , Perlman Stanley , McCray Paul B. , Gallagher Tom
Published: October 2016

Significance

Middle East respiratory syndrome coronavirus (MERS-CoV) can cause lethal pneumonia by infecting lung epithelial cells. Infection requires viral “spike” proteins, which catalyze virus–cell membrane fusion during cell entry. Fusion catalysis requires that spikes be first cleaved by cellular proteases. MERS-CoV spikes are cleaved in virus-producing cells before subsequent virus-cell entry, whereas other human coronaviruses have spikes that are cleaved in virus-infecting cells during virus-cell entry. Here, we found that the early MERS-CoV cleavages are required for the subsequent infection of human lung-like cells, but are dispensable for infection of several other cell types. Our findings demonstrate that the spike cleavage status of MERS-CoVs dictates cell tropism, and points to spike proteolytic processing as a correlate of MERS-CoV virulence.
Identifying the elusive link between amino acid sequence and charge selectivity in pentameric ligand-gated ion channels
Authors: Cymes Gisela D. , Grosman Claudio
Published: October 2016

Significance

The cation-versus-anion selectivity of pentameric ligand-gated ion channels cannot always be predicted on the basis of their amino acid sequences alone. Indeed, the relationship between amino acid sequence and function contains subtle elements that have eluded prior investigation. Here, we found that ion–ion interactions between the passing ions and ionized side chains in the first turn of the M2 α-helices dominate the permeation free-energy landscape, but we also found that the mere presence of an ionized residue in the first turn of M2 does not ensure that its charge is “felt” by permeating ions. Instead, there seems to be a requirement for a proper conformation for a charged side chain to exert its effect on selectivity.
Controlling the mode of operation of organic transistors through side-chain engineering
Authors: Giovannitti Alexander , Sbircea Dan-Tiberiu , Inal Sahika , Nielsen Christian B. , Bandiello Enrico , Hanifi David A. , Sessolo Michele , Malliaras George G. , McCulloch Iain , Rivnay Jonathan
Published: October 2016

Significance

Side-chain engineering is a versatile tool to modify the processability, as well as the physical, electrical, and optical properties, of conjugated polymers. This approach is used to tailor the operating mechanism of electrolyte-gated organic transistors, allowing for facile bulk doping and therefore efficient modulation of transistor channel conductance. Such transistors combine fast response with high current-to-voltage signal transduction necessary for active sensing and low-power circuit applications.
Bicarbonate-induced redox tuning in Photosystem II for regulation and protection
Authors: Brinkert Katharina , De Causmaecker Sven , Krieger-Liszkay Anja , Fantuzzi Andrea , Rutherford A. William
Published: October 2016

Significance

The
E

m

of

Q
A

/

Q
A

−
•

is the reference pegging the thermodynamics of Photosystem II (PSII) to an absolute value. This work resolves a long-standing discrepancy in the literature, removing this ambiguity at the heart of PSII bioenergetics. The discrepancy in the literature reflects the loss of bicarbonate in some titrations. This surprising finding shows that bicarbonate binding controls the
E

m

of

Q
A

/

Q
A

−
•

, and thus the redox state of Q
A
influences the binding of bicarbonate. This process constitutes a previously unrecognized regulation of PSII:

Q
A

−
•

triggers bicarbonate release, slowing electron transfer and tuning the potential of Q
A
to protect PSII against photodamage. This work provides an explanation for the existence of bicarbonate in PSII, a mystery for more than half a century.
Herpes simplex virus ICP27 regulates alternative pre-mRNA polyadenylation and splicing in a sequence-dependent manner
Authors: Tang Shuang , Patel Amita , Krause Philip R.
Published: October 2016

Significance

Although implicated, the role of herpes simplex virus (HSV) infected cell culture polypeptide 27 (ICP27) in cotranscriptional pre-mRNA processing remains poorly understood. We show that ICP27 promotes cotranscriptional cellular pre-mRNA 3′ end formation using cryptic polyadenylation signals in introns, generating hundreds of novel, intronless GC-rich cellular transcripts that resemble HSV genes. ICP27 also causes aberrant pre-mRNA splicing of some genes. ICP27-targeted genes share common features such as high GC content, cytosine-rich sequences, and suboptimal splice sites, providing an explanation for the observed target specificity of ICP27 and suggesting an overlapping mechanism for ICP27-mediated aberrant pre-mRNA splicing and polyadenylation. By specifically modifying pre-mRNA processing of HSV-like GC-rich transcripts that are likely spared by the virion host shutoff protein, ICP27 contributes to virus-induced host shutoff required for efficient viral growth.
Mitotic Golgi disassembly is required for bipolar spindle formation and mitotic progression
Authors: Guizzunti Gianni , Seemann Joachim
Published: October 2016

Significance

During mammalian cell division, the contiguous Golgi ribbon is first vesiculated and then partitioned into the daughter cells with the aid of the mitotic spindle. Whether Golgi vesiculation is required for cell division is unclear. Here, we show that inhibition of Golgi disassembly by the acute formation of a polymer in the Golgi lumen prior to mitotic entry blocks bipolar spindle formation and arrests cells in early mitosis with an active spindle assembly checkpoint (SAC). Importantly, mitotic progression is fully restored upon depletion of centrosomes. Our work thus reveals that mitotic Golgi disassembly is tightly monitored and acts as an upstream surveillance point for the canonical SAC to ensure the fidelity of Golgi inheritance and cell division.
Extracellular matrix stiffness causes systematic variations in proliferation and chemosensitivity in myeloid leukemias
Authors: Shin Jae-Won , Mooney David J.
Published: October 2016

Significance

Most chemotherapy drugs treat, but do not cure, cancer patients due to resistance. New high-throughput screening assays are emerging to better predict drug efficacy by recapitulating tumor microenvironments with three-dimensional hydrogels. Our platform exploits the mechanical tunability of alginate hydrogels to introduce biophysical cues into screening assays. The utility of this approach is demonstrated with the findings of unique modes of growth modulation by matrix stiffness and mechanosensitivity of drug actions in different myeloid leukemia subtypes. The same hydrogels were then adapted to confirm in vivo that matrix softening accelerates cancer growth kinetics and causes resistance to standard chemotherapy. We anticipate that this integrative workflow will be broadly useful to discover drugs that target cancer cells in different physical environments.
A conserved αβ transmembrane interface forms the core of a compact T-cell receptor–CD3 structure within the membrane
Authors: Krshnan Logesvaran , Park Soohyung , Im Wonpil , Call Melissa J. , Call Matthew E.
Published: October 2016

Significance

The T-cell antigen receptor (TCR) is an eight-subunit modular biosensor that detects the presence of pathogen-derived molecular fragments in infected cells and tissues. No atomic-resolution structure has been determined for the intact receptor complex, and the mechanism by which it transmits signals across the cell membrane remains poorly defined. Using a combination of biochemical, biophysical, and computational approaches to study the assembled complex in cellular membranes, we identified an evolutionarily conserved core transmembrane (TM) structure that organizes the complex into an intimately packed eight-helix bundle within the membrane and is critical for the structural integrity of the intact receptor. Our model provides insights into possible structural pathways involved in TM TCR signaling.
Theory of single-molecule controlled rotation experiments, predictions, tests, and comparison with stalling experiments in F
1
-ATPase
Authors: Volkán-Kacsó Sándor , Marcus Rudolph A.
Published: October 2016

Significance

The investigation of nucleotide binding and release dynamics vs. rotor shaft rotation in the F
1
-ATPase enzyme is necessary to reveal biological function. We elucidate the mechanism of the exponential-like change of binding and release rate (and thus the equilibrium) constants when probed against the rotor angle at the single-molecule level. We extend our group transfer theory proposed for the stalling experiments to treat controlled rotation experiments. The model correctly predicts the controlled rotation data on fluorescent ATP without any adjustable parameters. The theory provides a framework able to treat the binding and release of various nucleotides. In the process we also learn about the properties of the fluorescent nucleotide Cy3-ATP.
Overdrinking, swallowing inhibition, and regional brain responses prior to swallowing
Authors: Saker Pascal , Farrell Michael J. , Egan Gary F. , McKinley Michael J. , Denton Derek A.
Published: October 2016

Significance

Drinking represents a crucial behavior that subserves the survival of species by maintaining fluid balance within the body. The present study confirms in humans the presence of swallowing inhibition after excess liquid has been drunk, revealing a mechanism important for the regulation of fluid intake. The findings presented here support the view that swallowing inhibition is probably a “hard-wired” process that aids maintenance of fluid balance within the body, thereby avoiding the detrimental effects of overdrinking that can cause water intoxication and eventually death.
Mutational landscape of uterine and ovarian carcinosarcomas implicates histone genes in epithelial–mesenchymal transition
Authors: Zhao Siming , Bellone Stefania , Lopez Salvatore , Thakral Durga , Schwab Carlton , English Diana P. , Black Jonathan , Cocco Emiliano , Choi Jungmin , Zammataro Luca , Predolini Federica , Bonazzoli Elena , Bi Mark , Buza Natalia , Hui Pei , Wong Serena , Abu-Khalaf Maysa , Ravaggi Antonella , Bignotti Eliana , Bandiera Elisabetta , Romani Chiara , Todeschini Paola , Tassi Renata , Zanotti Laura , Odicino Franco , Pecorelli Sergio , Donzelli Carla , Ardighieri Laura , Facchetti Fabio , Falchetti Marcella , Silasi Dan-Arin , Ratner Elena , Azodi Masoud , Schwartz Peter E. , Mane Shrikant , Angioli Roberto , Terranova Corrado , Quick Charles Matthew , Edraki Babak , Bilgüvar Kaya , Lee Moses , Choi Murim , Stiegler Amy L. , Boggon Titus J. , Schlessinger Joseph , Lifton Richard P. , Santin Alessandro D.
Published: October 2016

Significance

Some cancers, termed carcinosarcomas (CSs), have mixed cell types, with either epithelial or mesenchymal features. Sequencing the genomes of uterine and ovarian CSs demonstrated that these different cell types derive from a common precursor cell that has many mutations typical of epithelial cancers. In addition, we find that these tumors have a significant burden of point mutations and amplification of histone genes, suggesting a potential role of these mutations in sarcomatous transformation. Consistent with this finding, expression of specific histone gene mutations in uterine carcinoma cells changed gene expression toward a mesenchymal state. These findings have potential implications for the treatment of these cancers.
Pronounced Genetic Structure and Site Fidelity among Native Muskellunge Populations in Lake Huron and Georgian Bay
Authors: Wilson Chris C. , Liskauskas Arunas P. , Wozney Kristyne M.
Published: October 2016

Conservation and management issues related to genetic diversity and stock structure of native populations of Muskellunge Esox masquinongy have largely been unexplored. In Lake Huron's North Channel and Georgian Bay, Muskellunge populations have been impacted by historical commercial fisheries, recreational fisheries, loss of spawning habitat, historical water quality issues, and ecosystem changes. To determine the spatial genetic structure of native Muskellunge in Lake Huron and Georgian Bay, spawning adults were sampled from 10 sites in the North Channel and eastern Georgian Bay. Genotyping with 20 microsatellite DNA loci showed substantial spatial genetic structure, with significant pairwise divergences among spawning sites. Individual‐ and population‐based analyses revealed hierarchical population structuring, with strong patterns of spawning site fidelity and isolation by distance; very low levels of dispersal and gene flow over historical and contemporary timescales were indicated. Estimation of effective population sizes highlighted the limited genetic resources that are present in these localized populations. The present results show that Muskellunge in Lake Huron and Georgian Bay consist of multiple small populations with limited ranges and high site fidelity and should be managed accordingly.

Received February 28, 2016; accepted July 1, 2016 Published online October 11, 2016
Global and pedestal confinement and pedestal structure in dimensionless collisionality scans of low-triangularity H-mode plasmas in JET-ILW
Authors: Frassinetti L. , Beurskens M.N.A. , Saarelma S. , Boom J.E. , Delabie E. , Flanagan J. , Kempenaars M. , Giroud C. , Lomas P. , Meneses L. , Maggi C.S. , Menmuir S. , Nunes I. , Rimini F. , Stefanikova E. , Urano H. , Verdoolaege G.
Published: October 2016

A dimensionless collisionality scan in low-triangularity plasmas in the Joint European Torus with the ITER-like wall (JET-ILW) has been performed. The increase of the normalized energy confinement (defined as the ratio between thermal energy confinement and Bohm confinement time) with decreasing collisionality is observed. Moreover, at low collisionality, a confinement factor H98, comparable to JET-C, is achieved. At high collisionality, the low normalized confinement is related to a degraded pedestal stability and a reduction in the density-profile peaking.

The increase of normalized energy confinement is due to both an increase in the pedestal and in the core regions. The improvement in the pedestal is related to the increase of the stability. The improvement in the core is driven by (i) the core temperature increase via the temperature-profile stiffness and by (ii) the density-peaking increase driven by the low collisionality.

Pedestal stability analysis performed with the ELITE (edge-localized instabilities in tokamak equilibria) code has a reasonable qualitative agreement with the experimental results. An improvement of the pedestal stability with decreasing collisionality is observed. The improvement is ascribed to the reduction of the pedestal width, the increase of the bootstrap current and the reduction of the relative shift between the positions of the pedestal density and pedestal temperature.

The EPED1 model predictions for the pedestal pressure height are qualitatively well correlated with the experimental results. Quantitatively, EPED1 overestimates the experimental pressure by 15–35%. In terms of the pedestal width, a correct agreement (within 10–15%) between the EPED1 and the experimental width is found at low collisionality. The experimental pedestal width increases with collisionality. Nonetheless, an extrapolation to low-collisionality values suggests that the width predictions from the KBM constraint are reasonable for ITER.
gsrc: an R package for genome structure rearrangement calling
Authors: Grandke Fabian , Snowdon Rod , Samans Birgit
Published: October 2016

Genome structure rearrangements are a common phenomenon in allopolyploid species. Deletions, duplications and homeologous non-reciprocal translocations (HNRT) between the highly similar subgenomes can be observed, which are known to have a large impact on phenotypic traits. Current research is limited because these rearrangements can be located genome wide only by cost intensive sequencing approaches and not reliably in high-density array genotyping data. We developed gsrc, an R-package to detect genome structure rearrangements from genotyping data in allopolyploid species including exchanges between subgenomes. We exemplarily apply gsrc to a publicly available Brassica napus dataset.

Availability and Implementation

The compiled R-package and source code are available at http://cran.r-project.org/web/packages/gsrc/.

Supplementary information

Supplementary data are available at Bioinformatics online.
Transfer learning across ontologies for phenome–genome association prediction
Authors: Petegrosso Raphael , Park Sunho , Hwang Tae Hyun , Kuang Rui
Published: October 2016

Motivation

To better predict and analyze gene associations with the collection of phenotypes organized in a phenotype ontology, it is crucial to effectively model the hierarchical structure among the phenotypes in the ontology and leverage the sparse known associations with additional training information. In this paper, we first introduce Dual Label Propagation (DLP) to impose consistent associations with the entire phenotype paths in predicting phenotype–gene associations in Human Phenotype Ontology (HPO). DLP is then used as the base model in a transfer learning framework (tlDLP) to incorporate functional annotations in Gene Ontology (GO). By simultaneously reconstructing GO term–gene associations and HPO phenotype–gene associations for all the genes in a protein–protein interaction network, tlDLP benefits from the enriched training associations indirectly through relation with GO terms.

Results

In the experiments to predict the associations between human genes and phenotypes in HPO based on human protein–protein interaction network, both DLP and tlDLP improved the prediction of gene associations with phenotype paths in HPO in cross-validation and the prediction of the most recent associations added after the snapshot of the training data. Moreover, the transfer learning through GO term–gene associations significantly improved association predictions for the phenotypes with no more specific known associations by a large margin. Examples are also shown to demonstrate how phenotype paths in phenotype ontology and transfer learning with gene ontology can improve the predictions.

Availability and Implementation

Source code is available at http://compbio.cs.umn.edu/ontophenome.

Supplementary information

Supplementary data are available at Bioinformatics online.
Neither
lieux de mémoire
, nor
non-lieux
: Towards a Concept of Precarious Spaces in Philippe Vasset’s
Un livre blanc
Authors: Colon Églantine
Published: October 2016

This article starts from the identification in French literature of a recent turn to the peripheries, at a time when the centre of Paris has become both museified and gentrified. Taking Philippe Vasset’s ‘récit’
Un livre blanc
(2007) as a case study of this turn, this article identifies urban peripheries as the space where the postcolonial and the post-industrial intersect, intensifying the precarity of those who live there. The analysis proceeds dialectically to unfold the ways in which Vasset both resorts to the neutralizing spatialism operated by cartography and distances himself from these postmodern co-ordinates, deploying a ‘poetics of precarity’ that encodes the unstable qualities of the peripheries. Arguing that neither of the two concepts currently used to define contemporary space — the
lieux de mémoire
and the
non-lieux
— is fully apt to describe the current socio-temporal configurations of urban peripheries, this article elaborates the concept of ‘precarious spaces’, redirecting the analysis towards the political pressures exerted by the globalized, fragile dimensions of our contemporary moment. Vasset’s text is thus analysed in its capacity to insist on the relevance of the notion of precarity in the study of contemporary French literature.
Consequences of elevated CO2 exposure across multiple life stages in a coastal forage fish
Authors: Murray Christopher S. , Fuiman Lee A. , Baumann Hannes
Published: October 2016

Ocean acidification may impact the fitness of marine fish, however, studies reporting neutral to moderate effects have mostly performed short-term exposures to elevated CO2, whereas longer-term studies across life stages are still scarce. We performed a CO2 exposure experiment, in which a large number (n > 2200) of Atlantic silverside Menidia menidia offspring from wild spawners were reared for 135 days through their embryonic, larval, and juvenile stages under control (500 µatm) and high CO2 conditions (2300 µatm). Although survival was high across treatments, subtle but significant differences in length, weight, condition factor and fatty acid (FA) composition were observed. On average, fish from the acidified treatment were 4% shorter and weighed 6% less, but expressed a higher condition factor than control juveniles. In addition, the metrics of length and weight distributions differed significantly, with juveniles from the high CO2 treatment occupying more extreme size classes and the length distribution shifting to a positive kurtosis. Six of twenty-seven FAs differed significantly between treatments. Our results suggest that high CO2 conditions alter long-term growth in M. menidia, particularly in the absence of excess food. It remains to be shown whether and how these differences will impact fish populations in the wild facing size-selective predation and seasonally varying prey abundance.
Seasonal movements and connectivity of an Atlantic cod (Gadus morhua) spawning component in the western Gulf of Maine
Authors: Zemeckis Douglas R. , Liu Chang , Cowles Geoffrey W. , Dean Micah J. , Hoffman William S. , Martins David , Cadrin Steven X.
Published: October 2016

Movement patterns of marine fishes can have considerable impacts on their population dynamics. A thorough understanding of fish movements is therefore required for informing stock identification, stock assessment, and fishery management. This study investigated the seasonal movements and connectivity of a spring-spawning component of Atlantic cod (Gadus morhua) in the western Gulf of Maine. From 2010 through 2013, spawning cod were sampled within an inshore spawning closure and tagged with conventional tags (n = 2368), acoustic transmitters (n = 106), and archival data storage tags (n = 266). Acoustic receivers were deployed on three inshore spawning sites to test for connectivity among sites. Data from archival tags were used to describe seasonal habitat occupancy and movement patterns via geolocation to statistical areas. Tagging data indicated that cod were primarily residential in the western Gulf of Maine, moving inshore to spawn during the spring (April–July), followed by an offshore migration to their feeding grounds for summer and fall. Cod generally inhabited waters from 45 to 175 m, with the deep offshore basins (>150 m) serving as overwintering habitat. Occupied water temperatures ranged from 4.0 to 13.3 °C, with the coldest temperatures experienced from March through July and the warmest temperatures experienced from September through January. Results provided evidence of spawning site fidelity and connectivity among spawning sites, with some fish visiting multiple spawning sites within or between years. The movements observed during and after the spring-spawning season serve as important mechanisms influencing metapopulation dynamics in the Gulf of Maine region, including both fine- and broad-scale population structure. The improved understanding of cod movement patterns will assist fishery managers in developing management plans, including spawning protection measures, and help to address remaining uncertainties with respect to cod population structure in the Gulf of Maine and other regions.