bluuebunny/crossref_metadata_2025 huggingface dataset:
Absence of magnetic ordering in the ground state of a SrTm2O4 single crystal
Authors: Li Hai-Feng , Senyshyn Anatoliy , Fabelo Oscar , Persson Jörg , Hou Binyang , Boehm Martin , Schmalzl Karin , Schmidt Wolfgang , Vassalli Jean-Pierre , Thakuria Pankaj , Sun Xiao , Wang Liming , Khazaradze Giorgi , Schmitz Berthold , Zhang Cong , Roth Georg , García Roca Javier , Wildes Andrew
Published: June 2015

We report on the first single crystal study of SrTm2O4.
Trajectory optimisation method by using independent component analysis for MIMO‐OTHR target tracking
Authors: Luo Yang , Zhao Zhiqin
Published: June 2015

Traditional sky‐wave over‐the‐horizon radar (OTHR) target tracking algorithms, such as multipath probabilistic data association, can achieve good performance if the multipath environment clutter is not strong enough. The computation complexity and tracking performance of these algorithms can be further improved by multiple‐input multiple‐output (MIMO) radar technology owing to its capability to utilise transmitting and receiving diversities. However, multipath propagation is still considered to degrade the performance because of the strong ionosphere and sea clutter. To deal with the interference of strong clutter in a multipath environment, a tracking trajectory optimisation method is proposed by applying the fast and robust fixed‐point independent component analysis algorithm which uses the projection pursuit approach to separate clutter and a true target moving trajectory from the received signals. Numerical simulations demonstrate the feasibility of the method, and it also shows that the multipath measurements can be utilised for MIMO‐OTHR target tracking.
Passive target tracking of marine traffic ships using onboard monocular camera for unmanned surface vessel
Authors: Park Jeonghong , Kim Jinwhan , Son Nam‐sun
Published: June 2015

Enhancing the performance of passive target tracking and trajectory estimation of marine traffic ships is focused using a monocular camera mounted on an unmanned surface vessel. To accurately estimate the trajectory of a target traffic ship, the relative bearing and range information between the observing ship and the target ship is required. Monocular vision provides bearing information with reasonable accuracy but with no explicit range information. The relative range information can be extracted from the bearing changes induced by the relative ship motion in the framework of bearings‐only tracking (BOT). BOT can be effective in crossing situations with large bearing angle changes. However, it often fails in head‐on or overtaking situations due to small bearing angle changes and the resulting low observability of the tracking filter. To deal with the lack of observability, the vertical pixel distance between the horizon and the target ship in the image is used, which improves the overall target tracking performance. The feasibility and performance of the proposed tracking approach were validated through field experiments at sea.
0.5–50 GHz dielectric characterisation of breast cancer tissues
Authors: Martellosio A. , Pasian M. , Bozzi M. , Perregrini L. , Mazzanti A. , Svelto F. , Summers P.E. , Renne G. , Bellomi M.
Published: June 2015

Cancer affects a significant percentage of people, and early detection techniques are important for prompt and effective treatment. The use of microwave frequencies to achieve non‐invasive and non‐destructive cancer detections is currently under investigation by several research groups. In this frequency range, the dielectric properties of the biological tissue determine the interactions of the tissue with electromagnetic fields. Knowledge of the dielectric properties of both the normal and the malignant human tissues is therefore a fundamental starting point. A dielectric spectroscopy system, based on the use of a reflectometry setup, was used to perform an extensive experimental campaign on fresh surgical specimens. The measurement system allowed achieving a broadband dielectric characterisation of biological tissues up to 50 GHz, thus including millmetre‐wave (mm‐wave) frequencies. In the case of breast tissues, the results showed that the malignant and normal tissues exhibit significantly different complex dielectric permittivities of up to 50 GHz, due to their respective high and low water content. This permittivity difference is well detectable, and this paves the way to new screening methods based on mm‐wave imaging systems.
Lagrangian coherent structures along atmospheric rivers
Authors: Garaboa-Paz Daniel , Eiras-Barca Jorge , Huhn Florian , Pérez-Muñuzuri Vicente
Published: June 2015

We show that filamentous Atmospheric Rivers (ARs) over the Northern Atlantic Ocean are closely linked to attracting Lagrangian Coherent Structures (LCSs) in the large scale wind field. The detected LCSs represent lines of attraction in the evolving flow with a significant impact on all passive tracers. Using Finite-Time Lyapunov Exponents, we extract LCSs from a two-dimensional flow derived from water vapor flux of atmospheric reanalysis data and compare them to the three-dimensional LCS obtained from the wind flow. We correlate the typical filamentous water vapor patterns of ARs with LCSs and find that LCSs bound the filaments on the back side. Passive advective transport of water vapor in the AR from tropical latitudes is potentially possible.
Interaction of a finite-span synthetic jet near the tip of a sweptback wing
Authors: Vasile Joseph D. , Amitay Michael
Published: June 2015

An experimental investigation was performed to study the three-dimensional flow interaction of a finite-span (aspect ratio of 18) synthetic jet located near the tip of a sweptback wing (cross-sectional profile of NACA 4421, aspect ratio of 4, and sweep angle of 30°) at a Reynolds number of 105 and at three angles of attack of 0°, 9°, and 15.5° (covering the range of attached to separated flow in the vicinity of the synthetic jet). Three blowing ratios were considered as 0.8, 1.2, and 2. Stereoscopic particle image velocimetry data were collected at multiple 2-D planes in the vicinity of the jet’s orifice, which were then used to reconstruct the flow volume, and the effect of the jet’s blowing ratio was analyzed using time-averaged and phase-averaged statistics. The study showed that the flow field in the vicinity of the synthetic jet orifice becomes highly three-dimensional and is governed by the streamwise structures that are associated with the finite span of the orifice (edge vortices). Furthermore, it was demonstrated that the baseline flow field that develops over a swept-back configuration (characterized by spanwise and streamwise vorticity components) is responsible for the immediate breakdown of the coherent structures that are introduced by the synthetic jet orifice and for the formation of the secondary flow structures that were seen in the time-averaged flow field. Moreover, the presence of a tip vortex results in the development of a non-uniform (in the spanwise direction) spanwise boundary layer that becomes more pronounced with increasing angle of attack. Consequently, the development of the flow structures is altered. Finally, the present work suggests that the location of the synthetic jet along the span is not as important (as the angle of attack and the blowing ratio) in the overall formation and evolution of the flow structures issued from the jet. However, the size and strength of these structures are affected by the jet’s spanwise location.
Beyond the single-file fluid limit using transfer matrix method: Exact results for confined parallel hard squares
Authors: Gurin Péter , Varga Szabolcs
Published: June 2015

We extend the transfer matrix method of one-dimensional hard core fluids placed between confining walls for that case where the particles can pass each other and at most two layers can form. We derive an eigenvalue equation for a quasi-one-dimensional system of hard squares confined between two parallel walls, where the pore width is between σ and 3σ (σ is the side length of the square). The exact equation of state and the nearest neighbor distribution functions show three different structures: a fluid phase with one layer, a fluid phase with two layers, and a solid-like structure where the fluid layers are strongly correlated. The structural transition between differently ordered fluids develops continuously with increasing density, i.e., no thermodynamic phase transition occurs. The high density structure of the system consists of clusters with two layers which are broken with particles staying in the middle of the pore.
Mixed quantum-classical equilibrium in global flux surface hopping
Authors: Sifain Andrew E. , Wang Linjun , Prezhdo Oleg V.
Published: June 2015

Global flux surface hopping (GFSH) generalizes fewest switches surface hopping (FSSH)—one of the most popular approaches to nonadiabatic molecular dynamics—for processes exhibiting superexchange. We show that GFSH satisfies detailed balance and leads to thermodynamic equilibrium with accuracy similar to FSSH. This feature is particularly important when studying electron-vibrational relaxation and phonon-assisted transport. By studying the dynamics in a three-level quantum system coupled to a classical atom in contact with a classical bath, we demonstrate that both FSSH and GFSH achieve the Boltzmann state populations. Thermal equilibrium is attained significantly faster with GFSH, since it accurately represents the superexchange process. GFSH converges closer to the Boltzmann averages than FSSH and exhibits significantly smaller statistical errors.
Tracking stochastic resonance curves using an assisted reference model
Authors: Calderón Ramírez Mario , Rico Martínez Ramiro , Ramírez Álvarez Elizeth , Parmananda P.
Published: June 2015

The optimal noise amplitude for Stochastic Resonance (SR) is located employing an Artificial Neural Network (ANN) reference model with a nonlinear predictive capability. A modified Kalman Filter (KF) was coupled to this reference model in order to compensate for semi-quantitative forecast errors. Three manifestations of stochastic resonance, namely, Periodic Stochastic Resonance (PSR), Aperiodic Stochastic Resonance (ASR), and finally Coherence Resonance (CR) were considered. Using noise amplitude as the control parameter, for the case of PSR and ASR, the cross-correlation curve between the sub-threshold input signal and the system response is tracked. However, using the same parameter the Normalized Variance curve is tracked for the case of CR. The goal of the present work is to track these curves and converge to their respective extremal points. The ANN reference model strategy captures and subsequently predicts the nonlinear features of the model system while the KF compensates for the perturbations inherent to the superimposed noise. This technique, implemented in the FitzHugh-Nagumo model, enabled us to track the resonance curves and eventually locate their optimal (extremal) values. This would yield the optimal value of noise for the three manifestations of the SR phenomena.
Interfacial hydrodynamic instabilities driven by cross-diffusion in reverse microemulsions
Authors: Budroni M. A. , Carballido-Landeira J. , Intiso A. , De Wit A. , Rossi F.
Published: June 2015

When two microemulsions are put in contact in the gravity field along a horizontal contact line, cross-diffusion can trigger the transport of one species in the presence of a gradient in concentration of another species. We show here theoretically that such cross-diffusion effects can induce buoyancy-driven convective instabilities at the interface between two solutions of different compositions even when initially the less dense solution lies on top of the denser one. Two different sources of convective modes are identified depending whether positive or negative cross-diffusion is involved. We evidence the two predicted cross-diffusion driven instabilities experimentally using a two-layer stratification of Aerosol-OT (AOT) water-in-oil microemulsions solutions with different water or AOT composition.
Single walled carbon nanotube network—Tetrahedral amorphous carbon composite film
Authors: Iyer Ajai , Kaskela Antti , Johansson Leena-Sisko , Liu Xuwen , Kauppinen Esko I. , Koskinen Jari
Published: June 2015

Single walled carbon nanotube network (SWCNTN) was coated by tetrahedral amorphous carbon (ta-C) using a pulsed Filtered Cathodic Vacuum Arc system to form a SWCNTN—ta-C composite film. The effects of SWCNTN areal coverage density and ta-C coating thickness on the composite film properties were investigated. X-Ray photoelectron spectroscopy measurements prove the presence of high quality sp3 bonded ta-C coating on the SWCNTN. Raman spectroscopy suggests that the single wall carbon nanotubes (SWCNTs) forming the network survived encapsulation in the ta-C coating. Nano-mechanical testing suggests that the ta-C coated SWCNTN has superior wear performance compared to uncoated SWCNTN.
Localized absorption in aluminum mask in visible spectrum due to longitudinal modes in vertical silicon nanowire arrays
Authors: Dhindsa Navneet , Saini Simarjeet Singh
Published: June 2015

Localized optical absorption in aluminum masks used for vertical silicon nanowire fabrication is demonstrated experimentally and supported using computer simulations. The mask is in the form of 30 nm thick aluminum nano-disks on top of silicon nanowires arranged in square lattices. The nanowires are 1 μm long, with diameters ranging from 60 nm to 100 nm and spaced 400 nm apart. New spectral features appear in the 500 nm–700 nm wavelengths range and are dependent on both the nanowire diameter and length. The former is due to the excitation of radial modes, whereas the latter stems from longitudinal (Fabry–Perot) resonances. The salient features associated with absorption in the aluminum mask and the role nanowire plays in this connection are discussed.
On the vapor-liquid equilibrium of attractive chain fluids with variable degree of molecular flexibility
Authors: van Westen Thijs , Vlugt Thijs J. H. , Gross Joachim
Published: June 2015

We study the isotropic (vapor and liquid) phase behavior of attractive chain fluids. Special emphasis is placed on the role of molecular flexibility, which is studied by means of a rod-coil model. Two new equations of state (EoSs) are developed for square-well- (SW) and Lennard-Jones (LJ) chain fluids. The EoSs are developed by applying the perturbation theory of Barker and Henderson (BH) to a reference fluid of hard chain molecules. The novelty of the approach is based on (1) the use of a recently developed hard-chain reference EoS that explicitly incorporates the effects of molecular flexibility, (2) the use of recent molecular simulation data for the radial distribution function of hard-chain fluids, and (3) a newly developed effective segment size, which effectively accounts for the soft repulsion between segments of LJ chains. It is shown that the effective segment size needs to be temperature-, density-, and chain-length dependent. To obtain a simplified analytical EoS, the perturbation terms are fitted by polynomials in density (SW and LJ), chain length (SW and LJ), and temperature (only for LJ). It is shown that the equations of state result in an accurate description of molecular simulation data for vapor-liquid equilibria (VLE) and isotherms of fully flexible SW- and LJ chain fluids and their mixtures. To evaluate the performance of the equations of state in describing the effects of molecular flexibility on VLE, we present new Monte Carlo simulation results for the VLE of rigid linear- and partially flexible SW- and LJ chain fluids. For SW chains, the developed EoS is in a good agreement with simulation results. For increased rigidity of the chains, both theory and simulations predict an increase of the VL density difference and a slight increase of the VL critical temperature. For LJ chains, the EoS proves incapable of reproducing part of these trends.
Getting the most from gene delivery by repeated DNA transfections
Authors: Montani Maura , Marchini Cristina , Badillo Pazmay Gretta Veronica , Andreani Cristina , Bartolacci Caterina , Amici Augusto , Pozzi Daniela , Caracciolo Giulio
Published: June 2015

Intracellular delivery of reporter genes causes cells to be luminescent or fluorescent, this condition being of tremendous relevance in applied physics research. Potential applications range from the study of spatial distribution and dynamics of plasma membrane and cytosolic proteins up to the rational design of nanocarriers for gene therapy. Since efficiency of gene delivery is the main limit in most biophysical studies, versatile methods that can maximize gene expression are urgently needed. Here, we describe a robust methodology based on repeated gene delivery in mammalian cells. We find this procedure to be much more efficient than the more traditional route of gene delivery making it possible to get high-quality data without affecting cell viability. Implications for biophysical investigations are discussed.
Photon energy dependence of photo-induced inverse spin-Hall effect in Pt/GaAs and Pt/Ge
Authors: Isella Giovanni , Bottegoni Federico , Ferrari Alberto , Finazzi Marco , Ciccacci Franco
Published: June 2015

We report the photon energy dependence of photo-induced inverse spin Hall effect (ISHE) in Pt/GaAs and Pt/Ge Schottky junctions. The experimental results are compared with a spin drift-diffusion model, which highlights the role played by the different spin lifetime in the two semiconductors, in determining the energy dependence of the ISHE signal detected in the Pt layer. The good qualitative agreement between experiments and modelling indicates that photo-induced ISHE can be used as a tool to characterize spin lifetime in semiconductors.
Flexible semi-around gate silicon nanowire tunnel transistors with a sub-kT/q switch
Authors: Lee Myeongwon , Jeon Youngin , Kim Minsuk , Kim Sangsig
Published: June 2015

Tunnel field-effect transistors (TFETs) with a subthreshold swing (SS) < 60 mV/dec are expected to be active devices in low-power flexible systems, potentially lowering operational voltage by virtue of steep switching behavior via band-to-band tunneling. In silicon (Si) channel materials, however, it still remains a challenge to obtain SS smaller than 60 mV/dec. In this study, we experimentally demonstrate the sub-60 mV/dec operation of a flexible semi-around gate TFET on a plastic substrate using Si nanowires (SiNWs) as the channel material. With the combined advantages of selectively thinned SiNW channels (width ∼ 15 nm and height ∼ 40 nm) and high-κ (Al2O3 ∼ 7 nm) gate dielectric, in conjunction with an abrupt degenerate source junction, the device with a channel length of ∼500 nm exhibits a minimal SS of ∼42 mV/dec at room temperature. Moreover, mechanical bendability of the device indicates that it has stable and good fatigue properties, providing an important step towards the realization of steep-slope switches for low-power and energy-efficient flexible electronics.
High efficiency Schottky junction solar cells by co-doping of graphene with gold nanoparticles and nitric acid
Authors: Liu X. , Zhang X. W. , Meng J. H. , Yin Z. G. , Zhang L. Q. , Wang H. L. , Wu J. L.
Published: June 2015

We have reported an effective method to enhance the efficiency of graphene-on-Si (Gr/Si) Schottky junction solar cells by co-doping of graphene with Au nanoparticles (NPs) and HNO3. Both Au NPs decoration and HNO3 treatment lead to p-type doping of graphene, and their combination is confirmed to be a more effective approach for achieving the higher work function and enhanced electrical conductivity of graphene. Consequently, the power conversion efficiency of Gr/Si solar cells is increased by 2.6 times, with a maximum value of 10.20%. This work suggests that the co-doping might be a promising way to realize high performance Gr/Si solar cells.
Strain dependence on polarization properties of AlGaN and AlGaN-based ultraviolet lasers grown on AlN substrates
Authors: Bryan Zachary , Bryan Isaac , Mita Seiji , Tweedie James , Sitar Zlatko , Collazo Ramón
Published: June 2015

Since the band ordering in AlGaN has a profound effect on the performance of UVC light emitting diodes (LEDs) and even determines the feasibility of surface emitting lasers, the polarization properties of emitted light from c-oriented AlGaN and AlGaN-based laser structures were studied over the whole composition range, as well as various strain states, quantum confinements, and carrier densities. A quantitative relationship between the theoretical valence band separation, determined using k•p theory, and the experimentally measured degree of polarization is presented. Next to composition, strain was found to have the largest influence on the degree of polarization while all other factors were practically insignificant. The lowest crossover point from the transverse electric to transverse magnetic polarized emission of 245 nm was found for structures pseudomorphically grown on AlN substrates. This finding has significant implications toward the efficiency and feasibility of surface emitting devices below this wavelength.
A nanoscale temperature-dependent heterogeneous nucleation theory
Authors: Cao Y. Y. , Yang G. W.
Published: June 2015

Classical nucleation theory relies on the hypothetical equilibrium of the whole nucleation system, and neglects the thermal fluctuations of the surface; this is because the high entropic gains of the (thermodynamically extensive) surface would lead to multiple stable states. In fact, at the nanometer scale, the entropic gains of the surface are high enough to destroy the stability of the thermal equilibrium during nucleation, comparing with the whole system. We developed a temperature-dependent nucleation theory to elucidate the heterogeneous nucleation process, by considering the thermal fluctuations based on classical nucleation theory. It was found that the temperature not only affected the phase transformation, but also influenced the surface energy of the nuclei. With changes in the Gibbs free energy barrier, nucleation behaviors, such as the nucleation rate and the critical radius of the nuclei, showed temperature-dependent characteristics that were different from those predicted by classical nucleation theory. The temperature-dependent surface energy density of a nucleus was deduced based on our theoretical model. The agreement between the theoretical and experimental results suggested that the developed nucleation theory has the potential to contribute to the understanding and design of heterogeneous nucleation at the nanoscale.
An extremely wideband and lightweight metamaterial absorber
Authors: Shen Yang , Pei Zhibin , Pang Yongqiang , Wang Jiafu , Zhang Anxue , Qu Shaobo
Published: June 2015

This paper presents a three-dimensional microwave metamaterial absorber based on the stand-up resistive film patch array. The absorber has wideband absorption, lightweight, and polarization-independent properties. Our design comes from the array of unidirectional stand-up resistive film patches backed by a metallic plane, which can excite multiple standing wave modes. By rolling the resistive film patches as a square enclosure, we obtain the polarization-independent property. Due to the multiple standing wave modes, the most incident energy is dissipated by the resistive film patches, and thus, the ultra-wideband absorption can be achieved by overlapping all the absorption modes at different frequencies. Both the simulated and experimental results show that the absorber possesses a fractional bandwidth of 148.2% with the absorption above 90% in the frequency range from 3.9 to 26.2 GHz. Moreover, the proposed absorber is extremely lightweight. The areal density of the fabricated sample is about 0.062 g/cm2, which is approximately equivalent to that of eight stacked standard A4 office papers. It is expected that our proposed absorber may find potential applications such as electromagnetic interference and stealth technologies.
Contingency and entrenchment in protein evolution under purifying selection
Authors: Shah Premal , McCandlish David M. , Plotkin Joshua B.
Published: June 2015

Significance

How large a role does history play in evolution? Do later events depend critically on specific earlier events, or do all events occur more or less independently? If a change occurs early in evolution, does it become easier or harder to revert the change as time proceeds? Here, we explore these ideas in the context of protein evolution, by simulating sequence evolution under purifying selection and then systematically permuting the order of amino acid substitutions. Our results suggest that the amino acid substitutions that occur in evolution are typically contingent on the presence of prior substitutions, and that substitutions that occur early in evolution become entrenched and difficult to modify as subsequent substitutions accrue.
Optogenetic stimulation of infralimbic PFC reproduces ketamine’s rapid and sustained antidepressant actions
Authors: Fuchikami Manabu , Thomas Alexandra , Liu Rongjian , Wohleb Eric S. , Land Benjamin B. , DiLeone Ralph J. , Aghajanian George K. , Duman Ronald S.
Published: June 2015

Significance

Clinical studies report that a single, low dose of ketamine produces a rapid antidepressant response in treatment-resistant depressed patients. Although rodent studies have begun to elucidate the molecular mechanisms underlying the behavioral actions of ketamine, the brain regions and cellular mechanisms have not been defined. Using a combination of pharmacological silencing and optogenetic stimulation approaches, the results of the current study demonstrate that ketamine infusion or optogenetic stimulation of the infalimbic prefrontal cortex produces antidepressant behavioral and synaptic responses similar to the actions of systemic ketamine. These findings further elucidate the mechanisms underlying the therapeutic actions of ketamine and will enhance the development of safer rapid-acting and efficacious agents.
Altered thalamocortical rhythmicity and connectivity in mice lacking Ca
V
3.1 T-type Ca
2+
channels in unconsciousness
Authors: Choi Soonwook , Yu Eunah , Lee Seongwon , Llinás Rodolfo R.
Published: June 2015

Significance

Defining the neuronal activity underlying unconscious states is a fundamental prerequisite to understanding cognitive brain function. The present findings indicate that the neuronal activity associated with unconsciousness is directly related to the voltage-gated ionic conductances supporting thalamic low-frequency electrical oscillations. In particular, voltage-gated calcium channels are important players in the generation of prolonged unconsciousness. Thus, mice with a deletion of voltage-gated Ca
V
3.1 channels are incapable of maintaining the low-frequency oscillatory activity associated with unconsciousness. These results indicate that Ca
V
3.1, though functionally very significant in the generation of physiological unconsciousness, is not the only channel involved in the generation of the low-frequency spontaneous brain activity that supports nonpathological unconsciousness.
Establishing task- and modality-dependent dissociations between the semantic and default mode networks
Authors: Humphreys Gina F. , Hoffman Paul , Visser Maya , Binney Richard J. , Lambon Ralph Matthew A.
Published: June 2015

Significance

Functional neuroimaging has established that most cognitive functions are supported by distributed neural networks. Hundreds of studies have investigated the semantic network (SN) and the default mode network (DMN) (neural deactivation when undertaking a variety of tasks). These stable networks are increasingly used as biomarkers in neurological and psychiatric investigations. Despite implicating overlapping neural regions and shared cognitive mechanisms, the relationship between the two networks has received minimal attention. Analyses of a large multitask distortion-corrected functional MRI (fMRI) dataset established that both networks fractionate, depending on the semantic nature of the task, stimulus type, modality, and task difficulty. The implications for the SN, variability in the DMN and its cognitive coherence, and interpretation of resting-state fMRI data are discussed.
Caffeine acts through neuronal adenosine A
2A
receptors to prevent mood and memory dysfunction triggered by chronic stress
Authors: Kaster Manuella P. , Machado Nuno J. , Silva Henrique B. , Nunes Ana , Ardais Ana Paula , Santana Magda , Baqi Younis , Müller Christa E. , Rodrigues Ana Lúcia S. , Porciúncula Lisiane O. , Chen Jiang Fan , Tomé Ângelo R. , Agostinho Paula , Canas Paula M. , Cunha Rodrigo A.
Published: June 2015

Significance

Epidemiological studies show that individuals exposed to repeated stress, a major trigger of depression, increase their caffeine intake, which correlates inversely with the incidence of depression. However, the mechanism underlying this protective effect is unknown. We used an animal model of chronic unpredictable stress (CUS) to show that caffeine prevents the maladaptive changes caused by CUS in a manner mimicked by the selective blockade of adenosine A
2A
receptors (A
2A
R). CUS enhanced A
2A
R in synapses, and the selective elimination of neuronal A
2A
R abrogated CUS modifications. Moreover, A
2A
R blockade also afforded a therapeutic benefit, paving the way to consider A
2A
R blockers as a strategy to manage the negative impact of chronic stress on mood and memory.
A simple nutrient-dependence mechanism for predicting the stoichiometry of marine ecosystems
Authors: Galbraith Eric D. , Martiny Adam C.
Published: June 2015

Significance

The elemental ratios of nitrogen, phosphorus, and carbon in marine phytoplankton can diverge significantly from the “Redfield ratio,” but the underlying reasons have been hard to elucidate. As a result, global biogeochemical models often ignore this stoichiometric variability. Here we show that, hidden within the noise of a large dataset of particulate measurements, a surprisingly consistent relationship exists between community P:C and dissolved phosphate concentrations. The plasticity of ecosystem stoichiometry in the face of nutrient scarcity, with greater plasticity for P relative to N, appears to explain the main divergences from the Redfield ratio. When included in a simple model, the relationship implies a more important role for low latitude nutrient cycling in the biological pump than is commonly assumed.
Disregulated expression of the transcription factor ThPOK during T-cell development leads to high incidence of T-cell lymphomas
Authors: Lee Hyung-Ok , He Xiao , Mookerjee-Basu Jayati , Zhongping Dai , Hua Xiang , Nicolas Emmanuelle , Sulis Maria Luisa , Ferrando Adolfo A. , Testa Joseph R. , Kappes Dietmar J.
Published: June 2015

Significance

We demonstrate a novel and unexpected role of the transcription factor ThPOK as a potent oncogene in mice. During normal T-cell development, T-helper-inducing POZ/Krueppel-like factor (ThPOK) is selectively expressed in thymocytes developing to the CD4 lineage and is necessary for their differentiation. However, when ThPOK is expressed indiscriminately in all thymocytes, it causes highly penetrant thymic lymphoma. Strong T-cell receptor (TCR) signal rescues thymocytes from ThPOK-dependent lymphoma development, whereas weak signals promote lymphomagenesis. These results demonstrate a novel correlation between ThPOK, TCR signal strength, and lymphomagenesis. We also present evidence that ectopic ThPOK expression gives rise to a preleukemic and self-perpetuating precursor population, akin to a tumor stem cell.
Inference of transcriptional regulation in cancers
Authors: Jiang Peng , Freedman Matthew L. , Liu Jun S. , Liu Xiaole Shirley
Published: June 2015

Significance

We developed an efficient and accurate computational framework, RABIT (regression analysis with background integration), and comprehensively integrated public transcription factor (TF)-binding profiles with TCGA tumor-profiling datasets in 18 cancer types. To systematically search for cancer-associated TFs, RABIT controls the effect of tumor-confounding factors on transcriptional regulation, such as copy number alteration, DNA methylation, and TF somatic mutation. Our predicted TF regulatory activity in tumors is highly consistent with the knowledge from cancer gene databases and reveals many previously unidentified cancer-associated TFs. We also analyzed RNA-binding protein regulation in cancer and demonstrated that RABIT is a general platform for predicting oncogenic gene expression regulators.
Cooperative folding of a polytopic α-helical membrane protein involves a compact N-terminal nucleus and nonnative loops
Authors: Paslawski Wojciech , Lillelund Ove K. , Kristensen Julie Veje , Schafer Nicholas P. , Baker Rosanna P. , Urban Sinisa , Otzen Daniel E.
Published: June 2015

Significance

How a protein folds in a membrane is a problem of central biological significance. Although extensively investigated for globular proteins, there are very limited data available for membrane proteins due to the difficulties of finding a tractable model system. We present a study of the folding of a six-transmembrane helix protein, the rhomboid protease GlpG, which folds according to a two-state model in a membrane-mimicking mixed micelle surfactant system. By recording the kinetics of folding and unfolding of 69 GlpG mutants and performing an extensive ϕ-value analysis, we propose a folding mechanism and discuss its possible interpretations and implications. These data serve as an excellent starting point for computational studies of membrane protein folding mechanisms and kinetics.
GABA
B
receptor deficiency causes failure of neuronal homeostasis in hippocampal networks
Authors: Vertkin Irena , Styr Boaz , Slomowitz Edden , Ofir Nir , Shapira Ilana , Berner David , Fedorova Tatiana , Laviv Tal , Barak-Broner Noa , Greitzer-Antes Dafna , Gassmann Martin , Bettler Bernhard , Lotan Ilana , Slutsky Inna
Published: June 2015

Significance

How neuronal circuits maintain stable activity despite continuous environmental changes is one of the most intriguing questions in neuroscience. Previous studies proposed that deficits in homeostatic control systems may underlie common neurological symptoms in a variety of brain disorders. However, the key regulatory molecules that control homeostasis of central neural circuits remain obscure. We show here that basal activity of GABA
B
receptors is required for firing rate homeostasis in hippocampal networks. We identified the principal mechanisms by which GABA
B
receptors control homeostatic augmentation of synaptic strength to chronic neuronal silencing. We propose that deficits in GABA
B
receptor signaling, associated with epilepsy and psychiatric disorders, may lead to aberrant brain activity by erasing homeostatic plasticity.
Host lysozyme-mediated lysis of
Lactococcus lactis
facilitates delivery of colitis-attenuating superoxide dismutase to inflamed colons
Authors: Ballal Sonia A. , Veiga Patrick , Fenn Kathrin , Michaud Monia , Kim Jason H. , Gallini Carey Ann , Glickman Jonathan N. , Quéré Gaëlle , Garault Peggy , Béal Chloé , Derrien Muriel , Courtin Pascal , Kulakauskas Saulius , Chapot-Chartier Marie-Pierre , van Hylckama Vlieg Johan , Garrett Wendy S.
Published: June 2015

Significance

Microbes hold promise as an inflammatory bowel disease (IBD) therapy.
Lactococcus lactis
, which has not been appreciated as a beneficial microbe, attenuated colitis in three preclinical mouse IBD models. Neither colonization nor an intact bacterium throughout the colon per se was required. Rather, host lysozyme-mediated lysis in an inflamed colon led to
L. lactis
’s release of its superoxide dismutase, which was necessary for its colitis-attenuating and oxidative stress-reducing activity. Overall, these findings unveil a mechanism by which a bacterium offers benefits to the host but requires the host for targeted release of this beneficial activity. Furthermore, because
L. lactis
is generally regarded as safe, it represents an opportunity for rapid bench-to-bedside testing in IBD.
Climate mediates hypoxic stress on fish diversity and nursery function at the land–sea interface
Authors: Hughes Brent B. , Levey Matthew D. , Fountain Monique C. , Carlisle Aaron B. , Chavez Francisco P. , Gleason Mary G.
Published: June 2015

Significance

Human populations are rapidly expanding along Earth's coastlines, increasing stress to coastal ecosystems and the services they provide. One of these stressors comes from an increase in nutrient inputs from coastal land development that can enter estuaries and coastal seas leading to algal blooms that deplete oxygen from the water, a condition known as hypoxia. In this study, we investigated how coastal hypoxia influences fish diversity, the nursery habitat for juvenile fish, and fisheries production in adjacent offshore waters. We found that severity in hypoxia corresponded with declines to fish diversity, nursery quality, and offshore fisheries. Furthermore, intensification of El Niño mediated hypoxia by improving dissolved oxygen conditions, demonstrating that climate can influence anthropogenic stressors affecting coastal ecosystem services.
Novel pathways for fuels and lubricants from biomass optimized using life-cycle greenhouse gas assessment
Authors: Balakrishnan Madhesan , Sacia Eric R. , Sreekumar Sanil , Gunbas Gorkem , Gokhale Amit A. , Scown Corinne D. , Toste F. Dean , Bell Alexis T.
Published: June 2015

Significance

The development of renewable liquid fuels and bioproducts is critical to reducing global reliance on petroleum and mitigating climate change, particularly for applications where few low-carbon alternatives exist. We combine chemical catalysis with life-cycle greenhouse gas (GHG) modeling to create a new platform for producing biobased aviation fuel and automotive lubricant base oils. The recyclable catalysts we developed are capable of converting sugar and biomass-derived alkyl methyl ketones into cyclic enones via condensation reactions. These products can subsequently be hydrodeoxygenated to create a new class of aviation fuel and lubricant candidates with superior cold flow properties, density, and viscosity that substantially reduce GHG emissions relative to conventional petroleum.
Transcriptional modulator
ZBED6
affects cell cycle and growth of human colorectal cancer cells
Authors: Akhtar Ali Muhammad , Younis Shady , Wallerman Ola , Gupta Rajesh , Andersson Leif , Sjöblom Tobias
Published: June 2015

Significance

The
ZBED6
(zinc finger, BED-type containing 6) transcription factor is unique to placental mammals. Its high degree of sequence conservation among placental mammals indicates that it has an essential function. Using two colorectal cancer cell lines we have, for the first time to our knowledge, completely inactivated ZBED6 by genome editing. Our results demonstrate that ZBED6 is not required for cell survival, but its ablation led to consistent changes in cell growth within cell lines but opposite trends between cell lines. The results are in line with the hypothesis that ZBED6 is a transcriptional modulator that does not determine whether or not its target genes are active but fine-tunes their expression. Thus, its effect on tumorigenesis will depend on the transcriptional state of the cell.
The notion of contextual locking: Previously learnt items are not accessible as such when appearing in a less common context
Authors: Perlman Amotz , Hoffman Yaakov , Tzelgov Joseph , Pothos Emmanuel M. , Edwards Darren J.
Published: June 2015

We examined the effect of context on the learning of spatial coding in four experiments. Two partially overlapping sets of stimuli, which had the very same stimulus–response spatial coding, were presented in unique contexts. Results show contextual locking—that is, response times to the very same item in a more common context (80%) were significantly shorter than those in a less common context (20%). Contextual locking was obtained both when the context was more salient (Experiments 1 and 2) and less salient (Experiments 3 and 4). In addition, results were obtained even when contextualization seemed less necessary (Experiments 2 and 4). Binding of information to context is discussed in relation to chunking, transfer effects, and practical applications pertaining to professional training.
The effect of identical word pairs on people's metamemory judgments: What are the contributions of processing fluency and beliefs about memory?
Authors: Mueller Michael L. , Dunlosky John , Tauber Sarah K.
Published: June 2015

Judgments of learning (JOLs) are higher for identical pairs (dog–dog) than for related pairs (dog–cat). This identical effect may be mediated (a) by processing fluency (i.e., identical pairs are processed faster than related pairs) or (b) by a belief that identical pairs are better remembered or (c) by both factors. In the present work, we assessed the contribution of both factors. We evaluated whether a measure of processing fluency (i.e., self-paced study) mediated the relationship between pair type and JOLs (Experiment 1) and attempted to disrupt processing fluency using an AlTeRnAtInG presentation format (Experiment 2). We also evaluated whether judgments made in the absence of processing fluency demonstrated the identical effect (Experiment 3), and, finally, we had participants read a vignette about an experiment that included both pair types and estimate which pairs would be best remembered (Experiment 4). Evidence from all experiments converged on the conclusion that people's beliefs about how variables affect memory—and not differential fluency—best explain the identical effect, although we cannot entirely rule out the possibility that fluency plays a small role. The outcomes were consistent with the analytic-processing theory of JOLs—namely, when instructed to make JOLs, people adopt an analytic problem-solving approach that involves identifying variation across pairs that plausibly relate to memory and then use this variation to make JOLs.
High-resolution view of the spring bloom initiation and net community production in the Subantarctic Southern Ocean using glider data
Authors: Thomalla Sandy J. , Racault Marie-Fanny , Swart Sebastiaan , Monteiro Pedro M. S.
Published: June 2015

In the Southern Ocean, there is increasing evidence that seasonal to subseasonal temporal scales, and meso- to submesoscales play an important role in understanding the sensitivity of ocean primary productivity to climate change. This drives the need for a high-resolution approach to resolving biogeochemical processes. In this study, 5.5 months of continuous, high-resolution (3 h, 2 km horizontal resolution) glider data from spring to summer in the Atlantic Subantarctic Zone is used to investigate: (i) the mechanisms that drive bloom initiation and high growth rates in the region and (ii) the seasonal evolution of water column production and respiration. Bloom initiation dates were analysed in the context of upper ocean boundary layer physics highlighting sensitivities of different bloom detection methods to different environmental processes. Model results show that in early spring (September to mid-November) increased rates of net community production (NCP) are strongly affected by meso- to submesoscale features. In late spring/early summer (late-November to mid-December) seasonal shoaling of the mixed layer drives a more spatially homogenous bloom with maximum rates of NCP and chlorophyll biomass. A comparison of biomass accumulation rates with a study in the North Atlantic highlights the sensitivity of phytoplankton growth to fine-scale dynamics and emphasizes the need to sample the ocean at high resolution to accurately resolve phytoplankton phenology and improve our ability to estimate the sensitivity of the biological carbon pump to climate change.
Analysis Situs, the Foundations of Mathematics, and a Geometry of Space
Authors: Risi Vincenzo De
Published: June 2015

This chapter focuses on Gottfried Wilhelm Leibniz’s writings on analysis situs—a collection of mathematical and philosophical investigations into the foundations, development, and formalization of geometry, examining how they contributed to the development of modern geometry. It first explains the concept of situation (situs) as the first source of Leibniz’s theory of a relational space and its use in metaphysics, then considers Leibniz’s development of a new formalism for geometry (a characteristica geometrica propria) and his use of (Euclidean) metric relations between figures or points as the main subject of his analysis situs. It also discusses Leibniz’s definition of space as an order of situations, his grand ambition to establish the principles of Euclidean geometry based on the abstract concept of a metric space, and how his writings on analysis situs became intertwined with metaphysics and the theory of knowledge. Finally, the chapter reviews Leibniz’s definition of space in relation to monads and bodies.
Happiness and Justice
Authors: Brown Gregory
Published: June 2015

This chapter focuses on Gottfried Wilhelm Leibniz’s philosophical reflections on happiness and justice. It begins with a discussion of the two central concepts of Leibniz’s moral theory: disinterested love and love (or charity) of the wise. It then looks at Leibniz’s efforts to ground the happiness of man in virtue and the good of others, as well as his views about the good that moves us to act. Leibniz argues that it is our perfection that constitutes our happiness, and that we can—and morally ought to—desire the good of others for its own sake. This chapter also analyzes Leibniz’s views on the motivations underlying just action, together with pleasure and perfection of the mind in relation to love and happiness.
Downsizing a giant: re-evaluating
Dreadnoughtus
body mass
Authors: Bates Karl T. , Falkingham Peter L. , Macaulay Sophie , Brassey Charlotte , Maidment Susannah C. R.
Published: June 2015

Estimates of body mass often represent the founding assumption on which biomechanical and macroevolutionary hypotheses are based. Recently, a scaling equation was applied to a newly discovered titanosaurian sauropod dinosaur (
Dreadnoughtus
), yielding a 59 300 kg body mass estimate for this animal. Herein, we use a modelling approach to examine the plausibility of this mass estimate for
Dreadnoughtus
. We find that 59 300 kg for
Dreadnoughtus
is highly implausible and demonstrate that masses above 40 000 kg require high body densities and expansions of soft tissue volume outside the skeleton several times greater than found in living quadrupedal mammals. Similar results from a small sample of other archosaurs suggests that lower-end mass estimates derived from scaling equations are most plausible for
Dreadnoughtus
, based on existing volumetric and density data from extant animals. Although volumetric models appear to more tightly constrain dinosaur body mass, there remains a clear need to further support these models with more exhaustive data from living animals. The relative and absolute discrepancies in mass predictions between volumetric models and scaling equations also indicate a need to systematically compare predictions across a wide size and taxonomic range to better inform studies of dinosaur body size.
Tensor methods for parameter estimation and bifurcation analysis of stochastic reaction networks
Authors: Liao Shuohao , Vejchodský Tomáš , Erban Radek
Published: June 2015

Stochastic modelling of gene regulatory networks provides an indispensable tool for understanding how random events at the molecular level influence cellular functions. A common challenge of stochastic models is to calibrate a large number of model parameters against the experimental data. Another difficulty is to study how the behaviour of a stochastic model depends on its parameters, i.e. whether a change in model parameters can lead to a significant qualitative change in model behaviour (bifurcation). In this paper, tensor-structured parametric analysis (TPA) is developed to address these computational challenges. It is based on recently proposed low-parametric tensor-structured representations of classical matrices and vectors. This approach enables simultaneous computation of the model properties for all parameter values within a parameter space. The TPA is illustrated by studying the parameter estimation, robustness, sensitivity and bifurcation structure in stochastic models of biochemical networks. A Matlab implementation of the TPA is available at
http://www.stobifan.org
.