bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nuclease Footprints in Sperm Project Past and Future Chromatin Regulatory Events
Authors: Johnson Graham D. , Jodar Meritxell , Pique-Regi Roger , Krawetz Stephen A. 
Published: May 2016

AbstractNuclear remodeling to a condensed state is a hallmark of spermatogenesis. This is achieved by replacement of histones with protamines. Regions retaining nucleosomes may be of functional significance. To determine their potential roles, sperm from wild type and transgenic mice harboring a single copy insert of the human protamine cluster were subjected to Micrococcal Nuclease-seq. CENTIPEDE, a hierarchical Bayesian model, was used to identify multiple spatial patterns, "footprints", of MNase-seq reads along the sperm genome. Regions predicted by CENTIPEDE analysis to be bound by a regulatory factor in sperm were correlated with genomic landmarks and higher order chromatin structure datasets to identify potential roles for these factors in regulating either prior or post spermatogenic, i.e., early embryonic events. This approach linked robust endogenous protamine transcription and transgene suppression to its chromatin environment within topologically associated domains. Of the candidate enhancer-bound regulatory proteins, Ctcf, was associated with chromatin domain boundaries in testes and embryonic stem cells. The continuity of Ctcf binding through the murine germline may permit rapid reconstitution of chromatin organization following fertilization. This likely reflects its preparation for early zygotic genome activation and comparatively accelerated preimplantation embryonic development program observed in mouse as compared to human and bull.
Prospect of quantum anomalous Hall and quantum spin Hall effect in doped kagome lattice Mott insulators
Authors: Guterding Daniel , Jeschke Harald O. , Valentí Roser 
Published: May 2016

AbstractElectronic states with non-trivial topology host a number of novel phenomena with potential for revolutionizing information technology. The quantum anomalous Hall effect provides spin-polarized dissipation-free transport of electrons, while the quantum spin Hall effect in combination with superconductivity has been proposed as the basis for realizing decoherence-free quantum computing. We introduce a new strategy for realizing these effects, namely by hole and electron doping kagome lattice Mott insulators through, for instance, chemical substitution. As an example, we apply this new approach to the natural mineral herbertsmithite. We prove the feasibility of the proposed modifications by performing ab-initio density functional theory calculations and demonstrate the occurrence of the predicted effects using realistic models. Our results herald a new family of quantum anomalous Hall and quantum spin Hall insulators at affordable energy/temperature scales based on kagome lattices of transition metal ions.
H3O+ tetrahedron induction in large negative linear compressibility
Authors: Wang Hui , Feng Min , Wang Yu-Fang , Gu Zhi-Yuan 
Published: May 2016

AbstractDespite the rarity, large negative linear compressibility (NLC) was observed in metal-organic framework material Zn(HO3PC4H8PO3H)∙2H2O (ZAG-4) in experiment. We find a unique NLC mechanism in ZAG-4 based on first-principle calculations. The key component to realize its large NLC is the deformation of H3O+ tetrahedron. With pressure increase, the oxygen apex approaches and then is inserted into the tetrahedron base (hydrogen triangle). The tetrahedron base subsequently expands, which results in the b axis expansion. After that, the oxygen apex penetrates the tetrahedron base and the b axis contracts. The negative and positive linear compressibility is well reproduced by the hexagonal model and ZAG-4 is the first MOFs evolving from non re-entrant to re-entrant hexagon framework with pressure increase. This gives a new approach to explore and design NLC materials.
Krüppel homolog 1 and E93 mediate Juvenile hormone regulation of metamorphosis in the common bed bug, Cimex lectularius
Authors: Gujar Hemant , Palli Subba Reddy 
Published: May 2016

AbstractThe common bed bug is an obligate hematophagous parasite of humans. We studied the regulation of molting and metamorphosis in bed bugs with a goal to identify key players involved. qRT-PCR studies on the expression of genes known to be involved in molting and metamorphosis showed high levels of Krüppel homolog 1 [Kr-h1, a transcription factor that plays key roles in juvenile hormone (JH) action] mRNA in the penultimate nymphal stage (N4). However, low levels of Kr-h1 mRNA were detected in the fifth and last nymphal stage (N5). Knockdown of Kr-h1 in N4 resulted in a precocious development of adult structures. Kr-h1 maintains the immature stage by suppressing E93 (early ecdysone response gene) in N4. E93 expression increases during the N5 in the absence of Kr-h1 and promotes the development of adult structures. Knockdown of E93 in N5 results in the formation of supernumerary nymphs. The role of JH in the suppression of adult structures through interaction with Kr-h1 and E93 was also studied by the topical application of JH analog, methoprene, to N5. Methoprene induced Kr-h1 and suppressed E93 and induced formation of the supernumerary nymph. These data show interactions between Kr-h1, E93 and JH in the regulation of metamorphosis in the bed bugs.
The rice thylakoid membrane-bound ascorbate peroxidase OsAPX8 functions in tolerance to bacterial blight
Authors: Jiang Guanghuai , Yin Dedong , Zhao Jiying , Chen Honglin , Guo Lequn , Zhu Lihuang , Zhai Wenxue 
Published: May 2016

AbstractThylakoid membrane-bound ascorbate peroxidase (tAPX) is a major H2O2-scavenging enzyme. To clarify its functions in tolerance to rice bacterial blight, we produced rice lines overexpressing and suppressing tAPX (OsAPX8). The overexpressing lines exhibited increased tolerance to bacterial pathogen. The RNA interference (RNAi) lines were considerably more sensitive than the control plant. Further analysis of the H2O2 content in these transgenic plants indicated that the H2O2 accumulation of OsAPX8-overexpressing plants was considerably less than that of wild-type and RNAi plants upon challenge with bacterial pathogen. Interestingly, H2O2 was the most important factor for the serious leaf dehydration and withering of rice without major resistance genes and was not the cause of hypersensitivity. It addition, wall tightening or loosening can occur according to the level of H2O2. In addition, OsAPX8 interacted with the susceptibility protein Os8N3/Xa13, and their binding repressed the reaction of OsAPX8 in tolerance to bacterial blight.
Loss of ubiquitin E2 Ube2w rescues hypersensitivity of Rnf4 mutant cells to DNA damage
Authors: Maure Jean-François , Moser Sandra C. , Jaffray Ellis G. , F. Alpi Arno , Hay Ronald T. 
Published: May 2016

AbstractSUMO and ubiquitin play important roles in the response of cells to DNA damage. These pathways are linked by the SUMO Targeted ubiquitin Ligase Rnf4 that catalyses transfer of ubiquitin from a ubiquitin loaded E2 conjugating enzyme to a polySUMO modified substrate. Rnf4 can functionally interact with multiple E2s, including Ube2w, in vitro. Chicken cells lacking Rnf4 are hypersensitive to hyroxyurea, DNA alkylating drugs and DNA crosslinking agents, but this sensitivity is suppressed by simultaneous depletion of Ube2w. Cells depleted of Ube2w alone are not hypersensitive to the same DNA damaging agents. Similar results were also obtained in human cells. These data indicate that Ube2w does not have an essential role in the DNA damage response, but is deleterious in the absence of Rnf4. Thus, although Rnf4 and Ube2w functionally interact in vitro, our genetic experiments indicate that in response to DNA damage Ube2w and Rnf4 function in distinct pathways.
Self-current induced spin-orbit torque in FeMn/Pt multilayers
Authors: Xu Yanjun , Yang Yumeng , Yao Kui , Xu Baoxi , Wu Yihong 
Published: May 2016

AbstractExtensive efforts have been devoted to the study of spin-orbit torque in ferromagnetic metal/heavy metal bilayers and exploitation of it for magnetization switching using an in-plane current. As the spin-orbit torque is inversely proportional to the thickness of the ferromagnetic layer, sizable effect has only been realized in bilayers with an ultrathin ferromagnetic layer. Here we demonstrate that, by stacking ultrathin Pt and FeMn alternately, both ferromagnetic properties and current induced spin-orbit torque can be achieved in FeMn/Pt multilayers without any constraint on its total thickness. The critical behavior of these multilayers follows closely three-dimensional Heisenberg model with a finite Curie temperature distribution. The spin torque effective field is about 4 times larger than that of NiFe/Pt bilayer with a same equivalent NiFe thickness. The self-current generated spin torque is able to switch the magnetization reversibly without the need for an external field or a thick heavy metal layer. The removal of both thickness constraint and necessity of using an adjacent heavy metal layer opens new possibilities for exploiting spin-orbit torque for practical applications.
Effects of acute aerobic exercise on neural correlates of attention and inhibition in adolescents with bipolar disorder
Authors: Metcalfe A W S , MacIntosh B J , Scavone A , Ou X , Korczak D , Goldstein B I 
Published: May 2016

AbstractExecutive dysfunction is common during and between mood episodes in bipolar disorder (BD), causing social and functional impairment. This study investigated the effect of acute exercise on adolescents with BD and healthy control subjects (HC) to test for positive or negative consequences on neural response during an executive task. Fifty adolescents (mean age 16.54±1.47 years, 56% female, 30 with BD) completed an attention and response inhibition task before and after 20 min of recumbent cycling at ~70% of age-predicted maximum heart rate. 3 T functional magnetic resonance imaging data were analyzed in a whole brain voxel-wise analysis and as regions of interest (ROI), examining Go and NoGo response events. In the whole brain analysis of Go trials, exercise had larger effect in BD vs HC throughout ventral prefrontal cortex, amygdala and hippocampus; the profile of these effects was of greater disengagement after exercise. Pre-exercise ROI analysis confirmed this 'deficit in deactivation' for BDs in rostral ACC and found an activation deficit on NoGo errors in accumbens. Pre-exercise accumbens NoGo error activity correlated with depression symptoms and Go activity with mania symptoms; no correlations were present after exercise. Performance was matched to controls and results survived a series of covariate analyses. This study provides evidence that acute aerobic exercise transiently changes neural response during an executive task among adolescents with BD, and that pre-exercise relationships between symptoms and neural response are absent after exercise. Acute aerobic exercise constitutes a biological probe that may provide insights regarding pathophysiology and treatment of BD.
The problem of empty names and Russellian Plenitude
Authors: Spencer Joshua 
Published: May 2016

Abstract‘Ahab is a whaler’ and ‘Holmes is a whaler’ express different propositions, even though neither ‘Ahab’ nor ‘Holmes’ has a referent. This seems to constitute a theoretical puzzle for the Russellian view of propositions. In this paper, I develop a variant of the Russellian view, Plenitudinous Russellianism. I claim that ‘Ahab is a whaler’ and ‘Holmes is a whaler’ express distinct gappy propositions. I discuss key metaphysical and semantic differences between Plenitudinous Russellianism and Traditional Russellianism and respond to objections that stem from those differences.
Influences of Summer Water Temperatures on the Movement, Distribution, and Resource Use of Fluvial Westslope Cutthroat Trout in the South Fork Clearwater River Basin
Authors: Dobos Marika E. , Corsi Matthew P. , Schill Daniel J. , DuPont Joseph M. , Quist Michael C. 
Published: May 2016

Abstract
Although many Westslope Cutthroat Trout Oncorhynchus clarkii lewisi populations in Idaho are robust and stable, population densities in some systems remain below management objectives. In many of those systems, such as in the South Fork Clearwater River (SFCR) system, environmental conditions (e.g., summer temperatures) are hypothesized to limit populations of Westslope Cutthroat Trout. Radiotelemetry and snorkeling methods were used to describe seasonal movement patterns, distribution, and habitat use of Westslope Cutthroat Trout in the SFCR during the summers of 2013 and 2014. Sixty-six radio transmitters were surgically implanted into Westslope Cutthroat Trout (170–405 mm TL) from May 30–June 25, 2013, and June 20–July 6, 2014. Sedentary and mobile summer movement patterns by Westslope Cutthroat Trout were observed in the SFCR. Westslope Cutthroat Trout were generally absent from the lower SFCR. In the upper region of the SFCR, fish generally moved from the main-stem SFCR into tributaries as water temperatures increased during the summer. Fish remained in the middle region of the SFCR where water temperatures were cooler than in the upper or lower regions of the SFCR. A spatially explicit water temperature model indicated that the upper and lower regions of the SFCR exceeded thermal tolerance levels of Westslope Cutthroat Trout throughout the summer. During snorkeling, 23 Westslope Cutthroat Trout were observed in 13 sites along the SFCR and at low density (mean ± SD, 0.0003 ± 0.0001 fish/m2). The distribution of fish observed during snorkeling was consistent with the distribution of radio-tagged fish in the SFCR during the summer. Anthropogenic activities (i.e., grazing, mining, road construction, and timber harvest) in the SFCR basin likely altered the natural flow dynamics and temperature regime and thereby limited stream habitat in the SFCR system for Westslope Cutthroat Trout.
Received June 15, 2015; accepted December 21, 2015 Published online May 16, 2016
Pellet refuelling of particle loss due to ELM mitigation with RMPs in the ASDEX Upgrade tokamak at low collisionality
Authors: Valovič M. , Lang P.T. , Kirk A. , Suttrop W. , Cavedon M. , Cseh G. , Dunne M. , Fischer L.R. , Garzotti L. , Guimarais L. , Kocsis G. , Mlynek A. , Plőckl B. , Scannell R. , Szepesi T. , Tardini G. , Thornton A. , Viezzer E. , Wolfrum E. 
Published: May 2016

Abstract
The complete refuelling of the plasma density loss (pump-out) caused by mitigation of edge localised modes (ELMs) is demonstrated on the ASDEX Upgrade tokamak. The plasma is refuelled by injection of frozen deuterium pellets and ELMs are mitigated by external resonant magnetic perturbations (RMPs). In this experiment relevant dimensionless parameters, such as relative pellet size, relative RMP amplitude and pedestal collisionality are kept at the ITER like values. Refuelling of density pump out of the size of

Δ
n
/
n
∼
30
%

requires a factor of two increase of nominal fuelling rate. Energy confinement and pedestal temperatures are not restored to pre-RMP values by pellet refuelling.
Interaction of adhered metallic dust with transient plasma heat loads
Authors: Ratynskaia S. , Tolias P. , Bykov I. , Rudakov D. , De Angeli M. , Vignitchouk L. , Ripamonti D. , Riva G. , Bardin S. , van der Meiden H. , Vernimmen J. , Bystrov K. , De Temmerman G. 
Published: May 2016

Abstract
The first study of the interaction of metallic dust (tungsten, aluminum) adhered on tungsten substrates with transient plasma heat loads is presented. Experiments were carried out in the Pilot-PSI linear device with transient heat fluxes up to 550 MW m−2 and in the DIII-D divertor tokamak. The central role of the dust-substrate contact area in heat conduction is highlighted and confirmed by heat transfer simulations. The experiments provide evidence of the occurrence of wetting-induced coagulation, a novel growth mechanism where cluster melting accompanied by droplet wetting leads to the formation of larger grains. The physical processes behind this mechanism are elucidated. The remobilization activity of the newly formed dust and the survivability of tungsten dust on hot surfaces are documented and discussed in the light of implications for ITER.
The disappearance of the helium-giant progenitor of the Type Ib supernova iPTF13bvn and constraints on its companion
Authors: Eldridge J. J. , Maund J. R. 
Published: May 2016

Abstract
We report and discuss post-explosion observations of supernova iPTF13bvn. We find that the brightness of the supernova (SN) at +740 d is below the level of the pre-explosion source and thus confirm that the progenitor has exploded. We estimate that the late-time brightness is still dominated by the SN, which constrains the magnitude and thus mass of a possible companion star to below approximately 10 M⊙. In turn, this implies that the progenitor's initial mass is constrained to a narrow range between 10 and 12 M⊙. The progenitor of iPTF13bvn would have been a helium giant rather than a Wolf–Rayet star. In addition, we suggest that sufficiently deep observations acquired in 2016 would now stand a chance to directly observe the companion star.
The low abundance and insignificance of dark discs in simulated Milky Way galaxies
Authors: Schaller Matthieu , Frenk Carlos S. , Fattahi Azadeh , Navarro Julio F. , Oman Kyle A. , Sawala Till 
Published: May 2016

Abstract
We investigate the presence and importance of dark matter discs in a sample of 24 simulated Milky Way galaxies in the apostle project, part of the eagle programme of hydrodynamic simulations in ΛCDM cosmology. It has been suggested that a dark disc in the Milky Way may boost the dark matter density and modify the velocity modulus relative to a smooth halo at the position of the Sun, with ramifications for direct detection experiments. From a kinematic decomposition of the dark matter and a real space analysis of all 24 haloes, we find that only one of the simulated Milky Way analogues has a detectable dark disc component. This unique event was caused by a merger at late time with an LMC-mass satellite at very low grazing angle. Considering that even this rare scenario only enhances the dark matter density at the solar radius by 35 per cent and affects the high-energy tail of the dark matter velocity distribution by less than 1 per cent, we conclude that the presence of a dark disc in the Milky Way is unlikely, and is very unlikely to have a significant effect on direct detection experiments.
A Randomized, Double-blinded Trial of a “Rule of Threes” Algorithm Versus Continuous Infusion of Oxytocin During Elective Cesarean Delivery
Authors: Kovacheva V.P. , Soens M.A. , Tsen L.C. 
Published: May 2016

(Anesthesiology. 2015;123:92–100)
Oxytocin is commonly used to improve uterine tone during cesarean delivery. However, if administered too quickly or in high doses it can lead to such adverse effects as hemodynamic instability, cardiovascular collapse, and even death. There are also currently no established recommended doses, timing, or rates of administration.
17-alpha-hydroxyprogesterone Caproate for Maintenance Tocolysis: A Systematic Review and Metaanalysis of Randomized Trials
Authors: Saccone G. , Suhag A. , Berghella V. 
Published: May 2016

(Am J Obstet Gynecol. 2015;213(1):16–22)
Preterm birth is the leading cause of neonatal death and morbidity in the United States. Preterm labor can be halted using tocolytic agents, but since a mother’s risk of preterm birth remains high even once preterm labor has been arrested, some suggest the use of continued maintenance tocolysis.
Once More Unto the Breech: Planned Vaginal Delivery Compared With Planned Cesarean Delivery
Authors: Joseph K.S. , Pressey Tracy , Lyons Janet , Bartholomew Sharon , Liu Shiliang , Muraca Giulia , Liston Robert M. 
Published: May 2016

(Obstet Gynecol. 2015;125:1162–1167)
This commentary provides an overview of the current evidence regarding planned vaginal versus planned cesarean delivery for breech presentation at term gestation, relying primarily on the 2001 Term Breech Trial and its 2-year follow-up study and the 2006 presentation and mode of delivery (PREMODA) study.
Trends in Care Practices, Morbidity, and Mortality of Extremely Preterm Neonates, 1993 to 2012
Authors: Stoll B.J. , Hansen N.I. , Bell E.F. , Walsh M.C. , Carlo W.A. , Shankaran S. , Laptook A.R. , Sánchez P.J. , Van Meurs K.P. , Wyckoff M. , Das A. , Hale E.C. , Ball M.B. , Newman N.S. , Schibler K. , Poindexter B.B. , Kennedy K.A. , Cotten C.M. , Watterberg K.L. , D’Angio C.T. , DeMauro S.B. , Truog W.E. , Devaskar U. , Higgins R.D. 
Published: May 2016

(JAMA. 2015;314(10):1039–1051)
Extremely preterm infants contribute disproportionately to the burden of neonatal morbidity, mortality, and long-term neurodevelopmental disability. This study of extremely preterm infants born at Human Development Neonatal Research Network (NRN) centers is the first comprehensive review to evaluate how care practices, major morbidities, and mortality have evolved over a 20-year period.
National Partnership for Maternal Safety: Consensus Bundle on Obstetric Hemorrhage
Authors: Main E.K. , Goffman B.M. , Kane L.K. , Bingham D. , Fontaine P.L. , Gorlin J.B. , Lagrew D.C. , Levy B.S. 
Published: May 2016

(Anesth Analg. 2015;121(1):142–48)
This consensus bundle compiles a selection of guidelines and recommendations for best clinical practices regarding obstetric hemorrhage. The consensus bundle on obstetric hemorrhage was developed by a workgroup of the Partnership for Maternal Safety within the Council on Patient Safety in Women’s Health Care, and represents all major women’s health care professional organizations. The goal of the partnership is implementation of the safety bundle in every birthing facility in the United States. As it is unlikely that many hospitals will have all of the elements of the consensus bundle in place, it is intended to serve as a checklist from which to work. The consensus bundle is divided into 4 action domains—readiness, recognition and prevention, response, and reporting and systems learning—and encompasses 13 key elements within these domains.
Induction of Labour Versus Expectant Management for Large-for-Date Fetuses: A Randomized-Controlled Trial
Authors: Boulvain M. , Senat M.V. , Perrotin F. , Winer N. , Beucher G. , Subtil D. , Bretelle F. , Azria E. , Hejaiej D. , Vendittelli F. , Capelle M. , Langer B. , Matis R. , Connan L. , Gillard P. , Kirkpatrick C. , Ceysens G. , Faron G. , Irion O. , Rozenberg P. 
Published: May 2016

(Lancet. 2015;385(9987):2600–2605)
As macrosomia is a risk factor for unfavorable delivery outcomes, including operative vaginal or cesarean delivery and shoulder dystocia (with its associated neonatal morbidity), it is important to determine the best clinical practices for the management of pregnancies with large-for-date fetuses. This randomized-controlled trial evaluated the risks and benefits of induction of labor versus expectant management in women with large-for-date fetuses, hypothesizing that induction of labor would prevent shoulder dystocia and other neonatal and maternal morbidity associated with macrosomia, without significantly affecting the risk of cesarean delivery.