bluuebunny/crossref_metadata_2025_split huggingface dataset:
RodZ modulates geometric localization of the bacterial actin MreB to regulate cell shape
Authors: Colavin Alexandre , Shi Handuo , Huang Kerwyn Casey 
Published: April 2018

AbstractIn the rod-shaped bacterium Escherichia coli, the actin-like protein MreB localizes in a curvature-dependent manner and spatially coordinates cell-wall insertion to maintain cell shape, although the molecular mechanism by which cell width is regulated remains unknown. Here we demonstrate that the membrane protein RodZ regulates the biophysical properties of MreB and alters the spatial organization of E. coli cell-wall growth. The relative expression levels of MreB and RodZ change in a manner commensurate with variations in growth rate and cell width, and RodZ systematically alters the curvature-based localization of MreB and cell width in a concentration-dependent manner. We identify MreB mutants that alter the bending properties of MreB filaments in molecular dynamics simulations similar to RodZ binding, and show that these mutants rescue rod-like shape in the absence of RodZ alone or in combination with wild-type MreB. Thus, E. coli can control its shape and dimensions by differentially regulating RodZ and MreB to alter the patterning of cell-wall insertion, highlighting the rich regulatory landscape of cytoskeletal molecular biophysics.
Small tumor necrosis factor receptor biologics inhibit the tumor necrosis factor-p38 signalling axis and inflammation
Authors: Mukaro Violet R. , Quach Alex , Gahan Michelle E. , Boog Bernadette , Huang Zhi H. , Gao Xiuhui , Haddad Carol , Mahalingam Suresh , Hii Charles S. , Ferrante Antonio 
Published: April 2018

AbstractDespite anti-TNF therapy advancements for inflammatory diseases such as rheumatoid arthritis, the burden of diseases remains high. An 11-mer TNF peptide, TNF70–80, is known to stimulate selective functional responses compared to the parent TNF molecule. Here, we show that TNF70–80binds to the TNF receptor, activating p38 MAP kinase through TNF receptor-associated factor 2. Using truncated TNFR mutants, we identify the sequence in TNFRI which enables p38 activation by TNF70–80. Peptides with this TNFRI sequence, such as TNFRI206–211bind to TNF and inhibit TNF-induced p38 activation, respiratory burst, cytokine production and adhesion receptor expression but not F-Met-Leu-Phe-induced respiratory burst in neutrophils. TNFRI206–211does not prevent TNF binding to TNFRI or TNF-induced stimulation of ERK, JNK and NF-κB. TNFRI206–211inhibits bacterial lipopolysaccharide-induced peritonitis, carrageenan-induced and antigen-induced paw inflammation, and respiratory syncytial virus-induced lung inflammation in mice. Our findings suggest a way of targeting TNF-p38 pathway to treat chronic inflammatory disorders.
Three-dimensional variations of the slab geometry correlate with earthquake distributions at the Cascadia subduction system
Authors: Gao Haiying 
Published: April 2018

AbstractSignificant along-strike variations of seismicity are observed at subduction zones, which are strongly influenced by physical properties of the plate interface and rheology of the crust and mantle lithosphere. However, the role of the oceanic side of the plate boundary on seismicity is poorly understood due to the lack of offshore instrumentations. Here tomographic results of the Cascadia subduction system, resolved with full-wave ambient noise simulation and inversion by integrating dense offshore and onshore seismic datasets, show significant variations of the oceanic lithosphere along strike and down dip from spreading centers to subduction. In central Cascadia, where seismicity is sparse, the slab is imaged as a large-scale low-velocity feature near the trench, which is attributed to a highly hydrated and strained oceanic lithosphere underlain by a layer of melts or fluids. The strong correlation suggests that the properties of the incoming oceanic plate play a significant role on seismicity.
Dissociating frontoparietal brain networks with neuroadaptive Bayesian optimization
Authors: Lorenz Romy , Violante Ines R. , Monti Ricardo Pio , Montana Giovanni , Hampshire Adam , Leech Robert 
Published: April 2018

AbstractUnderstanding the unique contributions of frontoparietal networks (FPN) in cognition is challenging because they overlap spatially and are co-activated by diverse tasks. Characterizing these networks therefore involves studying their activation across many different cognitive tasks, which previously was only possible with meta-analyses. Here, we use neuroadaptive Bayesian optimization, an approach combining real-time analysis of functional neuroimaging data with machine-learning, to discover cognitive tasks that segregate ventral and dorsal FPN activity. We identify and subsequently refine two cognitive tasks, Deductive Reasoning and Tower of London, which maximally dissociate the dorsal from ventral FPN. We subsequently investigate these two FPNs in the context of a wider range of FPNs and demonstrate the importance of studying the whole activity profile across tasks to uniquely differentiate any FPN. Our findings deviate from previous meta-analyses and hypothesized functional labels for these FPNs. Taken together the results form the starting point for a neurobiologically-derived cognitive taxonomy.
Nuclear disarmament verification via resonant phenomena
Authors: Hecla Jake J. , Danagoulian Areg 
Published: April 2018

AbstractNuclear disarmament treaties are not sufficient in and of themselves to neutralize the existential threat of the nuclear weapons. Technologies are necessary for verifying the authenticity of the nuclear warheads undergoing dismantlement before counting them toward a treaty partner’s obligation. Here we present a concept that leverages isotope-specific nuclear resonance phenomena to authenticate a warhead’s fissile components by comparing them to a previously authenticated template. All information is encrypted in the physical domain in a manner that amounts to a physical zero-knowledge proof system. Using Monte Carlo simulations, the system is shown to reveal no isotopic or geometric information about the weapon, while readily detecting hoaxing attempts. This nuclear technique can dramatically increase the reach and trustworthiness of future nuclear disarmament treaties.
Helraiser intermediates provide insight into the mechanism of eukaryotic replicative transposition
Authors: Grabundzija Ivana , Hickman Alison B. , Dyda Fred 
Published: April 2018

AbstractHelitrons are eukaryotic DNA transposons that have profoundly affected genome variability via capture and mobilization of host genomic sequences. Defining their mode of action is therefore important for understanding how genome landscapes evolve. Sequence similarities with certain prokaryotic mobile elements suggest a “rolling circle” mode of transposition, involving only a single transposon strand. Using the reconstituted Helraiser transposon to study Helitron transposition in cells and in vitro, we show that the donor site must be double-stranded and that single-stranded donors will not suffice. Nevertheless, replication and integration assays demonstrate the use of only one of the transposon donor strands. Furthermore, repeated reuse of Helraiser donor sites occurs following DNA synthesis. In cells, circular double-stranded intermediates that serve as transposon donors are generated and replicated by Helraiser transposase. Cell-free experiments demonstrate strand-specific cleavage and strand transfer, supporting observations made in cells.
High-speed and on-chip graphene blackbody emitters for optical communications by remote heat transfer
Authors: Miyoshi Yusuke , Fukazawa Yusuke , Amasaka Yuya , Reckmann Robin , Yokoi Tomoya , Ishida Kazuki , Kawahara Kenji , Ago Hiroki , Maki Hideyuki 
Published: April 2018

AbstractHigh-speed light emitters integrated on silicon chips can enable novel architectures for silicon-based optoelectronics, such as on-chip optical interconnects, and silicon photonics. However, conventional light sources based on compound semiconductors face major challenges for their integration with a silicon-based platform because of their difficulty of direct growth on a silicon substrate. Here we report ultra-high-speed (100-ps response time), highly integrated graphene-based on-silicon-chip blackbody emitters in the near-infrared region including telecommunication wavelength. Their emission responses are strongly affected by the graphene contact with the substrate depending on the number of graphene layers. The ultra-high-speed emission can be understood by remote quantum thermal transport via surface polar phonons of the substrates. We demonstrated real-time optical communications, integrated two-dimensional array emitters, capped emitters operable in air, and the direct coupling of optical fibers to the emitters. These emitters can open new routes to on-Si-chip, small footprint, and high-speed emitters for highly integrated optoelectronics and silicon photonics.
NKX2-5 regulates human cardiomyogenesis via a HEY2 dependent transcriptional network
Authors: Anderson David J. , Kaplan David I. , Bell Katrina M. , Koutsis Katerina , Haynes John M. , Mills Richard J. , Phelan Dean G. , Qian Elizabeth L. , Leitoguinho Ana Rita , Arasaratnam Deevina , Labonne Tanya , Ng Elizabeth S. , Davis Richard P. , Casini Simona , Passier Robert , Hudson James E. , Porrello Enzo R. , Costa Mauro W. , Rafii Arash , Curl Clare L. , Delbridge Lea M. , Harvey Richard P. , Oshlack Alicia , Cheung Michael M. , Mummery Christine L. , Petrou Stephen , Elefanty Andrew G. , Stanley Edouard G. , Elliott David A. 
Published: April 2018

AbstractCongenital heart defects can be caused by mutations in genes that guide cardiac lineage formation. Here, we show deletion of NKX2-5, a critical component of the cardiac gene regulatory network, in human embryonic stem cells (hESCs), results in impaired cardiomyogenesis, failure to activate VCAM1 and to downregulate the progenitor marker PDGFRα. Furthermore, NKX2-5 null cardiomyocytes have abnormal physiology, with asynchronous contractions and altered action potentials. Molecular profiling and genetic rescue experiments demonstrate that the bHLH protein HEY2 is a key mediator of NKX2-5 function during human cardiomyogenesis. These findings identify HEY2 as a novel component of the NKX2-5 cardiac transcriptional network, providing tangible evidence that hESC models can decipher the complex pathways that regulate early stage human heart development. These data provide a human context for the evaluation of pathogenic mutations in congenital heart disease.
Recurrent acquisition of cytosine methyltransferases into eukaryotic retrotransposons
Authors: de Mendoza Alex , Bonnet Amandine , Vargas-Landin Dulce B. , Ji Nanjing , Li Hongfei , Yang Feng , Li Ling , Hori Koichi , Pflueger Jahnvi , Buckberry Sam , Ohta Hiroyuki , Rosic Nedeljka , Lesage Pascale , Lin Senjie , Lister Ryan 
Published: April 2018

AbstractTransposable elements are in a constant arms race with the silencing mechanisms of their host genomes. One silencing mechanism commonly used by many eukaryotes is dependent on cytosine methylation, a covalent modification of DNA deposited by C5 cytosine methyltransferases (DNMTs). Here, we report how two distantly related eukaryotic lineages, dinoflagellates and charophytes, have independently incorporated DNMTs into the coding regions of distinct retrotransposon classes. Concomitantly, we show that dinoflagellates of the genus Symbiodinium have evolved cytosine methylation patterns unlike any other eukaryote, with most of the genome methylated at CG dinucleotides. Finally, we demonstrate the ability of retrotransposon DNMTs to methylate CGs de novo, suggesting that retrotransposons could self-methylate retrotranscribed DNA. Together, this is an example of how retrotransposons incorporate host-derived genes involved in DNA methylation. In some cases, this event could have implications for the composition and regulation of the host epigenomic environment.
Multi-omics analysis reveals neoantigen-independent immune cell infiltration in copy-number driven cancers
Authors: McGrail Daniel J. , Federico Lorenzo , Li Yongsheng , Dai Hui , Lu Yiling , Mills Gordon B. , Yi Song , Lin Shiaw-Yih , Sahni Nidhi 
Published: April 2018

AbstractTo realize the full potential of immunotherapy, it is critical to understand the drivers of tumor infiltration by immune cells. Previous studies have linked immune infiltration with tumor neoantigen levels, but the broad applicability of this concept remains unknown. Here, we find that while this observation is true across cancers characterized by recurrent mutations, it does not hold for cancers driven by recurrent copy number alterations, such as breast and pancreatic tumors. To understand immune invasion in these cancers, we developed an integrative multi-omics framework, identifying the DNA damage response protein ATM as a driver of cytokine production leading to increased immune infiltration. This prediction was validated in numerous orthogonal datasets, as well as experimentally in vitro and in vivo by cytokine release and immune cell migration. These findings demonstrate diverse drivers of immune cell infiltration across cancer lineages and may facilitate the clinical adaption of immunotherapies across diverse malignancies.
Species-specific host factors rather than virus-intrinsic virulence determine primate lentiviral pathogenicity
Authors: Joas Simone , Parrish Erica H. , Gnanadurai Clement W. , Lump Edina , Stürzel Christina M. , Parrish Nicholas F. , Learn Gerald H. , Sauermann Ulrike , Neumann Berit , Rensing Kerstin Mätz , Fuchs Dietmar , Billingsley James M. , Bosinger Steven E. , Silvestri Guido , Apetrei Cristian , Huot Nicolas , Garcia-Tellez Thalia , Müller-Trutwin Michaela , Hotter Dominik , Sauter Daniel , Stahl-Hennig Christiane , Hahn Beatrice H. , Kirchhoff Frank 
Published: April 2018

AbstractHIV-1 causes chronic inflammation and AIDS in humans, whereas related simian immunodeficiency viruses (SIVs) replicate efficiently in their natural hosts without causing disease. It is currently unknown to what extent virus-specific properties are responsible for these different clinical outcomes. Here, we incorporate two putative HIV-1 virulence determinants, i.e., a Vpu protein that antagonizes tetherin and blocks NF-κB activation and a Nef protein that fails to suppress T cell activation via downmodulation of CD3, into a non-pathogenic SIVagm strain and test their impact on viral replication and pathogenicity in African green monkeys. Despite sustained high-level viremia over more than 4 years, moderately increased immune activation and transcriptional signatures of inflammation, the HIV-1-like SIVagm does not cause immunodeficiency or any other disease. These data indicate that species-specific host factors rather than intrinsic viral virulence factors determine the pathogenicity of primate lentiviruses.
Lipoprotein lipase regulates hematopoietic stem progenitor cell maintenance through DHA supply
Authors: Liu Chao , Han Tianxu , Stachura David L. , Wang Huawei , Vaisman Boris L. , Kim Jungsu , Klemke Richard L. , Remaley Alan T. , Rana Tariq M. , Traver David , Miller Yury I. 
Published: April 2018

AbstractLipoprotein lipase (LPL) mediates hydrolysis of triglycerides (TGs) to supply free fatty acids (FFAs) to tissues. Here, we show that LPL activity is also required for hematopoietic stem progenitor cell (HSPC) maintenance. Knockout of Lpl or its obligatory cofactor Apoc2 results in significantly reduced HSPC expansion during definitive hematopoiesis in zebrafish. A human APOC2 mimetic peptide or the human very low-density lipoprotein, which carries APOC2, rescues the phenotype in apoc2 but not in lpl mutant zebrafish. Creating parabiotic apoc2 and lpl mutant zebrafish rescues the hematopoietic defect in both. Docosahexaenoic acid (DHA) is identified as an important factor in HSPC expansion. FFA-DHA, but not TG-DHA, rescues the HSPC defects in apoc2 and lpl mutant zebrafish. Reduced blood cell counts are also observed in Apoc2 mutant mice at the time of weaning. These results indicate that LPL-mediated release of the essential fatty acid DHA regulates HSPC expansion and definitive hematopoiesis.
Response of carbon cycle to drier conditions in the mid-Holocene in central China
Authors: Huang Xianyu , Pancost Richard D. , Xue Jiantao , Gu Yansheng , Evershed Richard P. , Xie Shucheng 
Published: April 2018

AbstractThe nature and extent to which hydrological changes induced by the Asian summer monsoon affected key biogeochemical processes remain poorly defined. This study explores the relationship between peatland drying and carbon cycling on centennial timescales in central China using lipid biomarkers. The difference between peat n-alkane δ2H and a nearby stalagmite δ18O record reveals that intervals of prominent peatland drying occurred during the mid-Holocene. Synchronous with these drier conditions, leaf wax δ13C values show large negative excursions, with the utilization of CO2 respired from the peatland subsurface for plant photosynthesis being a possible mechanism. Crucially, successive drying events appear to have had a cumulative impact on the susceptibility of peat carbon stores to climate change. Concurrently, bacterially derived hopane δ13C values suggest the occurrence of enhanced methane oxidation during the drier periods. Collectively, these observations expand our understanding of how respiration and degradation of peat are enhanced during drying events.
Photonic zero mode in a non-Hermitian photonic lattice
Authors: Pan Mingsen , Zhao Han , Miao Pei , Longhi Stefano , Feng Liang 
Published: April 2018

AbstractZero-energy particles (such as Majorana fermions) are newly predicted quasiparticles and are expected to play an important role in fault-tolerant quantum computation. In conventional Hermitian quantum systems, however, such zero states are vulnerable and even become vanishing if couplings with surroundings are of the same topological nature. Here we demonstrate a robust photonic zero mode sustained by a spatial non-Hermitian phase transition in a parity-time (PT) symmetric lattice, despite the same topological order across the entire system. The non-Hermitian-enhanced topological protection ensures the reemergence of the zero mode at the phase transition interface when the two semi-lattices under different PT phases are decoupled effectively in their real spectra. Residing at the midgap level of the PT symmetric spectrum, the zero mode is topologically protected against topological disorder. We experimentally validated the robustness of the zero-energy mode by ultrafast heterodyne measurements of light transport dynamics in a silicon waveguide lattice.
Observation of elastic topological states in soft materials
Authors: Li Shuaifeng , Zhao Degang , Niu Hao , Zhu Xuefeng , Zang Jianfeng 
Published: April 2018

AbstractTopological elastic metamaterials offer insight into classic motion law and open up opportunities in quantum and classic information processing. Theoretical modeling and numerical simulation of elastic topological states have been reported, whereas the experimental observation remains relatively unexplored. Here we present an experimental observation and numerical simulation of tunable topological states in soft elastic metamaterials. The on-demand reversible switch in topological phase has been achieved by changing filling ratio, tension, and/or compression of the elastic metamaterials. By combining two elastic metamaterials with distinct topological invariants, we further demonstrate the formation and dynamic tunability of topological interface states by mechanical deformation, and the manipulation of elastic wave propagation. Moreover, we provide a topological phase diagram of elastic metamaterials under deformation. Our approach to dynamically control interface states in soft materials paves the way to various phononic systems involving thermal management and soft robotics requiring better use of energy.
Archean phosphorus liberation induced by iron redox geochemistry
Authors: Herschy Barry , Chang Sae Jung , Blake Ruth , Lepland Aivo , Abbott-Lyon Heather , Sampson Jacqueline , Atlas Zachary , Kee Terence P. , Pasek Matthew A. 
Published: April 2018

AbstractThe element phosphorus (P) is central to ecosystem growth and is proposed to be a limiting nutrient for life. The Archean ocean may have been strongly phosphorus-limited due to the selective binding of phosphate to iron oxyhydroxide. Here we report a new route to solubilizing phosphorus in the ancient oceans: reduction of phosphate to phosphite by iron(II) at low (<200 °C) diagenetic temperatures. Reduction of phosphate to phosphite was likely widespread in the Archean, as the reaction occurs rapidly and is demonstrated from thermochemical modeling, experimental analogs, and detection of phosphite in early Archean rocks. We further demonstrate that the higher solubility of phosphite compared to phosphate results in the liberation of phosphorus from ferruginous sediments. This phosphite is relatively stable after its formation, allowing its accumulation in the early oceans. As such, phosphorus, not as phosphate but as phosphite, could have been a major nutrient in early pre-oxygenated oceans.
Stimulus dependent diversity and stereotypy in the output of an olfactory functional unit
Authors: Arneodo Ezequiel M. , Penikis Kristina B. , Rabinowitz Neil , Licata Angela , Cichy Annika , Zhang Jingji , Bozza Thomas , Rinberg Dmitry 
Published: April 2018

AbstractOlfactory inputs are organized in an array of functional units (glomeruli), each relaying information from sensory neurons expressing a given odorant receptor to a small population of output neurons, mitral/tufted (MT) cells. MT cells respond heterogeneously to odorants, and how the responses encode stimulus features is unknown. We recorded in awake mice responses from “sister” MT cells that receive input from a functionally characterized, genetically identified glomerulus, corresponding to a specific receptor (M72). Despite receiving similar inputs, sister MT cells exhibit temporally diverse, concentration-dependent, excitatory and inhibitory responses to most M72 ligands. In contrast, the strongest known ligand for M72 elicits temporally stereotyped, early excitatory responses in sister MT cells, consistent across a range of concentrations. Our data suggest that information about ligand affinity is encoded in the collective stereotypy or diversity of activity among sister MT cells within a glomerular functional unit in a concentration-tolerant manner.
Magnetically-driven phase transformation strengthening in high entropy alloys
Authors: Niu Changning , LaRosa Carlyn R. , Miao Jiashi , Mills Michael J. , Ghazisaeidi Maryam 
Published: April 2018

AbstractCrCoNi alloy exhibits a remarkable combination of strength and plastic deformation, even superior to the CrMnFeCoNi high-entropy alloy. We connect the magnetic and mechanical properties of CrCoNi, via a magnetically tunable phase transformation. While both alloys crystallize as single-phase face-centered-cubic (fcc) solid solutions, we find a distinctly lower-energy phase in CrCoNi alloy with a hexagonal close-packed (hcp) structure. Comparing the magnetic configurations of CrCoNi with those of other equiatomic ternary derivatives of CrMnFeCoNi confirms that magnetically frustrated Mn eliminates the fcc-hcp energy difference. This highlights the unique combination of chemistry and magnetic properties in CrCoNi, leading to a fcc-hcp phase transformation that occurs only in this alloy, and is triggered by dislocation slip and interaction with internal boundaries. This phase transformation sets CrCoNi apart from the parent quinary, and its other equiatomic ternary derivatives, and provides a new way for increasing strength without compromising plastic deformation.