bluuebunny/crossref_metadata_2025 huggingface dataset:
Microphysical transition in water clouds over the Amazon and China derived from space‐borne radar and radiometer data
Authors: Kawamoto Kazuaki , Suzuki Kentaroh
Published: January 2012

This study examines the transitional processes and relationships among cloud droplets, drizzle, and precipitation in single‐layer water clouds over the Amazon and China by synergistically analyzing products of active CloudSat and passive Moderate Resolution Imaging Spectroradiometer sensors. Cloud droplet number concentrations (Nc) are confirmed to generally be lower over the Amazon and higher over China, reflecting the difference in aerosol amount between these two regions at different seasons. Radar reflectivity (Ze) frequencies are consistent with the regional and seasonal differences in precipitation rate. Furthermore, the fractional occurrences of maximum Ze as a function of liquid water path (LWP) show an almost monotonic decline and increase for nonprecipitating and precipitating categories, respectively, denoting differences in the precipitation rate. The behavior of cloud parameters such as the cloud optical depth, effective particle radius, Nc, and LWP among different Ze categories indicates the cloud development stage and reveals regional differences in the microphysical characteristics. Finally, a vertical cloud structure is examined to illustrate that water clouds tend to become optically thinner and to produce precipitation (shifting to larger Ze) through the coalescence of droplets as Nc decreases. Regionally, precipitation over the Amazon takes place in optically thicker parts than over China.
Ghrelin Mediates Anticipation to a Palatable Meal in Rats
Authors: Merkestein Myrte , Brans Maike A.D. , Luijendijk Mieneke C.M. , de Jong Johannes W. , Egecioglu Emil , Dickson Suzanne L. , Adan Roger A.H.
Published: January 2012

Food anticipatory activity (FAA) is displayed in rats when access to food is restricted to a specific time frame of their circadian phase, a behavior thought to reflect both hunger and the motivation to eat. Rats also display FAA in a feeding schedule with ad libitum access to normal chow, but limited availability of a palatable meal, which is thought to involve mainly motivational aspects. The orexigenic hormone ghrelin has been implicated in FAA in rodents with restricted access to chow. Because ghrelin plays an important role not only in the control of food intake, but also in reward, we sought to determine the role of ghrelin in anticipation to a palatable meal. Plasma ghrelin levels of non‐restricted rats that anticipated chocolate correlated positively with FAA and were increased compared with chow‐fed control rats. Furthermore, centrally injected ghrelin increased, whereas an antagonist of the ghrelin receptor decreased, the anticipation to chocolate. Therefore, we hypothesize that central ghrelin signaling is able to mediate the motivational drive to eat.
Angiotensin-converting enzyme 2 regulates renal atrial natriuretic peptide through angiotensin-(1–7)
Authors: Bernardi Stella , Burns Wendy C. , Toffoli Barbara , Pickering Raelene , Sakoda Maryio , Tsorotes Despina , Grixti Edward , Velkoska Elena , Burrell Louise M. , Johnston Colin , Thomas Merlin C. , Fabris Bruno , Tikellis Christos
Published: January 2012

Deficiency of ACE2 (angiotensin-converting enzyme 2), which degrades Ang (angiotensin) II, promotes the development of glomerular lesions. However, the mechanisms explaining why the reduction in ACE2 is associated with the development of glomerular lesions have still to be fully clarified. We hypothesized that ACE2 may regulate the renoprotective actions of ANP (atrial natriuretic peptide). The aim of the present study was to investigate the effect of ACE2 deficiency on the renal production of ANP. We evaluated molecular and structural abnormalities, as well as the expression of ANP in the kidneys of ACE2-deficient mice and C57BL/6 mice. We also exposed renal tubular cells to AngII and Ang-(1–7) in the presence and absence of inhibitors and agonists of RAS (renin–angiotensin system) signalling. ACE2 deficiency resulted in increased oxidative stress, as well as pro-inflammatory and profibrotic changes. This was associated with a down-regulation of the gene and protein expression on the renal production of ANP. Consistent with a role for the ACE2 pathway in modulating ANP, exposing cells to either Ang-(1–7) or ACE2 or the Mas receptor agonist up-regulated ANP gene expression. This work demonstrates that ACE2 regulates renal ANP via the generation of Ang-(1–7). This is a new mechanism whereby ACE2 counterbalances the renal effects of AngII and which explains why targeting ACE2 may be a promising strategy against kidney diseases, including diabetic nephropathy.
Surgical Treatment of the Atrophic Mandibular Fractures by Locked Plates Systems: Our Experience and a Literature Review
Authors: Novelli Giorgio , Sconza Cristiano , Ardito Emanuela , Bozzetti Alberto
Published: January 2012

The management of atrophic mandibular fractures in edentulous patients represents an insidious issue for the maxillofacial surgeon due to the biological and biomechanical conditions that are unfavorable for fracture fixation and bone healing. The purpose of this study was to evaluate the results of the treatment of atrophic mandibular fractures and to compare the outcomes of different plating systems used for stabilization. We selected a study group of 16 patients with fractures of completely edentulous atrophic mandibles who were treated in our department between 2004 and 2010. All patients were surgically treated by open reduction and internal rigid fixation using 2.0-mm large-profile locking and 2.4-mm locking bone plates. All patients achieved a complete fracture healing and fast functional recovery of mandibular movements without intraoperative or postoperative surgical complications. The results of our study demonstrated the efficacy of this type of treatment in association with a low postoperative complication rate, a reduction in the recovery time, and the possibility to have an immediately functional rehabilitation. There were very similar results using each of the two bone plating methods considered: no case had hardware failure or nonunion of the fracture. The 2.0-mm large locking plate is thinner, exposes through the soft tissues less frequently, and is much easier to shape and adapt to the mandibular anatomy. However, the 2.4-mm locking plate system still represents the reference hardware in the condition of severe bone atrophy.
Evidence for low-temperature antiferromagnetic phase transition in Ising singlet magnet KTb(WO4)2
Authors: Khatsko E. , Paulsen C. , Rykova A.
Published: January 2012

The magnetic susceptibility and magnetization measured along the b axis of a KTb(WO4)2 single crystal was investigated experimentally in the temperature range 70 mK–6 K and in magnetic fields up to 8 T. The results allow us to make conclusion that singlet magnet KTb(WO4)2 undergoes an antiferromagnetic phase transition Tc = 0.65 K.
In situ calibration of rotating sensor coils for magnet testing
Authors: Arpaia P. , Buzio M. , Golluccio G. , Walckiers L.
Published: January 2012

An in situ procedure for calibrating equivalent magnetic area and rotation radius of rotating coils is proposed for testing accelerator magnets shorter than the measuring coil. The procedure exploits measurements of magnetic field and mechanical displacement inside a reference quadrupole magnet. In a quadrupole field, an offset between the magnet and coil rotation axes gives rise to a dipole component in the field series expansion. The measurements of the focusing strength, the displacement, and the resulting dipole term allow the equivalent area and radius of the coil to be determined analytically. The procedure improves the accuracy of coils with large geometrical irregularities in the winding. This is essential for short magnets where the coil dimensions constrain the measurement accuracy. Experimental results on different coils measuring small-aperture permanent magnets are shown.
Anisotropic dynamics and sub-grid energy transfer in wall-turbulence
Authors: Cimarelli A. , De Angelis E.
Published: January 2012

Purpose of the present work is the analysis of the generalized Kolmogorov equation applied to the direct numerical simulation data of a turbulent channel flow. The multi-dimensional description of the anisotropic behavior of turbulent energy production, transport, and dissipation is shown to be relevant for the understanding and modeling of the wall-turbulent physics with special care to the phenomenon of reverse energy flux. These results are proven instrumental also for the correct computation of wall-turbulence when a large eddy simulation approach is considered. The capability of a filtered velocity field to correctly reproduce the wall-turbulent dynamics at different ranges of scales and wall-distances as a function of the filter length will be assessed via filtered direct numerical simulation (DNS) and large eddy simulation data. The possibility of new modeling approaches is also highlighted.
Synthesis of single-component metallic glasses by thermal spray of nanodroplets on amorphous substrates
Authors: An Qi , Luo Sheng-Nian , Goddard William A. , Han W. Z. , Arman B. , Johnson William L.
Published: January 2012

We show that single component metallic glasses can be synthesized by thermal spray coating of nanodroplets onto an amorphous substrate. We demonstrate this using molecular dynamics simulations of nanodroplets up to 30 nm that the spreading of the nanodroplets during impact on a substrate leads to sufficiently rapid cooling (1012–1013 K/s) sustained by the large temperature gradients between the thinned nanodroplets and the bulk substrate. However, even under these conditions, in order to ensure that the glass transition outruns crystal nucleation, it is essential that the substrate be amorphous (eliminating sites for heterogeneous nucleation of crystallization).
Influence on electrical characteristics of the design of 4H-SiC ultraviolet photodetectors: Theoretical analysis and simulations
Authors: Biondo Stéphane , Vervisch Wilfried , Ottaviani Laurent , Palais Olivier
Published: January 2012

This paper deals with the simulation of the reverse current density of 4H-SiC ultraviolet- (UV) photodetector devices based on p-i-n diodes. Simulations using the finite-element method presented in this paper lead to an understanding of the photodetector current density levels in dark field, as well as under UV exposure. The theoretical study coming from these simulations allows us to propose some UV-photodetector performance enhancements. A way to improve the UV-photodetector performance is to increase the current density at reverse bias. This study demonstrates the improvement in electrical characteristics achievable by either optical or electrical means. Optical simulations prove that an increase in photon harvesting is possible by using a specific patterned surface, a surface grating which behaves as a photonic crystal. In addition to the absorption enhancement achieved caused by this kind of surface, we point out wavelength selectivity. Nevertheless, the electrical simulation confirms that the electric field placement is of primary importance. To ensure that the photon absorption is carried out inside the space-charge region, the simulation study leads us to propose a UV-photodetector comprising a “flat-top pyramid” surface.
A new quasi-steady method to measure gas permeability of weakly permeable porous media
Authors: Jannot Yves , Lasseux Didier
Published: January 2012

A new quasi-steady method for the determination of the apparent gas permeability of porous materials is presented in this paper along with the corresponding interpretative physical model derived from the unsteady flow equations. This method is mainly dedicated to the measurement of very low permeability of thin porous media, although thicker but more permeable samples may also be analyzed. The method relies on quasi-steady flow resulting from a (quasi) constant pressure maintained at the inlet face of the sample. Gas flow-rate, as low as 3 × 10−10 m3/s, is determined from the record of pressure increase in a reservoir connected to the outlet face of the sample. An estimate of the characteristic time, tc, to reach quasi-steady flow after imposing a constant pressure at the inlet is derived. It is validated by direct numerical simulations of the complete unsteady flow, clearly defining the required experimental duration for the method to apply. Experimental results obtained on rather permeable and thick rock samples are reported showing an excellent agreement of the measured permeability with that determined independently on the same sample whereas the experimental value of tc is also in very good agreement with the predicted one. The method is further employed on a composite material sheet allowing the identification of an apparent gas permeability of about 10−23 m2.
n-type doping in Cu2O with F, Cl, and Br: A first-principles study
Authors: Bai Qiong , Wang Weichao , Zhang Qiming , Tao Meng
Published: January 2012

The n-type doping in the cuprous oxide (Cu2O) synthesized from an acidic solution environment has been studied by the first-principles calculations. The dopants of F, Cl, and Br in substitution of an O atom have low formation energies. They present an n-type conduction behavior with donor levels below but close to the bottom of the conduction bands. The Cl dopant has the shallowest donor level among the three halogens. The results are in good agreement with the very recent experimental results.
Rectification of elastic waves in a thin plate
Authors: Tanaka Yukihiro , Murai Takahiro , Nishiguchi Norihiko
Published: January 2012

We propose a rectifier of elastic waves in a thin plate, which is made of an elastically isotropic material containing a periodic array of triangular holes as scatterers, and demonstrate numerically that it works both for the symmetric and anti-symmetric Lamb waves as well as shear horizontal waves. The rectification is caused by the geometric effects on wave scattering due to the asymmetric scatterers, while the interplay between the mode conversion and interference effects among the scattered waves owing to the periodic arrangement of scatterers complicates it. The mechanism makes it possible to rectify the typical elastic waves in the system above the threshold frequency corresponding to the wavelength equivalent to the periodicity of scatterers.
Metal-insulator transition and nonlinear conductivity in Mn-deficient (LaCa)MnO3
Authors: Fisher B. , Genossar J. , Patlagan L. , Reisner G. M.
Published: January 2012

We report on linear and nonlinear electronic transport in the La0.65+3vCa0.35-3vMn1-vO3 system (0 ≤ v ≤ 0.06), that exhibits a disorder driven metal-insulator (M-I) transition. This transition is compared with the compositionally induced M-I transition in the La1−xCaxMnO3 system (0.17 ≤ x ≤ 0.22). Nonlinear conductivity of electronic origin, as measured using short, single current pulses, was detected only in the disordered non-metallic samples (v = 0.04−0.06), in electric fields E≲500 V/cm. At low temperatures and high electric fields, the I-V characteristics exhibit power-law behavior. Conductivities two orders of magnitude higher than ohmic were obtained for v = 0.04.
Energy transfer and dynamics studies of photoluminescence of polythiophene derivative in blend thin films
Authors: Wang Zi-Han , Lee Haiwon , Cui Hai-Ning
Published: January 2012

Thin films of the blend luminescent poly 3-(2-(5-chlorobenzotriazolo)ethyl) thiophene (PCBET) with poly-(p-(methyl)-phenylmethacrylate) (PMPMA), polyvinylcarzole (PVK), and poly (methyl methacrylate) (PMMA) were deposited by spin coating. Systematic studies on optical properties, the concentration effect, and energy transfer of these conjugated polymers within the blend films are discussed. Fluorescence lifetimes of excited state in the blend films were investigated by nanosecond time-resolved spectroscopy, UV-vis, photoluminescence (PL), synchronous PL spectra. These results and analysis suggest that energy transfer, from good matrix material (PMPMA and PVK) with active chromophores to PCBET, leads to the enhancement of PL emission of PCBET in a blend system.
Environment and baking influence on charge retention on silicon nitride charge trap layers
Authors: Sridhara Karthik , Borowik Łukasz , Mariolle Denis , Chevalier Nicolas , Colonna Jean-Philippe
Published: January 2012

We report the charge storage capacity of silicon nitride using Kelvin force microscopy (KFM). KFM is performed under various environments and for different thicknesses of Si3N4 (3 nm, 6 nm, and 9 nm) on top of a 10-nm SiO2 blocking oxide. We prove increased storage capacity with increased thickness and strong localization of charge characteristics — under reduced surface contamination. We have found that surface contamination is here linked with baking and presence of nitrogen flux. The structure shows strong retention under ultra high vacuum and Si3N4 thickness dependency. The total charge stored in each of these structures is calculated using Poisson solver.
Accurate ab initio potential energy surface, thermochemistry, and dynamics of the Cl(2P, 2P3/2) + CH4 → HCl + CH3 and H + CH3Cl reactions
Authors: Czakó Gábor , Bowman Joel M.
Published: January 2012

We report a high-quality, ab initio, full-dimensional global potential energy surface (PES) for the Cl(2P, 2P3/2) + CH4 reaction, which describes both the abstraction (HCl + CH3) and substitution (H + CH3Cl) channels. The analytical PES is a least-squares fit, using a basis of permutationally invariant polynomials, to roughly 16 000 ab initio energy points, obtained by an efficient composite method, including counterpoise and spin-orbit corrections for the entrance channel. This composite method is shown to provide accuracy almost equal to all-electron CCSD(T)/aug-cc-pCVQZ results, but at much lower computational cost. Details of the PES, as well as additional high-level benchmark characterization of structures and energetics are reported. The PES has classical barrier heights of 2650 and 15 060 cm−1 (relative to Cl(2P3/2) + CH4(eq)), respectively, for the abstraction and substitution reactions, in good agreement with the corresponding new computed benchmark values, 2670 and 14 720 cm−1. The PES also accurately describes the potential wells in the entrance and exit channels for the abstraction reaction. Quasiclassical trajectory calculations using the PES show that (a) the inclusion of the spin-orbit corrections in the PES decreases the cross sections by a factor of 1.5–2.5 at low collision energies (Ecoll); (b) at Ecoll ≈ 13 000 cm−1 the substitution channel opens and the H/HCl ratio increases rapidly with Ecoll; (c) the maximum impact parameter (bmax) for the abstraction reaction is ∼6 bohr; whereas bmax is only ∼2 bohr for the substitution; (d) the HCl and CH3 products are mainly in the vibrational ground state even at very high Ecoll; and (e) the HCl rotational distributions are cold, in excellent agreement with experiment at Ecoll = 1280 cm−1.
Influence of monovalent ions on density fluctuations in hydrothermal aqueous solutions by small angle X-ray scattering
Authors: Da Silva - Cadoux Cécile , Hazemann Jean-Louis , Testemale Denis , Proux Olivier , Rochas Cyrille
Published: January 2012

Synchrotron small angle X-ray scattering measurements on water and alkaline bromine aqueous solutions (XBr, with X = Li, Rb, or Cs) were carried out from ambient to supercritical conditions. The temperature was increased from 300 to 750 K along several isobars between 24 and 35 MPa. The correlation length and the structure factor were extracted from the data following the Ornstein-Zernike formalism. We obtained experimental evidence of the shift of the critical point and isochore and their dependence on the ions concentration (0.33 mol/kg and 1.0 mol/kg). We also observed that the size of the density fluctuations and the structure factor increase with the presence of the ions and that this effect is positively correlated with the atomic number of the cation. These behaviors were compared with ZnBr2 and NaCl systems from the literature.
Position-controlled [100] InP nanowire arrays
Authors: Wang Jia , Plissard Sébastien , Hocevar Moïra , Vu Thuy T. T. , Zehender Tilman , Immink George G. W. , Verheijen Marcel A. , Haverkort Jos , Bakkers Erik P. A. M.
Published: January 2012

We investigate the growth of vertically standing [100] zincblende InP nanowire (NW) arrays on InP (100) substrates in the vapor-liquid-solid growth mode using low-pressure metal-organic vapor-phase epitaxy. Precise positioning of these NWs is demonstrated by electron beam lithography. The vertical NW yield can be controlled by different parameters. A maximum yield of 56% is obtained and the tapering caused by lateral growth can be prevented by in situ HCl etching. Scanning electron microscopy, high-resolution transmission electron microscopy, and micro-photoluminescence have been used to investigate the NW properties.
Single-photon generation from a nitrogen impurity center in GaAs
Authors: Ikezawa Michio , Sakuma Yoshiki , Zhang Liao , Sone Yosinori , Mori Tatsuya , Hamano Takenobu , Watanabe Masato , Sakoda Kazuaki , Masumoto Yasuaki
Published: January 2012

We have demonstrated single-photon emission from a nitrogen luminescence center in GaAs. An inhomogeneously broadened luminescence band formed by localized centers was observed in the spectral range from 1480 meV to 1510 meV at 5 K in nitrogen delta-doped GaAs. Optical properties of the individual centers were investigated by steady-state and time-resolved micro photoluminescence. We have found that a bright luminescence center emits single photons with a radiative lifetime of 650 ps, which is much shorter than the lifetime of NN pairs in previous reports.
Tunable magnetic properties in ultrathin Co/garnet heterostructures
Authors: Pashkevich M. , Stupakiewicz A. , Kirilyuk A. , Maziewski A. , Stognij A. , Novitskii N. , Kimel A. , Rasing Th.
Published: January 2012

We demonstrate how the magnetic properties of metal/dielectric Co/yttrium iron garnet heterostructures can be engineered by both changing the garnet thickness and adding an ultrathin Co cover layer. The observed magnetization reversal process in the heterostructures is explained by both cubic and perpendicular growth-induced magnetic anisotropy of the garnet films. In particular, the perpendicular magnetic anisotropy can be strongly increased for reduced thickness. A strong influence of a 2 nm Co layer on the domain structure geometry and magnetization processes has been found for 1.8 µm garnet films.
Negative differential thermal conductance through vacuum
Authors: Zhu Linxiao , Otey Clayton R. , Fan Shanhui
Published: January 2012

We propose a scheme for achieving negative differential thermal conductance in near-field electromagnetic thermal transfer. As an example, we show that the scheme can be implemented with two slabs of silicon carbide brought in close proximity to each other. We also describe how a bistable thermal switch can be constructed in this manner.
Non-ideal energy selective contacts and their effect on the performance of a hot carrier solar cell with an indium nitride absorber
Authors: Feng Y. , Aliberti P. , Veettil B. P. , Patterson R. , Shrestha S. , Green M. A. , Conibeer G.
Published: January 2012

The hot carrier solar cell is a third generation photovoltaic device that extracts photo-generated carriers before they thermalise. In this work, the efficiency of a hot carrier solar cell with a 50 nm indium nitride (InN) absorber layer has been calculated, taking into account the realistic transport properties of energy selective contacts. The cell performance has been modeled considering the carrier extraction through contacts as ballistic. A potential practical implementation of a hot carrier solar cell, with contacts based on an InXGa1−XN/InN/InXGa1−XN quantum well structure, has been proposed, with calculated maximum efficiency of 37.15% under 1000 suns.
Enhanced Primary Care improves GP service regularity in older patients without impacting on service frequency
Authors: Gibson David A. J. , Moorin Rachael E. , Preen David , Emery Jon , D'Arcy J. Holman C.
Published: January 2012

The objective of this study was to assess the impact of Enhanced Primary Care service utilisation on subsequent GP service regularity and frequency. The study involved a retrospective population-based longitudinal cohort using linked administrative health records of hospital and primary care services for people over the age of 65 years. Multinomial logistic regression modelling was used to evaluate changes in the relative likelihood of increased primary care service regularity and frequency in exposed and unexposed individuals adjusting for age, sex and recent chronic disease hospitalisation history. Enhanced Primary Care services significantly and substantially increased the relative likelihood of increased regularity with no corresponding higher likelihood of increased frequency of GP contact. Increased regularity was more likely with increasing age except for the oldest age group (90+ years). Some chronic disease histories (e.g. diabetes) showed a higher likelihood of improved regularity while others were less likely to produce an increased regularity (e.g. hypertension). The study suggests a capacity for modification of physician and patient behaviour using incentivised services within the current fee-for-service system in Australia.
Regional drought-induced reduction in the biomass carbon sink of Canada's boreal forests
Authors: Ma Zhihai , Peng Changhui , Zhu Qiuan , Chen Huai , Yu Guirui , Li Weizhong , Zhou Xiaolu , Wang Weifeng , Zhang Wenhua
Published: January 2012

The boreal forests, identified as a critical “tipping element” of the Earth's climate system, play a critical role in the global carbon budget. Recent findings have suggested that terrestrial carbon sinks in northern high-latitude regions are weakening, but there has been little observational evidence to support the idea of a reduction of carbon sinks in northern terrestrial ecosystems. Here, we estimated changes in the biomass carbon sink of natural stands throughout Canada's boreal forests using data from long-term forest permanent sampling plots. We found that in recent decades, the rate of biomass change decreased significantly in western Canada (Alberta, Saskatchewan, and Manitoba), but there was no significant trend for eastern Canada (Ontario and Quebec). Our results revealed that recent climate change, and especially drought-induced water stress, is the dominant cause of the observed reduction in the biomass carbon sink, suggesting that western Canada's boreal forests may become net carbon sources if the climate change–induced droughts continue to intensify.
Mitochondrial genomes from modern horses reveal the major haplogroups that underwent domestication
Authors: Achilli Alessandro , Olivieri Anna , Soares Pedro , Lancioni Hovirag , Kashani Baharak Hooshiar , Perego Ugo A. , Nergadze Solomon G. , Carossa Valeria , Santagostino Marco , Capomaccio Stefano , Felicetti Michela , Al-Achkar Walid , Penedo M. Cecilia T. , Verini-Supplizi Andrea , Houshmand Massoud , Woodward Scott R. , Semino Ornella , Silvestrelli Maurizio , Giulotto Elena , Pereira Luísa , Bandelt Hans-Jürgen , Torroni Antonio
Published: January 2012

Archaeological and genetic evidence concerning the time and mode of wild horse (Equus ferus) domestication is still debated. High levels of genetic diversity in horse mtDNA have been detected when analyzing the control region; recurrent mutations, however, tend to blur the structure of the phylogenetic tree. Here, we brought the horse mtDNA phylogeny to the highest level of molecular resolution by analyzing 83 mitochondrial genomes from modern horses across Asia, Europe, the Middle East, and the Americas. Our data reveal 18 major haplogroups (A–R) with radiation times that are mostly confined to the Neolithic and later periods and place the root of the phylogeny corresponding to the Ancestral Mare Mitogenome at ∼130–160 thousand years ago. All haplogroups were detected in modern horses from Asia, but F was only found inE. przewalskii—the only remaining wild horse. Therefore, a wide range of matrilineal lineages from the extinctE. ferusunderwent domestication in the Eurasian steppes during the Eneolithic period and were transmitted to modernE. caballusbreeds. Importantly, now that the major horse haplogroups have been defined, each with diagnostic mutational motifs (in both the coding and control regions), these haplotypes could be easily used to (i) classify well-preserved ancient remains, (ii) (re)assess the haplogroup variation of modern breeds, including Thoroughbreds, and (iii) evaluate the possible role of mtDNA backgrounds in racehorse performance.
Quantitative modeling of the terminal differentiation of B cells and mechanisms of lymphomagenesis
Authors: Martínez María Rodríguez , Corradin Alberto , Klein Ulf , Álvarez Mariano Javier , Toffolo Gianna M. , di Camillo Barbara , Califano Andrea , Stolovitzky Gustavo A.
Published: January 2012

Mature B-cell exit from germinal centers is controlled by a transcriptional regulatory module that integrates antigen and T-cell signals and, ultimately, leads to terminal differentiation into memory B cells or plasma cells. Despite a compact structure, the module dynamics are highly complex because of the presence of several feedback loops and self-regulatory interactions, and understanding its dysregulation, frequently associated with lymphomagenesis, requires robust dynamical modeling techniques. We present a quantitative kinetic model of three key gene regulators, BCL6, IRF4, and BLIMP, and use gene expression profile data from mature human B cells to determine appropriate model parameters. The model predicts the existence of two different hysteresis cycles that direct B cells through an irreversible transition toward a differentiated cellular state. By synthetically perturbing the interactions in this network, we can elucidate known mechanisms of lymphomagenesis and suggest candidate tumorigenic alterations, indicating that the model is a valuable quantitative tool to simulate B-cell exit from the germinal center under a variety of physiological and pathological conditions.
Mitochondrial ubiquitin ligase MITOL blocks S-nitrosylated MAP1B-light chain 1-mediated mitochondrial dysfunction and neuronal cell death
Authors: Yonashiro Ryo , Kimijima Yuya , Shimura Takuya , Kawaguchi Kohei , Fukuda Toshifumi , Inatome Ryoko , Yanagi Shigeru
Published: January 2012

Nitric oxide (NO) is implicated in neuronal cell survival. However, excessive NO production mediates neuronal cell death, in part via mitochondrial dysfunction. Here, we report that the mitochondrial ubiquitin ligase, MITOL, protects neuronal cells from mitochondrial damage caused by accumulation of S-nitrosylated microtubule-associated protein 1B-light chain 1 (LC1). S-nitrosylation of LC1 induces a conformational change that serves both to activate LC1 and to promote its ubiquination by MITOL, indicating that microtubule stabilization by LC1 is regulated through its interaction with MITOL. Excessive NO production can inhibit MITOL, and MITOL inhibition resulted in accumulation of S-nitrosylated LC1 following stimulation of NO production by calcimycin and N-methyl-D-aspartate. LC1 accumulation under these conditions resulted in mitochondrial dysfunction and neuronal cell death. Thus, the balance between LC1 activation by S-nitrosylation and down-regulation by MITOL is critical for neuronal cell survival. Our findings may contribute significantly to an understanding of the mechanisms of neurological diseases caused by nitrosative stress-mediated mitochondrial dysfunction.
Severe mammal declines coincide with proliferation of invasive Burmese pythons in Everglades National Park
Authors: Dorcas Michael E. , Willson John D. , Reed Robert N. , Snow Ray W. , Rochford Michael R. , Miller Melissa A. , Meshaka Walter E. , Andreadis Paul T. , Mazzotti Frank J. , Romagosa Christina M. , Hart Kristen M.
Published: January 2012

Invasive species represent a significant threat to global biodiversity and a substantial economic burden. Burmese pythons, giant constricting snakes native to Asia, now are found throughout much of southern Florida, including all of Everglades National Park (ENP). Pythons have increased dramatically in both abundance and geographic range since 2000 and consume a wide variety of mammals and birds. Here we report severe apparent declines in mammal populations that coincide temporally and spatially with the proliferation of pythons in ENP. Before 2000, mammals were encountered frequently during nocturnal road surveys within ENP. In contrast, road surveys totaling 56,971 km from 2003–2011 documented a 99.3% decrease in the frequency of raccoon observations, decreases of 98.9% and 87.5% for opossum and bobcat observations, respectively, and failed to detect rabbits. Road surveys also revealed that these species are more common in areas where pythons have been discovered only recently and are most abundant outside the python's current introduced range. These findings suggest that predation by pythons has resulted in dramatic declines in mammals within ENP and that introduced apex predators, such as giant constrictors, can exert significant top-down pressure on prey populations. Severe declines in easily observed and/or common mammals, such as raccoons and bobcats, bode poorly for species of conservation concern, which often are more difficult to sample and occur at lower densities.
Gating transitions in the selectivity filter region of a sodium channel are coupled to the domain IV voltage sensor
Authors: Capes Deborah L. , Arcisio-Miranda Manoel , Jarecki Brian W. , French Robert J. , Chanda Baron
Published: January 2012

Voltage-dependent ion channels are crucial for generation and propagation of electrical activity in biological systems. The primary mechanism for voltage transduction in these proteins involves the movement of a voltage-sensing domain (D), which opens a gate located on the cytoplasmic side. A distinct conformational change in the selectivity filter near the extracellular side has been implicated in slow inactivation gating, which is important for spike frequency adaptation in neural circuits. However, it remains an open question whether gating transitions in the selectivity filter region are also actuated by voltage sensors. Here, we examine conformational coupling between each of the four voltage sensors and the outer pore of a eukaryotic voltage-dependent sodium channel. The voltage sensors of these sodium channels are not structurally symmetric and exhibit functional specialization. To track the conformational rearrangements of individual voltage-sensing domains, we recorded domain-specific gating pore currents. Our data show that, of the four voltage sensors, only the domain IV voltage sensor is coupled to the conformation of the selectivity filter region of the sodium channel. Trapping the outer pore in a particular conformation with a high-affinity toxin or disulphide crossbridge impedes the return of this voltage sensor to its resting conformation. Our findings directly establish that, in addition to the canonical electromechanical coupling between voltage sensor and inner pore gates of a sodium channel, gating transitions in the selectivity filter region are also coupled to the movement of a voltage sensor. Furthermore, our results also imply that the voltage sensor of domain IV is unique in this linkage and in the ability to initiate slow inactivation in sodium channels.
Environmental stress increases the entry of cytoplasmic organellar DNA into the nucleus in plants
Authors: Wang Dong , Lloyd Andrew H. , Timmis Jeremy N.
Published: January 2012

Mitochondria and chloroplasts (photosynthetic members of the plastid family of cytoplasmic organelles) in eukaryotic cells originated more than a billion years ago when an ancestor of the nucleated cell engulfed two different prokaryotes in separate sequential events. Extant cytoplasmic organellar genomes contain very few genes compared with their candidate free-living ancestors, as most have functionally relocated to the nucleus. The first step in functional relocation involves the integration of inactive DNA fragments into nuclear chromosomes, and this process continues at high frequency with attendant genetic, genomic, and evolutionary consequences. Using two different transplastomic tobacco lines, we show that DNA migration from chloroplasts to the nucleus is markedly increased by mild heat stress. In addition, we show that insertion of mitochondrial DNA fragments during the repair of induced double-strand breaks is increased by heat stress. The experiments demonstrate that the nuclear influx of organellar DNA is a potentially a source of mutation for nuclear genomes that is highly susceptible to temperature fluctuations that are well within the range experienced naturally.
Nonequilibrium atmospheric secondary organic aerosol formation and growth
Authors: Perraud Véronique , Bruns Emily A. , Ezell Michael J. , Johnson Stanley N. , Yu Yong , Alexander M. Lizabeth , Zelenyuk Alla , Imre Dan , Chang Wayne L. , Dabdub Donald , Pankow James F. , Finlayson-Pitts Barbara J.
Published: January 2012

Airborne particles play critical roles in air quality, health effects, visibility, and climate. Secondary organic aerosols (SOA) formed from oxidation of organic gases such as α-pinene account for a significant portion of total airborne particle mass. Current atmospheric models typically incorporate the assumption that SOA mass is a liquid into which semivolatile organic compounds undergo instantaneous equilibrium partitioning to grow the particles into the size range important for light scattering and cloud condensation nuclei activity. We report studies of particles from the oxidation of α-pinene by ozone and NO
3
radicals at room temperature. SOA is primarily formed from low-volatility ozonolysis products, with a small contribution from higher volatility organic nitrates from the NO
3
reaction. Contrary to expectations, the particulate nitrate concentration is not consistent with equilibrium partitioning between the gas phase and a liquid particle. Rather the fraction of organic nitrates in the particles is only explained by irreversible, kinetically determined uptake of the nitrates on existing particles, with an uptake coefficient that is 1.6% of that for the ozonolysis products. If the nonequilibrium particle formation and growth observed in this atmospherically important system is a general phenomenon in the atmosphere, aerosol models may need to be reformulated. The reformulation of aerosol models could impact the predicted evolution of SOA in the atmosphere both outdoors and indoors, its role in heterogeneous chemistry, its projected impacts on air quality, visibility, and climate, and hence the development of reliable control strategies.
The protein SdhA maintains the integrity of the
Legionella
-containing vacuole
Authors: Creasey Elizabeth A. , Isberg Ralph R.
Published: January 2012

Legionella pneumophila
directs the formation of a specialized vacuole within host cells, dependent on protein substrates of the Icm/Dot translocation system. Survival of the host cell is essential for intracellular replication of
L. pneumophila
. Strains lacking the translocated substrate SdhA are defective for intracellular replication and activate host cell death pathways in primary macrophages. To understand how SdhA promotes evasion of death pathways, we performed a mutant hunt to identify bacterial suppressors of the
ΔsdhA
growth defect. We identified the secreted phospholipase PlaA as key to activation of death pathways by the
ΔsdhA
strain. Based on homology between PlaA and SseJ, a
Salmonella
protein associated with vacuole degradation, we determined the roles of SdhA and PlaA in controlling vacuole integrity. In the absence of
sdhA
, the
Legionella
-containing vacuole was unstable, resulting in access to the host cytosol. Both vacuole disruption and host cell death were largely dependent on PlaA. Consistent with these observations, the
ΔsdhA
strain colocalized with galectin-3, a marker of vacuole rupture, in a PlaA-dependent process. Access of
ΔsdhA
strains to the macrophage cytosol triggered multiple responses in the host cell, including degradation of bacteria, induction of the type I IFN response, and activation of inflammasomes. Therefore, we have demonstrated that the
Legionella
-containing vacuole is actively stabilized by the SdhA protein during intracellular replication. This vacuolar niche affords the bacterium protection from cytosolic host factors that degrade bacteria and initiate immune responses.
A long noncoding RNA regulates photoperiod-sensitive male sterility, an essential component of hybrid rice
Authors: Ding Jihua , Lu Qing , Ouyang Yidan , Mao Hailiang , Zhang Pingbo , Yao Jialing , Xu Caiguo , Li Xianghua , Xiao Jinghua , Zhang Qifa
Published: January 2012

Hybrid rice has greatly contributed to the global increase of rice productivity. A major component that facilitated the development of hybrids was a mutant showing photoperiod-sensitive male sterility (PSMS) with its fertility regulated by day length. Transcriptome studies have shown that large portions of the eukaryotic genomic sequences are transcribed to long noncoding RNAs (lncRNAs). However, the potential roles for only a few lncRNAs have been brought to light at present. Thus, great efforts have to be invested to understand the biological functions of lncRNAs. Here we show that a lncRNA of 1,236 bases in length, referred to as long-day–specific male-fertility–associated RNA (LDMAR), regulates PSMS in rice. We found that sufficient amount of the LDMAR transcript is required for normal pollen development of plants grown under long-day conditions. A spontaneous mutation causing a single nucleotide polymorphism (SNP) between the wild-type and mutant altered the secondary structure of LDMAR. This change brought about increased methylation in the putative promoter region of LDMAR, which reduced the transcription of LDMAR specifically under long-day conditions, resulting in premature programmed cell death (PCD) in developing anthers, thus causing PSMS. Thus, a lncRNA could directly exert a major effect on a trait like a structure gene, and a SNP could alter the function of a lncRNA similar to amino acid substitution in structural genes. Molecular elucidating of PSMS has important implications for understanding molecular mechanisms of photoperiod regulation of many biological processes and also for developing male sterile germplasms for hybrid crop breeding.
Hypertension with or without adrenal hyperplasia due to different inherited mutations in the potassium channel
KCNJ5
Authors: Scholl Ute I. , Nelson-Williams Carol , Yue Peng , Grekin Roger , Wyatt Robert J. , Dillon Michael J. , Couch Robert , Hammer Lisa K. , Harley Frances L. , Farhi Anita , Wang Wen-Hui , Lifton Richard P.
Published: January 2012

We recently implicated two recurrent somatic mutations in an adrenal potassium channel, KCNJ5, as a cause of aldosterone-producing adrenal adenomas (APAs) and one inherited KCNJ5 mutation in a Mendelian form of early severe hypertension with massive adrenal hyperplasia. The mutations identified all altered the channel selectivity filter, producing increased Na
+
conductance and membrane depolarization, the signal for aldosterone production and proliferation of adrenal glomerulosa cells. We report herein members of four kindreds with early onset primary aldosteronism of unknown cause. Sequencing of
KCNJ5
revealed that affected members of two kindreds had

KCNJ5
G151R

mutations, identical to one of the prevalent recurrent mutations in APAs. These individuals had severe progressive aldosteronism and hyperplasia requiring bilateral adrenalectomy in childhood for blood pressure control. Affected members of the other two kindreds had

KCNJ5
G151E

mutations, which are not seen in APAs. These subjects had easily controlled hypertension and no evidence of hyperplasia. Surprisingly, electrophysiology of channels expressed in 293T cells demonstrated that KCNJ5
G151E
was the more extreme mutation, producing a much larger Na
+
conductance than KCNJ5
G151R
, resulting in rapid Na
+
-dependent cell lethality. We infer that this increased lethality limits adrenocortical cell mass and the severity of aldosteronism in vivo, accounting for the milder phenotype among these patients. These findings demonstrate striking variations in phenotypes and clinical outcome resulting from different mutations of the same amino acid in KCNJ5 and have implications for the diagnosis and pathogenesis of primary aldosteronism with and without adrenal hyperplasia.
Glut1-mediated glucose transport regulates HIV infection
Authors: Loisel-Meyer Séverine , Swainson Louise , Craveiro Marco , Oburoglu Leal , Mongellaz Cédric , Costa Caroline , Martinez Marion , Cosset François-Loic , Battini Jean-Luc , Herzenberg Leonard A. , Herzenberg Leonore A. , Atkuri Kondala R. , Sitbon Marc , Kinet Sandrina , Verhoeyen Els , Taylor Naomi
Published: January 2012

Cell cycle entry is commonly considered to positively regulate HIV-1 infection of CD4 T cells, raising the question as to how quiescent lymphocytes, representing a large portion of the viral reservoir, are infected in vivo. Factors such as the homeostatic cytokine IL-7 have been shown to render quiescent T cells permissive to HIV-1 infection, presumably by transiently stimulating their entry into the cell cycle. However, we show here that at physiological oxygen (O2) levels (2–5% O2tension in lymphoid organs), IL-7 stimulation generates an environment permissive to HIV-1 infection, despite a significantly attenuated level of cell cycle entry. We identify the IL-7–induced increase in Glut1 expression, resulting in augmented glucose uptake, as a key factor in rendering these T lymphocytes susceptible to HIV-1 infection. HIV-1 infection of human T cells is abrogated either by impairment of Glut1 signal transduction or by siRNA-mediated Glut1 down-regulation. Consistent with this, we show that the susceptibility of human thymocyte subsets to HIV-1 infection correlates with Glut1 expression; single-round infection is markedly higher in the Glut1-expressing double-positive thymocyte population than in any of the Glut1-negative subsets. Thus, our studies reveal the Glut1-mediated metabolic pathway as a critical regulator of HIV-1 infection in human CD4 T cells and thymocytes.
Collision effects on high-n ballooning modes with a full Lorentz collision operator
Authors: Liu Jianxun , Chen Shaoyong , Tang Changjian
Published: January 2012

The dispersion relation for high-n ballooning modes is obtained from the customary drift gyro-kinetic equation employing the energy-dependent Lorenz collision operator. There are significant differences between our results and those with the Krook collision operator. The present results show that collision seems to have much weaker stabilizing effects, if any, on the high-n ballooning modes than those with the Krook collision operator when the collisionality, υ*e, is smaller than a critical value. However, contrary to the phenomenon, the collision shows strong stabilizing effects on the ballooning mode once the collisionality exceeds a critical value. These differences are supposed to arise from boundary layer behaviour which refers to the electron perturbation at the boundary between trapped and passing electrons in velocity space, but the physical process cannot be described by non-conserving Krook collision operators. This destabilizing mechanism of boundary layer behaviour is discussed in this paper. In addition, the critical value shows a considerably strong dependence on ηe (ηe ≡ d ln T
e/d ln N
e).