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transitive inference

Xiaoming Guo, Halima Tabani, Dylan Griswold, Ali Tayebi Meybodi, Jose Juan Gonzalez Sanchez, Michael T Lawton, Arnau Benet
BACKGROUND: Identification and protection of the cochlea during anterior petrosectomy is key to prevent hearing loss. Currently, there is no optimal method to infer the position of the cochlea in relation to the Kawase quadrangle, therefore damage to the cochlea during anterior petrosectomy remains a substantial risk. OBJECTIVES: To identify and define landmarks available during anterior petrosectomy to locate the cochlea and prevent its damage. METHODS: Kawase approach was simulated in eleven specimens...
November 29, 2016: World Neurosurgery
Greg A Breed, Emily A Golson, M Tim Tinker
The home-range concept is central in animal ecology and behavior, and numerous mechanistic models have been developed to understand home range formation and maintenance. These mechanistic models usually assume a single, contiguous home range. Here we describe and implement a simple home-range model that can accommodate multiple home-range centers, form complex shapes, allow discontinuities in use patterns, and infer how external and internal variables affect movement and use patterns. The model assumes individuals associate with two or more home-range centers and move among them with some estimable probability...
October 6, 2016: Ecology
Oleg Simakov, Takeshi Kawashima
Metazoan evolution encompasses a vast evolutionary time scale spanning over 600 million years. Our ability to infer ancestral metazoan characters, both morphological and functional, is limited by our understanding of the nature and evolutionary dynamics of the underlying regulatory networks. Increasing coverage of metazoan genomes enables us to identify the evolutionary changes of the relevant genomic characters such as the loss or gain of coding sequences, gene duplications, micro- and macro-synteny, and non-coding element evolution in different lineages...
November 25, 2016: Developmental Biology
Pierina Cheung, Miriam Rubenson, David Barner
Recent accounts of number word learning posit that when children learn to accurately count sets (i.e., become "cardinal principle" or "CP" knowers), they have a conceptual insight about how the count list implements the successor function - i.e., that every natural number n has a successor defined as n+1 (Carey, 2004, 2009; Sarnecka & Carey, 2008). However, recent studies suggest that knowledge of the successor function emerges sometime after children learn to accurately count, though it remains unknown when this occurs, and what causes this developmental transition...
November 24, 2016: Cognitive Psychology
Somayeh Raiesdana
It is thought that the critical brain dynamics in sleep is modulated during frequent periods of wakefulness. This paper utilizes the capacity of EEG based scaling analysis to quantify sleep fragmentation in patients with obstructive sleep apnea. The scale-free (fractal) behavior refers to a state where no characteristic scale dominates the dynamics of the underlying process which is evident as long range correlations in a time series. Here, Multiscaling (multifractal) spectrum is utilized to quantify the disturbed dynamic of an OSA brain with fragmented sleep...
November 18, 2016: Technology and Health Care: Official Journal of the European Society for Engineering and Medicine
Sahand Hormoz, Zakary S Singer, James M Linton, Yaron E Antebi, Boris I Shraiman, Michael B Elowitz
As they proliferate, living cells undergo transitions between specific molecularly and developmentally distinct states. Despite the functional centrality of these transitions in multicellular organisms, it has remained challenging to determine which transitions occur and at what rates without perturbations and cell engineering. Here, we introduce kin correlation analysis (KCA) and show that quantitative cell-state transition dynamics can be inferred, without direct observation, from the clustering of cell states on pedigrees (lineage trees)...
November 23, 2016: Cell Systems
A Gholamipour-Shirazi, M S Carvalho, M F G Huila, K Araki, P Dommersnes, J O Fossum
Colloidal clay in water suspensions are known to exhibit a multitude of bulk phases depending on initial colloidal concentration and ionic strength, and examples of this include repulsive Wigner colloidal glasses at low ionic strength and attractive gels at higher ionic strength due to screened electrostatic forces by the electrolyte. From confocal Raman microscopy combined with elasticity measurements, we infer that clay trapped at quasi two-dimensional interfaces between oil and water also exhibit confined glass-like or gel-like states...
November 24, 2016: Scientific Reports
Petra Stamm, Alexander T Topham, Nur K Mukhtar, Matthew Jackson, Daniel Tome, Jim L Beynon, George W Bassel
The seed to seedling transition is driven exclusively by cell shape changes within the axis of the plant embryo. Using digital single cell analysis of 3D cellular growth, here we identify the presence of two spatially and temporally distinct cell expansion modules within subdomains of the growing embryo. The second growth module is within the hypocotyl and drives the final phase of the completion of germination under optimal conditions. Using network inference, we identified the transcription factor ATHB5 as a genetic factor specifically induced and localized to the hypocotyl prior to its expansion...
November 21, 2016: Plant Physiology
Antoine G Godin, Juan A Varela, Zhenghong Gao, Noémie Danné, Julien P Dupuis, Brahim Lounis, Laurent Groc, Laurent Cognet
The brain is a dynamic structure with the extracellular space (ECS) taking up almost a quarter of its volume. Signalling molecules, neurotransmitters and nutrients transit via the ECS, which constitutes a key microenvironment for cellular communication and the clearance of toxic metabolites. The spatial organization of the ECS varies during sleep, development and aging and is probably altered in neuropsychiatric and degenerative diseases, as inferred from electron microscopy and macroscopic biophysical investigations...
November 21, 2016: Nature Nanotechnology
Emiliano Brunamonti, Floriana Costanzo, Anna Mammì, Cristina Rufini, Diletta Veneziani, Pierpaolo Pani, Stefano Vicari, Stefano Ferraina, Deny Menghini
Objective: Here we explored whether children with ADHD have a deficit in relational reasoning, a skill subtending the acquisition of many cognitive abilities and social rules. Method: We analyzed the performance of a group of children with ADHD during a transitive inference task, a task requiring first to learn the reciprocal relationship between adjacent items of a rank ordered series (e.g., A>B; B>C; C>D; D>E; E>F), and second, to deduct the relationship between novel pairs of items never matched during the learning (e...
November 21, 2016: Neuropsychology
Marwin H S Segler, Mark Waller
The ability to reason beyond established knowledge allows Organic Chemists to solve synthetic problems and to invent novel transformations. Here, we propose a model which mimics chemical reasoning and formalises reaction prediction as finding missing links in a knowledge graph. We have constructed a knowledge graph containing 14.4 million molecules and 8.2 million binary reactions, which represents the bulk of all chemical reactions ever published in the scientific literature. Our model outperforms a rule-based expert system in the reaction prediction task for 180,000 randomly selected binary reactions...
November 11, 2016: Chemistry: a European Journal
Dawn Chen, Hongjing Lu, Keith J Holyoak
A key property of relational representations is their generativity: From partial descriptions of relations between entities, additional inferences can be drawn about other entities. A major theoretical challenge is to demonstrate how the capacity to make generative inferences could arise as a result of learning relations from non-relational inputs. In the present paper, we show that a bottom-up model of relation learning, initially developed to discriminate between positive and negative examples of comparative relations (e...
November 17, 2016: Cognitive Science
Yafeng Wang, Neil Pederson, Aaron M Ellison, Hannah L Buckley, Bradley S Case, Eryuan Liang, J Julio Camarero
The most widespread response to global warming among alpine treeline ecotones is not an upward shift, but an increase in tree density. However, the impact of increasing density on interactions among trees at treeline is not well understood. Here, we test if treeline densification induced by climatic warming leads to increasing intraspecific competition. We mapped and measured the size and age of Smith fir trees growing in two treelines located in the southeastern Tibetan Plateau. We used spatial point-pattern and codispersion analyses to describe the spatial association and covariation among seedlings, juveniles, and adults grouped in 30-yr age classes from the 1860s to the present...
July 2016: Ecology
Shingo Tanaka, Mineki Oguchi, Masamichi Sakagami
To behave appropriately in a complex and uncertain world, the brain makes use of several distinct learning systems. One such system is called the "model-free process", via which conditioning allows the association between a stimulus or response and a given reward to be learned. Another system is called the "model-based process". Via this process, the state transition between a stimulus and a response is learned so that the brain is able to plan actions prior to their execution. Several studies have tried to relate the difference between model-based and model-free processes to the difference in functions of the lateral prefrontal cortex (LPFC) and the striatum...
November 2016: Brain and Nerve, Shinkei Kenkyū No Shinpo
Jing Wang, Zihao Ma, Steven A Carr, Philipp Mertins, Hui Zhang, Zhen Zhang, Daniel W Chan, Matthew J C Ellis, R Reid Townsend, Richard D Smith, Jason E McDermott, Xian Chen, Amanda G Paulovich, Emily S Boja, Mehdi Mesri, Christopher R Kinsinger, Henry Rodriguez, Karin D Rodland, Daniel C Liebler, Bing Zhang
Co-expression of mRNAs under multiple conditions is commonly used to infer co-functionality of their gene products despite well-known limitations of this "guilt-by-association" (GBA) approach. Recent advancements in mass spectrometry-based proteomic technologies have enabled global expression profiling at the protein level; however, whether proteome profiling data can outperform transcriptome profiling data for co-expression based gene function prediction has not been systematically investigated. Here, we address this question by constructing and analyzing mRNA and protein co-expression networks for three cancer types with matched mRNA and protein profiling data from The Cancer Genome Atlas (TCGA) and the Clinical Proteomic Tumor Analysis Consortium (CPTAC)...
November 11, 2016: Molecular & Cellular Proteomics: MCP
Andrew Thompson, Francisco E Robles, Jesse W Wilson, Sanghamitra Deb, Robert Calderbank, Warren S Warren
Pump-probe microscopy is an emerging technique that provides detailed chemical information of absorbers with sub-micrometer spatial resolution. Recent work has shown that the pump-probe signals from melanin in human skin cancers correlate well with clinical concern, but it has been difficult to infer the molecular origins of these differences. Here we develop a mathematical framework to describe the pump-probe dynamics of melanin in human pigmented tissue samples, which treats the ensemble of individual chromophores that make up melanin as Gaussian absorbers with bandwidth related via Frenkel excitons...
November 11, 2016: Scientific Reports
Zitao Liu, Milos Hauskrecht
The linear dynamical system (LDS) model is arguably the most commonly used time series model for real-world engineering and financial applications due to its relative simplicity, mathematically predictable behavior, and the fact that exact inference and predictions for the model can be done efficiently. In this work, we propose a new generalized LDS framework, gLDS, for learning LDS models from a collection of multivariate time series (MTS) data based on matrix factorization, which is different from traditional EM learning and spectral learning algorithms...
May 2016: Proceedings of the ... SIAM International Conference on Data Mining
Zhuqing Zhang, Yanhua Ouyang, Tao Chen
Since single-point mutant perturbation has been used to probe protein folding mechanisms in experiments, the ϕ-value has become a critical parameter to infer the transition state (TS) for two-state proteins. Experimentally, large scale analysis has shown a nearly single uniform ϕ-value with normally distributed error from 24 different proteins; moreover, in zero stability conditions, the intrinsic variable ϕ(0) is around 0.36. To explore how and to what extent theoretical models can capture experimental phenomena, we here use structure-based explicit chain coarse-grained models to investigate the influence of single-point mutant perturbation on protein folding for single domain two-state proteins...
November 16, 2016: Physical Chemistry Chemical Physics: PCCP
Ruiyue Yang, Zhongwei Huang, Wei Yu, Gensheng Li, Wenxi Ren, Lihua Zuo, Xiaosi Tan, Kamy Sepehrnoori, Shouceng Tian, Mao Sheng
A complex fracture network is generally generated during the hydraulic fracturing treatment in shale gas reservoirs. Numerous efforts have been made to model the flow behavior of such fracture networks. However, it is still challenging to predict the impacts of various gas transport mechanisms on well performance with arbitrary fracture geometry in a computationally efficient manner. We develop a robust and comprehensive model for real gas transport in shales with complex non-planar fracture network. Contributions of gas transport mechanisms and fracture complexity to well productivity and rate transient behavior are systematically analyzed...
November 7, 2016: Scientific Reports
Hongzhi Lu, Zhengqin Qi, Lin Lin, Li Ma, Li Li, Hong Zhang, Li Feng, Ying Su
MiR-375 has been recognized as an important tumor suppressor and is usually downregulated in cervical cancer. However, how it is downregulated in cervical cancer is not clear. By using cancerous and normal cervical tissues, we observed that miR-375 and Dicer are both downregulated and were positively correlated. Overexpression of miR-375 resulted in decreased viral E6 and increased Dicer expression in both Hela and SiHa cells. Previous studies suggest that E6 can induce an accelerated degradation of TAp63β, while TAp63 can bind to and transactivate the Dicer promoter, exerting a direct regulation on transcription of Dicer...
November 3, 2016: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
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