bluuebunny/crossref_metadata_2025 huggingface dataset:
Charge Transfer at Junctions of a Single Layer of Graphene and a Metallic Single Walled Carbon Nanotube
Authors: Paulus Geraldine L. C. , Wang Qing Hua , Ulissi Zachary W. , McNicholas Thomas P. , Vijayaraghavan Aravind , Shih Chih‐Jen , Jin Zhong , Strano Michael S.
Published: December 2012

Junctions between a single walled carbon nanotube (SWNT) and a monolayer of graphene are fabricated and studied for the first time. A single layer graphene (SLG) sheet grown by chemical vapor deposition (CVD) is transferred onto a SiO2/Si wafer with aligned CVD‐grown SWNTs. Raman spectroscopy is used to identify metallic‐SWNT/SLG junctions, and a method for spectroscopic deconvolution of the overlapping G peaks of the SWNT and the SLG is reported, making use of the polarization dependence of the SWNT. A comparison of the Raman peak positions and intensities of the individual SWNT and graphene to those of the SWNT‐graphene junction indicates an electron transfer of 1.12 × 1013 cm−2 from the SWNT to the graphene. This direction of charge transfer is in agreement with the work functions of the SWNT and graphene. The compression of the SWNT by the graphene increases the broadening of the radial breathing mode (RBM) peak from 3.6 ± 0.3 to 4.6 ± 0.5 cm−1 and of the G peak from 13 ± 1 to 18 ± 1 cm−1, in reasonable agreement with molecular dynamics simulations. However, the RBM and G peak position shifts are primarily due to charge transfer with minimal contributions from strain. With this method, the ability to dope graphene with nanometer resolution is demonstrated.
Correct Spectral Conversion between Surface‐Enhanced Raman and Plasmon Resonance Scattering from Nanoparticle Dimers for Single‐Molecule Detection
Authors: Lee Kyuwan , Irudayaraj Joseph
Published: December 2012

Simultaneous measurement of surface‐enhanced Raman scattering (SERS) and localized surface plasmon resonance (LSPR) in nanoparticle dimers presents outstanding opportunities in molecular identification and in the elucidation of physical properties, such as the size, distance, and deformation of target species. SERS–LSPR instrumentation exists and has been used under limited conditions, but the extraction of SERS and LSPR readouts from a single measurement is still a challenge. Herein, the extraction of LSPR spectra from SERS signals is reported and a tool for measuring the interparticle distance from Raman enhancement data by the standardization of the SERS signal is proposed. The SERS nanoruler mechanism incorporates two important aspects (the LSPR scattering peak shift and the Raman shift for measuring interparticle distance), and signifies their exact one‐to‐one correspondence after spectral correction. The developed methodology is applied to calculate the interparticle distance between nanoparticle dimers from SERS signals, to detect and quantify DNA at the single‐molecule level in a base‐pair‐specific manner. It is also shown that the SERS nanoruler concept can be used in structural analysis for the specific detection of the interaction of immunoglobulin G (IgG) with its target from bianalyte Raman signals with identical shaping at single‐molecule resolution. The SERS profile shaping approach not only offers a new detection mechanism for single molecules, but also has excellent potential for studying protein interactions and the intracellular detection of mRNA.
Mechanical Exfoliation and Characterization of Single‐ and Few‐Layer Nanosheets of WSe2, TaS2, and TaSe2
Authors: Li Hai , Lu Gang , Wang Yanlong , Yin Zongyou , Cong Chunxiao , He Qiyuan , Wang Lu , Ding Feng , Yu Ting , Zhang Hua
Published: December 2012

Single‐ and few‐layer transition‐metal dichalcogenide nanosheets, such as WSe2, TaS2, and TaSe2, are prepared by mechanical exfoliation. A Raman microscope is employed to characterize the single‐layer (1L) to quinary‐layer (5L) WSe2 nanosheets and WSe2 single crystals with a laser excitation power ranging from 20 μW to 5.1 mW. Typical first‐order together with some second‐order and combinational Raman modes are observed. A new peak at around 308 cm−1 is observed in WSe2 except for the 1L WSe2, which might arise from interlayer interactions. Red shifting of the A1g mode and the Raman peak around 308 cm−1 is observed from 1L to 5L WSe2. Interestingly, hexagonal‐ and monoclinic‐structured WO3 thin films are obtained during the local oxidation of thinner (1L–3L) and thicker (4L and 5L) WSe2 nanosheets, while laser‐burned holes are found during the local oxidation of the WSe2 single crystal. In addition, the characterization of TaS2 and TaSe2 thin layers is also conducted.
A New Double Calcium Treatment Method for Clean Steel Refining
Authors: Deng Zhiyin , Zhu Miaoyong
Published: December 2012

A new double calcium treatment method was proposed according to industrial experiment. In the new process, the evolution of inclusion was analyzed and the controlling standard of T.[Ca]/T.[O] ratio for calcium treatment was discussed. The results show that good castability with low calcium content about 12 ppm was obtained by this method, and the inclusion grade of D type thin series decreases from 1.5 to 1.0 in final product. CaOMgOAl2O3 system inclusions containing small amount of CaO are mainly presented after LF refining. After the 1st calcium treatment, most inclusions are in the liquid region with low melting point and the MgO content decreases obviously. After the 2nd calcium treatment, the distribution of inclusion composition is more concentrated compared with the 1st calcium treatment, and the MgO content decreases further with the inclusion composition very close to CaOAl2O3 system and almost all in liquid region. In order to get a good calcium treatment result, T.[Ca]/T.[O] ratio should be controlled above 0.91, and the ratio between 0.91 and 1.25 is suitable in present work.
Assessment of the continuous wavelet transform in the modal parameters estimation of 2MM and 3MM systems
Authors: Loussifi Hichem , Nouri Khaled , Benhadj Braiek Naceur
Published: December 2012

In this paper, our interest is in the identification of a special class of electromechanical systems: a motor‐drive system using the continuous wavelet transform method. This new modal analysis technique is evaluated in terms of its accuracy in the estimation of the modal parameters, its ability in distinguishing and separating several modes, its resistance to noisy conditions, and its usability with different excitations types. For this investigation, two models of elastic drive systems are considered: the two‐mass model and the three‐mass model. Simulation results of the study are presented, and the effectiveness of the developed identification method is discussed. © 2012 Institute of Electrical Engineers of Japan. Published by John Wiley & Sons, Inc.
An investigation on attenuation UCT with wave paths enhancement for breast ultrasound
Authors: Sanpanich Arthorn , Hamamoto Kazuhiko , Pintavirooj Chuchart
Published: December 2012

Breast cancer is one of the most prevalent health hazards in women all over the world. An annual screening test using a diagnostic ultrasound seems to be an appropriate method to handle this physical threat. In this paper, we propose the use of a two‐dimensional reflection‐mode ultrasonic tomography system for a general breast ultrasound investigation enhanced by an echo wave path using a wave reflecting plate. Our virtual imaging setup system is composed of a 128‐element conventional linear array transducer placed on the top of a water bath and a wave reflector attached around this setup. The shape of the wave reflector was designed as a single plate shape, rectangular shape and curve shape. For projection data, we estimate a line integral insonifying data by using a classical integration slope of attenuation coefficient method in which its derivative is independent of transmittance, reflectance, and noise. By imaging a virtual breast phantom model, the reconstruction results obtained from an iterative algebraic reconstruction technique (ART) algorithm show a promising image. The image is not only indicates a tissue characterization from quantitative attenuation data, but also restores an area covered by hard tissue due to an increased wave path direction from our nonrotational imaging system. These results encourage us to implement our concept with a clinical study in the near future. © 2012 Institute of Electrical Engineers of Japan. Published by John Wiley & Sons, Inc.
Validation for capacitance national standard based on long‐term monitoring results of standard capacitors
Authors: Domae Atsushi , Sakamoto Norihiko , Kaneko Nobu‐Hisa
Published: December 2012

The National Metrology Institute of Japan (NMIJ) has developed a new national standard of capacitance (capacitance standard) and also established its traceability system. Calibration and measurement capabilities (CMCs) of the new capacitance standard were validated in the international comparison with foreign National Metrology Institutes (NMIs). However, it is not easy to frequently carry out such international comparison which requires close coordination among the participating NMIs. In order to maintain high reliability of the capacitance standard, therefore, it is important to verify its CMCs during the period when the comparisons are not carried out. To verify the CMCs, NMIJ has been performing long‐term monitoring of standard capacitors and of capacitance differences among a number of standard capacitors. In this paper, we will report the details of the long‐term monitoring of the standard capacitor, the long‐term monitoring results of capacitance differences, and verification of CMCs based on the analysis of these results. Validation of the CMCs based on results of monitoring conducted after the massive earthquake on March 11, 2011 is also described as specific case. © 2012 Institute of Electrical Engineers of Japan. Published by John Wiley & Sons, Inc.
Multiobjective particle swarm optimization for a novel fuzzy portfolio selection problem
Authors: Wang Bo , Watada Junzo
Published: December 2012

On the basis of the portfolio selection theory, this paper proposes a novel fuzzy multiobjective model that can evaluate investment risk properly and increase the probability of obtaining an expected return. In building this model, fuzzy value‐at‐risk (VaR) is used to evaluate the exact future risk in terms of loss. The VaR can directly reflect the greatest loss of a selection case under a given confidence level. Conversely, variance, the measure of the spread of a distribution around its expected value, is utilized to make the selection more stable. This model can provide investors with more significant information for decision making. To solve this model, an improved Pareto‐optimal‐set‐based multiobjective particle swarm optimization (IMOPSO) algorithm is designed to obtain better solutions in the Pareto front. The proposed model and algorithm are exemplified by specific numerical examples. Furthermore, comparisons are made between IMOPSO and other existing approaches. Experiments show that the model and algorithm are effective in solving the multiobjective portfolio selection problem. © 2012 Institute of Electrical Engineers of Japan. Published by John Wiley & Sons, Inc.
A new application‐level link aggregation and its implementation on Android terminals
Authors: Takiguchi Takafumi , Hidaka Akira , Masui Hiromu , Sugizaki Yoshio , Mizuno Osamu , Asatani Koichi
Published: December 2012

Link aggregation bundles multiple physical links on a single virtual link, enabling very high‐speed and large‐capacity data communications. It also enables redundant communications. Several link aggregation methods have been proposed. These methods utilize transport/or lower layer link aggregation. In this paper, a new application‐level link aggregation is proposed and implemented on Android operating system (OS), which is one of the popular OSs for mobile devices such as smartphones and tablet PCs. The proposed application‐level link aggregation method is verified with use of an implemented terminal. Copyright © 2012 John Wiley & Sons, Ltd.
SNR and throughput analysis of distributed collaborative beamforming in locally‐scattered environments
Authors: Zaidi Slim , Affes Sofiène
Published: December 2012

Three main collaborative beamforming (CB) solutions based on different channel models exist: the optimal CSI‐based CB (OCB), the conventional or monochromatic (i.e., single‐ray) distributed CB (M‐DCB), and the recently developed bichromatic (i.e., two‐ray) distributed CB (B‐DCB). In this paper, we perform an analytical comparison, under practical constraints, between these CB solutions in terms of achieved signal‐to‐noise ratio (SNR) as well as achieved throughput. Assuming the presence of local scattering in the source vicinity and accounting for implementation errors incurred by each CB solution, we derive for the first time closed‐form expressions of their true achieved SNRs. For low angular spread (AS), where both solutions nominally achieve the same SNR in ideal conditions, we show that the B‐DCB always outperforms OCB, more so and at larger regions of AS values when errors increase. Excluding exceptional circumstances of unrealistic low quantization levels (i.e., very large quantization errors) that are hard to justify in practice, we also show that the new B‐DCB always outperforms the M‐DCB as recently found nominally in ideal conditions. This work is also the first to push the performance analysis of CB to the throughput level by taking into account the feedback overhead cost incurred by each solution. We prove both by concordant analysis and simulations that the B‐DCB is able to outperform, even for high AS values, the OCB which is penalized by its prohibitive implementation overhead, especially for a large number of collaborating terminals and/or high Doppler frequencies. Indeed, it is shown that the operational regions in terms of AS values over which the new B‐DCB is favored against OCB in terms of achieved throughput can reach up to 40°. Copyright © 2012 John Wiley & Sons, Ltd.
Compressed sensing construction of spectrum map for routing in cognitive radio networks
Authors: Shih Sung‐Yin , Chen Kwang‐Cheng
Published: December 2012

Cooperative relay enables multihop cognitive radio networks of cognitive radios (CRs) and nodes of primary system. However, successful CR networking functions such as routing prefer on the knowledge of radio resource availability associated with location, which is a challenge of traditional spectrum sensing. We introduce the concept of spectrum map encompassing spectrum and location information to facilitate multihop routing in highly dynamic environment, in addition to utilizing statistics of opportunistic links. Because traditional spectrum sensing only knows local information of CR transmitter, it is difficult and resource consuming to construct the entire spectrum map. We therefore extend the compressed sensing technique requiring very limited local sensing to establish spectrum map. We analyze the communication overhead and practically construct the spectrum map via expander graph. Finally, we demonstrate using spectrum map to reliably route packets of CRs in an end‐to‐end way, under the guaranteed outage for nodes in primary system and maximizing the throughput among cooperative CRs. Copyright © 2012 John Wiley & Sons, Ltd.
Selection of multinomial logit models via association rules analysis
Authors: Changpetch Pannapa , Lin Dennis K.J.
Published: December 2012

In this research, we propose a novel approach for a multinomial logit model selection procedure: specifically, we apply association rules analysis to identifying potential interactions for multinomial logit modeling. Interaction effects are very common in reality, but conventional multinomial logit model selection methods typically ignore them. This is especially true for higher‐order interactions. Here, we develop a model selection framework to address this problem. Specifically, we focus on building an optimal multinomial logit model by (1) exploring the combinations of input variables that have a significant impact on response (via association rules analysis); (2) selecting potential (low‐order and high‐order) interactions; (3) converting these potential interactions into new dummy variables; and (4) performing variable selections among all the input variables and the newly created dummy variables (interactions). Our model selection procedure is the first approach to provide a global search for potential interactions and establish the optimal combination of main effects and interaction effects in the multinomial logit model. In our investigation, we consider both simulated and real‐life datasets, thereby confirming the effectiveness and efficiency of this method. WIREs Comput Stat 2013, 5:68–77. doi: 10.1002/wics.1242

This article is categorized under:

Data: Types and Structure > Categorical Data

Statistical Models > Generalized Linear Models

Statistical Models > Model Selection
A low molecular mass cutinase of Thielavia terrestris efficiently hydrolyzes poly(esters)
Authors: Yang Shaoqing , Xu Haibo , Yan Qiaojuan , Liu Yu , Zhou Peng , Jiang Zhengqiang
Published: December 2012

A low molecular mass cutinase (designated TtcutA) from Thielavia terrestris was purified and biochemically characterized. The thermophilic fungus T. terrestris CAU709 secreted a highly active cutinase (90.4 U ml−1) in fermentation broth containing wheat bran as the carbon source. The cutinase was purified 19-fold with a recovery yield of 4.8 %. The molecular mass of the purified TtcutA was determined as 25.3 and 22.8 kDa using SDS-PAGE and gel filtration, respectively. TtcutA displayed optimal activity at pH 4.0 and 50 °C. It was highly stable up to 65 °C and in the broad pH range 2.5–10.5. Extreme stability in high concentrations (80 %, v/v) of solvents such as methanol, ethanol, acetone, acetonitrile, isopropanol, and dimethyl sulfoxide was observed for the enzyme. The K  m values for this enzyme towards p-nitrophenyl (pNP) acetate, pNP butyrate, and pNP caproate were 7.7, 1.0, and 0.52 mM, respectively. TtcutA was able to efficiently degrade various ester polymers, including cutin, polyethylene terephthalate (PET), polycaprolactone (PCL), and poly(butylene succinate) (PBS) at hydrolytic rates of 3 μmol h−1 mg−1 protein, 1.1 mg h−1 mg−1 protein, 203.6 mg h−1 mg−1 protein, and 56.4 mg h−1 mg−1 protein, respectively. Because of these unique biochemical properties, TtcutA of T. terrestris may be useful in various industrial applications in the future.
Crystal structure of human angiogenin with an engineered loop exhibits conformational flexibility at the functional regions of the molecule
Authors: Thiyagarajan Nethaji , Acharya K. Ravi
Published: December 2012

Human angiogenin (ANG) is an angiogenic molecule and a ribonucleolytic enzyme with significant amino acid sequence identity to pancreatic RNase A, plays a critical role in the establishment and growth of tumours. An association between ANG and cancer has been observed in more than 25 clinical studies to date. In addition, ANG has now been shown to be implicated in Amyotrophic Lateral Sclerosis (ALS) and Parkinson's Disease (PD). Structural and biochemical studies so far have showed several distinguishing features of ANG molecule compared to RNase A and provided details of the putative cell binding site, active site, nuclear translocation sequence and the roles of residues in binding and cleaving RNA. A key finding elucidated from the structural study on ANG is the presence of a ‘blocked’ C‐terminus (part of the active site apparatus) compared with RNase A. Here we report the crystal structure of ANG with an ‘engineered‐loop’ from eosinophil derived neurotoxin (a homologue of ANG) which has resulted with local perturbations (conformational flexibility) at the cell binding site and at the C‐terminus of the molecule. This experimental observation will now provide a new avenue to design compounds (potent inhibitors) through a structure guided drug design route.
Inanspruchnahme von Hilfen bei Pathologischem Glücksspielen
Authors: Bischof Anja , Meyer Christian , Bischof Gallus , Kastirke Nadin , John Ulrich , Rumpf Hans-Jürgen
Published: December 2012

Ziel: Die vorliegende Studie berichtet über die Inanspruchnahme von suchtspezifischen Hilfen bei Pathologischen Glücksspielern. Methode: Die Bevölkerungsstichprobe basiert auf 15 023 Probanden, deren Telefonnummern zufällig gezogen wurden. Zusätzlich wurden in 39 Glücksspielstätten 303 Spieler befragt. Mit einem computergestützten telefonischen Interview wurden Spielverhalten und Spielprobleme bezogen auf die Lebenszeit erfragt. In beiden Stichproben zusammen wurden 232 Probanden erfasst, die im Verlauf ihres Lebens pathologisch gespielt hatten. Von ihnen erhielten 105 Personen ein vertiefendes klinisches Interview. Ergebnisse: Von den Befragten berichteten 20 % Kontakt zum Hilfesystem im Verlauf ihres Lebens. Weitergehenden Kontakt berichteten 10,5 %, am häufigsten wurden Suchtberatungsstellen (5,7 %), Selbsthilfegruppen (4,8 %) und ambulante Psychotherapie (3,8 %) genannt. Inanspruchnahme formeller Hilfen war mit der Problemschwere assoziiert (p = .022). Außerdem zeigte sich ein Zusammenhang zwischen bestimmten DSM-IV Kriterien und dem Kontakt zum Hilfesystem. Schlussfolgerungen: Es ist von einer gravierenden Unterversorgung Pathologischer Glücksspieler auszugehen. Glücksspielspezifische Hilfeangebote scheinen die Betroffenen bislang nicht in ausreichendem Maße zu erreichen.
The fuzzy coat of pathological human Tau fibrils is a two-layered polyelectrolyte brush
Authors: Wegmann Susanne , Medalsy Izhar D. , Mandelkow Eckhard , Müller Daniel J.
Published: December 2012

The structure and properties of amyloid-like Tau fibrils accumulating in neurodegenerative diseases have been debated for decades. Although the core of Tau fibrils assembles from short β-strands, the properties of the much longer unstructured Tau domains protruding from the fibril core remain largely obscure. Applying immunogold transmission EM, and force-volume atomic force microscopy (AFM), we imaged human Tau fibrils at high resolution and simultaneously mapped their mechanical and adhesive properties. Tau fibrils showed a ≈16-nm–thick fuzzy coat that resembles a two-layered polyelectrolyte brush, which is formed by the unstructured short C-terminal and long N-terminal Tau domains. The mechanical and adhesive properties of the fuzzy coat are modulated by electrolytes and pH, and thus by the cellular environment. These unique properties of the fuzzy coat help in understanding how Tau fibrils disturb cellular interactions and accumulate in neurofibrillary tangles.
Activation of NF-κB signalling by fusicoccin-induced dimerization
Authors: Skwarczynska Malgorzata , Molzan Manuela , Ottmann Christian
Published: December 2012

Chemically induced dimerization is an important tool in chemical biology for the analysis of protein function in cells. Here we report the use of the natural product fusicoccin (FC) to induce dimerization of 14–3-3–fused target proteins with proteins tagged to the C terminus (CT) of the H
+
-ATPase PMA2. To prevent nonproductive or detrimental interactions of the 14-3-3 proteins and CT fusions with endogenous cell proteins, their interaction surface was engineered to facilitate FC-induced dimerization exclusively between the introduced protein constructs. Live-cell imaging documented the reversible FC-induced translocation of 14-3-3 and CT to different cell compartments depending on localization sequences fused to their dimerization partner protein. The functionality of this system was demonstrated by the FC-induced importation of the NF-κB-CT into the nucleus. In HeLa cells, FC-mediated dimerization of the NF-κB-CT with a constitutively nuclear-localized 14-3-3 protein led to an NF-κB–specific cellular response by inducing IL-8 secretion.
Genealogies of rapidly adapting populations
Authors: Neher Richard A. , Hallatschek Oskar
Published: December 2012

The genetic diversity of a species is shaped by its recent evolutionary history and can be used to infer demographic events or selective sweeps. Most inference methods are based on the null hypothesis that natural selection is a weak or infrequent evolutionary force. However, many species, particularly pathogens, are under continuous pressure to adapt in response to changing environments. A statistical framework for inference from diversity data of such populations is currently lacking. Towards this goal, we explore the properties of genealogies in a model of continual adaptation in asexual populations. We show that lineages trace back to a small pool of highly fit ancestors, in which almost simultaneous coalescence of more than two lineages frequently occurs. Whereas such multiple mergers are unlikely under the neutral coalescent, they create a unique genetic footprint in adapting populations. The site frequency spectrum of derived neutral alleles, for example, is nonmonotonic and has a peak at high frequencies, whereas Tajima’s
D
becomes more and more negative with increasing sample size. Because multiple merger coalescents emerge in many models of rapid adaptation, we argue that they should be considered as a null model for adapting populations.
AtABCA9 transporter supplies fatty acids for lipid synthesis to the endoplasmic reticulum
Authors: Kim Sangwoo , Yamaoka Yasuyo , Ono Hirofumi , Kim Hanul , Shim Donghwan , Maeshima Masayoshi , Martinoia Enrico , Cahoon Edgar B. , Nishida Ikuo , Lee Youngsook
Published: December 2012

Fatty acids, the building blocks of biological lipids, are synthesized in plastids and then transported to the endoplasmic reticulum (ER) for assimilation into specific lipid classes. The mechanism of fatty acid transport from plastids to the ER has not been identified. Here we report that AtABCA9, an ABC transporter in
Arabidopsis thaliana
, mediates this transport. AtABCA9 was localized to the ER, and
atabca9
null mutations reduced seed triacylglycerol (TAG) content by 35% compared with WT. Developing
atabca9
seeds incorporated 35% less
14
C-oleoyl-CoA into TAG compared with WT seeds. Furthermore, overexpression of
AtABCA9
enhanced TAG deposition by up to 40%. These data strongly support a role for AtABCA9 as a supplier of fatty acid substrates for TAG biosynthesis at the ER during the seed-filling stage. AtABCA9 may be a powerful tool for increasing lipid production in oilseeds.
Neuroligin-1 controls synaptic abundance of NMDA-type glutamate receptors through extracellular coupling
Authors: Budreck Elaine C. , Kwon Oh-Bin , Jung Jung Hoon , Baudouin Stephane , Thommen Albert , Kim Hye-Sun , Fukazawa Yugo , Harada Harumi , Tabuchi Katsuhiko , Shigemoto Ryuichi , Scheiffele Peter , Kim Joung-Hun
Published: December 2012

Despite the pivotal functions of the NMDA receptor (NMDAR) for neural circuit development and synaptic plasticity, the molecular mechanisms underlying the dynamics of NMDAR trafficking are poorly understood. The cell adhesion molecule neuroligin-1 (NL1) modifies NMDAR-dependent synaptic transmission and synaptic plasticity, but it is unclear whether NL1 controls synaptic accumulation or function of the receptors. Here, we provide evidence that NL1 regulates the abundance of NMDARs at postsynaptic sites. This function relies on extracellular, NL1 isoform-specific sequences that facilitate biochemical interactions between NL1 and the NMDAR GluN1 subunit. Our work uncovers NL1 isoform-specific
cis
-interactions with ionotropic glutamate receptors as a key mechanism for controlling synaptic properties.
Striatal GABAergic and cortical glutamatergic neurons mediate contrasting effects of cannabinoids on cortical network synchrony
Authors: Sales-Carbonell Carola , Rueda-Orozco Pavel E. , Soria-Gómez Edgar , Buzsáki György , Marsicano Giovanni , Robbe David
Published: December 2012

Activation of type 1 cannabinoid receptors (CB1R) decreases GABA and glutamate release in cortical and subcortical regions, with complex outcomes on cortical network activity. To date there have been few attempts to disentangle the region- and cell-specific mechanisms underlying the effects of cannabinoids on cortical network activity in vivo. Here we addressed this issue by combining in vivo electrophysiological recordings with local and systemic pharmacological manipulations in conditional mutant mice lacking CB1R expression in different neuronal populations. First we report that cannabinoids induce hypersynchronous thalamocortical oscillations while decreasing the amplitude of faster cortical oscillations. Then we demonstrate that CB1R at striatonigral synapses (basal ganglia direct pathway) mediate the thalamocortical hypersynchrony, whereas activation of CB1R expressed in cortical glutamatergic neurons decreases cortical synchrony. Finally we show that activation of CB1 expressed in cortical glutamatergic neurons limits the cannabinoid-induced thalamocortical hypersynchrony. By reporting that CB1R activations in cortical and subcortical regions have contrasting effects on cortical synchrony, our study bridges the gap between cellular and in vivo network effects of cannabinoids. Incidentally, the thalamocortical hypersynchrony we report suggests a potential mechanism to explain the sensory “high” experienced during recreational consumption of marijuana.
Surface structural-chemical characterization of a single-site d
0
heterogeneous arene hydrogenation catalyst having 100% active sites
Authors: Williams Linda A. , Guo Neng , Motta Alessandro , Delferro Massimiliano , Fragalà Ignazio L. , Miller Jeffrey T. , Marks Tobin J.
Published: December 2012

Structural characterization of the catalytically significant sites on solid catalyst surfaces is frequently tenuous because their fraction, among all sites, typically is quite low. Here we report the combined application of solid-state
13
C-cross-polarization magic angle spinning nuclear magnetic resonance (
13
C-CPMAS-NMR) spectroscopy, density functional theory (DFT), and Zr X-ray absorption spectroscopy (XAS) to characterize the adsorption products and surface chemistry of the precatalysts (η
5
-C
5
H
5
)
2
ZrR
2
(R = H, CH
3
) and [η
5
-C
5
(CH
3
)
5
]Zr(CH
3
)
3
adsorbed on Brønsted superacidic sulfated alumina (AlS). The latter complex is exceptionally active for benzene hydrogenation, with ∼100% of the Zr sites catalytically significant as determined by kinetic poisoning experiments. The
13
C-CPMAS-NMR, DFT, and XAS data indicate formation of organozirconium cations having a largely electrostatic [η
5
-C
5
(CH
3
)
5
]Zr(CH
3
)
2
+
···AlS
−
interaction with greatly elongated Zr···O
AlS
distances of ∼2.35(2) Å. The catalytic benzene hydrogenation cycle is stepwise understandable by DFT, and proceeds via turnover-limiting H
2
delivery to surface [η
5
-C
5
(CH
3
)
5
]ZrH
2
(benzene)
+
···AlS
−
species, observable by solid-state NMR and XAS.
Movement and Habitat Differentiation among Adult Shoal Bass, Largemouth Bass, and Spotted Bass in the Upper Flint River, Georgia
Authors: Goclowski Matthew R. , Kaeser Adam J. , Sammons Steven M.
Published: December 2012

The Shoal Bass Micropterus cataractae is a fluvial specialist endemic to the Apalachicola River drainage in Alabama, Florida, and Georgia that has experienced declines throughout much of its range. The Flint River, Georgia, represents the largest remaining intact ecosystem for Shoal Bass in their native range. Spotted Bass M. punctulatus have recently been introduced into this system, causing concern about the potential negative impacts the species may have on the native populations of Shoal Bass and Largemouth Bass M. salmoides. To assess the symmetry and strength of competition and gain the greatest perspective on the interrelationships among these sympatric, congeneric species, we compared the movement patterns and habitat use of all three species of black bass present in this system. Fifteen Shoal Bass, 10 Largemouth Bass, and 6 Spotted Bass were implanted with radio transmitters in the Flint River and tracked for a period of 1 year (2008). Daily and hourly movements did not vary among species or season, though individuals of each species were observed moving >5 km to shoal complexes during spring. Habitat overlap varied between species during the study; overlap was highest between Spotted Bass and Largemouth Bass, intermediate between Spotted Bass and Shoal Bass, and lowest between Shoal Bass and Largemouth Bass. Shoal Bass tended to select coarse rocky habitat, while Largemouth Bass tended to select depositional habitat. Spotted Bass exhibited the widest niche breadth and generally used habitat in proportion to its availability. Use of similar habitats by these three species during the spring spawning period highlights the potential risk of genetic introgression of the two native species by introduced Spotted Bass. Physical barriers that restrict access to habitat during long-distance seasonal movements, as observed for several Shoal Bass in this study, may negatively impact populations of this species.

Received March 31, 2012; accepted October 12, 2012
Network Analysis of Functional Genomics Data: Application to Avian Sex-Biased Gene Expression
Authors: Frings Oliver , Mank Judith E. , Alexeyenko Andrey , Sonnhammer Erik L. L.
Published: December 2012

Gene expression analysis is often used to investigate the molecular and functional underpinnings of a phenotype. However, differential expression of individual genes is limited in that it does not consider how the genes interact with each other in networks. To address this shortcoming we propose a number of network-based analyses that give additional functional insights into the studied process. These were applied to a dataset of sex-specific gene expression in the chicken gonad and brain at different developmental stages. We first constructed a global chicken interaction network. Combining the network with the expression data showed that most sex-biased genes tend to have lower network connectivity, that is, act within local network environments, although some interesting exceptions were found. Genes of the same sex bias were generally more strongly connected with each other than expected. We further studied the fates of duplicated sex-biased genes and found that there is a significant trend to keep the same pattern of sex bias after duplication. We also identified sex-biased modules in the network, which reveal pathways or complexes involved in sex-specific processes. Altogether, this work integrates evolutionary genomics with systems biology in a novel way, offering new insights into the modular nature of sex-biased genes.
Muscle Wasting and Resistance of Muscle Anabolism: The “Anabolic Threshold Concept” for Adapted Nutritional Strategies during Sarcopenia
Authors: Dardevet Dominique , Rémond Didier , Peyron Marie-Agnès , Papet Isabelle , Savary-Auzeloux Isabelle , Mosoni Laurent
Published: December 2012

Skeletal muscle loss is observed in several physiopathological situations. Strategies to prevent, slow down, or increase recovery of muscle have already been tested. Besides exercise, nutrition, and more particularly protein nutrition based on increased amino acid, leucine or the quality of protein intake has generated positive acute postprandial effect on muscle protein anabolism. However, on the long term, these nutritional strategies have often failed in improving muscle mass even if given for long periods of time in both humans and rodent models. Muscle mass loss situations have been often correlated to a resistance of muscle protein anabolism to food intake which may be explained by an increase of the anabolic threshold toward the stimulatory effect of amino acids. In this paper, we will emphasize how this anabolic resistance may affect the intensity and the duration of the muscle anabolic response at the postprandial state and how it may explain the negative results obtained on the long term in the prevention of muscle mass. Sarcopenia, the muscle mass loss observed during aging, has been chosen to illustrate this concept but it may be kept in mind that it could be extended to any other catabolic states or recovery situations.
Sorafenib Inhibits Tumor Growth and Improves Survival in a Transgenic Mouse Model of Pancreatic Islet Cell Tumors
Authors: Fendrich Volker , Maschuw Katja , Rehm Johannes , Buchholz Malte , Holler Julia P. , Slater Emily P. , Bartsch Detlef K. , Waldmann Jens
Published: December 2012

Background. The purpose of the study was to evaluate Sorafenib (BAY 43-9006) derived receptor tyrosine kinase inhibition on tumor progression in murine islet cell tumors. Sorafenib is considered to be a potent inhibitor of tumor angiogenesis and neovascularization in various solid tumors. Rip1Tag2 mice were treated in two different groups according to the model of tumor progression: the early treatment group received vehicle or Sorafenib from 10 to 14 weeks of age and the late treatment group from week 12 until death. Tumor surface, tumor cell proliferation, and apoptosis were measured in both treatment groups to assess the in vivo effects of Sorafenib. Survival was recorded for the late treatment group. In the early treatment group Sorafenib led to a dramatic decrease in tumor volume compared to the control group. Apoptosis was significantly augmented and cell proliferation was inhibited. As a single therapy Sorafenib significantly improved survival in the late treatment group.Conclusion. Sorafenib may provide a new paradigm for the therapy of islet cell tumors.
Chronic-Alcohol-Abuse-Induced Oxidative Stress in the Development of Acute Respiratory Distress Syndrome
Authors: Liang Yan , Yeligar Samantha M. , Brown Lou Ann S.
Published: December 2012

Chronic alcohol ingestion increases the risk of developing acute respiratory distress syndrome (ARDS), a severe form of acute lung injury, characterized by alveolar epithelial and endothelial barrier disruption and intense inflammation. Alcohol abuse is also associated with a higher incidence of sepsis or pneumonia resulting in a higher rate of admittance to intensive care, longer inpatient stays, higher healthcare costs, and a 2–4 times greater mortality rate. Chronic alcohol ingestion induced severe oxidative stress associated with increased ROS generation, depletion of the critical antioxidant glutathione (GSH), and oxidation of the thiol/disulfide redox potential in the alveolar epithelial lining fluid and exhaled breath condensate. Across intracellular and extracellular GSH pools in alveolar type II cells and alveolar macrophages, chronic alcohol ingestion consistently induced a 40–60 mV oxidation of GSH/GSSG suggesting that the redox potentials of different alveolar GSH pools are in equilibrium. Alcohol-induced GSH depletion or oxidation was associated with impaired functions of alveolar type II cells and alveolar macrophages but could be reversed by restoring GSH pools in the alveolar lining fluid. The aims of this paper are to address the mechanisms for alcohol-induced GSH depletion and oxidation and the subsequent effects in alveolar barrier integrity, modulation of the immune response, and apoptosis.
Gene Expression Network Reconstruction by LEP Method Using Microarray Data
Authors: You Na , Mou Peng , Qiu Ting , Kou Qiang , Zhu Huaijin , Chen Yuexi , Wang Xueqin
Published: December 2012

Gene expression network reconstruction using microarray data is widely studied aiming to investigate the behavior of a gene cluster simultaneously. Under the Gaussian assumption, the conditional dependence between genes in the network is fully described by the partial correlation coefficient matrix. Due to the high dimensionality and sparsity, we utilize the LEP method to estimate it in this paper. Compared to the existing methods, the LEP reaches the highest PPV with the sensitivity controlled at the satisfactory level. A set of gene expression data from the HapMap project is analyzed for illustration.
Mental Health Recovery: Evaluation of a Recovery-Oriented Training Program
Authors: Wilrycx G. K. M. L. , Croon M. A. , van den Broek A. H. S. , van Nieuwenhuizen Ch.
Published: December 2012

Aim. This study investigates the effectiveness of a recovery-oriented training program on knowledge and attitudes of mental health care professionals towards recovery of people with serious mental illness.Methods. Using data from a longitudinal study of recovery, changes in knowledge and attitudes of 210 mental health care professionals towards recovery were explored using the Recovery Attitude Questionnaire and the Recovery Knowledge Inventory. The study uses a two-group multiple intervention interrupted time-series design which is a variant of the stepped-wedge trial design. A total of six measurements occasions took place.Results. This study shows that professionals' attitudes towards recovery from mental illness can improve with training. After two intensive recovery-oriented training sessions, mental health care professionals have a more positive attitude towards recovery in clinical practice.Conclusion. A recovery-oriented training program can change attitudes of mental health care professionals towards recovery of serious mental illness.
The Effect of Metabolic Syndrome upon the Success of Varicocelectomy
Authors: Ozturk Ufuk , Sener Nevzat Can , Nalbant Ismail , Karabacak Osman Raif , Ulusoy Mustafa Gurhan , Imamoglu M. Abdurrahim
Published: December 2012

We aimed to investigate the impact of metabolic syndrome (MetS) on the varicocele treatment. 101 patients underwent spermatic vein ligation between 2007 and 2010 were retrospectively analyzed. Those patients were divided into two groups as without (n: 56, Group 1) or with MetS (n: 48, Group 2). All the patients underwent left microsurgical subinguinal spermatic vein ligation. Groups were compared by the improvement on sperm parameters and spontaneous pregnancy rates at a mean of 19 (±4) months followup. When sperm parameters were compared postoperatively, the significant improvement in total sperm count, motile sperm count percentage, and normal sperm percentage was reported. The groups were compared to each other and the improvement seemed significantly better in Group 1. There was no statistically significant improvement difference in the normal sperm percentage between groups. Spontaneous pregnancy rate after two years was 45% in Group 1 and 34% in Group 2 (). Patients with MetS and varicocele improved after surgery, but not as well as the similar group without MetS. This may help to show that MetS can be a factor for male infertility.
ATARiS: Computational quantification of gene suppression phenotypes from multisample RNAi screens
Authors: Shao Diane D. , Tsherniak Aviad , Gopal Shuba , Weir Barbara A. , Tamayo Pablo , Stransky Nicolas , Schumacher Steven E. , Zack Travis I. , Beroukhim Rameen , Garraway Levi A. , Margolin Adam A. , Root David E. , Hahn William C. , Mesirov Jill P.
Published: December 2012

Genome-scale RNAi libraries enable the systematic interrogation of gene function. However, the interpretation of RNAi screens is complicated by the observation that RNAi reagents designed to suppress the mRNA transcripts of the same gene often produce a spectrum of phenotypic outcomes due to differential on-target gene suppression or perturbation of off-target transcripts. Here we present a computational method, Analytic Technique for Assessment of RNAi by Similarity (ATARiS), that takes advantage of patterns in RNAi data across multiple samples in order to enrich for RNAi reagents whose phenotypic effects relate to suppression of their intended targets. By summarizing only such reagent effects for each gene, ATARiS produces quantitative, gene-level phenotype values, which provide an intuitive measure of the effect of gene suppression in each sample. This method is robust for data sets that contain as few as 10 samples and can be used to analyze screens of any number of targeted genes. We used this analytic approach to interrogate RNAi data derived from screening more than 100 human cancer cell lines and identifiedHNF1Bas a transforming oncogene required for the survival of cancer cells that harborHNF1Bamplifications. ATARiS is publicly available athttp://broadinstitute.org/ataris.
A Digital Signal Processing Module for Time-Division Multiplexed Microcalorimeter Arrays
Authors: Tan H , Walby M , Hennig W , Warburton W , Grudberg P , Reintsema C , Bennett D , Doriese W , Ullom J
Published: December 2012

We have developed a digital signal processing module for real time processing of time-division multiplexed data from SQUID-coupled transition-edge sensor microcalorimeter arrays. It is a 3U PXI card consisting of a standardized core processor board and a daughter board. Through fiber-optic links on its front panel, the daughter board receives time-division multiplexed data (comprising error and feedback signals) and clocks from the digital-feedback cards developed at the National Institute of Standards and Technology. After mixing the error signal with the feedback signal in a field-programmable gate array, the daughter board transmits demultiplexed data to the core processor. Real-time processing in the field-programmable gate array of the core processor board includes pulse detection, pileup inspection, pulse height computation, and histogramming into on-board spectrum memory. Data from up to 128 microcalorimeter pixels can be processed by a single module in real time. Energy spectra, waveform, and run statistics data can be read out in real time through the PCI bus by a host computer at a maximum rate of ~100 MB/s. The module's hardware architecture, mechanism for synchronizing with NIST's digital-feedback, and count rate capability are presented.
Model‐Driven and Risk‐Based Performance Analysis of Industrial Emergency Plans
Authors: Karagiannis Georgios Marios , Piatyszek Eric , Flaus Jean‐Marie
Published: December 2012

This paper presents a methodology for the assessment of the performance of industrial hazardous materials emergency plans. This approach is based on a structuro‐functional model of the emergency plan, which highlights the plan's functions, resources, support services and interactions. A resource taxonomy is used to manage the complexity of the emergency response system. The model can be used both as a planning guide and for the analysis of the performance of the emergency response system, based on the risk assessment of the system. The failure probability is estimated through the plan's functions and resources fault trees. The failure severity of each function is determined by using the facility's hazard study. The failure criticality of each function is hence obtained.
An assessment of the antioxidant potential of coriander extracts in ghee when stored at high temperature and during deep fat frying
Authors: Patel Shriyesh , Shende Sneha , Arora Sumit , Singh Ashish K
Published: December 2012

A coriander extract was evaluated for its potential to increase oxidative stability of ghee. Antioxidant activity using β‐carotene–linoleic acid model system and radical scavenging activity by 2‐diphenyl‐1‐picrylhydrazyl hydrate free (DPPH) was higher in steam distilled extract compared to its oleoresin counterpart. Steam distilled extract and oleoresin were significantly effective in retarding the deterioration of ghee relative to control, as observed in peroxide value, conjugated dienes, thiobarbituric acid (TBA) value and oxidative stability index at the end of 21 days of storage. However, these were less effective than butylated hydroxyanisole (BHA). During deep fat frying, steam distilled extracts showed higher antioxidant activity compared to oleoresin and BHA.