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Transitive inferences

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
Yang Liu, Ye Jin, Jun Li, Lei Zhao, Zhengtian Li, Jun Xu, Fuya Zhao, Jing Feng, Huinan Chen, Chengyuan Fang, Rojina Shilpakar, Yunwei Wei
Disturbance of the gut microbiota is common in liver cirrhosis (LC) patients, the underlying mechanisms of which are yet to be unfolded. This study aims to explore the relationship between small bowel transit (SBT) and gut microbiota in LC patients. Cross-sectional design was applied with 36 LC patients and 20 healthy controls (HCs). The gut microbiota was characterized by 16S rRNA gene sequencing. The Firmicutes/Bacteroidetes (F/B) ratio and the Microbial Dysbiosis index (MDI) were used to evaluate the severity of microbiota dysbiosis...
2018: Frontiers in Physiology
Manuela Sann, Oliver Niehuis, Ralph S Peters, Christoph Mayer, Alexey Kozlov, Lars Podsiadlowski, Sarah Bank, Karen Meusemann, Bernhard Misof, Christoph Bleidorn, Michael Ohl
BACKGROUND: Apoid wasps and bees (Apoidea) are an ecologically and morphologically diverse group of Hymenoptera, with some species of bees having evolved eusocial societies. Major problems for our understanding of the evolutionary history of Apoidea have been the difficulty to trace the phylogenetic origin and to reliably estimate the geological age of bees. To address these issues, we compiled a comprehensive phylogenomic dataset by simultaneously analyzing target DNA enrichment and transcriptomic sequence data, comprising 195 single-copy protein-coding genes and covering all major lineages of apoid wasps and bee families...
May 18, 2018: BMC Evolutionary Biology
Alireza Mashaghi, Abolfazl Ramezanpour
We study a diagnostic strategy which is based on the anticipation of the diagnostic process by simulation of the dynamical process starting from the initial findings. We show that such a strategy could result in more accurate diagnoses compared to a strategy that is solely based on the direct implications of the initial observations. We demonstrate this by employing the mean-field approximation of statistical physics to compute the posterior disease probabilities for a given subset of observed signs (symptoms) in a probabilistic model of signs and diseases...
March 2018: Physical Review. E
Sanku Paul, M S Santhanam
It is well known that, in the chaotic regime, all the Floquet states of kicked rotor system display an exponential profile resulting from dynamical localization. If the kicked rotor is placed in an additional stationary infinite potential well, its Floquet states display power-law profile. It has also been suggested in general that the Floquet states of periodically kicked systems with singularities in the potential would have power-law profile. In this work, we study the Floquet states of a kicked particle in finite potential barrier...
March 2018: Physical Review. E
Emmanuel Klinger, Dennis Rickert, Jan Hasenauer
Summary: Likelihood-free methods are often required for inference in systems biology. While Approximate Bayesian Computation (ABC) provides a theoretical solution, its practical application has often been challenging due to its high computational demands. To scale likelihood-free inference to computationally demanding stochastic models we developed pyABC: a distributed and scalable ABC-Sequential Monte Carlo (ABC-SMC) framework. It implements a scalable, runtime-minimizing parallelization strategy for multi-core and distributed environments scaling to thousands of cores...
May 14, 2018: Bioinformatics
J Brocal, S De Decker, R José-López, E G Manzanilla, J Penderis, C Stalin, S Bertram, J J Schoenebeck, C Rusbridge, N Fitzpatrick, R Gutierrez-Quintana
The number of cervical vertebrae in mammals is almost constant at seven, regardless of their neck length, implying that there is selection against variation in this number. Homebox (Hox) genes are involved in this evolutionary mammalian conservation, and homeotic transformation of cervical into thoracic vertebrae (cervical ribs) is a common phenotypic abnormality when Hox gene expression is altered. This relatively benign phenotypic change can be associated with fatal traits in humans. Mutations in genes upstream of Hox, inbreeding and stressors during organogenesis can also cause cervical ribs...
May 14, 2018: Journal of Anatomy
Niels Møller Israelsen, Michael Maria, Mette Mogensen, Sophie Bojesen, Mikkel Jensen, Merete Haedersdal, Adrian Podoleanu, Ole Bang
Optical coherence tomography (OCT) imaging of the skin is gaining recognition and is increasingly applied to dermatological research. A key dermatological parameter inferred from an OCT image is the epidermal (Ep) thickness as a thickened Ep can be an indicator of a skin disease. Agreement in the literature on the signal characters of Ep and the subjacent skin layer, the dermis (D), is evident. Ambiguities of the OCT signal interpretation in the literature is however seen for the transition region between the Ep and D, which from histology is known as the dermo-epidermal junction (DEJ); a distinct junction comprised of the lower surface of a single cell layer in epidermis (the stratum basale) connected to an even thinner membrane (the basement membrane)...
May 1, 2018: Biomedical Optics Express
Wengang Zhang, Jack F Douglas, Francis W Starr
There is significant variation in the reported magnitude and even the sign of [Formula: see text] shifts in thin polymer films with nominally the same chemistry, film thickness, and supporting substrate. The implicit assumption is that methods used to estimate [Formula: see text] in bulk materials are relevant for inferring dynamic changes in thin films. To test the validity of this assumption, we perform molecular simulations of a coarse-grained polymer melt supported on an attractive substrate. As observed in many experiments, we find that [Formula: see text] based on thermodynamic criteria (temperature dependence of film height or enthalpy) decreases with decreasing film thickness, regardless of the polymer-substrate interaction strength ε...
May 14, 2018: Proceedings of the National Academy of Sciences of the United States of America
Alexandre Antonelli, Alexander Zizka, Fernanda Antunes Carvalho, Ruud Scharn, Christine D Bacon, Daniele Silvestro, Fabien L Condamine
The American tropics (the Neotropics) are the most species-rich realm on Earth, and for centuries, scientists have attempted to understand the origins and evolution of their biodiversity. It is now clear that different regions and taxonomic groups have responded differently to geological and climatic changes. However, we still lack a basic understanding of how Neotropical biodiversity was assembled over evolutionary timescales. Here we infer the timing and origin of the living biota in all major Neotropical regions by performing a cross-taxonomic biogeographic analysis based on 4,450 species from six major clades across the tree of life (angiosperms, birds, ferns, frogs, mammals, and squamates), and integrate >1...
May 14, 2018: Proceedings of the National Academy of Sciences of the United States of America
Miguel A Caro, Volker L Deringer, Jari Koskinen, Tomi Laurila, Gábor Csányi
We study the deposition of tetrahedral amorphous carbon (ta-C) films from molecular dynamics simulations based on a machine-learned interatomic potential trained from density-functional theory data. For the first time, the high sp^{3} fractions in excess of 85% observed experimentally are reproduced by means of computational simulation, and the deposition energy dependence of the film's characteristics is also accurately described. High confidence in the potential and direct access to the atomic interactions allow us to infer the microscopic growth mechanism in this material...
April 20, 2018: Physical Review Letters
F J Fattoyev, J Piekarewicz, C J Horowitz
The historical first detection of a binary neutron star merger by the LIGO-Virgo Collaboration [B. P. Abbott et al., Phys. Rev. Lett. 119, 161101 (2017)PRLTAO0031-900710.1103/PhysRevLett.119.161101] is providing fundamental new insights into the astrophysical site for the r process and on the nature of dense matter. A set of realistic models of the equation of state (EOS) that yield an accurate description of the properties of finite nuclei, support neutron stars of two solar masses, and provide a Lorentz covariant extrapolation to dense matter are used to confront its predictions against tidal polarizabilities extracted from the gravitational-wave data...
April 27, 2018: Physical Review Letters
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...
May 7, 2018: Neuroscience and Biobehavioral Reviews
Yongjie Zhang, Sen Lin, Yan Chen, Fei Yang, Shenlin Liu
Introduction: Epithelial-mesenchymal transition (EMT) is regarded as a crucial process of invasion and metastasis, which contribute greatly to cancer-related relapse and death. Based on research results that hypoxia can trigger gastric cancer EMT and decreasing lactate production can selectively kill hypoxic cancer cells, we infer that lactate dehydrogenase A (LDH-A) transforming pyruvate into lactate is at least in part responsible for poor prognosis of gastric cancer. Materials and methods: We used siRNA to knock down LDH-A in intestinal-type gastric cancer (ITGC) cell lines SGC7901 and BGC823...
2018: OncoTargets and Therapy
Haiyu Wang, Lu Yao, Yuda Gong, Bo Zhang
Tripartite motif 31(TRIM31) is a new member of the E3 ubiquitin ligase family, which plays a role in many biological processes. It has been indicated that TRIM31 is strongly correlated with tumorigenesis. However, the impact of TRIM31 in colorectal cancer (CRC) and its underlying mechanisms are largely unknown. In this study, we found an increase in TRIM31 expression in CRC cells and a positive correlation between TRIM31 and CRC malignancy. Applying genetic interventions and cellular function tests, our results showed that TRIM31 acted as an epithelial-mesenchymal transition (EMT) inducer to promote CRC invasion and metastasis...
2018: American Journal of Translational Research
Yueming Jin, Qi Dou, Hao Chen, Lequan Yu, Jing Qin, Chi-Wing Fu, Pheng-Ann Heng
We propose an analysis of surgical videos that is based on a novel recurrent convolutional network (SV-RCNet), specifically for automatic workflow recognition from surgical videos online, which is a key component for developing the context-aware computer-assisted intervention systems. Different from previous methods which harness visual and temporal information separately, the proposed SV-RCNet seamlessly integrates a convolutional neural network (CNN) and a recurrent neural network (RNN) to form a novel recurrent convolutional architecture in order to take full advantages of the complementary information of visual and temporal features learned from surgical videos...
May 2018: IEEE Transactions on Medical Imaging
David Boldrin, Andrei Mihai, Bin Zou, Jan Zemen, Ryan Thompson, Ecaterina Ware, Bogdan Neamtu, Luis Ghivelder, Bryan Esser, David W McComb, Peter K Petrov, Lesley F Cohen
Controlling magnetism with electric field directly or through strain-driven piezoelectric coupling remains a key goal of spintronics. Here we demonstrate that giant piezomagnetism, a linear magneto-mechanic coupling effect, is manifest in antiperovskite Mn3NiN, facilitated by its geometrically frustrated antiferromagnetism opening the possibility of new memory device concepts. Films of Mn3NiN with intrinsic biaxial strains of ±0.25% result in Néel transition shifts up to 60K and magnetisation changes consistent with theory...
May 4, 2018: ACS Applied Materials & Interfaces
Tabitha J Hookey, Robert C Backus, Allison M Wara
More than one-third of humans and companion dogs in Western societies are overweight or obese. In people, vitamin D deficiency is widespread and associated with obesity, a now recognised inflammatory state. Low vitamin D status occurs in dogs with inflammatory conditions, but its relationship with obesity has not been investigated. In otherwise healthy privately owned adult dogs of ideal body condition (control, n 7) and dogs with overweight to obese body condition (treatment, n 8), serum 25-hydroxyvitamin D (25(OH)D) concentration and body composition as inferred from 2 H-labelled water dilution space were evaluated...
2018: Journal of Nutritional Science
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