bluuebunny/crossref_metadata_2025_split huggingface dataset:
Shallow slip amplification and enhanced tsunami hazard unravelled by dynamic simulations of mega-thrust earthquakes
Authors: Murphy S. , Scala A. , Herrero A. , Lorito S. , Festa G. , Trasatti E. , Tonini R. , Romano F. , Molinari I. , Nielsen S. 
Published: October 2016

AbstractThe 2011 Tohoku earthquake produced an unexpected large amount of shallow slip greatly contributing to the ensuing tsunami. How frequent are such events? How can they be efficiently modelled for tsunami hazard? Stochastic slip models, which can be computed rapidly, are used to explore the natural slip variability; however, they generally do not deal specifically with shallow slip features. We study the systematic depth-dependence of slip along a thrust fault with a number of 2D dynamic simulations using stochastic shear stress distributions and a geometry based on the cross section of the Tohoku fault. We obtain a probability density for the slip distribution, which varies both with depth, earthquake size and whether the rupture breaks the surface. We propose a method to modify stochastic slip distributions according to this dynamically-derived probability distribution. This method may be efficiently applied to produce large numbers of heterogeneous slip distributions for probabilistic tsunami hazard analysis. Using numerous M9 earthquake scenarios, we demonstrate that incorporating the dynamically-derived probability distribution does enhance the conditional probability of exceedance of maximum estimated tsunami wave heights along the Japanese coast. This technique for integrating dynamic features in stochastic models can be extended to any subduction zone and faulting style.
Effect of adding nanometre-sized heterogeneities on the structural dynamics and the excess wing of a molecular glass former
Authors: Gupta S. , Fischer J. K. H. , Lunkenheimer P. , Loidl A. , Novak E. , Jalarvo N. , Ohl M. 
Published: October 2016

AbstractWe present the relaxation dynamics of glass-forming glycerol mixed with 1.1 nm sized polyhedral oligomeric silsesquioxane (POSS) molecules using dielectric spectroscopy (DS) and two different neutron scattering (NS) techniques. Both, the reorientational dynamics as measured by DS and the density fluctuations detected by NS reveal a broadening of the α relaxation when POSS molecules are added. Moreover, we find a significant slowing down of the α-relaxation time. These effects are in accord with the heterogeneity scenario considered for the dynamics of glasses and supercooled liquids. The addition of POSS also affects the excess wing in glycerol arising from a secondary relaxation process, which seems to exhibit a dramatic increase in relative strength compared to the α relaxation.
Leukocyte immunoglobulin-like receptor B4 regulates key signalling molecules involved in FcγRI-mediated clathrin-dependent endocytosis and phagocytosis
Authors: Park Mijeong , Raftery Mark J. , Thomas Paul S. , Geczy Carolyn L. , Bryant Katherine , Tedla Nicodemus 
Published: October 2016

AbstractFcγRI cross-linking on monocytes may trigger clathrin-mediated endocytosis, likely through interaction of multiple intracellular molecules that are controlled by phosphorylation and dephosphorylation events. However, the identity of phospho-proteins and their regulation are unknown. We proposed the leukocyte immunoglobulin-like receptor B4 (LILRB4) that inhibits FcγRI-mediated cytokine production via Tyr dephosphorylation of multiple kinases, may also regulate endocytosis/phagocytosis through similar mechanisms. FcγRI and/or LILRB4 were antibody-ligated on THP-1 cells, lysates immunoprecipitated using anti-pTyr antibody and peptides sequenced by mass spectrometry. Mascot Search identified 25 Tyr phosphorylated peptides with high confidence. Ingenuity Pathway Analysis revealed that the most significantly affected pathways were clathrin-mediated endocytosis and Fc-receptor dependent phagocytosis. Tyr phosphorylation of key candidate proteins in these pathways included common γ-chain of the Fc receptors, Syk, clathrin, E3 ubiquitin protein ligase Cbl, hepatocyte growth factor-regulated tyrosine kinase substrate, tripartite motif-containing 21 and heat shock protein 70. Importantly, co-ligation of LILRB4 with FcγRI caused significant dephosphorylation of these proteins and was associated with suppression of Fc receptor-dependent uptake of antibody-opsonised bacterial particles, indicating that LILRB4. These results suggest that Tyr phosphorylation may be critical in FcγRI-dependent endocytosis/phagocytosis that may be regulated by LILRB4 by triggering dephosphorylation of key signalling proteins.
Differentially expressed galactinol synthase(s) in chickpea are implicated in seed
vigor and longevity by limiting the age induced ROS accumulation
Authors: Salvi Prafull , Saxena Saurabh Chandra , Petla Bhanu Prakash , Kamble Nitin Uttam , Kaur Harmeet , Verma Pooja , Rao Venkateswara , Ghosh Shraboni , Majee Manoj 
Published: October 2016

AbstractGalactinol synthase (GolS) catalyzes the first and rate limiting step of Raffinose
Family Oligosaccharide (RFO) biosynthetic pathway, which is a highly specialized
metabolic event in plants. Increased accumulation of galactinol and RFOs in seeds
have been reported in few plant species, however their precise role in seed vigor
and longevity remain elusive. In present study, we have shown that galactinol
synthase activity as well as galactinol and raffinose content progressively increase
as seed development proceeds and become highly abundant in pod and mature dry seeds,
which gradually decline as seed germination progresses in chickpea (Cicer
arietinum). Furthermore, artificial aging also stimulates galactinol
synthase activity and consequent galactinol and raffinose accumulation in seed.
Molecular analysis revealed that GolS in chickpea are encoded by two divergent genes
(CaGolS1 and CaGolS2) which potentially encode five CaGolS
isoforms through alternative splicing. Biochemical analysis showed that only two
isoforms (CaGolS1 and CaGolS2) are biochemically active with similar yet distinct
biochemical properties. CaGolS1 and CaGolS2 are differentially regulated in
different organs, during seed development and germination however exhibit similar
subcellular localization. Furthermore, seed-specific overexpression ofCaGolS1 and CaGolS2 in Arabidopsis results improved seed
vigor and longevity through limiting the age induced excess ROS and consequent lipid
peroxidation.
Oesophageal carcinoma: comparison of ex vivo high-resolution 3.0 T MR imaging with histopathological findings
Authors: Wei Yi , Wu Sen , Shi Dapeng , Dou Shewei , Sun Tingyi , Ning Peigang , Zhao Cuihua , Li Ziyuan , Li Xiaodong , Gao Feifei , Li Linlin , Zheng Dandan , Zhu Shaocheng 
Published: October 2016

AbstractHigh-resolution magnetic resonance (MR) images clearly depict the normal oesophageal wall as consisting of eight layers, which correlates well with histopathological findings. In 56 (91.8%) of 61 lesions, the depth of oesophageal wall invasion determined through MR imaging was consistent with histopathological staging (r = 0.975, P < 0.001). The sensitivity, specificity and accuracy for the mucosa were 71.4%, 98.1%, and 95.1%, respectively, and the corresponding values for the submucosa were 82.4%, 95.5%, and 91.8%; for the muscularis propria, the sensitivity, specificity and accuracy were 100%, 95.7%, and 96.7%, respectively, and for the adventitia, these values were 100%, 100%, and 100%. The Cohen k values for interobserver agreement were excellent: K = 0.839, P < 0.001 (observer 1 vs. observer 2); K = 0.908, P < 0.001 (observer 1 vs. observer 3); and K = 0.885, P < 0.01 (observer 2 vs. observer 3). High-resolution ex vivo MR images obtained with a 3.0 T scanner can be used to precisely evaluate oesophageal carcinoma invasion and provide good diagnostic sensitivity, specificity and accuracy.
Misfit Strain Relaxation of Ferroelectric PbTiO3/LaAlO3 (111) Thin Film System
Authors: Xu Y. B. , Tang Y. L. , Zhu Y. L. , Liu Y. , Li S. , Zhang S. R. , Ma X. L. 
Published: October 2016

AbstractFerroelectric thin films grown on high index substrates show unusual structural and switching dynamics due to their special strain states. Understanding the misfit relaxation behavior is crucial to facilitate the high index thin film growth with improved quality. In this paper, ferroelectric PbTiO3 thin films were grown on LaAlO3 (111) substrates by pulsed laser deposition technique. The microstructures were investigated by combinations of conventional and aberration-corrected transmission electron microscopy. Diffraction contrast analysis and high resolution imaging reveal that high density interfacial dislocations were distributed at the interfaces. These dislocations have mixed character with Burgers vectors of a <110> and line directions of <112>. The edge components of the dislocations, with the Burgers vectors parallel to the interface, accommodate the lattice mismatch and are the main contributor to the misfit relaxation of this system. The formation mechanism of these dislocations is proposed and discussed to elucidate the novel mismatch relaxation behavior of <111> oriented perovskite films.
High-solid Anaerobic Co-digestion of Sewage Sludge and Cattle Manure: The Effects of Volatile Solid Ratio and pH
Authors: Dai Xiaohu , Chen Yang , Zhang Dong , Yi Jing 
Published: October 2016

AbstractHigh-solid anaerobic digestion is an attractive solution to the problem of sewage sludge disposal. One method that can be used to enhance the production of volatile fatty acids (VFAs) and the generation of methane from anaerobic digestion involves combining an alkaline pretreatment step with the synergistic effects of sewage sludge and cattle manure co-digestion, which improves the activity of key enzymes and microorganisms in the anaerobic co-digestion system to promote the digestion of organic waste. In this study, we describe an efficient strategy that involves adjusting the volatile solid (VS) ratio (sewage sludge/cattle manure: 3/7) and initial pH (9.0) to improve VFA production and methane generation from the co-digestion of sludge and manure. The experimental results indicate that the maximum VFA production was 98.33 g/kg-TS (total solid) at the optimal conditions. Furthermore, methane generation in a long-term semi-continuously operated reactor (at a VS ratio of 3/7 and pH of 9.0) was greater than 120.0 L/kg-TS.
The rs6771157 C/G polymorphism in SCN10A is associated with the risk of atrial fibrillation in a Chinese Han population
Authors: Fang Zhen , Jiang Yue , Wang Yifeng , Lin Yuan , Liu Yaowu , Zhao Liyan , Xu Yan , Toorabally Mohammad Bilaal , He Shenghu , Zhang Fengxiang 
Published: October 2016

AbstractA recent genome wide associated study in European descent population identified the association of Atrial fibrillation (AF) risk with a single nucleotide polymorphism (SNP) in SCN10A. The aim of this study was to evaluate whether SCN10A polymorphisms are associated with AF risk in the Chinese Han population. A total of 2,300 individuals of Chinese Han origin were recruited and three potentially functional SNPs were genotyped. Logistic regression models were utilized to calculate odds ratios (ORs) at a 95% confidence intervals (CIs). Logistic regression analysis in an additive genetic model revealed that one SNP in SCN10A (rs6771157) was associated with an increased risk of AF (adjusted OR = 1.20, 95% CI: 1.06 - 1.36, P = 0.003). Stratification analysis of several main AF risk factors indicated that the risk associations with rs6771157 were not statistically different among different subgroups. In summary, our study suggests the possible involvement of the SCN10A variant in AF development in Chinese Han populations. Further biological function analyses are required to confirm our finding.
Modulation of fear extinction processes using transcranial electrical stimulation
Authors: Abend R , Jalon I , Gurevitch G , Sar-el R , Shechner T , Pine D S , Hendler T , Bar-Haim Y 
Published: October 2016

AbstractResearch associates processes of fear conditioning and extinction with treatment of anxiety and stress-related disorders. Manipulation of these processes may therefore be beneficial for such treatment. The current study examines the effects of electrical brain stimulation on fear extinction processes in healthy humans in order to assess its potential relevance for treatment enhancement. Forty-five participants underwent a 3-day fear conditioning and extinction paradigm. Electrical stimulation targeting the medial prefrontal cortex was applied during the extinction-learning phase (Day 2). Participants were randomly assigned to three stimulation conditions: direct-current (DC) stimulation, aimed at enhancing extinction-learning; low-frequency alternating-current (AC) stimulation, aimed at interfering with reconsolidation of the activated fear memory; and sham stimulation. The effect of stimulation on these processes was assessed in the subsequent extinction recall phase (Day 3), using skin conductance response and self-reports. Results indicate that AC stimulation potentiated the expression of fear response, whereas DC stimulation led to overgeneralization of fear response to non-reinforced stimuli. The current study demonstrates the capability of electrical stimulation targeting the medial prefrontal cortex to modulate fear extinction processes. However, the stimulation parameters tested here yielded effects opposite to those anticipated and could be clinically detrimental. These results highlight the potential capacity of stimulation to manipulate processes relevant for treatment of anxiety and stress-related disorders, but also emphasize the need for additional research to identify delivery parameters to enable its translation into clinical practice. Clinical trial identifiers: Modulation of Fear Extinction Processes Using Transcranial Electrical Stimulation; https://clinicaltrials.gov/show/NCT02723188; NCT02723188 NCT02723188.
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.
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.
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.
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.
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.
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.
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.