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Transitive inferences

Hooman Davoudiasl, Christopher W Murphy
A very light boson of mass O(10^{-22})  eV may potentially be a viable dark matter (DM) candidate, which can avoid phenomenological problems associated with cold DM. Such "fuzzy DM (FDM)" may naturally be an axion with a decay constant f_{a}∼10^{16}-10^{18}  GeV and a mass m_{a}∼μ^{2}/f_{a} with μ∼10^{2}  eV. Here, we propose a concrete model, where μ arises as a dynamical scale from infrared confining dynamics, analogous to QCD. Our model is an alternative to the usual approach of generating μ through string theoretic instanton effects...
April 7, 2017: Physical Review Letters
Wei-Wei Yu, Hong Jiang, Cun-Tai Zhang, Yang Peng
miR-128 is expressed in various tumors, but its expression and function in gastric cancer have not been defined. Thus, the goal of this study was to characterize miR-128 in gastric cancer. We found first that miR-128 is down-regulated in gastric cancer cell lines and tissues, and this dysregulation is correlated with DNA methylation and the transcription factor SNAIL. Using prediction tools, western blotting, and luciferase reporter assays, we found that Bmi-1 was the direct target of miR-128. Additionally, overexpression of miR-128 inhibited gastric cancer cell migration, invasion, and proliferation by targeting Bmi-1 in vitro and in vivo...
April 5, 2017: Oncotarget
Sushmita Roy, Rupa Sridharan
Changes in chromatin state play important roles in cell fate transitions. Current computational approaches to analyze chromatin modifications across multiple cell types do not model how the cell types are related on a lineage or over time. To overcome this limitation, we have developed a method called CMINT (Chromatin Module INference on Trees), a probabilistic clustering approach to systematically capture chromatin state dynamics across multiple cell types. Compared to existing approaches, CMINT can handle complex lineage topologies, capture higher quality clusters, and reliably detect chromatin transitions between cell types...
April 19, 2017: Genome Research
Neil Brocklehurst
The evolution of herbivory in early tetrapods was crucial in the establishment of terrestrial ecosystems, although it is so far unclear what effect this innovation had on the macro-evolutionary patterns observed within this clade. The clades that entered this under-filled region of ecospace might be expected to have experienced an "adaptive radiation": an increase in rates of morphological evolution and speciation driven by the evolution of a key innovation. However such inferences are often circumstantial, being based on the coincidence of a rate shift with the origin of an evolutionary novelty...
2017: PeerJ
Karl J Friston, Richard Rosch, Thomas Parr, Cathy Price, Howard Bowman
How do we navigate a deeply structured world? Why are you reading this sentence first - and did you actually look at the fifth word? This review offers some answers by appealing to active inference based on deep temporal models. It builds on previous formulations of active inference to simulate behavioural and electrophysiological responses under hierarchical generative models of state transitions. Inverting these models corresponds to sequential inference, such that the state at any hierarchical level entails a sequence of transitions in the level below...
April 14, 2017: Neuroscience and Biobehavioral Reviews
Mani Priyadarshini, Venkata Rajanikanth Machavaram, Akella Sivaramakrishna, Pachiyappan Arulmozhivarman
Temperature-induced crystallization events in an aqueous calcium chloride solution in the concentration range of 15-40 mass% are monitored using an optical fiber Fresnel reflection sensor in the temperature range of 30°C to -200°C. The deviation of the phase boundary from equilibrium and the formation of an eutectic mixture followed by its densification during rapid cooling are inferred from the distinct signatures of the optical fiber sensor via the changes in refractive index. During the natural heating at laboratory ambient conditions, the optical signals impart the completion of dissolution of ice and CaCl<sub>2</sub>·6H<sub>2</sub>O...
April 10, 2017: Applied Optics
Yoana Dimitrova, Andreas J Gruber, Nitish Mittal, Souvik Ghosh, Beatrice Dimitriades, Daniel Mathow, William Aaron Grandy, Gerhard Christofori, Mihaela Zavolan
BACKGROUND: The transition between epithelial and mesenchymal phenotypes (EMT) occurs in a variety of contexts. It is critical for mammalian development and it is also involved in tumor initiation and progression. Master transcription factor (TF) regulators of this process are conserved between mouse and human. METHODS: From a computational analysis of a variety of high-throughput sequencing data sets we initially inferred that TFAP2A is connected to the core EMT network in both species...
April 17, 2017: Biology Direct
Francesco Ambrosio, Giacomo Miceli, Alfredo Pasquarello
We provide a consistent description of the electronic levels associated to localized and delocalized excess electrons in liquid water by combining hybrid-functional molecular dynamics simulations with a grand canonical formulation of solutes in aqueous solution. The excess electron localizes in a cavity with an average radius of 1.8 Å and a majority coordination of five water molecules. The vertical binding energy, the optical s-p transitions, and the adiabatic redox level are found to agree closely with their experimental counterparts...
April 13, 2017: Journal of Physical Chemistry Letters
Sandra R Schachat
The evolution of wing pattern in Lepidoptera is a popular area of inquiry but few studies have examined microlepidoptera, with fewer still focusing on intraspecific variation. The tineid genus Moerarchis Durrant, 1914 includes two species with high intraspecific variation of wing pattern. A subset of the specimens examined here provide, to my knowledge, the first examples of wing patterns that follow both the 'alternating wing-margin' and 'uniform wing-margin' models in different regions along the costa. These models can also be evaluated along the dorsum of Moerarchis, where a similar transition between the two models can be seen...
March 2017: Royal Society Open Science
Sterling J Nesbitt, Richard J Butler, Martín D Ezcurra, Paul M Barrett, Michelle R Stocker, Kenneth D Angielczyk, Roger M H Smith, Christian A Sidor, Grzegorz Niedźwiedzki, Andrey G Sennikov, Alan J Charig
The relationship between dinosaurs and other reptiles is well established, but the sequence of acquisition of dinosaurian features has been obscured by the scarcity of fossils with transitional morphologies. The closest extinct relatives of dinosaurs either have highly derived morphologies or are known from poorly preserved or incomplete material. Here we describe one of the stratigraphically lowest and phylogenetically earliest members of the avian stem lineage (Avemetatarsalia), Teleocrater rhadinus gen. et sp...
April 12, 2017: Nature
Michael G Branstetter, Ana Ješovnik, Jeffrey Sosa-Calvo, Michael W Lloyd, Brant C Faircloth, Seán G Brady, Ted R Schultz
The evolution of ant agriculture, as practised by the fungus-farming 'attine' ants, is thought to have arisen in the wet rainforests of South America about 55-65 Ma. Most subsequent attine agricultural evolution, including the domestication event that produced the ancestor of higher attine cultivars, is likewise hypothesized to have occurred in South American rainforests. The 'out-of-the-rainforest' hypothesis, while generally accepted, has never been tested in a phylogenetic context. It also presents a problem for explaining how fungal domestication might have occurred, given that isolation from free-living populations is required...
April 12, 2017: Proceedings. Biological Sciences
Nicholas Deardorff, Katharine Cashman
Microcrystalline inclusions within microlite-poor matrix are surprisingly common in low intensity eruptions around the world, yet their origin is poorly understood. Inclusions are commonly interpreted as evidence of crystallization along conduit margins. Alternatively, these clasts may be recycled from low level eruptions where they recrystallize by heating within the vent. We conducted a series of experiments heating basaltic andesite lapilli from temperatures below the glass transition (~690 °C) to above inferred eruption temperatures (>1150 °C) for durations of 2 to >60 minutes...
April 12, 2017: Scientific Reports
Jose M Martin-Duran, Joseph F Ryan, Bruno Vellutini, Kevin Pang, Andreas Hejnol
Gains and losses shape the gene complement of animal lineages and are a fundamental aspect of genomic evolution. Acquiring a comprehensive view of the evolution of gene repertoires is limited by the intrinsic limitations of common sequence similarity searches and available databases. Thus, a subset of the gene complement of an organism consists of hidden orthologs, i.e., those with no apparent homology to sequenced animal lineages - mistakenly considered new genes - but actually representing rapidly evolving orthologs or undetected paralogs...
April 11, 2017: Genome Research
Bo-Ran Shen, Cheng-Hua Zhu, Zhen Yao, Li-Li Cui, Jian-Jun Zhang, Cheng-Wei Yang, Zheng-Hui He, Xin-Xiang Peng
Various chloroplast transit peptides (CTP) have been used to successfully target some foreign proteins into chloroplasts, but for other proteins these same CTPs have reduced localization efficiencies or fail completely. The underlying cause of the failures remains an open question, and more effective CTPs are needed. In this study, we initially observed that two E.coli enzymes, EcTSR and EcGCL, failed to be targeted into rice chloroplasts by the commonly-used rice rbcS transit peptide (rCTP) and were subsequently degraded...
April 11, 2017: Scientific Reports
Luke T Dunning, Marjorie R Lundgren, Jose J Moreno-Villena, Mary Namaganda, Erika J Edwards, Patrik Nosil, Colin P Osborne, Pascal-Antoine Christin
The origins of novel traits are often studied using species trees and modeling phenotypes as different states of the same character, an approach that cannot always distinguish multiple origins from fewer origins followed by reversals. We address this issue by studying the origin of C4 photosynthesis, an adaptation to warm and dry conditions, in the grass Alloteropsis. We dissect the C4 trait into its components, and show two independent origins of the C4 phenotype via different anatomical modifications, and the use of distinct sets of genes...
April 10, 2017: Evolution; International Journal of Organic Evolution
Yong-Qiang Ren, Hui-Jun Wang, Yong-Qing Zhang, Yan-Bing Liu
PURPOSE: The mechanisms underlying the oncogenic properties of WW domain binding protein 2 (WBP2) in breast cancer have not been fully understood. In this study, we explored the role of WBP2 in cell cycle regulation in ER+ breast cancer cells and how it is regulated in the cancer cells. METHODS: The association between WBP2 expression and prognosis in ER+ breast cancer was assessed by data mining in Breast Cancer Gene-Expression Miner v4.0. Cell cycle was assessed by PI staining and flow cytometry...
April 8, 2017: Cancer Chemotherapy and Pharmacology
A Miskowiec, Z N Buck, F Y Hansen, H Kaiser, H Taub, M Tyagi, S O Diallo, E Mamontov, K W Herwig
We have used high-resolution quasielastic neutron scattering (QENS) to investigate the dynamics of water molecules (time scale of motion ∼10(-11)-10(-9) s) in proximity to single-supported bilayers of the zwitterioniclipid DMPC (1,2-dimyristoyl-sn-glycero-3-phosphorylcholine) and the anionic lipid DMPG (1,2-dimyristoyl-sn-glycero-3-phosphoglycerol) in the temperature range 160-295 K. For both membranes, the temperature dependence of the intensity of neutronsscattered elastically and incoherently from these samples indicates a series of freezing/melting transitions of the membrane-associated water, which have not been observed in previous studies of multilayer membranes...
March 28, 2017: Journal of Chemical Physics
Paolo Cabras, Florent Nageotte, Philippe Zanne, Christophe Doignon
BACKGROUND: Flexible bendable instruments are key tools for performing surgical endoscopy. Being able to measure the 3D position of such instruments can be useful for various tasks, such as controlling automatically robotized instruments and analyzing motions. METHODS: An automatic method is proposed to infer the 3D pose of a single bending section instrument, using only the images provided by a monocular camera embedded at the tip of the endoscope. The proposed method relies on colored markers attached onto the bending section...
April 7, 2017: International Journal of Medical Robotics + Computer Assisted Surgery: MRCAS
Wenjia Song, Yan Lavallée, Fabian B Wadsworth, Kai-Uwe Hess, Donald B Dingwell
A major hazard to jet engines posed by volcanic ash is linked to the wetting and spreading of molten ash droplets on engine component surfaces. Here, using the sessile drop method, we study the evolution of the wettability and spreading of volcanic ash. We employ rapid temperature changes up to 1040-1450 °C, to replicate the heating conditions experienced by volcanic ash entering an operating jet engine. In this scenario, samples densify as particles coalesce under surface tension until they form a large system-sized droplet (containing remnant gas bubbles and crystals), which subsequently spreads on the surface...
April 20, 2017: Journal of Physical Chemistry Letters
Martha Liliana Serrano-Serrano, Jonathan Rolland, John L Clark, Nicolas Salamin, Mathieu Perret
The effects of specific functional groups of pollinators in the diversification of angiosperms are still to be elucidated. We investigated whether the pollination shifts or the specific association with hummingbirds affected the diversification of a highly diverse angiosperm lineage in the Neotropics. We reconstructed a phylogeny of 583 species from the Gesneriaceae family and detected diversification shifts through time, inferred the timing and amount of transitions among pollinator functional groups, and tested the association between hummingbird pollination and speciation and extinction rates...
April 12, 2017: Proceedings. Biological Sciences
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