bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantum chaos in the Heisenberg spin chain: The effect of Dzyaloshinskii-Moriya interaction
Authors: Vahedi J. , Ashouri A. , Mahdavifar S.
Published: October 2016

Using one-dimensional spin-1/2 systems as prototypes of quantum many-body systems, we study the emergence of quantum chaos. The main purpose of this work is to answer the following question: how the spin-orbit interaction, as a pure quantum interaction, may lead to the onset of quantum chaos? We consider the three integrable spin-1/2 systems: the Ising, the XX, and the XXZ limits and analyze whether quantum chaos develops or not after the addition of the Dzyaloshinskii-Moriya interaction. We find that depending on the strength of the anisotropy parameter, the answer is positive for the XXZ and Ising models, whereas no such evidence is observed for the XX model. We also discuss the relationship between quantum chaos and thermalization.
Computational prediction of the diversity of monolayer boron phosphide allotropes
Authors: Zhu Zhili , Cai Xiaolin , Niu Chunyao , Wang Chongze , Jia Yu
Published: October 2016

We propose previously unrecognized allotropes of monolayer boron phosphorus (BP) based on ab initio density functional calculations. In addition to the hexagonal structure of h-BP, four types of boron phosphide compounds were predicted to be stable as monolayers. They can form sp2 hybridized planar structures composed of 6-membered rings, and buckled geometries including 4–8 or 3–9 membered rings with sp3 like bonding for P atoms. The calculated Bader charges illustrate their ionic characters with the charge transfers from B to P atoms. The competing between the electrostatic energy and the bonding energy of sp2 and sp3 hybridizations reflected in P atoms results in multiple structures of BP. These 2D BP structures can be semiconducting or metallic depending on their geometric structures. Our findings significantly broaden the diversity of monolayer BP allotropes and provide valuable guidance to other 2D group-III-V allotropes.
Engineering micro-supercapacitors of graphene nanowalls/Ni heterostructure based on microfabrication technology
Authors: Li Jinhua , Zhu Minjie , Wang Zhuqing , Ono Takahito
Published: October 2016

Heterostructure of graphene nanowalls (GNW) supported Ni thin-layer was fabricated to form an on-chip pseudocapacitor via a standard microelectromechanical system process. Beyond a high-rate capability of the micro-supercapacitors, a large specific energy density of 2.1 mW h cm−3 and power density up to 5.91 W cm−3 have been achieved, which are two orders of magnitude higher than those commercial electrolytic capacitors and thin-film batteries, respectively. Rational analysis revealed a rapid GNW growth originated from the Pt current collector embedment by catalyzing hydrocarbon dissociating. The unique concept in our design includes that Ni was evaporated onto GNW to serve as both the shadow mask for microelectrode patterning and subsequently a precursor to be in-situ electrochemically converted into pseudo-capacitive Ni(OH)2 for capacitance enhancing. Addressing the challenge to uniformly coat in complex nanoporous structures, this strategy renders a conformal deposition of pseudo-capacitive material on individual graphene nanoflakes, leading to efficient merits harnessing of huge accessible surfaces from the conductive GNW networks and great capacitance of the Ni-based active materials for high performance delivery. The proof of concept can be potentially extended to other transition metals and paves the way to further apply GNW hybrids in diverse microsystems.
Direct measurement of single-dot coercivity and statistical analysis of switching field distribution in bit-patterned media using scanning hard-X-ray nanoprobe
Authors: Suzuki Motohiro , Kondo Yuji , Ariake Jun
Published: October 2016

To investigate the possible sources of the switching field distribution in bit-patterned media, we applied a scanning hard-X-ray nanoprobe technique based on X-ray magnetic circular dichroism spectroscopy to an array of Co-Pt dots with the typical diameters of 200 nm. Element-specific magnetization curves at the Pt L3 edge were measured for individual dots isolated from each other, and the magnetization switching field (coercivity) values were determined for more than 100 individual dots. To assess the effect of dot diameters as a possible source of switching field distribution, a statistical analysis of the coercivity values and dot diameters measured for many dots was performed. The resulting switching field distribution had a mean of ⟨HSW⟩=1.80 kOe and a standard deviation of σHSW = 0.64 kOe. The relative deviation of σHSW/⟨HSW⟩=36% was not in good agreement with the relative dispersion in a dot diameter of σD/⟨D⟩=2.7%, and no clear correlation between the coercivity and dot diameter was observed. These results may suggest other possible sources of switching field distribution than dot diameter, such as dispersion in the c-axis orientation and in magnetocrystalline anisotropy.
Exploiting nonlinear amplitude-frequency dependence for temperature compensation in silicon micromechanical resonators
Authors: Defoort M. , Taheri-Tehrani P. , Horsley D. A.
Published: October 2016

Resonators used in frequency-reference oscillators must maintain a stable frequency output even when subjected to temperature variations. The traditional solution is to construct the resonator from a material with a low temperature coefficient, such as AT-cut quartz, which can achieve absolute frequency stability on the order of ±25 ppm over commercial temperature ranges. In comparison, Si microresonators suffer from the disadvantage that silicon's temperature coefficient of frequency (TCF) is approximately two orders of magnitude greater than that of AT-cut quartz. In this paper, we present an in situ passive temperature compensation scheme for Si microresonators based on nonlinear amplitude-frequency coupling which reduces the TCF to a level comparable with that of an AT-quartz resonator. The implementation of this passive technique is generic to a variety of Si microresonators and can be applied to a number of frequency control and timing applications.
Light-induced performance increase of silicon heterojunction solar cells
Authors: Kobayashi Eiji , De Wolf Stefaan , Levrat Jacques , Christmann Gabriel , Descoeudres Antoine , Nicolay Sylvain , Despeisse Matthieu , Watabe Yoshimi , Ballif Christophe
Published: October 2016

Silicon heterojunction solar cells consist of crystalline silicon (c-Si) wafers coated with doped/intrinsic hydrogenated amorphous silicon (a-Si:H) bilayers for passivating-contact formation. Here, we unambiguously demonstrate that carrier injection either due to light soaking or (dark) forward-voltage bias increases the open circuit voltage and fill factor of finished cells, leading to a conversion efficiency gain of up to 0.3% absolute. This phenomenon contrasts markedly with the light-induced degradation known for thin-film a-Si:H solar cells. We associate our performance gain with an increase in surface passivation, which we find is specific to doped a-Si:H/c-Si structures. Our experiments suggest that this improvement originates from a reduced density of recombination-active interface states. To understand the time dependence of the observed phenomena, a kinetic model is presented.
Monolithic translucent BaMgAl10O17:Eu2+ phosphors for laser-driven solid state lighting
Authors: Cozzan Clayton , Brady Michael J. , O’Dea Nicholas , Levin Emily E. , Nakamura Shuji , DenBaars Steven P. , Seshadri Ram
Published: October 2016

With high power light emitting diodes and laser diodes being explored for white light generation and visible light communication, thermally robust encapsulation schemes for color-converting inorganic phosphors are essential. In the current work, the canonical blue-emitting phosphor, high purity Eu-doped BaMgAl10O17, has been prepared using microwave-assisted heating (25 min) and densified into translucent ceramic phosphor monoliths using spark plasma sintering (30 min). The resulting translucent ceramic monoliths convert UV laser light to blue light with the same efficiency as the starting powder and provide superior thermal management in comparison with silicone encapsulation.
Optimization of audio - ultrasonic plasma system parameters
Authors: Haleem N. A. , Abdelrahman M. M. , Ragheb M.S.
Published: October 2016

The present plasma is a special glow plasma type generated by an audio ultrasonic discharge voltage. A definite discharge frequency using a gas at a narrow band pressure creates and stabilizes this plasma type. The plasma cell is a self-extracted ion beam; it is featured with its high output intensity and its small size. The influence of the plasma column length on the output beam due to the variation of both the audio discharge frequency and the power applied to the plasma electrodes is investigated. In consequence, the aim of the present work is to put in evidence the parameters that influence the self-extracted collected ion beam and to optimize the conditions that enhance the collected ion beam. The experimental parameters studied are the nitrogen gas, the applied frequency from 10 to 100 kHz, the plasma length that varies from 8 to 14 cm, at a gas pressure of ≈ 0.25 Torr and finally the discharge power from 50 to 500 Watt. A sheet of polyethylene of 5 micrometer covers the collector electrode in order to confirm how much ions from the beam can go through the polymer and reach the collector. To diagnose the occurring events of the beam on the collector, the polymer used is analyzed by means of the FTIR and the XRF techniques. Optimization of the plasma cell parameters succeeded to enhance and to identify the parameters that influence the output ion beam and proved that its particles attaining the collector are multi-energetic.
Functional connectivity with the retrosplenial cortex predicts cognitive aging in rats
Authors: Ash Jessica A. , Lu Hanbing , Taxier Lisa R. , Long Jeffrey M. , Yang Yihong , Stein Elliot A. , Rapp Peter R.
Published: October 2016

Significance

Neural network dynamics thought to play a key role in cognition are substantially disrupted in both normal and pathological aging. Using a rat model, here we aimed to define the effects of aging on the integrity of cortical resting state functional connectivity distinct from the potential contribution of neurodegenerative disease. The findings highlight that disrupted circuit connectivity with the retrosplenial/posterior cingulate cortex is coupled with variability in memory function during aging, and that adaptive plasticity in the aged brain appears to contribute to successful cognitive aging. The development of interventions that promote neuroadaptive network plasticity is a potentially valuable alternative to strategies currently under investigation, toward bending the trajectory of aging away from neurodegeneration.
Physical interaction between neurofibromin and serotonin 5-HT
6
receptor promotes receptor constitutive activity
Authors: Deraredj Nadim Wissem , Chaumont-Dubel Séverine , Madouri Fahima , Cobret Laetitia , De Tauzia Marie-Ludivine , Zajdel Pawel , Bénédetti Hélène , Marin Philippe , Morisset-Lopez Séverine
Published: October 2016

Significance

This study provides evidence of a physical interaction between neurofibromin, an Ras-GTPase activating protein, and a G protein-coupled receptor (GPCR), the serotonin 5 hydroxytryptamine 6 (5-HT
6
) receptor. It also shows that constitutive activity of a GPCR depends on its association with GPCR-interacting proteins. Finally, it suggests that the 5-HT
6
receptor may be considered as a potentially relevant therapeutic target to correct some neurofibromatosis type 1-related cognitive deficits, a genetic disorder caused by mutations in the gene encoding neurofibromin.
Allosteric binding site in a Cys-loop receptor ligand-binding domain unveiled in the crystal structure of ELIC in complex with chlorpromazine
Authors: Nys Mieke , Wijckmans Eveline , Farinha Ana , Yoluk Özge , Andersson Magnus , Brams Marijke , Spurny Radovan , Peigneur Steve , Tytgat Jan , Lindahl Erik , Ulens Chris
Published: October 2016

Significance

Cys-loop receptors belong to a family of ion channels that are involved in fast synaptic transmission. Allosteric modulators of Cys-loop receptors hold therapeutic potential as they tweak receptor function while preserving the normal fluctuations in neurotransmitter signaling at the synapse. Here, we take advantage of a model Cys-loop receptor, the
Erwinia
ligand-gated ion channel (ELIC). We determined cocrystal structures of ELIC in complex with chlorpromazine (IC
50
, ∼160 μM) and its brominated derivative bromopromazine, which unveil an allosteric binding site localized at the interface between the extracellular ligand-binding domain and the pore-forming transmembrane domain. Our results demonstrate that the different allosteric binding sites present in Cys-loop receptors form an almost continuous path stretching from top to bottom of the receptor.
Thermogenic methane release as a cause for the long duration of the PETM
Authors: Frieling Joost , Svensen Henrik H. , Planke Sverre , Cramwinckel Marlow J. , Selnes Haavard , Sluijs Appy
Published: October 2016

The Paleocene–Eocene Thermal Maximum (PETM) (∼56 Ma) was a ∼170,000-y (∼170-kyr) period of global warming associated with rapid and massive injections of
13
C-depleted carbon into the ocean–atmosphere system, reflected in sedimentary components as a negative carbon isotope excursion (CIE). Carbon cycle modeling has indicated that the shape and magnitude of this CIE are generally explained by a large and rapid initial pulse, followed by ∼50 kyr of
13
C-depleted carbon injection. Suggested sources include submarine methane hydrates, terrigenous organic matter, and thermogenic methane and CO
2
from hydrothermal vent complexes. Here, we test for the contribution of carbon release associated with volcanic intrusions in the North Atlantic Igneous Province. We use dinoflagellate cyst and stable carbon isotope stratigraphy to date the active phase of a hydrothermal vent system and find it to postdate massive carbon release at the onset of the PETM. Crucially, however, it correlates to the period within the PETM of longer-term
13
C-depleted carbon release. This finding represents actual proof of PETM carbon release from a particular reservoir. Based on carbon cycle box model [i.e., Long-Term Ocean–Atmosphere–Sediment Carbon Cycle Reservoir (LOSCAR) model] experiments, we show that 4–12 pulses of carbon input from vent systems over 60 kyr with a total mass of 1,500 Pg of C, consistent with the vent literature, match the shape of the CIE and pattern of deep ocean carbonate dissolution as recorded in sediment records. We therefore conclude that CH
4
from the Norwegian Sea vent complexes was likely the main source of carbon during the PETM, following its dramatic onset.
ATM/G6PD-driven redox metabolism promotes FLT3 inhibitor resistance in acute myeloid leukemia
Authors: Gregory Mark A. , D’Alessandro Angelo , Alvarez-Calderon Francesca , Kim Jihye , Nemkov Travis , Adane Biniam , Rozhok Andrii I. , Kumar Amit , Kumar Vijay , Pollyea Daniel A. , Wempe Michael F. , Jordan Craig T. , Serkova Natalie J. , Tan Aik Choon , Hansen Kirk C. , DeGregori James
Published: October 2016

Significance

FMS-like tyrosine kinase 3 (FLT3) inhibitors have shown impressive activity in clinical trials for acute myeloid leukemia (AML); however, these inhibitors invariably fail to achieve sustained remissions. Here we demonstrate that FLT3 inhibition causes severe deficiencies in redox metabolism and accumulation of reactive oxygen species (ROS) in the mitochondria of AML cells. We discovered that the metabolic regulators ataxia telangiectasia mutated and glucose 6-phosphate dehydrogenase help maintain antioxidant capacity and survival of a subpopulation of AML cells in the face of FLT3 inhibition. Inactivation of these factors escalates mitochondrial ROS and enhances AML cell eradication. Importantly, we show that the use of a drug that increases mitochondrial ROS enhances the efficacy of FLT3 inhibitor therapy, suggesting a combinatorial therapeutic strategy.
V-1 regulates capping protein activity in vivo
Authors: Jung Goeh , Alexander Christopher J. , Wu Xufeng S. , Piszczek Grzegorz , Chen Bi-Chang , Betzig Eric , Hammer John A.
Published: October 2016

Significance

F-actin is assembled downstream of major actin nucleators like the actin-related proteins 2/3 (Arp2/3) complex and formins. Capping Protein (CP), conversely, halts actin assembly. The ankyrin-repeat protein V-1 has been shown to block CP activity in vitro. Here we show that V-1 overexpression and knockout in
Dictyostelium
amoeba phenocopy CP knockdown and overexpression, respectively. Moreover, V-1 must be capable of binding CP to exhibit overexpression phenotypes and rescue V-1–null cells. Finally, we present evidence that V-1’s ability to sequester CP is regulated by phosphorylation. Together, our data demonstrate that V-1 controls major actin-dependent cellular processes in vivo by virtue of its ability to inhibit CP and that its influence may be modulated in cells.
Molecular insight into the nanoconfined calcite–solution interface
Authors: Diao Yijue , Espinosa-Marzal Rosa M.
Published: October 2016

Significance

Calcium carbonate mineralization occurring in confined spaces and nanopores is central to many natural processes occurring at or near the Earth’s surface. We study the effect of divalent ion concentration, in an attempt to provide a general conceptual picture of Derjaguin–Landau–Verwey–Overbeek (DLVO) and non-DLVO forces considering calcite’s nonclassical Stern layer. From the careful measurement of the hydration forces in aqueous solutions, we propose a model for the nanoconfined calcite–solution interface. Colloidal probe AFM resolves subnanometer film thickness transitions of the nanoconfined aqueous solution induced by the squeezing out of water and hydrated calcium ions by applying an external work. The fundamental knowledge derived from this work provides guidance to understand the physicochemical phenomena occurring at nanoconfined mineral interfaces.
PPARγ-coactivator-1α gene transfer reduces neuronal loss and amyloid-β generation by reducing β-secretase in an Alzheimer’s disease model
Authors: Katsouri Loukia , Lim Yau M. , Blondrath Katrin , Eleftheriadou Ioanna , Lombardero Laura , Birch Amy M. , Mirzaei Nazanin , Irvine Elaine E. , Mazarakis Nicholas D. , Sastre Magdalena
Published: October 2016

Significance

The PPARγ-coactivator-1α (PGC-1α) is a transcriptional regulator of genes involved in energy metabolism. We observed previously that PGC-1α decreases the generation of Aβ in cell culture, and its levels are reduced in Alzheimer’s disease (AD) brains. To determine its potential therapeutic role in vivo, we delivered PGC-1α in specific brain areas of an AD model by using viral vectors. We found that PGC-1α–injected mice showed decreased Aβ plaques by reducing the expression of the main enzyme involved in Aβ production, preserving most neurons in the brain and performing as well as wild-type mice in cognitive tests. Therefore, PGC-1α selective delivery shows promising therapeutic value in AD.
Spatiotemporal periodicity of dislocation dynamics in a two-dimensional microfluidic crystal flowing in a tapered channel
Authors: Gai Ya , Leong Chia Min , Cai Wei , Tang Sindy K. Y.
Published: October 2016

Significance

Collective interactions in many-body systems can give rise to unexpected order. Such interactions underlie a wide range of complex phenomena such as swarming in animals and traffic patterns. This work reports an unexpected order in the flow of highly confined and highly concentrated water-in-oil drops, which can be explained and modeled as a soft crystal being extruded in the nanoscale. The findings are important to the understanding of out-of-equilibrium many-body systems, and the flow control of these drops used as microreactors in droplet microfluidics. Furthermore, contrary to the unpredictable microscale crystal deformation process, the discoveries here indicate that nanoscale crystal deformation can be highly ordered and predictable, and imply that the manufacturing of nanocrystalline materials may be easier than perceived.
miRNA92a targets KLF2 and the phosphatase PTEN signaling to promote human T follicular helper precursors in T1D islet autoimmunity
Authors: Serr Isabelle , Fürst Rainer W. , Ott Verena B. , Scherm Martin G. , Nikolaev Alexei , Gökmen Füsun , Kälin Stefanie , Zillmer Stephanie , Bunk Melanie , Weigmann Benno , Kunschke Nicole , Loretz Brigitta , Lehr Claus-Michael , Kirchner Benedikt , Haase Bettina , Pfaffl Michael , Waisman Ari , Willis Richard A. , Ziegler Anette-G. , Daniel Carolin
Published: October 2016

Significance

The onset of type 1 diabetes autoimmunity is indicated by the development of multiple islet autoantibodies, produced by B cells with the help of T follicular helper (TFH) cells. MicroRNAs (miRNAs) are small noncoding RNAs that regulate cellular states, as immune activation, making them suitable targets for disease intervention. Here, we show an enrichment of insulin-specific C-X-C chemokine receptor type 5 (CXCR5)
+
CD4
+
TFH precursors correlating with high miRNA92a abundance during onset of autoimmunity and identify Krueppel-like factor 2 (KLF2) as a target for miRNA92a. We demonstrate that miRNA92a inhibition blocks TFH induction and reduces murine islet autoimmunity in vivo. Therefore, we propose miRNA92a and the phosphatase and tension homolog-phosphoinositol-3-kinase-KLF2 signaling network as possible innovative precision medicine targets to interfere with aberrant immune activation in islet autoimmunity.
Impact of anthropogenic climate change on wildfire across western US forests
Authors: Abatzoglou John T. , Williams A. Park
Published: October 2016

Significance

Increased forest fire activity across the western United States in recent decades has contributed to widespread forest mortality, carbon emissions, periods of degraded air quality, and substantial fire suppression expenditures. Although numerous factors aided the recent rise in fire activity, observed warming and drying have significantly increased fire-season fuel aridity, fostering a more favorable fire environment across forested systems. We demonstrate that human-caused climate change caused over half of the documented increases in fuel aridity since the 1970s and doubled the cumulative forest fire area since 1984. This analysis suggests that anthropogenic climate change will continue to chronically enhance the potential for western US forest fire activity while fuels are not limiting.
Gene transfers from diverse bacteria compensate for reductive genome evolution in the chromatophore of
Paulinella chromatophora
Authors: Nowack Eva C. M. , Price Dana C. , Bhattacharya Debashish , Singer Anna , Melkonian Michael , Grossman Arthur R.
Published: October 2016

Significance

Eukaryotic photosynthetic organelles (plastids) originated >1 billion y ago via the endosymbiosis of a β-cyanobacterium. The resulting proliferation of primary producers fundamentally changed our planet’s history, allowing for the establishment of human populations. Early stages of plastid integration, however, remain poorly understood, including the role of horizontal gene transfer from nonendosymbiotic bacteria. Rules governing organellogenesis are difficult, if not impossible, to evaluate using the highly derived algal and plant systems. Insights into this issue are provided by the amoeba
Paulinella chromatophora
, which contains more recently established photosynthetic organelles of α-cyanobacterial origin. Here we show that the impact of Muller’s ratchet that leads to endosymbiont genome reduction seems to drive the fixation of horizontally acquired “compensatory” bacterial genes in the host nuclear genome.
Single cell lineage tracing reveals a role for TgfβR2 in intestinal stem cell dynamics and differentiation
Authors: Fischer Jared M. , Calabrese Peter P. , Miller Ashleigh J. , Muñoz Nina M. , Grady William M. , Shibata Darryl , Liskay R. Michael
Published: October 2016

Significance

Although Tgfβ signaling is important in intestinal development and cancer, little is known about the consequences of sporadic transforming growth factor β receptor 2 (
TgfβR2
) mutation in intestinal stem cells (ISCs). By labeling single,
TgfβR2
-mutant ISCs, we measured the effects of
TgfβR2
loss on competition-driven clonal dynamics and differentiation. Specifically, we found that stochastic loss of
TgfβR2
increases clonal survival while paradoxically decreasing clonal expansion and crypt fission, further elucidating mechanisms responsible for the role of Tgfβ signaling in ISCs on tumor initiation and tissue regeneration. In addition, we found that Tgfβ signaling modulates the generation of secretory cell precursors, revealing a role for Tgfβ signaling in altering ISC differentiation with implications for cancer, tissue regeneration, and inflammation.
Context-specific inhibition of translation by ribosomal antibiotics targeting the peptidyl transferase center
Authors: Marks James , Kannan Krishna , Roncase Emily J. , Klepacki Dorota , Kefi Amira , Orelle Cédric , Vázquez-Laslop Nora , Mankin Alexander S.
Published: October 2016

Significance

Chloramphenicol and linezolid interfere with translation by targeting the ribosomal catalytic center and are viewed as universal inhibitors of peptide bond formation. We show that, contrary to this view, the activity of these antibiotics critically depends on the nature of specific amino acids of the nascent chain carried by the ribosome and by the identity of the residue entering the A site. These findings indicate that the nascent protein modulates the properties of the ribosomal catalytic center and affects binding of its ligands. Understanding the principles of context specificity of ribosomal drugs may help develop better antibiotics.
Differential roles of the RNases H in preventing chromosome instability
Authors: Zimmer Anjali D. , Koshland Douglas
Published: October 2016

Significance

DNA damage can lead to chromosome instability and loss of genetic information, resulting in cell death or diseases such as cancer. One source of damage is DNA:RNA hybrids that form when RNA transcripts hybridize to homologous sequences in the genome. Cells from all branches of life possess two enzymes that can degrade DNA:RNA hybrids: RNase H1 and RNase H2. In this study we explore the differential functions of the RNase H1 and H2 in preventing chromosome instability in the model organism
Saccharomyces cerevisiae
. We present evidence that RNase H2 acts on hybrids genome-wide to prevent chromosome instability. In contrast, RNase H1 acts at a subset of hybrids to repress locus-restricted chromosome instability.
Rippling ultrafast dynamics of suspended 2D monolayers, graphene
Authors: Hu Jianbo , Vanacore Giovanni M. , Cepellotti Andrea , Marzari Nicola , Zewail Ahmed H.
Published: October 2016

Significance

Rippling is an intrinsic feature of 2D materials, responsible for their structural stability, transport properties, and electron–hole charge redistribution. Modulating these ripples in a controlled manner not only provides a better understanding of their structural properties, but also has potential impact for applications. Here, we examine graphene monolayer as a prototypical 2D material. An ultrafast attenuation of the ripples intrinsically present in the graphene plane is followed by a significant enhancement of the rippling effect on a longer time scale, as driven by the successive excitation of in-plane and out-of-plane phonon modes. The methodology described is of a general nature and is suitable for the investigation of other 2D materials, where we expect to observe similar rippling effects.
Genetic architecture of natural variation in visual senescence in
Drosophila
Authors: Carbone Mary Anna , Yamamoto Akihiko , Huang Wen , Lyman Rachel A. , Meadors Tess Brune , Yamamoto Ryoan , Anholt Robert R. H. , Mackay Trudy F. C.
Published: October 2016

Significance

Functional decline with age—senescence—is a major determinant of health span in an aging population, but its genetic basis remains largely unknown. In humans, visual decline often heralds the onset of senescence. We used the fruit fly,
Drosophila melanogaster
, to explore the genetic basis of natural variation in phototaxis, the innate tendency to move toward light, and age-dependent decline in phototaxis as a proxy for visual senescence. We found the genetic basis for visual senescence is distinct from that which determines variation in life span. Furthermore, genes shaping early development of the nervous system, in particular the visual system, also contribute to senescence at later age, demonstrating that senescence is part of a genetic continuum throughout the life span.
Crystal structure of the DNA binding domain of the transcription factor T-bet suggests simultaneous recognition of distant genome sites
Authors: Liu Ce Feng , Brandt Gabriel S. , Hoang Quyen Q. , Naumova Natalia , Lazarevic Vanja , Hwang Eun Sook , Dekker Job , Glimcher Laurie H. , Ringe Dagmar , Petsko Gregory A.
Published: October 2016

Significance

The transcription factor T-bet (Tbox protein expressed in T cells), a master regulator of T-cell lineage commitment, is a member of the Tbox family but coordinately regulates many more genes than other Tbox proteins. How T-bet simultaneously recognizes distant elements that may be thousands of base pairs apart is unknown. We have determined the crystal structure of the Tbox DNA binding domain of T-bet complexed with a 24-bp palindromic DNA. The structure shows a dimer where each monomer binds simultaneously to two independent DNA molecules. Fluorescence-based assays show T-bet can synapse two DNA molecules in solution. Chromosome conformation capture assays confirm that T-bet can directly mediate the formation of chromatin loops at the IFN-γ gene locus in the absence of other transcription-related proteins.
Orthopedic surgery modulates neuropeptides and BDNF expression at the spinal and hippocampal levels
Authors: Zhang Ming-Dong , Barde Swapnali , Yang Ting , Lei Beilei , Eriksson Lars I. , Mathew Joseph P. , Andreska Thomas , Akassoglou Katerina , Harkany Tibor , Hökfelt Tomas G. M. , Terrando Niccolò
Published: October 2016

Significance

Orthopedic surgery sometimes causes persistent pain and, especially in the elderly, delirium and cognitive dysfunction. Using an established mouse bone-fracture model associating with memory deficits, we assessed pain behavior and expression of several molecules in sensory neurons, spinal cord, and brain. An increase in cold sensitivity and up-regulation of several injury markers, including activating transcription factor 3, the neuropeptide galanin, and growth factor brain-derived neurotrophic factor (BDNF), were observed in sensory ganglia. In the hippocampus, BDNF protein levels were increased in mossy fibers. In contrast, the Bdnf transcript was not increased in the parent granule cell bodies, and c-Fos levels were decreased, as was neurogenesis. Thus, impaired hippocampal BDNF signaling may contribute to mental deficits observed after surgery.
Human attention filters for single colors
Authors: Sun Peng , Chubb Charles , Wright Charles E. , Sperling George
Published: October 2016

Significance

The eyes present the brain much more information than it could possibly process. One important way to prioritize information is by selective attention to features, processing only items containing the attended features and blocking others (i.e., forming an attention filter). Here we demonstrate an extremely efficient paradigm and a powerful analysis to quantitatively measure, as accurately as one might measure physical color filters, 32 such human attention filters for single colors. These data are an essential basis for a theory of attention to color. The centroid paradigm itself, because it quickly and quantitatively characterizes basic attention processes, has numerous applications.
Graded activation and free energy landscapes of a muscarinic G-protein–coupled receptor
Authors: Miao Yinglong , McCammon J. Andrew
Published: October 2016

Significance

G-protein–coupled receptors (GPCRs) represent primary targets of about one-third of currently marketed drugs. The structure, dynamics, and function of GPCRs result from complex free energy landscapes. In this work, we have applied Gaussian accelerated molecular dynamics (GaMD) to study the ligand-dependent behavior of the M
2
muscarinic GPCR. Extensive GaMD simulations have revealed distinct structural flexibility and free energy profiles that depict graded activation of the M
2
receptor. We have captured both dissociation and binding of an orthosteric ligand in a single all-atom GPCR simulation. GaMD is well poised to study large biomolecules and ligand recognition for drug discovery.
Structure and assembly model for the
Trypanosoma cruzi
60S ribosomal subunit
Authors: Liu Zheng , Gutierrez-Vargas Cristina , Wei Jia , Grassucci Robert A. , Ramesh Madhumitha , Espina Noel , Sun Ming , Tutuncuoglu Beril , Madison-Antenucci Susan , Woolford John L. , Tong Liang , Frank Joachim
Published: October 2016

Significance

The pathogenic trypanosomatids—
Trypanosoma cruzi
,
Trypanosoma brucei
, and
Leishmania
spp.—are the causative agents of Chagas disease, African trypanosomiasis, and leishmaniasis, respectively. These diseases, with high morbidity and mortality rates, affect millions of people worldwide. Current treatments typically use drugs with high toxicity and marginal efficacy. Here we present, a 2.5-Å structure of the
T. cruzi
ribosome large subunit by single-particle cryo-EM. Our structure highlights distinctive trypanosome interactions and has allowed us to propose a tentative model for assembly of the 60S large ribosomal subunit. These atomic details highlighting trypanosome-specific interactions and the differences between
T. cruzi
and the human ribosome can be used directly for structure-based drug design of antitrypanosome drugs.
NMR detection of intermolecular interaction sites in the dimeric 5′-leader of the HIV-1 genome
Authors: Keane Sarah C. , Van Verna , Frank Heather M. , Sciandra Carly A. , McCowin Sayo , Santos Justin , Heng Xiao , Summers Michael F.
Published: October 2016

Significance

A nucleotide-specific
2
H-edited NMR approach was used to determine the nature of the intermolecular interface in the intact, dimeric HIV type-1 (HIV-1) 5′-leader RNA (230 kD). The studies distinguish between previously proposed extended duplex and kissing hairpin models and identify additional intermolecular interaction sites. A one-dimensional
2
H-edited NMR method that allows temporal monitoring of intermolecular base-pair formation revealed that the observed “extended dimer interface” forms rapidly, even in the absence of RNA chaperones. In addition to addressing long-standing questions about retroviral genome dimerization, these studies illustrate the utility of
2
H-edited NMR for determining the structures and folding kinetics of relatively large RNAs.
Mechanism of O2activation and substrate hydroxylation in noncoupled binuclear copper monooxygenases
Authors: Cowley Ryan E. , Tian Li , Solomon Edward I.
Published: October 2016

Significance

Nature has evolved several strategies for using dioxygen (O2) for chemical oxidations. These enzymatic processes typically use metal cofactors to impart selectivity and minimize production of deleterious reactive oxygen species. In particular, hormone biosynthesis and neurotransmitter regulation are accomplished by copper- and O2-dependent enzymes possessing a unique copper active site; however, the mechanism has been debated and the role of the unique active site structure in enabling the chemistry is unclear. To understand this, structural and spectroscopic data are used to computationally model the full reaction mechanism to define the molecular basis for O2reactivity and define the role of the active site structure in controlling proper enzymatic function.
Thermal Regimes, Nonnative Trout, and Their Influences on Native Bull Trout in the Upper Klamath River Basin, Oregon
Authors: Benjamin Joseph R. , Heltzel Jeannie M. , Dunham Jason B. , Heck Michael , Banish Nolan
Published: October 2016

The occurrence of fish species may be strongly influenced by a stream's thermal regime (magnitude, frequency, variation, and timing). For instance, magnitude and frequency provide information about sublethal temperatures, variability in temperature can affect behavioral thermoregulation and bioenergetics, and timing of thermal events may cue life history events, such as spawning and migration. We explored the relationship between thermal regimes and the occurrences of native Bull Trout Salvelinus confluentus and nonnative Brook Trout Salvelinus fontinalis and Brown Trout Salmo trutta across 87 sites in the upper Klamath River basin, Oregon. Our objectives were to associate descriptors of the thermal regime with trout occurrence, predict the probability of Bull Trout occurrence, and estimate upper thermal tolerances of the trout species. We found that each species was associated with a different suite of thermal regime descriptors. Bull Trout were present at sites that were cooler, had fewer high‐temperature events, had less variability, and took longer to warm. Brook Trout were also observed at cooler sites with fewer high‐temperature events, but the sites were more variable and Brook Trout occurrence was not associated with a timing descriptor. In contrast, Brown Trout were present at sites that were warmer and reached higher temperatures faster, but they were not associated with frequency or variability descriptors. Among the descriptors considered, magnitude (specifically June degree‐days) was the most important in predicting the probability of Bull Trout occurrence, and model predictions were strengthened by including Brook Trout occurrence. Last, all three trout species exhibited contrasting patterns of tolerating longer exposures to lower temperatures. Tolerance limits for Bull Trout were lower than those for Brook Trout and Brown Trout, with contrasts especially evident for thermal maxima. Our results confirm the value of exploring a suite of thermal regime descriptors for understanding the distribution and occurrence of fishes. Moreover, these descriptors and their relationships to fish should be considered with future changes in land use, water use, or climate.

Received March 4, 2016; accepted July 27, 2016 Published online October 11, 2016
Trophic Feasibility of Reintroducing Anadromous Salmonids in Three Reservoirs on the North Fork Lewis River, Washington: Prey Supply and Consumption Demand of Resident Fishes
Authors: Sorel Mark H. , Hansen Adam G. , Connelly Kristin A. , Beauchamp David A.
Published: October 2016

The reintroduction of anadromous salmonids in reservoirs is being proposed with increasing frequency, requiring baseline studies to evaluate feasibility and estimate the capacity of reservoir food webs to support reintroduced populations. Using three reservoirs on the north fork Lewis River as a case study, we demonstrate a method to determine juvenile salmonid smolt rearing capacities for lakes and reservoirs. To determine if the Lewis River reservoirs can support reintroduced populations of juvenile stream‐type Chinook Salmon Oncorhynchus tshawytscha, we evaluated the monthly production of daphnia Daphnia spp. (the primary zooplankton consumed by resident salmonids in the system) and used bioenergetics to model the consumption demand of resident fishes in each reservoir. To estimate the surplus of Daphnia prey available for reintroduced salmonids, we assumed a maximum sustainable exploitation rate and accounted for the consumption demand of resident fishes. The number of smolts that could have been supported was estimated by dividing any surplus Daphnia production by the simulated consumption demand of an individual Chinook Salmon fry rearing in the reservoir to successful smolt size. In all three reservoirs, densities of Daphnia were highest in the epilimnion, but warm epilimnetic temperatures and the vertical distribution of planktivores suggested that access to abundant epilimnetic prey was limited. By comparing accessible prey supply and demand on a monthly basis, we were able to identify potential prey supply bottlenecks that could limit smolt production and growth. These results demonstrate that a bioenergetics approach can be a valuable method of examining constraints on lake and reservoir rearing capacity, such as thermal structure and temporal food supply. This method enables numerical estimation of rearing capacity, which is a useful metric for managers evaluating the feasibility of reintroducing Pacific salmon Oncorhynchus spp. in lentic systems.

Received April 24, 2016; accepted July 28, 2016 Published online October 11, 2016
Recovery of Sockeye Salmon in the Elwha River, Washington, after Dam Removal: Dependence of Smolt Production on the Resumption of Anadromy by Landlocked Kokanee
Authors: Hansen Adam G. , Gardner Jennifer R. , Beauchamp David A. , Paradis Rebecca , Quinn Thomas P.
Published: October 2016

Pacific salmon Oncorhynchus spp. are adept at colonizing habitat that has been reopened to anadromous passage. Sockeye Salmon O. nerka are unique in that most populations require lakes to fulfill their life history. Thus, for Sockeye Salmon to colonize a system, projects like dam removals must provide access to lakes. However, if the lakes contain landlocked kokanee (lacustrine Sockeye Salmon), the recovery of Sockeye Salmon could be mediated by interactions between the two life history forms and the processes associated with the resumption of anadromy. Our objective was to evaluate the extent to which estimates of Sockeye Salmon smolt production and recovery are sensitive to the resumption of anadromy by kokanee after dam removal. We informed the analysis based on the abiotic and biotic features of Lake Sutherland, which was recently opened to passage after dam removal on the Elwha River, Washington. We first developed maximum expectations for the smolt‐producing capacity of Lake Sutherland by using two predictive models developed from Sockeye Salmon populations in Alaska and British Columbia: one model was based on the mean seasonal biomass of macrozooplankton, and the other was based on the euphotic zone volume of the lake. We then constructed a bioenergetics‐based simulation model to evaluate how the capacity of Lake Sutherland to rear yearling smolts could change with varying degrees of anadromy among O. nerka fry. We demonstrated that (1) the smolt‐producing capacity of a nursery lake for juvenile Sockeye Salmon changes in nonlinear ways with changes in smolt growth, mortality, and the extent to which kokanee resume anadromy after dam removal; (2) kokanee populations may be robust to changes in abundance after dam removal, particularly if lakes are located higher in the watershed on tributaries separate from where dams were removed; and (3) the productivity of newly establishing Sockeye Salmon can vary considerably depending on whether the population becomes rearing limited or is recruitment limited and depending on how adult escapement is managed.

Received March 9, 2016; accepted August 6, 2016 Published online October 11, 2016
Methodology for heat flux investigation on leading edges using infrared thermography
Authors: Corre Y. , Gardarein J.-L. , Dejarnac R. , Gaspar J. , Gunn J.P. , Aumeunier M.-H. , Courtois X. , Missirlian M. , Rigollet F.
Published: October 2016

During steady state plasma operation in fusion devices, leading edges of the actively cooled plasma-facing components can be impacted by plasma flux with nearly normal angle of incidence, causing local overheating. The overheating can be a critical issue in high-power machines, especially in the presence of mechanical misalignments. Due to heat diffusion through the material, the edge power overload also leads to a local increase of temperature on the top part of the tile that can be detected by the infrared imaging system (viewed from the top of the machine). In the Tore Supra tokamak, heat flux impinging on the top and the leading edge of the carbon fibre composite (CFC) flat tiles are characterized with both an infrared (IR) thermographic system and 2D thermal modelling of the tile. A specific sensor correction based on a laboratory blackbody-slit experiment has been developed to simulate the spatial resolution related effects (necessary here since the temperature gradient near the leading edge is smaller than the pixel size of the IR system). The transfer function of the IR system is characterized by a Gaussian distribution function. The standard deviation is found to be σ  =  1.75 mm for a pixel size of 3.1 mm. The heat flux calculation is applied to CFC flat tiles and, after being processed with the transfer function, compared to experimental IR data for two geometrical situations: one with 0.2 mm misalignment between two adjacent tiles and the other without misalignment (well-aligned tiles). The heat flux ratio between the leading edge and top is found to be ~25 in the case of the protruding tile, which is lower than the expected ratio using the guiding-centre ballistic approximation with no cross-field heat flux (57).
The trouble with H0
Authors: Bernal José Luis , Verde Licia , Riess Adam G.
Published: October 2016

We perform a comprehensive cosmological study of theH0tension between the direct local measurement and the model-dependent value inferred from the Cosmic Microwave Background. With the recent measurement ofH0this tension has raised to more than 3 σ. We consider changes in the early time physics without modifying the late time cosmology. We also reconstruct the late time expansion history in a model independent way with minimal assumptions using distance measurements from Baryon Acoustic Oscillations and Type Ia Supernovae, finding that atz < 0.6 the recovered shape of the expansion history is less than 5% different than that of a standard ΛCDM model. These probes also provide a model insensitive constraint on the low-redshift standard ruler, measuring directly the combinationrshwhereH0 = h × 100 Mpc−1km/s andrsis the sound horizon at radiation drag (the standard ruler), traditionally constrained by CMB observations. ThusrsandH0provide absolute scales for distance measurements (anchors) at opposite ends of the observable Universe. We calibrate the cosmic distance ladder and obtain a model-independent determination of the standard ruler for acoustic scale,rs. The tension inH0reflects a mismatch between our determination ofrsand its standard, CMB-inferred value. Without including high-ℓ Planck CMB polarization data (i.e., only considering the ``recommended baseline" low-ℓ polarisation and temperature and the high ℓ temperature data), a modification of the early-time physics to include a component of dark radiation with an effective number of species around 0.4 would reconcile the CMB-inferred constraints, and the localH0and standard ruler determinations. The inclusion of the ``preliminary" high-ℓ Planck CMB polarisation data disfavours this solution.
Re‐Examining the Reported Rates of Return to Food and Agricultural Research and Development: Comment
Authors: Oehmke James F.
Published: October 2016

Hurley, Rao, and Pardey (2014) argue to replace the internal rate of return with the modified internal rate of return for the evaluation of public research investment. The crux of their argument is that the internal rate of return “assumes intermediate cash flows can be reinvested (or borrowed) at same return as the initial investment, which is generally not correct or reasonable,” (page 1492). This article first demonstrates that reinvestment decisions are embodied in the project specification, and that the internal rate of return makes no inherent reinvestment assumption. The article then clarifies the algebraic properties of the marginal internal rate of return and the reinvestment implications of the internal rate of return and modified internal rate of return within the context of public agricultural research evaluation.