bluuebunny/crossref_metadata_2025_split huggingface dataset:
The neural dynamics of sensory focus
Authors: Clarke Stephen E. , Longtin André , Maler Leonard 
Published: November 2015

AbstractCoordinated sensory and motor system activity leads to efficient localization behaviours; but what neural dynamics enable object tracking and what are the underlying coding principles? Here we show that optimized distance estimation from motion-sensitive neurons underlies object tracking performance in weakly electric fish. First, a relationship is presented for determining the distance that maximizes the Fisher information of a neuron’s response to object motion. When applied to our data, the theory correctly predicts the distance chosen by an electric fish engaged in a tracking behaviour, which is associated with a bifurcation between tonic and burst modes of spiking. Although object distance, size and velocity alter the neural response, the location of the Fisher information maximum remains invariant, demonstrating that the circuitry must actively adapt to maintain ‘focus’ during relative motion.
Ikaros mediates gene silencing in T cells through Polycomb repressive complex 2
Authors: Oravecz Attila , Apostolov Apostol , Polak Katarzyna , Jost Bernard , Le Gras Stéphanie , Chan Susan , Kastner Philippe 
Published: November 2015

AbstractT-cell development is accompanied by epigenetic changes that ensure the silencing of stem cell-related genes and the activation of lymphocyte-specific programmes. How transcription factors influence these changes remains unclear. We show that the Ikaros transcription factor forms a complex with Polycomb repressive complex 2 (PRC2) in CD4−CD8− thymocytes and allows its binding to more than 500 developmentally regulated loci, including those normally activated in haematopoietic stem cells and others induced by the Notch pathway. Loss of Ikaros in CD4−CD8− cells leads to reduced histone H3 lysine 27 trimethylation and ectopic gene expression. Furthermore, Ikaros binding triggers PRC2 recruitment and Ikaros interacts with PRC2 independently of the nucleosome remodelling and deacetylation complex. Our results identify Ikaros as a fundamental regulator of PRC2 function in developing T cells.
Whole genome re-sequencing of date palms yields insights into diversification of a fruit tree crop
Authors: Hazzouri Khaled M. , Flowers Jonathan M. , Visser Hendrik J. , Khierallah Hussam S. M. , Rosas Ulises , Pham Gina M. , Meyer Rachel S. , Johansen Caryn K. , Fresquez Zoë A. , Masmoudi Khaled , Haider Nadia , El Kadri Nabila , Idaghdour Youssef , Malek Joel A. , Thirkhill Deborah , Markhand Ghulam S. , Krueger Robert R. , Zaid Abdelouahhab , Purugganan Michael D. 
Published: November 2015

AbstractDate palms (Phoenix dactylifera) are the most significant perennial crop in arid regions of the Middle East and North Africa. Here, we present a comprehensive catalogue of approximately seven million single nucleotide polymorphisms in date palms based on whole genome re-sequencing of a collection of 62 cultivars. Population structure analysis indicates a major genetic divide between North Africa and the Middle East/South Asian date palms, with evidence of admixture in cultivars from Egypt and Sudan. Genome-wide scans for selection suggest at least 56 genomic regions associated with selective sweeps that may underlie geographic adaptation. We report candidate mutations for trait variation, including nonsense polymorphisms and presence/absence variation in gene content in pathways for key agronomic traits. We also identify a copia-like retrotransposon insertion polymorphism in the R2R3 myb-like orthologue of the oil palm virescens gene associated with fruit colour variation. This analysis documents patterns of post-domestication diversification and provides a genomic resource for this economically important perennial tree crop.
IL-6 Inhibits Starvation-induced Autophagy via the STAT3/Bcl-2 Signaling Pathway
Authors: Qin Beibei , Zhou Zhuo , He Jianqin , Yan Chunlan , Ding Shiping 
Published: November 2015

AbstractIL-6, a pleiotropic cytokine, has been investigated for its role in regulating autophagy. Yet, its mechanism of action remains unclear. Here, we show that IL-6 exerted anti-autophagic effects on U937 cells through the STAT3 signaling pathway in vitro. The addition of IL-6 to starved U937 cells significantly activated the phosphorylation level of STAT3 (p-STAT3) at Tyr705 and reduced the protein levels of microtubule-associated protein 1 light chain 3 of type II (LC3-II) and Beclin 1. By immunoblotting, we also observed a positive correlation between the p-STAT3 level and Bcl-2 level. Furthermore, treatment with a STAT3 inhibitor, LLL12, or overexpression of a mutant form, STAT3Y705F, reversed the inhibitory effect of IL-6 on autophagy. Knockdown of Beclin 1 or Atg14 by siRNA and over-expression of Beclin 1 indicated the involvement of class III PI3K complex in IL-6-mediated inhibition of autophagy. Taken together, these data indicate that IL-6 inhibits starvation-induced autophagy and that p-STAT3 mediates the signal transduction from IL-6 to downstream proteins including Bcl-2 and Beclin1.
Electrically Tunable Epsilon-Near-Zero (ENZ) Metafilm Absorbers
Authors: Park Junghyun , Kang Ju-Hyung , Liu Xiaoge , Brongersma Mark L. 
Published: November 2015

AbstractEnhancing and spectrally controlling light absorption is of great practical and fundamental importance. In optoelectronic devices consisting of layered semiconductors and metals, absorption has traditionally been manipulated with the help of Fabry-Pérot resonances. Even further control over the spectral light absorption properties of thin films has been achieved by patterning them into dense arrays of subwavelength resonant structures to form metafilms. As the next logical step, we demonstrate electrical control over light absorption in metafilms constructed from dense arrays of actively tunable plasmonic cavities. This control is achieved by embedding indium tin oxide (ITO) into these cavities. ITO affords significant tuning of its optical properties by means of electrically-induced carrier depletion and accumulation. We demonstrate that particularly large changes in the reflectance from such metafilms (up to 15% P) can be achieved by operating the ITO in the epsilon-near-zero (ENZ) frequency regime where its electrical permittivity changes sign from negative to positive values.
Superinfection exclusion is absent during acute Junin virus infection of Vero and A549 cells
Authors: Gaudin Raphaël , Kirchhausen Tomas 
Published: November 2015

AbstractMany viruses have evolved strategies of so-called “superinfection exclusion” to prevent re-infection of a cell that the same virus has already infected. Although Old World arenavirus infection results in down-regulation of its viral receptor and thus superinfection exclusion, whether New World arenaviruses have evolved such a mechanism remains unclear. Here we show that acute infection by the New World Junin virus (JUNV) failed to down-regulate the transferrin receptor and did not induce superinfection exclusion. We observed that Vero cells infected by a first round of JUNV (Candid1 strain) preserve an ability to internalize new incoming JUNV particles that is comparable to that of non-infected cells. Moreover, we developed a dual infection assay with the wild-type Candid1 JUNV and a recombinant JUNV-GFP virus to discriminate between first and second infections at the transcriptional and translational levels. We found that Vero and A549 cells already infected by JUNV were fully competent to transcribe viral RNA from a second round of infection. Furthermore, flow cytometry analysis of viral protein expression indicated that viral translation was normal, regardless of whether cells were previously infected or not. We conclude that in acutely infected cells, Junin virus lacks a superinfection exclusion mechanism.
Photo-generated metamaterials induce modulation of CW terahertz quantum cascade lasers
Authors: Mezzapesa Francesco P. , Columbo Lorenzo L. , Rizza Carlo , Brambilla Massimo , Ciattoni Alessandro , Dabbicco Maurizio , Vitiello Miriam S. , Scamarcio Gaetano 
Published: November 2015

AbstractPeriodic patterns of photo-excited carriers on a semiconductor surface profoundly modifies its effective permittivity, creating a stationary all-optical quasi-metallic metamaterial. Intriguingly, one can tailor its artificial birefringence to modulate with unprecedented degrees of freedom both the amplitude and phase of a quantum cascade laser (QCL) subject to optical feedback from such an anisotropic reflector. Here, we conceive and devise a reconfigurable photo-designed Terahertz (THz) modulator and exploit it in a proof-of-concept experiment to control the emission properties of THz QCLs. Photo-exciting sub-wavelength metastructures on silicon, we induce polarization-dependent changes in the intra-cavity THz field, that can be probed by monitoring the voltage across the QCL terminals. This inherently flexible approach promises groundbreaking impact on THz photonics applications, including THz phase modulators, fast switches and active hyperbolic media.
Forager bees (Apis mellifera) highly express immune and detoxification genes in tissues associated with nectar processing
Authors: Vannette Rachel L. , Mohamed Abbas , Johnson Brian R. 
Published: November 2015

AbstractPollinators, including honey bees, routinely encounter potentially harmful microorganisms and phytochemicals during foraging. However, the mechanisms by which honey bees manage these potential threats are poorly understood. In this study, we examine the expression of antimicrobial, immune and detoxification genes in Apis mellifera and compare between forager and nurse bees using tissue-specific RNA-seq and qPCR. Our analysis revealed extensive tissue-specific expression of antimicrobial, immune signaling and detoxification genes. Variation in gene expression between worker stages was pronounced in the mandibular and hypopharyngeal gland (HPG), where foragers were enriched in transcripts that encode antimicrobial peptides (AMPs) and immune response. Additionally, forager HPGs and mandibular glands were enriched in transcripts encoding detoxification enzymes, including some associated with xenobiotic metabolism. Using qPCR on an independent dataset, we verified differential expression of three AMP and three P450 genes between foragers and nurses. High expression of AMP genes in nectar-processing tissues suggests that these peptides may contribute to antimicrobial properties of honey or to honey bee defense against environmentally-acquired microorganisms. Together, these results suggest that worker role and tissue-specific expression of AMPs and immune and detoxification enzymes may contribute to defense against microorganisms and xenobiotic compounds acquired while foraging.
LKB1 Regulates Cerebellar Development by Controlling Sonic Hedgehog-mediated Granule Cell Precursor Proliferation and Granule Cell Migration
Authors: Men Yuqin , Zhang Aizhen , Li Haixiang , Jin Yecheng , Sun Xiaoyang , Li Huashun , Gao Jiangang 
Published: November 2015

AbstractThe Liver Kinase B1 (LKB1) gene plays crucial roles in cell differentiation, proliferation and the establishment of cell polarity. We created LKB1 conditional knockout mice (LKB1Atoh1 CKO) to investigate the function of LKB1 in cerebellar development. The LKB1Atoh1 CKO mice displayed motor dysfunction. In the LKB1Atoh1 CKO cerebellum, the overall structure had a larger volume and morelobules. LKB1 inactivationled to an increased proliferation of granule cell precursors (GCPs), aberrant granule cell migration and overproduction of unipolar brush cells. To investigate the mechanism underlying the abnormal foliation, we examined sonic hedgehog signalling (Shh) by testing its transcriptional mediators, the Gli proteins, which regulate the GCPs proliferation and cerebellar foliation during cerebellar development. The expression levels of Gli genes were significantly increased in the mutant cerebellum. In vitro assays showed that the proliferation of cultured GCPs from mutant cerebellum significantly increased, whereas the proliferation of mutant GCPs significantly decreased in the presence of a Shh inhibitor GDC-0049. Thus, LKB1 deficiency in the LKB1Atoh1 CKO mice enhanced Shh signalling, leading to the excessive GCP proliferation and the formation of extra lobules. We proposed that LKB1 regulates cerebellar development by controlling GCPs proliferation through Shh signalling during cerebellar development.
The determining factor of a preferred orientation of GaN domains grown on m-plane sapphire substrates
Authors: Jue Miyeon , Kim Cheol-Woon , Kang Seoung-Hun , Yoon Hansub , Jang Dongsoo , Kwon Young-Kyun , Kim Chinkyo 
Published: November 2015

AbstractEpitaxial lateral overgrowth in tandem with the first-principles calculation was employed to investigate the determining factor of a preferred orientation of GaN on SiO2-patterned m-plane sapphire substrates. We found that the (1"Equation missing"00)-orientation is favored over the (1"Equation missing"0"Equation missing")-orientation in the region with a small filling factor of SiO2, while the latter orientation becomes preferred in the region with a large filling factor. This result suggests that the effective concentration determines the preferred orientation of GaN: the (1"Equation missing"00)- and (1"Equation missing"0"Equation missing")-orientations preferred at their low and high concentrations, respectively. Our computational study revealed that at a low coverage of Ga and N atoms, the local atomic arrangement resembles that on the (1"Equation missing"0"Equation missing") surface, although the (1"Equation missing"00) surface is more stable at their full coverage. Such a (1"Equation missing"0"Equation missing")-like atomic configuration crosses over to the local structure resembling that on the (1"Equation missing"00) surface as the coverage increases. Based on results, we determined that high effective concentration of Ga and N sources expedites the growth of the (1"Equation missing"0"Equation missing")-orientation while keeping from transition to the (1"Equation missing"00)-orientation. At low effective concentration, on the other hand, there is a sufficient time for the added Ga and N sources to rearrange the initial (1"Equation missing"0"Equation missing")-like orientation to form the (1"Equation missing"00)-orientation.
Multimodal super-resolution optical microscopy visualizes the close connection between membrane and the cytoskeleton in liver sinusoidal endothelial cell fenestrations
Authors: Mönkemöller Viola , Øie Cristina , Hübner Wolfgang , Huser Thomas , McCourt Peter 
Published: November 2015

AbstractLiver sinusoidal endothelial cells (LSECs) act as a filter between blood and the hepatocytes. LSECs are highly fenestrated cells; they contain transcellular pores with diameters between 50 to 200 nm. The small sizes of the fenestrae have so far prohibited any functional analysis with standard and advanced light microscopy techniques. Only the advent of super-resolution optical fluorescence microscopy now permits the recording of such small cellular structures. Here, we demonstrate the complementary use of two different super-resolution optical microscopy modalities, 3D structured illumination microscopy (3D-SIM) and single molecule localization microscopy in a common optical platform to obtain new insights into the association between the cytoskeleton and the plasma membrane that supports the formation of fenestrations. We applied 3D-SIM to multi-color stained LSECs to acquire highly resolved overviews of large sample areas. We then further increased the spatial resolution for imaging fenestrations by single molecule localization microscopy applied to select small locations of interest in the same sample on the same microscope setup. We optimized the use of fluorescent membrane stains for these imaging conditions. The combination of these techniques offers a unique opportunity to significantly improve studies of subcellular ultrastructures such as LSEC fenestrations.
Size does matter: 18 amino acids at the N-terminal tip of an amino acid transporter in Leishmania determine substrate specificity
Authors: Schlisselberg Doreen , Mazarib Eldar , Inbar Ehud , Rentsch Doris , Myler Peter J. , Zilberstein Dan 
Published: November 2015

AbstractLong N-terminal tails of amino acid transporters are known to act as sensors of the internal pool of amino acids and as positive regulators of substrate flux rate. In this study we establish that N-termini of amino acid transporters can also determine substrate specificity. We show that due to alternative trans splicing, the human pathogen Leishmania naturally expresses two variants of the proline/alanine transporter, one 18 amino acid shorter than the other. We demonstrate that the longer variant (LdAAP24) translocates both proline and alanine, whereas the shorter variant (∆18LdAAP24) translocates just proline. Remarkably, co-expressing the hydrophilic N-terminal peptide of the long variant with ∆18LdAAP24 was found to recover alanine transport. This restoration of alanine transport could be mediated by a truncated N-terminal tail, though truncations exceeding half of the tail length were no longer functional. Taken together, the data indicate that the first 18 amino acids of the negatively charged N-terminal LdAAP24 tail are required for alanine transport and may facilitate the electrostatic interactions of the entire negatively charged N-terminal tail with the positively charged internal loops in the transmembrane domain, as this mechanism has been shown to underlie regulation of substrate flux rate for other transporters.
Molecular Characterization of Growth Hormone-producing Tumors in the GC Rat Model of Acromegaly
Authors: Martín-Rodríguez Juan F. , Muñoz-Bravo Jose L. , Ibañez-Costa Alejandro , Fernandez-Maza Laura , Balcerzyk Marcin , Leal-Campanario Rocío , Luque Raúl M. , Castaño Justo P. , Venegas-Moreno Eva , Soto-Moreno Alfonso , Leal-Cerro Alfonso , Cano David A. 
Published: November 2015

AbstractAcromegaly is a disorder resulting from excessive production of growth hormone (GH) and consequent increase of insulin-like growth factor 1 (IGF-I), most frequently caused by pituitary adenomas. Elevated GH and IGF-I levels results in wide range of somatic, cardiovascular, endocrine, metabolic and gastrointestinal morbidities. Subcutaneous implantation of the GH-secreting GC cell line in rats leads to the formation of tumors. GC tumor-bearing rats develop characteristics that resemble human acromegaly including gigantism and visceromegaly. However, GC tumors remain poorly characterized at a molecular level. In the present work, we report a detailed histological and molecular characterization of GC tumors using immunohistochemistry, molecular biology and imaging techniques. GC tumors display histopathological and molecular features of human GH-producing tumors, including hormone production, cell architecture, senescence activation and alterations in cell cycle gene expression. Furthermore, GC tumors cells displayed sensitivity to somatostatin analogues, drugs that are currently used in the treatment of human GH-producing adenomas, thus supporting the GC tumor model as a translational tool to evaluate therapeutic agents. The information obtained would help to maximize the usefulness of the GC rat model for research and preclinical studies in GH-secreting tumors.
Shock assisted ionization injection in laser-plasma accelerators
Authors: Thaury C. , Guillaume E. , Lifschitz A. , Ta Phuoc K. , Hansson M. , Grittani G. , Gautier J. , Goddet J.-P. , Tafzi A. , Lundh O. , Malka V. 
Published: November 2015

AbstractIonization injection is a simple and efficient method to trap an electron beam in a laser plasma accelerator. Yet, because of a long injection length, this injection technique leads generally to the production of large energy spread electron beams. Here, we propose to use a shock front transition to localize the injection. Experimental results show that the energy spread can be reduced down to 10 MeV and that the beam energy can be tuned by varying the position of the shock. This simple technique leads to very stable and reliable injection even for modest laser energy. It should therefore become a unique tool for the development of laser-plasma accelerators.
Anisotropic electronic conduction in stacked two-dimensional titanium carbide
Authors: Hu Tao , Zhang Hui , Wang Jiemin , Li Zhaojin , Hu Minmin , Tan Jun , Hou Pengxiang , Li Feng , Wang Xiaohui 
Published: November 2015

AbstractStacked two-dimensional titanium carbide is an emerging conductive material for electrochemical energy storage which requires an understanding of the intrinsic electronic conduction. Here we report the electronic conduction properties of stacked Ti3C2T2 (T = OH, O, F) with two distinct stacking sequences (Bernal and simple hexagonal). On the basis of first-principles calculations and energy band theory analysis, both stacking sequences give rise to metallic conduction with Ti 3d electrons contributing most to the conduction. The conduction is also significantly anisotropic due to the fact that the effective masses of carriers including electrons and holes are remarkably direction-dependent. Such an anisotropic electronic conduction is evidenced by the I−V curves of an individual Ti3C2T2 particulate, which demonstrates that the in-plane electrical conduction is at least one order of magnitude higher than that vertical to the basal plane.
Identifying robust communities and multi-community nodes by combining top-down and bottom-up approaches to clustering
Authors: Gaiteri Chris , Chen Mingming , Szymanski Boleslaw , Kuzmin Konstantin , Xie Jierui , Lee Changkyu , Blanche Timothy , Chaibub Neto Elias , Huang Su-Chun , Grabowski Thomas , Madhyastha Tara , Komashko Vitalina 
Published: November 2015

AbstractBiological functions are carried out by groups of interacting molecules, cells or tissues, known as communities. Membership in these communities may overlap when biological components are involved in multiple functions. However, traditional clustering methods detect non-overlapping communities. These detected communities may also be unstable and difficult to replicate, because traditional methods are sensitive to noise and parameter settings. These aspects of traditional clustering methods limit our ability to detect biological communities and therefore our ability to understand biological functions. To address these limitations and detect robust overlapping biological communities, we propose an unorthodox clustering method called SpeakEasy which identifies communities using top-down and bottom-up approaches simultaneously. Specifically, nodes join communities based on their local connections, as well as global information about the network structure. This method can quantify the stability of each community, automatically identify the number of communities and quickly cluster networks with hundreds of thousands of nodes. SpeakEasy shows top performance on synthetic clustering benchmarks and accurately identifies meaningful biological communities in a range of datasets, including: gene microarrays, protein interactions, sorted cell populations, electrophysiology and fMRI brain imaging.