bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sound can suppress visual perception
Authors: Hidaka Souta , Ide Masakazu 
Published: May 2015

AbstractIn a single modality, the percept of an input (e.g., voices of neighbors) is often suppressed by another (e.g., the sound of a car horn nearby) due to close interactions of neural responses to these inputs. Recent studies have also suggested that close interactions of neural responses could occur even across sensory modalities, especially for audio-visual interactions. However, direct behavioral evidence regarding the audio-visual perceptual suppression effect has not been reported in a study with humans. Here, we investigated whether sound could have a suppressive effect on visual perception. We found that white noise bursts presented through headphones degraded visual orientation discrimination performance. This auditory suppression effect on visual perception frequently occurred when these inputs were presented in a spatially and temporally consistent manner. These results indicate that the perceptual suppression effect could occur across auditory and visual modalities based on close and direct neural interactions among those sensory inputs.
Assessing the potential of atomistic molecular dynamics simulations to probe reversible protein-protein recognition and binding
Authors: Abriata Luciano A. , Dal Peraro Matteo 
Published: May 2015

AbstractProtein-protein recognition and binding are governed by diffusion, noncovalent forces and conformational flexibility, entangled in a way that only molecular dynamics simulations can dissect at high resolution. Here we exploited ubiquitin’s noncovalent dimerization equilibrium to assess the potential of atomistic simulations to reproduce reversible protein-protein binding, by running submicrosecond simulations of systems with multiple copies of the protein at millimolar concentrations. The simulations essentially fail because they lead to aggregates, yet they reproduce some specificity in the binding interfaces as observed in known covalent and noncovalent ubiquitin dimers. Following similar observations in literature we hint at electrostatics and water descriptions as the main liable force field elements and propose that their optimization should consider observables relevant to multi-protein systems and unfolded proteins. Within limitations, analysis of binding events suggests salient features of protein-protein recognition and binding, to be retested with improved force fields. Among them, that specific configurations of relative direction and orientation seem to trigger fast binding of two molecules, even over 50 Å distances; that conformational selection can take place within surface-to-surface distances of 10 to 40 Å i.e. well before actual intermolecular contact; and that establishment of contacts between molecules further locks their conformations and relative orientations.
Effects of Aβ exposure on long-term associative memory and its neuronal mechanisms in a defined neuronal network
Authors: Ford Lenzie , Crossley Michael , Williams Thomas , Thorpe Julian R. , Serpell Louise C. , Kemenes György 
Published: May 2015

AbstractAmyloid beta (Aβ) induced neuronal death has been linked to memory loss, perhaps the most devastating symptom of Alzheimer’s disease (AD). Although Aβ-induced impairment of synaptic or intrinsic plasticity is known to occur before any cell death, the links between these neurophysiological changes and the loss of specific types of behavioral memory are not fully understood. Here we used a behaviorally and physiologically tractable animal model to investigate Aβ-induced memory loss and electrophysiological changes in the absence of neuronal death in a defined network underlying associative memory. We found similar behavioral but different neurophysiological effects for Aβ 25-35 and Aβ 1-42 in the feeding circuitry of the snail Lymnaea stagnalis. Importantly, we also established that both the behavioral and neuronal effects were dependent upon the animals having been classically conditioned prior to treatment, since Aβ application before training caused neither memory impairment nor underlying neuronal changes over a comparable period of time following treatment.
Extreme ultra-low lasing threshold of full-polymeric fundamental microdisk printed with room-temperature atmospheric ink-jet technique
Authors: Yoshioka Hiroaki , Ota Tomoya , Chen Cong , Ryu Soichiro , Yasui Kei , Oki Yuji 
Published: May 2015

AbstractWe experimentally demonstrated an extreme ultra-low lasing threshold from full-polymeric fundamental microdisk cavities fabricated by a novel fabrication method, the ink-jet printing method, which is much simpler and easier than previous methods such as lithography. The ink-jet printing method provides additive, room-temperature atmospheric, rapid fabrication with only two steps: (i) stacking cladding pedestal and waveguiding disk spots using the ink-jet technique and (ii) partial etching of the cladding pedestal envelope. Two kinds of low-viscosity polymers successfully formed microdisks with high surface homogeneity and one of the polymers doped with LDS798 dye yielded whispering-gallery-mode lasing. The fundamental disks exhibited an extremely ultra-low lasing threshold of 0.33 μJ/mm2 at a wavelength of 817.3 nm. To the best of our knowledge, this lasing threshold is the lowest threshold obtained among both organic and inorganic fundamental microdisk cavity lasers with a highly confined structure.
Reduced Carrier Recombination in PbS - CuInS2 Quantum Dot Solar Cells
Authors: Sun Zhenhua , Sitbon Gary , Pons Thomas , Bakulin Artem A. , Chen Zhuoying 
Published: May 2015

AbstractEnergy loss due to carrier recombination is among the major factors limiting the performance of TiO2/PbS colloidal quantum dot (QD) heterojunction solar cells. In this work, enhanced photocurrent is achieved by incorporating another type of hole-transporting QDs, Zn-doped CuInS2 (Zn-CIS) QDs into the PbS QD matrix. Binary QD solar cells exhibit a reduced charge recombination associated with the spatial charge separation between these two types of QDs. A ~30% increase in short-circuit current density and a ~20% increase in power conversion efficiency are observed in binary QD solar cells compared to cells built from PbS QDs only. In agreement with the charge transfer process identified through ultrafast pump/probe spectroscopy between these two QD components, transient photovoltage characteristics of single-component and binary QDs solar cells reveal longer carrier recombination time constants associated with the incorporation of Zn-CIS QDs. This work presents a straightforward, solution-processed method based on the incorporation of another QDs in the PbS QD matrix to control the carrier dynamics in colloidal QD materials and enhance solar cell performance.
Endotoxic shock-expanded murine CD11clowCD45RB+ regulatory dendritic cells modulate inflammatory T cell responses through multiple mechanisms
Authors: Wang Xiaoqian , Wang Qingyang , Zhang Xueying , Li Yajing , Wang Jingyang , Hou Chunmei , Chen Juan , Shen Beifen , Shi Yanchun , Zhang Jiyan 
Published: May 2015

AbstractChanges in the number and function of dendritic cells (DCs) have been reported to play an important role in endotoxin tolerance. It has been reported that expansion of splenic CD11clowCD45RB+ DCs occurs in mice injected with sublethal doses of lipopolysaccharide (LPS). However, the function of endotoxic shock-expanded CD11clowCD45RB+ DCs has not been examined. In this work, we show that endotoxic shock promotes the expansion of CD11clowCD45RB+ cells with dendritic morphology and the production of low levels of inflammatory cytokines and costimulatory molecules. The expanded cells induce the generation of regulatory T cells (Tregs), show incapability to stimulate T cells and induce apoptosis of CD4+ T cells in vitro. As compared to CD11chiCD45RB− conventional DCs, the expanded cells exert better protection against colitis induction by CD4+ CD25− T cells, even though both subpopulations show similar ability to induce Tregs in vivo. The better control of proinflammatory cytokine responses in vivo by the expanded cells is associated with more apoptosis in the Payer’s patches and in colonic tissue-infiltrating cells. Thus, the expanded cells can modulate inflammatory T cell responses through multiple mechanisms. Our study facilitates a better understanding how innate immune responses may shape adaptive immunity and immune suppression following LPS-induced acute inflammation.
Detection of Nitro-Based and Peroxide-Based Explosives by Fast Polarity-Switchable Ion Mobility Spectrometer with Ion Focusing in Vicinity of Faraday Detector
Authors: Zhou Qinghua , Peng Liying , Jiang Dandan , Wang Xin , Wang Haiyan , Li Haiyang 
Published: May 2015

AbstractIon mobility spectrometer (IMS) has been widely deployed for on-site detection of explosives. The common nitro-based explosives are usually detected by negative IMS while the emerging peroxide-based explosives are better detected by positive IMS. In this study, a fast polarity-switchable IMS was constructed to detect these two explosive species in a single measurement. As the large traditional Faraday detector would cause a trailing reactant ion peak (RIP), a Faraday detector with ion focusing in vicinity was developed by reducing the detector radius to 3.3 mm and increasing the voltage difference between aperture grid and its front guard ring to 591 V, which could remove trailing peaks from RIP without loss of signal intensity. This fast polarity-switchable IMS with ion focusing in vicinity of Faraday detector was employed to detect a mixture of 10 ng 2,4,6-trinitrotoluene (TNT) and 50 ng hexamethylene triperoxide diamine (HMTD) by polarity-switching and the result suggested that [TNT-H]− and [HMTD+H]+ could be detected in a single measurement. Furthermore, the removal of trailing peaks from RIP by the Faraday detector with ion focusing in vicinity also promised the accurate identification of KClO4, KNO3 and S in common inorganic explosives, whose product ion peaks were fairly adjacent to RIP.
Cross-species comparative analysis of Dicer proteins during Sindbis virus infection
Authors: Girardi Erika , Lefèvre Mathieu , Chane-Woon-Ming Béatrice , Paro Simona , Claydon Bill , Imler Jean-Luc , Meignin Carine , Pfeffer Sébastien 
Published: May 2015

AbstractIn plants and invertebrates RNA silencing is a major defense mechanism against virus infections. The first event in RNA silencing is dicing of long double stranded RNAs into small interfering RNAs (siRNAs). The Dicer proteins involved in this process are phylogenetically conserved and have the same domain organization. Accordingly, the production of viral derived siRNAs has also been observed in the mouse, but only in restricted cell types. To gain insight on this restriction, we compare the dicing activity of human Dicer and fly Dicer-2 in the context of Sindbis virus (SINV) infection. Expression of human Dicer in flies inefficiently rescues the production of viral siRNAs but confers some protection against SINV. Conversely, expression of Dicer-2 in human cells allows the production of viral 21 nt small RNAs. However, this does not confer resistance to viral infection, but on the contrary results in stronger accumulation of viral RNA. We further show that Dicer-2 expression in human cells perturbs interferon (IFN) signaling pathways and antagonizes protein kinase R (PKR)-mediated antiviral immunity. Overall, our data suggest that a functional incompatibility between the Dicer and IFN pathways explains the predominance of the IFN response in mammalian somatic cells.
A variant of PSMD6 is associated with the therapeutic efficacy of oral antidiabetic drugs in Chinese type 2 diabetes patients
Authors: Chen Miao , Hu Cheng , Zhang Rong , Jiang Feng , Wang Jie , Peng Danfeng , Tang Shanshan , Sun Xue , Yan Jing , Wang Shiyun , Wang Tao , Bao Yuqian , Jia Weiping 
Published: May 2015

AbstractThe PSMD6 variant rs831571 has been identified as a susceptibility locus for type 2 diabetes mellitus (T2DM). This study aimed to investigate the association of this variant with therapeutic effects of oral antidiabetic drugs in Chinese T2DM patients. 209 newly diagnosed T2DM patients were randomly assigned to treatment with repaglinide or rosiglitazone for 48 weeks and the therapeutic effects were compared. In the rosiglitazone cohort, rs831571 showed significant associations with fasting plasma glucose (FPG), 2-h glucose and decrement of glycated haemoglobin (HbA1c) levels after 24 weeks of treatment (P = 0.0368, 0.0468 and 0.0247, respectively). The C allele was significantly associated with a better attainment of FPG at 24 and 32 weeks (P = 0.0172 and 0.0257, respectively). Survival analyses showed CC homozygotes were more likely to attain a standard FPG level (P = 0.0654). In the repaglinide cohort, rs831571 was significantly associated with decreased HbA1c levels after 24 weeks of treatment, the homeostatic model assessment of insulin resistance and fasting insulin level after 48 weeks of treatment with repaglinide (P = 0.0096, 0235 and 0.0212, respectively). In conclusion, we observed that the PSMD6 variant rs831571 might be associated with the therapeutic effects of rosiglitazone and repaglinide in Chinese T2DM patients. However, these findings need to be confirmed in the future.
Nonequilibrium fluctuations as a distinctive feature of weak localization
Authors: Barone C. , Romeo F. , Pagano S. , Attanasio C. , Carapella G. , Cirillo C. , Galdi A. , Grimaldi G. , Guarino A. , Leo A. , Nigro A. , Sabatino P. 
Published: May 2015

AbstractTwo-dimensional materials, such as graphene, topological insulators, and two-dimensional electron gases, represent a technological playground to develop coherent electronics. In these systems, quantum interference effects and in particular weak localization, are likely to occur. These coherence effects are usually characterized by well-defined features in dc electrical transport, such as a resistivity increase and negative magnetoresistance below a crossover temperature. Recently, it has been shown that in magnetic and superconducting compounds, undergoing a weak-localization transition, a specific low-frequency 1/f noise occurs. An interpretation in terms of nonequilibrium universal conductance fluctuations has been given. The universality of this unusual electric noise mechanism has been here verified by detailed voltage-spectral density investigations on ultrathin copper films. The reported experimental results validate the proposed theoretical framework and also provide an alternative methodology to detect weak-localization effects by using electric noise spectroscopy.
Complex Interactions Between the Macrophyte Acorus Calamus and Microbial Fuel Cells During Pyrene and Benzo[a]Pyrene Degradation in Sediments
Authors: Yan Zaisheng , Jiang Helong , Cai Haiyuan , Zhou Yanli , Krumholz Lee R. 
Published: May 2015

AbstractThis study investigated the interaction of the macrophyte Acorus calamus and sediment microbial fuel cells (SMFC) during the degradation of high molecular weight-polycyclic aromatic hydrocarbons (HMW-PAHs) in sediments. Over 367-days, the combination of macrophyte and SMFC led to an increase in pyrene and benzo[a]pyrene degradation rates by at least 70% compared to SMFC or macrophyte alone. While either the macrophyte or SMFC increased redox potential in sediments, redox potentials near the anode (approximately 6 cm depth) in the macrophyte-SMFC combination were markedly lower than that in the only macrophyte treatment. Moreover, rhizospheric bacterial communities in macrophyte-SMFC and macrophyte treatments were distinctly different. Aerobic genera (Vogesella, Pseudomonas, Flavobacterium and Rhizobium) and anaerobic genera (Longilinea, Bellilinea, Desulfobacca and Anaeromyxobacter) became dominant in the rhizosphere in macrophyte and macrophyte-SMFC treatments, respectively. In addition, the macrophyte-SMFC combination improved the numbers of not only aerobic but anaerobic PAHs degraders in sediments. So, the SMFC employment facilitated the formation of anoxic zones in sediments with oxygen loss and exudates from the roots. As a result, cooperation of anaerobic/aerobic microbial metabolism for accelerating HMW-PAHs removal occurred within sediments after combining macrophytes with SMFC.
Host species vary in infection probability, sub-lethal effects and costs of immune response when exposed to an amphibian parasite
Authors: Bielby Jon , Fisher Matthew C. , Clare Frances C. , Rosa Gonçalo M. , Garner Trenton W. J. 
Published: May 2015

AbstractThe amphibian parasite Batrachochytrium dendrobatidis (Bd) is regarded as an extreme generalist, infecting over 500 species, but amongst these hosts there exists a great deal of variation in the susceptibility to and the costs of parasite exposure. We use two infection experiments to determine whether inter-specific variation in the sublethal and lethal effects of parasite exposure exist in two host species. We then tested the relative roles of host density and diversity on infection probability of a focal susceptible host. Our results show significant heterogeneity in host species response to parasite exposure and that both lethal and sub-lethal costs exist in individuals that are able to resist infection, indicating that successful immune response to infection comes at a cost. Further, we show that increasing host density significantly increased the likelihood of susceptible individuals becoming infected with Bd irrespective of host diversity and variation in host susceptibility. These results suggest that populations of resistant species are likely to suffer ill-effects of exposure to Bd regardless of their infection status and that at the stage of initial infection there was no support for the dilution of transmission events, in contrast to other studies that focus on subsequent transmission of infection.
Power quality improvement in a low‐voltage DC ceiling grid powered system
Authors: Nallusamy Subashini , Velayutham Dharmalingam , Govindarajan Uma , Parvathyshankar Deivasundari 
Published: May 2015

Power quality is an important issue in low‐voltage DC (LVDC) grids which drives light‐emitting diode lighting system and many other DC loads in residential applications. The requirement of high‐quality power to the lighting system necessitates power factor correction (PFC). This study presents a three‐phase modular AC‐to‐DC converter with a simple controller for PFC in LVDC grids under balanced and unbalanced supply voltage conditions. The proposed circuit consists of three separate single‐phase boost converter modules. Each module includes a diode rectifier at the front end, followed by a boost converter. The main advantage of this converter is module loss operation where the DC supply given to the lighting system and other DC loads will be continued even in case of failure of one module. The 24 V DC output voltage is regulated using an outer proportional‐integral controller and the input current wave shape in each phase is improved by three individual hysteresis controllers. The controller works successfully in tracking the reference voltage changes in order to vary the regulated DC output voltage. The effectiveness of the controller has been verified by the results obtained through MATLAB/SIMULINK. A prototype model has been developed to validate this system and tested using dSPACE1104 processor.
Direct observation of DNA overwinding by reverse gyrase
Authors: Ogawa Taisaku , Yogo Katsunori , Furuike Shou , Sutoh Kazuo , Kikuchi Akihiko , Kinosita Kazuhiko 
Published: May 2015

Significance
Reverse gyrase resides in bacteria that live in hot conditions. The enzyme further intertwines the double helix of DNA to make it tighter. In biochemical assays, reverse gyrase appears quite inefficient, requiring many enzyme molecules per DNA and yet taking many minutes to wind it up. Here, we show that one reverse gyrase molecule rapidly overwinds relaxed DNA but begins to idle as torsion accumulates. Excess torsion would hamper replication/transcription activities, whereas quick restoration of modest torsion prevents thermal denaturation of DNA. We discuss how reverse gyrase lets one strand of DNA pass the other in a preferred direction to achieve overwinding.
Liver X receptors alpha and beta promote myelination and remyelination in the cerebellum
Authors: Meffre Delphine , Shackleford Ghjuvan’Ghjacumu , Hichor Mehdi , Gorgievski Victor , Tzavara Eleni T. , Trousson Amalia , Ghoumari Abdel M. , Deboux Cyrille , Nait Oumesmar Brahim , Liere Philippe , Schumacher Michael , Baulieu Etienne-Emile , Charbonnier Frédéric , Grenier Julien , Massaad Charbel 
Published: May 2015

Significance
Liver X receptors (LXRs) α and β are the two major receptors of oxysterols, oxygenated derivatives of cholesterol. They control the homeostasis of cholesterol, an important lipid constituent of myelin sheaths. In the central nervous system, these insulating structures are generated by oligodendrocytes and are stabilized by myelin proteins. Here, we provide evidence of a new role of LXRs in the myelin physiology of the cerebellum. Mice invalidated for both LXRs exhibit alteration in motor coordination and spatial learning linked with myelination deficits. We demonstrated that LXRs intervene both in oligodendroglial cell maturation and in the transcriptional control of myelin gene expression during (re)myelination processes.
Utilization of Bacillus sp. strain TAT105 as a biological additive to reduce ammonia emissions during composting of swine feces
Authors: Kuroda Kazutaka , Waki Miyoko , Yasuda Tomoko , Fukumoto Yasuyuki , Tanaka Akihiro , Nakasaki Kiyohiko 
Published: May 2015

Abstract
Bacillus sp. strain TAT105 is a thermophilic, ammonium-tolerant bacterium that grows assimilating ammonium nitrogen and reduces ammonia emission during composting of swine feces. To develop a practical use of TAT105, a dried solid culture of TAT105 (5.3 × 109 CFU/g of dry matter) was prepared as an additive. It could be stored for one year without significant reduction of TAT105. Laboratory-scale composting of swine feces was conducted by mixing the additive. When the additive, mixed with an equal weight of water one day before use, was added to obtain a TAT105 concentration of above 107 CFU/g of dry matter in the initial material, the ammonia concentration emitted was lower and nitrogen loss was approximately 22% lower in the treatment with the additive than in the control treatment without the additive. The colony formation on an agar medium containing high ammonium could be used for enumeration of TAT105 in the composted materials.
antaRNA: ant colony-based RNA sequence design
Authors: Kleinkauf Robert , Mann Martin , Backofen Rolf 
Published: May 2015

Abstract
Motivation: RNA sequence design is studied at least as long as the classical folding problem. Although for the latter the functional fold of an RNA molecule is to be found, inverse folding tries to identify RNA sequences that fold into a function-specific target structure. In combination with RNA-based biotechnology and synthetic biology, reliable RNA sequence design becomes a crucial step to generate novel biochemical components.
Results: In this article, the computational tool antaRNA is presented. It is capable of compiling RNA sequences for a given structure that comply in addition with an adjustable full range objective GC-content distribution, specific sequence constraints and additional fuzzy structure constraints. antaRNA applies ant colony optimization meta-heuristics and its superior performance is shown on a biological datasets.
Availability and implementation: http://www.bioinf.uni-freiburg.de/Software/antaRNA
Contact: backofen@informatik.uni-freiburg.de
Supplementary information: Supplementary data are available at Bioinformatics online.