bluuebunny/crossref_metadata_2025_split huggingface dataset:
The enigmatic SAR202 cluster up close: shedding light on a globally distributed dark ocean lineage involved in sulfur cycling
Authors: Mehrshad Maliheh , Rodriguez-Valera Francisco , Amoozegar Mohammad Ali , López-García Purificación , Ghai Rohit 
Published: November 2017

Abstract
The dark ocean microbiota represents the unknown majority in the global ocean waters. The SAR202 cluster belonging to the phylum Chloroflexi was the first microbial lineage discovered to specifically inhabit the aphotic realm, where they are abundant and globally distributed. The absence of SAR202 cultured representatives is a significant bottleneck towards understanding their metabolic capacities and role in the marine environment. In this work, we use a combination of metagenome-assembled genomes from deep-sea datasets and publicly available single-cell genomes to construct a genomic perspective of SAR202 phylogeny, metabolism and biogeography. Our results suggest that SAR202 cluster members are medium sized, free-living cells with a heterotrophic lifestyle, broadly divided into two distinct clades. We present the first evidence of vertical stratification of these microbes along the meso- and bathypelagic ocean layers. Remarkably, two distinct species of SAR202 cluster are highly abundant in nearly all deep bathypelagic metagenomic datasets available so far. SAR202 members metabolize multiple organosulfur compounds, many appear to be sulfite-oxidizers and are predicted to play a major role in sulfur turnover in the dark water column. This concomitantly suggests an unsuspected availability of these nutrient sources to allow for the high abundance of these microbes in the deep sea.
Interleukin-13 receptor alpha 2 cooperates with EGFRvIII signaling to promote glioblastoma multiforme
Authors: Newman Jennifer P. , Wang Grace Y. , Arima Kazuhiko , Guan Shou P. , Waters Michael R. , Cavenee Webster K. , Pan Edward , Aliwarga Edita , Chong Siao T. , Kok Catherine Y. L. , Endaya Berwini B. , Habib Amyn A. , Horibe Tomohisa , Ng Wai H. , Ho Ivy A. W. , Hui Kam M. , Kordula Tomasz , Lam Paula Y. P. 
Published: November 2017

AbstractThe interleukin-13 receptor alpha2 (IL-13Rα2) is a cancer-associated receptor overexpressed in human glioblastoma multiforme (GBM). This receptor is undetectable in normal brain which makes it a highly suitable target for diagnostic and therapeutic purposes. However, the pathological role of this receptor in GBM remains to be established. Here we report that IL-13Rα2 alone induces invasiveness of human GBM cells without affecting their proliferation. In contrast, in the presence of the mutant EGFR (EGFRvIII), IL-13Rα2 promotes GBM cell proliferation in vitro and in vivo. Mechanistically, the cytoplasmic domain of IL-13Rα2 specifically binds to EGFRvIII, and this binding upregulates the tyrosine kinase activity of EGFRvIII and activates the RAS/RAF/MEK/ERK and STAT3 pathways. Our findings support the “To Go or To Grow” hypothesis whereby IL-13Rα2 serves as a molecular switch from invasion to proliferation, and suggest that targeting both receptors with STAT3 signaling inhibitor might be a therapeutic approach for the treatment of GBM.
Harnessing heterogeneous nucleation to control tin orientations in electronic interconnections
Authors: Ma Z. L. , Belyakov S. A. , Sweatman K. , Nishimura T. , Nishimura T. , Gourlay C. M. 
Published: November 2017

AbstractWhile many aspects of electronics manufacturing are controlled with great precision, the nucleation of tin in solder joints is currently left to chance. This leads to a widely varying melt undercooling and different crystal orientations in each joint, which results in a different resistance to electromigration, thermomechanical fatigue, and other failure modes in each joint. Here we identify a family of nucleants for tin, prove their effectiveness using a novel droplet solidification technique, and demonstrate an approach to incorporate the nucleants into solder joints to control the orientation of the tin nucleation event. With this approach, it is possible to change tin nucleation from a stochastic to a deterministic process, and to generate single-crystal joints with their c-axis orientation tailored to best combat a selected failure mode.
Complete 3-Qubit Grover search on a programmable quantum computer
Authors: Figgatt C. , Maslov D. , Landsman K. A. , Linke N. M. , Debnath S. , Monroe C. 
Published: November 2017

AbstractThe Grover quantum search algorithm is a hallmark application of a quantum computer with a well-known speedup over classical searches of an unsorted database. Here, we report results for a complete three-qubit Grover search algorithm using the scalable quantum computing technology of trapped atomic ions, with better-than-classical performance. Two methods of state marking are used for the oracles: a phase-flip method employed by other experimental demonstrations, and a Boolean method requiring an ancilla qubit that is directly equivalent to the state marking scheme required to perform a classical search. We also report the deterministic implementation of a Toffoli-4 gate, which is used along with Toffoli-3 gates to construct the algorithms; these gates have process fidelities of 70.5% and 89.6%, respectively.
Dendrogenin A drives LXR to trigger lethal autophagy in cancers
Authors: Segala Gregory , David Marion , de Medina Philippe , Poirot Mathias C. , Serhan Nizar , Vergez François , Mougel Aurelie , Saland Estelle , Carayon Kevin , Leignadier Julie , Caron Nicolas , Voisin Maud , Cherier Julia , Ligat Laetitia , Lopez Frederic , Noguer Emmanuel , Rives Arnaud , Payré Bruno , Saati Talal al , Lamaziere Antonin , Despres Gaëtan , Lobaccaro Jean-Marc , Baron Silvere , Demur Cecile , de Toni Fabienne , Larrue Clément , Boutzen Helena , Thomas Fabienne , Sarry Jean-Emmanuel , Tosolini Marie , Picard Didier , Record Michel , Récher Christian , Poirot Marc , Silvente-Poirot Sandrine 
Published: November 2017

AbstractDendrogenin A (DDA) is a newly discovered cholesterol metabolite with tumor suppressor properties. Here, we explored its efficacy and mechanism of cell death in melanoma and acute myeloid leukemia (AML). We found that DDA induced lethal autophagy in vitro and in vivo, including primary AML patient samples, independently of melanoma Braf status or AML molecular and cytogenetic classifications. DDA is a partial agonist on liver-X-receptor (LXR) increasing Nur77, Nor1, and LC3 expression leading to autolysosome formation. Moreover, DDA inhibited the cholesterol biosynthesizing enzyme 3β-hydroxysterol-Δ8,7-isomerase (D8D7I) leading to sterol accumulation and cooperating in autophagy induction. This mechanism of death was not observed with other LXR ligands or D8D7I inhibitors establishing DDA selectivity. The potent anti-tumor activity of DDA, its original mechanism of action and its low toxicity support its clinical evaluation. More generally, this study reveals that DDA can direct control a nuclear receptor to trigger lethal autophagy in cancers.
A Paleocene penguin from New Zealand substantiates multiple origins of gigantism in fossil Sphenisciformes
Authors: Mayr Gerald , Scofield R. Paul , De Pietri Vanesa L. , Tennyson Alan J. D. 
Published: November 2017

AbstractOne of the notable features of penguin evolution is the occurrence of very large species in the early Cenozoic, whose body size greatly exceeded that of the largest extant penguins. Here we describe a new giant species from the late Paleocene of New Zealand that documents the very early evolution of large body size in penguins. Kumimanu biceae, n. gen. et sp. is larger than all other fossil penguins that have substantial skeletal portions preserved. Several plesiomorphic features place the new species outside a clade including all post-Paleocene giant penguins. It is phylogenetically separated from giant Eocene and Oligocene penguin species by various smaller taxa, which indicates multiple origins of giant size in penguin evolution. That a penguin rivaling the largest previously known species existed in the Paleocene suggests that gigantism in penguins arose shortly after these birds became flightless divers. Our study therefore strengthens previous suggestions that the absence of very large penguins today is likely due to the Oligo-Miocene radiation of marine mammals.
Three distinct developmental pathways for adaptive and two IFN-γ-producing γδ T subsets in adult thymus
Authors: Buus Terkild Brink , Ødum Niels , Geisler Carsten , Lauritsen Jens Peter Holst 
Published: November 2017

AbstractMurine γδ T cells include subsets that are programmed for distinct effector functions during their development in the thymus. Under pathological conditions, different γδ T cell subsets can be protective or can exacerbate a disease. Here we show that CD117, CD200 and CD371, together with other markers, identify seven developmental stages of γδ T cells. These seven stages can be divided into three distinct developmental pathways that are enriched for different TCRδ repertoires and exhibit characteristic expression patterns associated with adaptive (γδTn), IFN-γ-producing (γδT1) and IFN-γ/IL-4-co-producing γδ T cells (γδNKT). Developmental progression towards both IFN-γ-producing subsets can be induced by TCR signalling, and each pathway results in thymic emigration at a different stage. Finally, we show that γδT1 cells are the predominating IFN-γ-producing subset developing in the adult thymus. Thus, this study maps out three distinct development pathways that result in the programming of γδTn, γδT1 and γδNKT cells.
Lysosomal integral membrane protein-2 as a phospholipid receptor revealed by biophysical and cellular studies
Authors: Conrad Karen S. , Cheng Ting-Wen , Ysselstein Daniel , Heybrock Saskia , Hoth Lise R. , Chrunyk Boris A. , am Ende Christopher W. , Krainc Dimitri , Schwake Michael , Saftig Paul , Liu Shenping , Qiu Xiayang , Ehlers Michael D. 
Published: November 2017

AbstractLysosomal integral membrane protein-2 (LIMP-2/SCARB2) contributes to endosomal and lysosomal function. LIMP-2 deficiency is associated with neurological abnormalities and kidney failure and, as an acid glucocerebrosidase receptor, impacts Gaucher and Parkinson’s diseases. Here we report a crystal structure of a LIMP-2 luminal domain dimer with bound cholesterol and phosphatidylcholine. Binding of these lipids alters LIMP-2 from functioning as a glucocerebrosidase-binding monomer toward a dimeric state that preferentially binds anionic phosphatidylserine over neutral phosphatidylcholine. In cellular uptake experiments, LIMP-2 facilitates transport of phospholipids into murine fibroblasts, with a strong substrate preference for phosphatidylserine. Taken together, these biophysical and cellular studies define the structural basis and functional importance of a form of LIMP-2 for lipid trafficking. We propose a model whereby switching between monomeric and dimeric forms allows LIMP-2 to engage distinct binding partners, a mechanism that may be shared by SR-BI and CD36, scavenger receptor proteins highly homologous to LIMP-2.
Random access quantum information processors using multimode circuit quantum electrodynamics
Authors: Naik R. K. , Leung N. , Chakram S. , Groszkowski Peter , Lu Y. , Earnest N. , McKay D. C. , Koch Jens , Schuster D. I. 
Published: November 2017

AbstractQubit connectivity is an important property of a quantum processor, with an ideal processor having random access—the ability of arbitrary qubit pairs to interact directly. This a challenge with superconducting circuits, as state-of-the-art architectures rely on only nearest-neighbor coupling. Here, we implement a random access superconducting quantum information processor, demonstrating universal operations on a nine-qubit memory, with a Josephson junction transmon circuit serving as the central processor. The quantum memory uses the eigenmodes of a linear array of coupled superconducting resonators. We selectively stimulate vacuum Rabi oscillations between the transmon and individual eigenmodes through parametric flux modulation of the transmon frequency. Utilizing these oscillations, we perform a universal set of quantum gates on 38 arbitrary pairs of modes and prepare multimode entangled states, all using only two control lines. We thus achieve hardware-efficient random access multi-qubit control in an architecture compatible with long-lived microwave cavity-based quantum memories.
Dissipatively coupled waveguide networks for coherent diffusive photonics
Authors: Mukherjee Sebabrata , Mogilevtsev Dmitri , Slepyan Gregory Ya. , Doherty Thomas H. , Thomson Robert R. , Korolkova Natalia 
Published: November 2017

AbstractA photonic circuit is generally described as a structure in which light propagates by unitary exchange and transfers reversibly between channels. In contrast, the term ‘diffusive’ is more akin to a chaotic propagation in scattering media, where light is driven out of coherence towards a thermal mixture. Based on the dynamics of open quantum systems, the combination of these two opposites can result in novel techniques for coherent light control. The crucial feature of these photonic structures is dissipative coupling between modes, via an interaction with a common reservoir. Here, we demonstrate experimentally that such systems can perform optical equalisation to smooth multimode light, or act as a distributor, guiding it into selected channels. Quantum thermodynamically, these systems can act as catalytic coherent reservoirs by performing perfect non-Landauer erasure. For lattice structures, localised stationary states can be supported in the continuum, similar to compacton-like states in conventional flat-band lattices.
Mechanism of early light signaling by the
carboxy-terminal output module of Arabidopsis phytochrome B
Authors: Qiu Yongjian , Pasoreck Elise K. , Reddy Amit K. , Nagatani Akira , Ma Wenxiu , Chory Joanne , Chen Meng 
Published: November 2017

AbstractPlant phytochromes are thought to transduce light signals by mediating the degradation of phytochrome-interacting transcription factors (PIFs) through the N-terminal photosensory module, while the C-terminal module, including a histidine kinase-related domain (HKRD), does not participate in signaling. Here we show that the C-terminal module of Arabidopsis phytochrome B (PHYB) is sufficient to mediate the degradation of PIF3 specifically and to activate photosynthetic genes in the dark. The HKRD is a dimerization domain for PHYB homo and heterodimerization. A D1040V mutation, which disrupts the dimerization of HKRD and the interaction between C-terminal module and PIF3, abrogates PHYB nuclear accumulation, photobody biogenesis, and PIF3 degradation. By contrast, disrupting the interaction between PIF3 and PHYB’s N-terminal module has little effect on PIF3 degradation. Together, this study demonstrates that the dimeric form of the C-terminal module plays important signaling roles by targeting PHYB to subnuclear photobodies and interacting with PIF3 to trigger its degradation.
Efficient and flexible implementation of Langevin simulation for gene burst production
Authors: Yan Ching-Cher Sanders , Chepyala Surendhar Reddy , Yen Chao-Ming , Hsu Chao-Ping 
Published: November 2017

AbstractGene expression involves bursts of production of both mRNA and protein, and the fluctuations in their number are increased due to such bursts. The Langevin equation is an efficient and versatile means to simulate such number fluctuation. However, how to include these mRNA and protein bursts in the Langevin equation is not intuitively clear. In this work, we estimated the variance in burst production from a general gene expression model and introduced such variation in the Langevin equation. Our approach offers different Langevin expressions for either or both transcriptional and translational bursts considered and saves computer time by including many production events at once in a short burst time. The errors can be controlled to be rather precise (<2%) for the mean and <10% for the standard deviation of the steady-state distribution. Our scheme allows for high-quality stochastic simulations with the Langevin equation for gene expression, which is useful in analysis of biological networks.
Brain Structural Bases of Tendency to Forgive: evidence from a young adults sample using voxel-based morphometry
Authors: Li Haijiang , Chen Qunlin , Lu Jiamei , Qiu Jiang 
Published: November 2017

AbstractTendency to forgive refers to one’s global dispositional level of forgiveness across situations and relationships. Brain imaging studies examined activation patterns underlying forgiving response, yet focal differences in brain structures related to tendency to forgive have never been investigated. In this study, voxel-based morphometry was used to investigate relations between gray matter/white matter volume (GMV/WMV) and individual differences in tendency to forgive in a large young sample. Participants were 199 young students (60 men) who completed the tendency to forgive scale (TTF) and underwent an anatomical magnetic resonance imaging scan. Results showed that higher TTF scores were associated with larger GMV in the regions of dorsolateral prefrontal cortex, and smaller GMV in the regions of the right insular cortex and inferior frontal gyrus (IFG). Moreover, higher TTF scores were also related to smaller WMV in the regions of the left IFG. Together, these findings suggest structural variations for individual differences in the tendency to forgive, distributed across different brain regions associated with empathic response and cognitive control.
Dietary amino acids and incidence of hypertension: A principle component analysis approach
Authors: Teymoori Farshad , Asghari Golaleh , Mirmiran Parvin , Azizi Fereidoun 
Published: November 2017

AbstractThe current study aimed to investigate the association between dietary amino acid patterns and incidence of hypertension, using principal components factor analyses. This study was conducted within the framework of Tehran Lipid and Glucose Study on 4288 adults, who were free of hypertension at baseline (2008–2011) and were followed for three years (2011–2014). Principal component factor analyses were conducted based on eight amino acid groups and three amino acid patterns were extracted. The first pattern was characterized by branched chain, aromatic, and alcoholic amino acids, and proline. Acidic amino acids and proline were highly loaded in the second pattern and the third was characterized by sulphuric and small amino acids. Adjusted odds ratio of the highest quartile of the first pattern was 1.83 (95%CI: 1.21–2.77, P for trend = 0.002) compared to the lowest one. The first pattern had high positive correlation with dietary intakes of animal protein and dairy, but was negatively correlated with plant protein, fruit, and vegetable. There was no significant association for the second and third patterns. Findings indicate that the dietary amino acid pattern, rich in branched chain, aromatic, and alcoholic amino acids, and proline could increase the risk of hypertension.
Characteristics of soil C:N ratio and δ13C in wheat-maize cropping system of the North China Plain and influences of the Yellow River
Authors: Shi Huijin , Wang Xiujun , Xu Minggang , Zhang Haibo , Luo Yongming 
Published: November 2017

AbstractTo better understand the characteristics of soil organic matter (SOM) in the North China Plain, we evaluate the large scale variations of soil organic carbon (SOC), total nitrogen (TN), carbon to nitrogen (C:N) ratio and stable carbon isotopic compositions (δ13C) in SOC over 0–100 cm. To assess the influence of the Yellow River, 31 sites are selected from the wheat-maize double cropping system, and grouped into two: 10 sites near and 21 sites far from the river. Our data show that mean soil C:N ratio is low (7.6–9.9) across the region, and not affected by the Yellow River. However, SOC and TN are significantly (P < 0.05) lower in subsoil near the Yellow River (2.0 and 0.2–0.3 g kg−1 for SOC and TN) than far away (3.1 and 0.4 g kg−1); δ13C is significantly more negative below 60 cm near the river (−23.3 to −22.6‰) than far away (−21.8 to −21.4‰). We estimate that the contributions of wheat and maize to SOC are 61.3–68.1% and 31.9–38.8%, respectively. Our analyses indicate that the overall low levels of SOC in the North China Plain may be associated with the low soil C:N ratio and less clay content. The hydrological processes may also partly be responsible, particularly for those near the Yellow River.
Three-dimensional organotypic matrices from alternative collagen sources as pre-clinical models for cell biology
Authors: Conway James R. W. , Vennin Claire , Cazet Aurélie S. , Herrmann David , Murphy Kendelle J. , Warren Sean C. , Wullkopf Lena , Boulghourjian Alice , Zaratzian Anaiis , Da Silva Andrew M. , Pajic Marina , Morton Jennifer P. , Cox Thomas R. , Timpson Paul 
Published: November 2017

AbstractOrganotypic co-cultures bridge the gap between standard two-dimensional culture and mouse models. Such assays increase the fidelity of pre-clinical studies, to better inform lead compound development and address the increasing attrition rates of lead compounds within the pharmaceutical industry, which are often a result of screening in less faithful two-dimensional models. Using large-scale acid-extraction techniques, we demonstrate a step-by-step process to isolate collagen I from commercially available animal byproducts. Using the well-established rat tail tendon collagen as a benchmark, we apply our novel kangaroo tail tendon collagen as an alternative collagen source for our screening-ready three-dimensional organotypic co-culture platform. Both collagen sources showed equal applicability for invasive, proliferative or survival assessment of well-established cancer models and clinically relevant patient-derived cancer cell lines. Additional readouts were also demonstrated when comparing these alternative collagen sources for stromal contributions to stiffness, organization and ultrastructure via atomic force microscopy, second harmonic generation imaging and scanning electron microscopy, among other vital biological readouts, where only minor differences were found between the preparations. Organotypic co-cultures represent an easy, affordable and scalable model to investigate drug responses within a physiologically relevant 3D platform.
QuPath: Open source software for digital pathology image analysis
Authors: Bankhead Peter , Loughrey Maurice B. , Fernández José A. , Dombrowski Yvonne , McArt Darragh G. , Dunne Philip D. , McQuaid Stephen , Gray Ronan T. , Murray Liam J. , Coleman Helen G. , James Jacqueline A. , Salto-Tellez Manuel , Hamilton Peter W. 
Published: November 2017

AbstractQuPath is new bioimage analysis software designed to meet the growing need for a user-friendly, extensible, open-source solution for digital pathology and whole slide image analysis. In addition to offering a comprehensive panel of tumor identification and high-throughput biomarker evaluation tools, QuPath provides researchers with powerful batch-processing and scripting functionality, and an extensible platform with which to develop and share new algorithms to analyze complex tissue images. Furthermore, QuPath’s flexible design makes it suitable for a wide range of additional image analysis applications across biomedical research.