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transitive inference

Pietro Enrico di Prampero, Cristian Osgnach
Team sports are characterised by frequent episodes of accelerated/decelerated running. The corresponding energy cost can be estimated on the basis of the biomechanical equivalence between accelerated/decelerated running on flat terrain and constant speed running uphill/downhill. This approach allows one to: (i) estimate the time course of the instantaneous metabolic power requirement of any given player and (ii) infer therefrom the overall energy expenditure of any given time window of a soccer drill or match...
June 14, 2018: International Journal of Sports Medicine
Yin Tong, Beibei Ru, Jiangwen Zhang
Summary: MicroRNAs play critical roles in oncogenesis by targeting a few key regulators or a large cohort of genes impinging on downstream signaling pathways. Conversely, miRNA activity is also titrated by ceRNA such as lncRNA with sponge effect. Web-based server, miRNACancerMap, aims to unravel lncRNA-miRNA-mRNA tripartite complexity to predict the function and clinical relevance of miRNA with network perspective. In conjunction with large-scale data and information integration, miRNACancerMap implements various algorithms and pipelines to construct dynamic miRNA-centered network with rigorous Systems Biology approaches and the state-of-the-art visualization tool...
April 20, 2018: Bioinformatics
Mohammad Hadigol, Hossein Khiabanian
BACKGROUND: Rapid progress in high-throughput sequencing (HTS) and the development of novel library preparation methods have improved the sensitivity of detecting mutations in heterogeneous samples, specifically in high-depth (> 500×) clinical applications. However, HTS methods are bounded by their technical and theoretical limitations and sequencing errors cannot be completely eliminated. Comprehensive quantification of the background noise can highlight both the efficiency and the limitations of any HTS methodology, and help differentiate true mutations at low abundance from artifacts...
June 8, 2018: BMC Bioinformatics
S Shanmukharao Samatham, Akhilesh Kumar Patel, Alexey V Lukoyanov, K G Suresh
We report on the combined results of structural, magnetic, transport and calorimetric properties of Mn<sub>5</sub>Si<sub>3</sub>-type hexagonal Gd<sub>5</sub>Sb<sub>3</sub>, together with <i>ab-initio</i> calculations. It exhibits a ferromagnetic (FM)-like transition at 265 K, antiferromagnetic (AFM) Néel transition at 95.5 K followed by a spin-orientation transition at 62 K...
June 7, 2018: Journal of Physics. Condensed Matter: An Institute of Physics Journal
Lauren Sumner-Rooney
Light is a fundamentally important biological cue used by almost every animal on earth, to maintain daily rhythms, navigate, forage, find mates or avoid predators. But an enormous number of species live in darkness: in subterranean caves, deep oceans, underground burrows, and within parasitic host bodies, and the loss of eyes appears consistently across these ecosystems. However, the evolutionary mechanisms that lead to the reduction of the visual system remain the subject of great interest and debate more than 150 years after Darwin tackled the issue...
June 4, 2018: Integrative and Comparative Biology
Masanori Inui, Alfred Q R Baron, Yukio Kajihara, Kazuhiro Matsuda, Shinya Hosokawa, Koji Kimura, Yoshimi Tsuchiya, Fuyuki Shimojo, Makoto Yao, Satoshi Tsutsui, Daisuke Ishikawa, Kozaburo Tamura
We investigate the dynamic structure factor of the melt of the well known glass former, As<sub>2</sub>Se<sub>3</sub>, using inelastic x-ray scattering (IXS) for temperatures, <i>T</i>, 1073 =< <i>T</i> =< 1673 K and momentum transfers <i>Q</i> from 1.6 =< <i>Q</i> =< 11 nm<sup>-1</sup>. An anomaly was observed at a momentum transfer <i>Q</i>=2...
June 6, 2018: Journal of Physics. Condensed Matter: An Institute of Physics Journal
Elyse S Freitas, Aaron M Bauer, Cameron D Siler, Donald G Broadley, Todd R Jackman
The aridification of Africa resulted in the fragmentation of forests and the expansion of an arid corridor stretching from the northeast to southwest portion of sub-Saharan Africa, but the role this corridor has had in species-level diversification of southern African vertebrates is poorly understood. The, skink species Mochlus afer and M. sundevallii inhabit wide areas of the arid corridor and are therefore an ideal species pair for studying patterns of genetic and phenotypic diversity associated with this landscape...
June 2, 2018: Molecular Phylogenetics and Evolution
Mathias Brochhausen, Jonathan Bona, Bernd Blobel
In the biomedical domain, there exist a number of common data models (CDM) that have experienced wide uptake. However, none of these has emerged as the common model. Recently, the demand for integrating and analyzing increasingly large data sets in clinical and translational research has led to numerous efforts to harmonize existing CDMs and integrate data curated based on those models. These efforts raise the question of how to appropriately represent the semantics of data, and, furthermore, they highlight the fact that quite often different groups have greatly different definitions of 'semantics'...
2018: Studies in Health Technology and Informatics
Tien-Lam Pham, Nguyen-Duong Nguyen, Van-Doan Nguyen, Hiori Kino, Takashi Miyake, Hieu-Chi Dam
We have developed a descriptor named Orbital Field Matrix (OFM) for representing material structures in datasets of multi-element materials. The descriptor is based on the information regarding atomic valence shell electrons and their coordination. In this work, we develop an extension of OFM called OFM1. We have shown that these descriptors are highly applicable in predicting the physical properties of materials and in providing insights on the materials space by mapping into a low embedded dimensional space...
May 28, 2018: Journal of Chemical Physics
C Alisha Quandt, Will Patterson, Joseph W Spatafora
Host specialization is common among parasitic fungi; however, there are examples when transitions in host specificity between disparately related hosts have occurred. Here, we examine the interkingdom host jump from insect pathogenicity and mycoparasitism in Tolypocladium. Previous phylogenetic inferences made using only a few genes and with poor support reconstructed an ancestral character state of insect pathogenesis, a transition to mycoparasitism, and reversions to insect pathogenesis. To further explore the directionality and genes underlying the transitions in host, we sequenced two additional species of Tolypocladium (T...
January 2018: Mycologia
Arkady Konovalov, Ian Krajbich
The brain is often able to learn complex structures of the environment using a very limited amount of evidence, which is crucial for model-based planning and sequential prediction. However, little is known about the neurocomputational mechanisms of deterministic sequential prediction, as prior work has primarily focused on stochastic transition structures. Here we find that human subjects' beliefs about a sequence of states, captured by reaction times, are well explained by a Bayesian pattern-learning model that tracks beliefs about both the current state and the underlying structure of the environment, taking into account prior beliefs about possible patterns in the sequence...
May 19, 2018: Neuron
Simon M Tierney, Barbara Langille, William F Humphreys, Andrew D Austin, Steve J B Cooper
Two tribes of subterranean dytiscid diving beetles independently colonised groundwater systems of the Western Australian arid zone, a habitat transition that was most likely driven by the contraction of surface water bodies following late Neogene aridification of the Australian continent. These 'stygofauna' are now trapped within discrete calcrete aquifers that have formed in palaeodrainage valleys, resulting in the world's most diverse radiations of subterranean dytiscid beetles. Approximately 100 species from three genera exhibit partial or fully regressed visual systems and are essentially blind...
May 31, 2018: Integrative and Comparative Biology
Hao Liu, Randall E Youngman, Saurabh Kapoor, Lars R Jensen, Morten M Smedskjaer, Yuanzheng Yue
We investigate the structure, phase separation, glass transition, and crystallization in a mixed network former glass series, i.e., B2O3-Al2O3-SiO2-P2O5 glasses with varying SiO2/B2O3 molar ratio. All the studied glasses exhibit two separate glassy phases: droplet phase (G1) with the size of 50-100 nm and matrix phase (G2), corresponding to a lower calorimetric glass transition temperature (Tg1) and a higher one (Tg2), respectively. Both Tg values decrease linearly with the substitution of B2O3 for SiO2, but the magnitude of the decrease is larger for Tg1...
May 31, 2018: Physical Chemistry Chemical Physics: PCCP
Yun-Hsuan Kuo, Yun-Wei Chiang
Solvent is essential for protein dynamics and function, but its role in regulating the dynamics remains debated. Here, we employ saturation transfer electron spin resonance (ST-ESR) to explore the issue and characterize the dynamics on a longer (from μs to s) time scale than has been extensively studied. We first demonstrate the reliability of ST-ESR by showing that the dynamical changeovers revealed in the spectra agree to liquid-liquid transition (LLT) in the state diagram of the glycerol/water system. Then, we utilize ST-ESR with four different probes to systematically map out the variation in local (site-specific) dynamics around a protein surface at subfreezing temperatures (180-240 K) in 10 mol % glycerol/water mixtures...
May 23, 2018: ACS Central Science
Daniel J Field, Antoine Bercovici, Jacob S Berv, Regan Dunn, David E Fastovsky, Tyler R Lyson, Vivi Vajda, Jacques A Gauthier
The fossil record and recent molecular phylogenies support an extraordinary early-Cenozoic radiation of crown birds (Neornithes) after the Cretaceous-Paleogene (K-Pg) mass extinction [1-3]. However, questions remain regarding the mechanisms underlying the survival of the deepest lineages within crown birds across the K-Pg boundary, particularly since this global catastrophe eliminated even the closest stem-group relatives of Neornithes [4]. Here, ancestral state reconstructions of neornithine ecology reveal a strong bias toward taxa exhibiting predominantly non-arboreal lifestyles across the K-Pg, with multiple convergent transitions toward predominantly arboreal ecologies later in the Paleocene and Eocene...
May 12, 2018: Current Biology: CB
S Dheivamalar, L Sugi, K Ravichandran, S Sriram
C20 is the most important fullerene cage and alanine is the simplest representation of a backbone unit of the protein. The absorption feasibility of alanine molecule in the Si-doped C20 and B-doped C20 fullerenes has been studied based on calculated electronic properties of fullerenes using density functional theory (DFT). In this work, we explore the ability of Si-doped C20 , B-doped C20 fullerene to interact with alanine at the DFT-B3LYP/6-31G, RHF level of theory. We find that noticeable structural change takes place in C20 when one of its carbon is substituted with Si or B...
May 14, 2018: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
Nathan Will, Kwangwoon Lee, Fatlum Hajredini, David H Giles, Rinat R Abzalimov, Michael Clarkson, Kevin N Dalby, Ranajeet Ghose
Eukaryotic elongation factor 2 kinase (eEF-2K), the only known calmodulin (CaM) activated α-kinase, phosphorylates eukaryotic elongation factor 2 (eEF-2) on a specific threonine (Thr-56) diminishing its affinity for the ribosome and reducing the rate of nascent chain elongation during translation. Despite its critical cellular role, the precise mechanisms underlying the CaM-mediated activation of eEF-2K remain poorly defined. Here, employing a minimal eEF-2K construct (TR) that exhibits activity comparable to the wild-type enzyme and is fully activated by CaM in vitro and in cells, and using a variety of complimentary biophysical techniques in combination with computational modeling, we provide a structural mechanism by which CaM activates eEF-2K...
May 22, 2018: Journal of Molecular Biology
Guangxu Ma, Tao Wang, Pasi K Korhonen, Ching-Seng Ang, Nicholas A Williamson, Neil D Young, Andreas J Stroehlein, Ross S Hall, Anson V Koehler, Andreas Hofmann, Robin B Gasser
In this study, we explored the molecular alterations in the developmental switch from the L3 to the exsheathed L3 (×L3) and to the L4 stage of Haemonchus contortus in vitro using an integrated transcriptomic, proteomic and bioinformatic approach. Totals of 9,754 mRNAs, 88 microRNAs (miRNAs) and 1,591 proteins were identified, and 6,686 miRNA-mRNA pairs inferred in all larval stages studied. Approximately 16% of transcripts in the combined transcriptome (representing all three larval stages) were expressed as proteins, and there were positive correlations (r = 0...
May 22, 2018: International Journal for Parasitology
Yu Luo, Jiaying Zhao
A remarkable ability of the cognitive system is to make novel inferences on the basis of prior experiences. What mechanism supports such inferences? We propose that statistical learning is a process through which transitive inferences of new associations are made between objects that have never been directly associated. After viewing a continuous sequence containing two base pairs (e.g., A-B, B-C), participants automatically inferred a transitive pair (e.g., A-C) where the two objects had never co-occurred before (Experiment 1)...
May 1, 2018: Psychological Science
Neil Brocklehurst
It has been suggested that a transition between a pelycosaurian-grade synapsid dominated fauna of the Cisuralian (early Permian) and the therapsid dominated fauna of the Guadalupian (middle Permian) was accompanied by, and possibly driven by, a mass extinction dubbed Olson's Extinction. However, this interpretation of the record has recently been criticised as being a result of inappropriate time-binning strategies: calculating species richness within international stages or substages combines extinctions occurring throughout the late Kungurian stage into a single event...
2018: PeerJ
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