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transitive inference

Dean C Adams, Michael L Collyer
Phylogenetic regression is frequently utilized in macroevolutionary studies, and its statistical properties have been thoroughly investigated. By contrast, phylogenetic ANOVA has received relatively less attention, and the conditions leading to incorrect statistical and biological inferences when comparing multivariate phenotypes among groups remains under-explored. Here we propose a refined method of randomizing residuals in a permutation procedure (RRPP) for evaluating phenotypic differences among groups while conditioning the data on the phylogeny...
April 22, 2018: Evolution; International Journal of Organic Evolution
M Deluca, Z G Al-Jlaihawi, K Reichmann, A M T Bell, A Feteira
In situ Raman spectroscopy shows the simultaneous incorporation of small amounts of Bi3+ and Yb3+ into the lattice of BaTiO3 to break the average symmetry inferred from X-ray powder diffraction analysis and permittivity measurements. In particular, Bi3+ with a stereochemically active lone-pair of electrons induces severe lattice strain and the coexistence of different local crystal symmetries over a wide temperature range, effectively controlling the physical properties, such as the temperature dependence of the permittivity and the Curie temperature...
April 7, 2018: Journal of Materials Chemistry. A, Materials for Energy and Sustainability
Takayuki Ishii, Rong Huang, Hongzhan Fei, Iuliia Koemets, Zhaodong Liu, Fumiya Maeda, Liang Yuan, Lin Wang, Dmitry Druzhbin, Takafumi Yamamoto, Shrikant Bhat, Robert Farla, Takaaki Kawazoe, Noriyoshi Tsujino, Eleonora Kulik, Yuji Higo, Yoshinori Tange, Tomoo Katsura
The 660-km seismic discontinuity, which is a significant structure in the Earth's mantle, is generally interpreted as the post-spinel transition, as indicated by the decomposition of ringwoodite to bridgmanite + ferropericlase. All precise high-pressure and high-temperature experiments nevertheless report 0.5-2 GPa lower transition pressures than those expected at the discontinuity depth (i.e. 23.4 GPa). These results are inconsistent with the post-spinel transition hypothesis and, therefore, do not support widely accepted models of mantle composition such as the pyrolite and CI chondrite models...
April 20, 2018: Scientific Reports
Alberto Gianinetti, Franca Finocchiaro, Paolo Bagnaresi, Antonella Zechini, Primetta Faccioli, Luigi Cattivelli, Giampiero Valè, Chiara Biselli
Red rice fully dormant seeds do not germinate even under favorable germination conditions. In several species, including rice, seed dormancy can be removed by dry-afterripening (warm storage); thus, dormant and non-dormant seeds can be compared for the same genotype. A weedy (red) rice genotype with strong dormancy was used for mRNA expression profiling, by RNA-Seq, of dormant and non-dormant dehulled caryopses (here addressed as seeds) at two temperatures (30 °C and 10 °C) and two durations of incubation in water (8 h and 8 days)...
April 19, 2018: Plants (Basel, Switzerland)
J Sperling, A Eckstein, W R Clements, M Moore, J J Renema, W S Kolthammer, S W Nam, A Lita, T Gerrits, I A Walmsley, G S Agarwal, W Vogel
In Sperling et al. [Phys. Rev. Lett. 118 , 163602 (2017)], we introduced and applied a detector-independent method to uncover nonclassicality. Here, we extend those techniques and give more details on the performed analysis. We derive a general theory of the positive-operator-valued measure that describes multiplexing layouts with arbitrary detectors. From the resulting quantum version of a multinomial statistics, we infer nonclassicality probes based on a matrix of normally ordered moments. We discuss these criteria and apply the theory to our data which are measured with superconducting transition-edge sensors...
July 2017: Physical Review. A
Hongxu Ding, Eugene F Douglass, Adam M Sonabend, Angeliki Mela, Sayantan Bose, Christian Gonzalez, Peter D Canoll, Peter A Sims, Mariano J Alvarez, Andrea Califano
We and others have shown that transition and maintenance of biological states is controlled by master regulator proteins, which can be inferred by interrogating tissue-specific regulatory models (interactomes) with transcriptional signatures, using the VIPER algorithm. Yet, some tissues may lack molecular profiles necessary for interactome inference (orphan tissues), or, as for single cells isolated from heterogeneous samples, their tissue context may be undetermined. To address this problem, we introduce metaVIPER, an algorithm designed to assess protein activity in tissue-independent fashion by integrative analysis of multiple, non-tissue-matched interactomes...
April 16, 2018: Nature Communications
Tessa Lord, Jon M Oatley
Historically, research in spermatogonial biology has been hindered by a lack of validated approaches to identify and isolate pure populations of the various spermatogonial subsets for in-depth analysis. In particular, although a number of markers of the undifferentiated spermatogonial population have now been characterized, standardized methodology for assessing their specificity to the spermatogonial stem cell (SSC) and transit amplifying progenitor pools has been lacking. To date, SSC content within an undefined population of spermatogonia has been inferred using either lineage tracing or spermatogonial transplantation analyses which generate qualitative and quantitative data, respectively...
April 3, 2018: Stem Cell Research
Eric W Goolsby, Abigail J Moore, Lillian P Hancock, Jurriaan M De Vos, Erika J Edwards
PREMISE OF THE STUDY: Next-generation sequencing facilitates rapid production of well-sampled phylogenies built from very large genetic data sets, which can then be subsequently exploited to examine the molecular evolution of the genes themselves. We present an evolutionary analysis of 83 gene families (19 containing carbon-concentrating mechanism (CCM) genes, 64 containing non-CCM genes) in the portullugo clade (Caryophyllales), a diverse lineage of mostly arid-adapted plants that contains multiple evolutionary origins of all known photosynthesis types in land plants (C3 , C4 , CAM, C4 -CAM, and various intermediates)...
April 16, 2018: American Journal of Botany
Yongtao Zou, Wei Zhang, Xuefei Li, Maining Ma, Xing'ao Li, Chun-Hai Wang, Bin He, Shanmin Wang, Zhiqiang Chen, Yusheng Zhao, Baosheng Li
Here, we report a high-pressure study of orthorhombic structured β-Sb2O3 (valentinite) by the combination of synchrotron in situ X-ray diffraction and first-principles theoretical calculations at pressures up to 40.5 GPa. Our results reveal that the metastable β-Sb2O3 undergoes an isostructural phase transition at high pressure, yielding a distorted β phase at 7-15 GPa through symmetry breaking and structural distortion as inferred from our XRD analyses and DFT theoretical calculations where pressure-induced elasticity softening is observed at pressures of 7-15 GPa...
April 12, 2018: Physical Chemistry Chemical Physics: PCCP
Yamila V Vazquez, Silvia E Barbosa
The aim of this work is to develop compatibilization strategies for High Impact Polystyrene (HIPS)/ Acrylonitrile-Butadiene-Styrene (ABS) blends from WEEE in order to add value to these recycled plastics by improving their mechanical performance. Results from a screening study of HIPS/ABS blends compatibilization by the addition of Styrene-Butadiene Rubber (SBR) are presented. Two different weight proportion of HIPS/ABS physical blends were analyzed, 80/20 and 20/80, with three different concentration of SBR: 2, 10 and 20 wt%...
April 3, 2018: Journal of Environmental Management
S Shanmukharao Samatham, K G Suresh
The critical magnetic properties of a non-centrosymmetric B20 cubic helimagnet Fe<sub>0.6</sub>Co<sub>0.4</sub>Si are investigated using magnetization isotherms. It belongs to 3D-Heisenberg universality class with short range magnetic coupling as inferred from the self-consistent critical exponents β = 0.411 ± 0.003, γ = 1.325 ± 0.062, δ = 4.223 ± 0.004 and α = -0.115 ± 0.007 in combination with exchange interaction <i>J</i>(r) ∼ r<sup>-4...
April 6, 2018: Journal of Physics. Condensed Matter: An Institute of Physics Journal
Jihwan Park, Rojesh Shrestha, Chengxiang Qiu, Ayano Kondo, Shizheng Huang, Max Werth, Mingyao Li, Jonathan Barasch, Katalin Suszták
Our understanding of kidney disease pathogenesis is limited by an incomplete molecular characterization of the cell types responsible for the organ's multiple homeostatic functions. To help fill this knowledge gap, we characterized 57,979 cells from healthy mouse kidneys using unbiased single-cell RNA sequencing. Based on gene expression patterns, we infer that inherited kidney diseases that arise from distinct genetic mutations but share the same phenotypic manifestation originate from the same cell differentiated type...
April 5, 2018: Science
Zhimin Zhang, Dapeng Li, Mohamed M Refaey, Weitong Xu, Rong Tang, Li Li
Host development influences gut microbial assemblies that may be confounded partly by dietary shifts and the changing environmental microbiota during ontogenesis. However, little is known about microbial colonization by excluding dietary effects and compositional differences in microbiota between the gut and environment at different ontogenetic stages. Herein, a developmental gut microbial experiment under controlled laboratory conditions was conducted with carnivorous southern catfish Silurus meridionalis fed on an identical prey with commensal and abundant microbiota...
2018: Frontiers in Microbiology
Zhiliang Zhang, Leonid E Popov, Lars E Holmer, Zhifei Zhang
BACKGROUND: Our understanding of the ontogeny of Palaeozoic brachiopods has changed significantly during the last two decades. However, the micromorphic acrotretoids have received relatively little attention, resulting in a poor knowledge of their ontogeny, origin and earliest evolution. The uniquely well preserved early Cambrian fossil records in South China provide a great new opportunity to investigate the phylogenetically important ontogeny of the earliest acrotretoid brachiopods, and give new details of the dramatic changes in anatomy of acrotretoid brachiopods during the transition from planktotrophic larvae to filter feeding sedentary juveniles...
April 2, 2018: BMC Evolutionary Biology
Andrew Storfer, Austin Patton, Alexandra K Fraik
As next-generation sequencing data become increasingly available for non-model organisms, a shift has occurred in the focus of studies of the geographic distribution of genetic variation. Whereas landscape genetics studies primarily focus on testing the effects of landscape variables on gene flow and genetic population structure, landscape genomics studies focus on detecting candidate genes under selection that indicate possible local adaptation. Navigating the transition between landscape genomics and landscape genetics can be challenging...
2018: Frontiers in Genetics
Chunquan Yu, Elizabeth A Day, Maarten V de Hoop, Michel Campillo, Saskia Goes, Rachel A Blythe, Robert D van der Hilst
Global seismic discontinuities near 410 and 660 km depth in Earth's mantle are expressions of solid-state phase transitions. These transitions modulate thermal and material fluxes across the mantle and variations in their depth are often attributed to temperature anomalies. Here we use novel seismic array analysis of SS waves reflecting off the 410 and 660 below the Hawaiian hotspot. We find amplitude-distance trends in reflectivity that imply lateral variations in wavespeed and density contrasts across 660 for which thermodynamic modeling precludes a thermal origin...
March 28, 2018: Nature Communications
B Bishal Paudel, Leonard A Harris, Keisha N Hardeman, Arwa A Abugable, Corey E Hayford, Darren R Tyson, Vito Quaranta
Targeted therapy is an effective standard of care in BRAF-mutated malignant melanoma. However, the duration of tumor remission varies unpredictably among patients, and relapse is almost inevitable. Here, we examine the responses of several BRAF-mutated melanoma cell lines (including isogenic subclones) to BRAF inhibitors. We observe complex response dynamics across cell lines, with short-term responses (<100 h) varying from cell line to cell line. In the long term, however, we observe equilibration of all drug-treated populations into a nonquiescent state characterized by a balanced rate of death and division, which we term the "idling" state, and to our knowledge, this state has not been previously reported...
March 27, 2018: Biophysical Journal
Tomotaka Matsumoto, Hiroshi Akashi
Inferred ancestral nucleotide states are increasingly employed in analyses of within and between species genome variation. Although numerous studies have focused on ancestral inference among distantly related lineages, approaches to infer ancestral states in polymorphism data have received less attention. Recently developed approaches that employ complex transition matrices allow us to infer ancestral nucleotide sequence in several evolutionary scenarios of base composition. However, the requirement of a single gene tree to calculate a likelihood is an important limitation for conducting ancestral inference using within-species variation in recombining genomes...
March 27, 2018: G3: Genes—Genomes—Genetics
Jing-Zhi Gong, Qiu-Jie Li, Xi Wang, Yue-Ping Ma, Xiao-Hui Zhang, Liang Zhao, Zhao-Yang Chang, Louis Ronse De Craene
Background and Aims: Camptotheca is endemic to China and there are limited data about the breeding system and morphogenesis of the flowers. Camptotheca is thought to be related to Nyssa and Davidia in Nyssaceae, which has sometimes been included in Cornaceae. However, molecular phylogenetic studies confirmed the inclusion of Camptotheca in Nyssaceae and its exclusion from Cornaceae. The aim of this study was to reveal developmental features of the inflorescence and flowers in Camptotheca to compare with related taxa in Cornales...
March 22, 2018: Annals of Botany
Haosheng Pang, Minglin Li, Chenghui Gao, Haili Huang, Weirong Zhuo, Jianyue Hu, Yaling Wan, Jing Luo, Weidong Wang
The single-layer molybdenum disulfide (SLMoS2) nanosheets have been experimentally discovered to exist in two different polymorphs, which exhibit different electrical properties, metallic or semiconducting. Herein, molecular dynamics (MD) simulations of nanoindentation and uniaxial compression were conducted to investigate the phase transition of SLMoS2 nanosheets. Typical load-deflection curves, stress-strain curves, and local atomic structures were obtained. The loading force decreases sharply and then increases again at a critical deflection under the nanoindentation, which is inferred to the phase transition...
March 27, 2018: Materials
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