bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantum Bayesian perspective for intelligence reservoir characterization, monitoring and management
Authors: Lozada Aguilar Miguel Ángel , Khrennikov Andrei , Oleschko Klaudia , de Jesús Correa María 
Published: October 2017

The paper starts with a brief review of the literature about uncertainty in geological, geophysical and petrophysical data. In particular, we present the viewpoints of experts in geophysics on the application of Bayesian inference and subjective probability. Then we present arguments that the use of classical probability theory (CP) does not match completely the structure of geophysical data. We emphasize that such data are characterized by contextuality and non-Kolmogorovness (the impossibility to use the CP model), incompleteness as well as incompatibility of some geophysical measurements. These characteristics of geophysical data are similar to the characteristics of quantum physical data. Notwithstanding all this, contextuality can be seen as a major deviation of quantum theory from classical physics. In particular, the contextual probability viewpoint is the essence of the Växjö interpretation of quantum mechanics. We propose to use quantum probability (QP) for decision-making during the characterization, modelling, exploring and management of theintelligent hydrocarbon reservoir. Quantum Bayesianism (QBism), one of the recently developed information interpretations of quantum theory, can be used as the interpretational basis for such QP decision-making in geology, geophysics and petroleum projects design and management.This article is part of the themed issue ‘Second quantum revolution: foundational questions’.
A model of adaptive decision-making from representation of information environment by quantum fields
Authors: Bagarello F. , Haven E. , Khrennikov A. 
Published: October 2017

We present the mathematical model of decision-making (DM) of agents acting in a complex and uncertain environment (combining huge variety of economical, financial, behavioural and geopolitical factors). To describe interaction of agents with it, we apply the formalism of quantum field theory (QTF). Quantum fields are a purely informational nature. The QFT model can be treated as a far relative of the expected utility theory, where the role of utility is played by adaptivity to an environment (bath). However, this sort of utility–adaptivity cannot be represented simply as a numerical function. The operator representation in Hilbert space is used and adaptivity is described as in quantum dynamics. We are especially interested in stabilization of solutions for sufficiently large time. The outputs of this stabilization process, probabilities for possible choices, are treated in the framework of classical DM. To connect classical and quantum DM, we appeal to Quantum Bayesianism. We demonstrate the quantum-like interference effect in DM, which is exhibited as a violation of the formula of total probability, and hence the classical Bayesian inference scheme.This article is part of the themed issue ‘Second quantum revolution: foundational questions’.
Novel Compensatory Mechanisms Enable the Mutant KCNT1 Channels to Induce Seizures
Authors: Ehaideb Salleh N. , Decker Gentry T. , Smith Petrina , Davis Daniel , Zhang Bing 
Published: October 2017

AbstractMutations in the sodium-activated potassium channel (KCNT1) gene are linked to epilepsy. Surprisingly, all KCNT1 mutations examined to date increase K+current amplitude. These findings present a major neurophysiological paradox: how do gain-of-function KCNT1 mutations expected to silence neurons cause epilepsy? Here, we useDrosophilato show that expressing mutant KCNT1 in GABAergic neurons leads to seizures, consistent with the notion that silencing inhibitory neurons tips the balance towards hyperexcitation. Unexpectedly, mutant KCNT1 expressed in motoneurons also causes seizures. One striking observation is that mutant KCNT1 causes abnormally large and spontaneous EJPs (sEJPs). Our data suggest that these sEJPs result from local depolarization of synaptic terminals due to a reduction in Shaker channel levels and more active Na+channels. Hence, we provide the firstin vivoevidence that both disinhibition of inhibitory neurons and compensatory plasticity in motoneurons can account for the paradoxical effects of gain-of-function mutant KCNT1 in epilepsy.
miR-128-induced LINE-1 restriction is dependent on down-regulation of hnRNPA1
Authors: Fung Lianna , Guzman Herlinda , Sevrioukov Evgueni , Idica Adam , Park Eddie , Bochnakien Aurore , Daugaard Iben , Jury Douglas , Mortazavi Ali , Zisoulis Dimitrios G , Pedersen Irene Munk 
Published: October 2017

ABSTRACTThe majority of the human genome is made of transposable elements, giving rise to interspaced repeats, including Long Interspersed Element-1s (LINE-1s or L1s). L1s are active human DNA parasites involved in genomic diversity and evolution, but can also contribute to genomic instability and diseases. L1s require host factors to complete their life cycles, whereas the host has evolved numerous mechanisms to restrict L1-induced mutagenesis. Restriction mechanisms in somatic cells include methylation of the L1 promoter, anti-viral factors and RNA-mediated processes such as small RNAs. microRNAs (miRNAs or miRs) are small non-coding RNAs that post-transcriptionally repress multiple target genes often found in the same cellular pathways. We have recently established that the interferon-inducible miR-128 function as a novel restriction factor inhibiting L1 mobilization in somatic cells. We have further demonstrated that miR-128 function through a dual mechanism; by directly targeting L1 RNA for degradation and indirectly by inhibiting a cellular co-factor which L1 is dependent on to transpose to new genomic locations (TNPO1). Here we add another piece to the puzzle of the enigmatic L1 life cycle. We show that miR-128 also inhibits another key cellular factor, hnRNPA1, by significantly reducing mRNA and protein levels through direct interaction with the coding sequence (CDS) of hnRNPA1 mRNA. Furthermore, we demonstrate that repression of hnRNPA1 using shRNA significantly decreasesde novoL1 retrotransposition and that induced hnRNPA1 expression enhances L1 mobilization. Finally, we determine that hnRNPA1 is a functional target of miR-128 and that induced hnRNPA1 expression in miR-128-overexpressing cells can partly rescue the miR-128-induced repression of L1’s ability to transpose to different genomic locations. Thus, we have identified an additional mechanism by which miR-128 represses L1 retrotransposition and mediate genomic stability.
Atg8 is essential specifically for an autophagy-independent function in apicoplast biogenesis in blood-stage malaria parasites
Authors: Walczak Marta , Ganesan Suresh M. , Niles Jacquin C. , Yeh Ellen 
Published: October 2017

AbstractPlasmodiumparasites and related pathogens contain an essential non-photosynthetic plastid organelle, the apicoplast, derived from secondary endosymbiosis. Intriguingly, a highly conserved eukaryotic protein, autophagy-related protein 8 (Atg8), has an autophagy-independent function in the apicoplast. Little is known about the novel apicoplast function of Atg8 and its importance in blood-stageP. falciparum. Using aP. falciparumstrain in which Atg8 expression was conditionally regulated, we showed thatPfAtg8 is essential for parasite replication. Significantly, growth inhibition caused by the loss ofPfAtg8 was reversed by addition of isopentenyl pyrophosphate (IPP), which was previously shown to rescue apicoplast defects inP. falciparum. Parasites deficient inPfAtg8, but growth rescued by IPP, had lost their apicoplast. We designed a suite of functional assays, including a new fluorescencein situhybridization (FISH) method for detection of the low-copy apicoplast genome, to interrogate specific steps in apicoplast biogenesis and detect apicoplast defects which preceded the block in parasite replication. Though protein import and membrane expansion of the apicoplast were unaffected, the apicoplast was not inherited by daughter parasites. Our findings demonstrate that, though multiple autophagy-dependent and independent functions have been proposed forPfAtg8, only its role in apicoplast biogenesis is essential. We propose thatPfAtg8 is required for fission or segregation of the apicoplast during parasite replication.
Offline Replay Supports Planning: fMRI Evidence from Reward Revaluation
Authors: Momennejad Ida , Ross Otto A. , Daw Nathaniel D. , Norman Kenneth A. 
Published: October 2017

AbstractMaking decisions in sequentially structured tasks requires integrating distally acquired information. The extensive computational cost of such integration challenges planning methods that integrate online, at decision time. Furthermore, it remains unclear whether “offline” integration during replay supports planning, and if so which memories should be replayed. Inspired by machine learning, we propose that (a) offline replay of trajectories facilitates integrating representations that guide decisions, and (b) unsigned prediction errors (uncertainty) trigger such integrative replay. We designed a 2-step revaluation task for fMRI, whereby participants needed to integrate changes in rewards with past knowledge to optimally replan decisions. As predicted, we found that (a) multi-voxel pattern evidence for off-task replay predicts subsequent replanning; (b) neural sensitivity to uncertainty predicts subsequent replay and replanning; (c) off-task hippocampus and anterior cingulate activity increase when revaluation is required. These findings elucidate how the brain leverages offline mechanisms in planning and goal-directed behavior under uncertainty.
Optimal Therapy Scheduling Based on a Pair of Collaterally Sensitive Drugs
Authors: Yoon Nara , Vander Velde Robert , Marusyk Andriy , Scott Jacob G. 
Published: October 2017

AbstractDespite major strides in the treatment of cancer, the development of drug resistance remains a major hurdle. One strategy which has been proposed to address this is the sequential application of drug therapies where resistance to one drug induces sensitivity to another drug, a concept called collateral sensitivity. The optimal timing of drug switching in these situations, however, remains unknown.To study this, we developed a dynamical model of sequential therapy on heterogeneous tumors comprised of resistant and sensitive cells. A pair of drugs (DrugA, DrugB) are utilized and are periodically switched during therapy. Assuming resistant cells to one drug are collaterally sensitive to the opposing drug, we classified cancer cells into two groups,ARandBR, each of which is a subpopulation of cells resistant to the indicated drug and concurrently sensitive to the other, and we subsequently explored the resulting population dynamics.Specifically, based on a system of ordinary differential equations forARandBR, we determined that the optimal treatment strategy consists of two stages: an initial stage in which a chosen effective drug is utilized until a specific time point,T, and a second stage in which drugs are switched repeatedly, during which each drug is used for a relative duration (i.e.fΔt-long forDrugAand (1 –f) Δt-long forDrugBwith 0 ≤f≤ 1 and Δt≥ 0). We prove that the optimal duration of the initial stage, in which the first drug is administered,T, is shorter than the period in which it remains effective in decreasing the total population, contrary to current clinical intuition.We further analyzed the relationship between population makeup,, and the effect of each drug. We determine a critical ratio, which we term, at which the two drugs are equally effective. As the first stage of the optimal strategy is applied,changes monotonically toand then, during the second stage, remains atthereafter.Beyond our analytic results, we explored an individual based stochastic model and presented the distribution of extinction times for the classes of solutions found. Taken together, our results suggest opportunities to improve therapy scheduling in clinical oncology.
Competitive learning modulates memory consolidation during sleep
Authors: Antony James W. , Cheng Larry Y. , Pacheco Paula , Paller Ken A. , Norman Kenneth A. 
Published: October 2017

AbstractCompetition between memories can cause weakening of those memories. Here we investigated memory competition during sleep by presenting auditory cues that had been linked to two distinct picture-location pairs during wake. We manipulated competition during learning by requiring subjects to rehearse item pairs associated with the same sound either competitively (choosing to rehearse one over the other, leading to greater competition) or separately; we hypothesized that greater competition during learning would lead to greater competition when memories were cued during sleep. With separate-pair learning, we found that cueing benefited spatial retention. With competitive-pair learning, no benefit of cueing was observed on retention, but cueing impaired retention of well-learned pairs (where we expected strong competition). During sleep, post-cue beta power (16-30 Hz) indexed competition-based weakening and forgetting, whereas sigma power (11-16 Hz) indexed memory strengthening. These findings show that memory consolidation during sleep fundamentally engages competition and selective memory weakening.
Fast Virome Explorer: A Pipeline for Virus and Phage Identification and Abundance Profiling in Metagenomics Data
Authors: Tithi Saima Sultana , Jensen Roderick V. , Zhang Liqing 
Published: October 2017

AbstractIdentifying viruses and phages in a metagenomics sample has important implication in improving human health, preventing viral outbreaks, and developing personalized medicine. With the rapid increase in data files generated by next generation sequencing, existing tools for identifying and annotating viruses and phages in metagenomics samples suffer from expensive running time. In this paper, we developed a stand-alone pipeline, FastViromeExplorer, for rapid identification and abundance quantification of viruses and phages in big metagenomic data. Both real and simulated data validated FastViromeExplorer as a reliable tool to accurately identify viruses and their abundances in large data, as well as in a time efficient manner.
Hunters or gardeners? Linking community structure and function of trap-associated microbes to the nutrient acquisition strategy of a carnivorous plant
Authors: Sirová Dagmara , Bárta Jiří , Šimek Karel , Posch Thomas , Pech Jiří , Stone James , Borovec Jakub , Adamec Lubomír , Vrba Jaroslav 
Published: October 2017

AbstractAll higher eukaryotes live in a relationship with diverse microorganisms which colonize their bodily surfaces; plants are no exception. However, we still lack a satisfactory understanding of how these loosely associated microbiomes with immense diversity and functional potential interact with their hosts or how these interactions shape processes within populations and ecosystems. There is considerable similarity between microbial communities colonizing plant surfaces such as roots, and those of the animal gut. This often overlooked parallel allows us to look at microbial as well as host ecophysiology from a fresh perspective. The traps of carnivorous plants are sophisticated digestive organs and interface environments between the supply and the demand for nutrients. We selected the miniature ecosystem in the traps of aquatic carnivorousUtriculariaplants as our model system. By assessing the trap-associated microbial community structure, diversity, function, as well as the nutrient recycling potential of bacterivory, we gained insight into the nutrient acquisition strategies of theUtriculariahosts. We conclude that trap ecophysiological function is in many aspects highly analogous to that of the herbivore gut and centers around complex microbial consortia, which act synergistically to covert complex organic matter, often of algal origin, into a source of nutrients for the plants.
A radial pillar device (RAPID) for continuous and high-throughput separation of multi-sized particles
Authors: Mehendale Ninad , Sharma Oshin , D’Costa Claudy , Paul Debjani 
Published: October 2017

AbstractPillar-based microfluidic sorting devices are preferred for isolation of rare cells due to their simple designs and passive operation. Dead-end pillar filters can efficiently capture large rare cells, such as, circulating tumor cells (CTCs), nucleated red blood cells (NRBCs), etc., but they get clogged easily. Cross flow filters are preferred for smaller rare particles (e.g. separating bacteria from blood), but they need additional buffer inlets and a large device footprint for efficient operation. We have designed a new microparticle separation device i.e.RadialPillarDevice (RAPID) that combines the advantages of dead-end and cross flow filters. RAPID can simultaneously isolate both large and small rare particles from a mixed population, while functioning for several hours without clogging. We have achieved simultaneous separation of 10µm and 2µm polystyrene particles from a mixture of 2µm, 7µm and 10µm beads. RAPID achieved average separation purity and recovery in excess of ⟂ 90%. The throughput of our device (⟂ 3ml/min) is 10 and 100 times higher compared to cross flow and dead-end filters respectively, thereby justifying the name RAPID.
Assessing Selectivity in the Basal Ganglia: The “Gearbox” Hypothesis
Authors: Fountas Zafeirios , Shanahan Murray 
Published: October 2017

AbstractDespite experimental evidence, the literature so far contains no systematic attempt to address the impact of cortical oscillations on the ability of the basal ganglia (BG) to select. In this study, we employed a state-of-the-art spiking neural model of the BG circuitry and investigated the effectiveness of this circuitry as an action selection device. We found that cortical frequency, phase, dopamine and the examined time scale, all have a very important impact on this process. Our simulations resulted in a canonical profile of selectivity, termed selectivity portraits, which suggests that the cortex is the structure that determines whether selection will be performed in the BG and what strategy will be utilized. Some frequency ranges promote the exploitation of highly salient actions, others promote the exploration of alternative options, while the remaining frequencies halt the selection process. Based on this behaviour, we propose that the BG circuitry can be viewed as the “gearbox” of action selection. Coalitions of rhythmic cortical areas are able to switch between a repertoire of available BG modes which, in turn, change the course of information flow within the cortico-BG-thalamo-cortical loop. Dopamine, akin to “control pedals”, either stops or initiates a decision, while cortical frequencies, as a “gear lever”, determine whether a decision can be triggered and what type of decision this will be. Finally, we identified a selection cycle with a period of around 200ms, which was used to assess the biological plausibility of the popular cognitive architectures.Author summaryOur brains are continuously called to select the most appropriate action between alternative competing choices. A plethora of evidence and theoretical work indicates that a fundamental brain region called the basal ganglia might be the locus where this competition occurs. But how is the winning choice determined each time? Using a detailed computational model, based on neurophysiological properties of this region, we suggest that, whereas the basal ganglia might indeed contain the circuitry of action selection, the cerebral cortex is, in fact, the brain region that dictates this process. Similarly to a gearbox in a car, the basal ganglia provide modes for the exploitation of the safest option (forward gears), exploration of alternative options (reverse gear) and a neutral state, in case that the selection process needs to be halted. Our results further indicate that the instructions for mode-switching are relayed to the basal ganglia through specific low frequencies of oscillations within cortical areas. Finally, we provide estimations for the frequency ranges that can be used to activate each selectivity mode, as well as the duration of the selection process under various conditions.
Partial restoration of mutational robustness after addition of genetic polymorphism and in the presence of sexual selection
Authors: Nieberding Caroline M. , San Martin Gilles , Saenko Suzanne , Allen Cerisse E. , Brakefield Paul M. , Visser Bertanne 
Published: October 2017

AbstractThe interaction between mutational (i.e. genetic) robustness, cryptic genetic variation and epistasis is currently under much debate, as is the question whether mutational robustness evolved under direct selection or as a by-product of environmental robustness. Here we report that mutational robustness was restored in a mutant line of the butterflyBicyclus anynanaafter the spontaneous mutation,comet, appeared in a genetically polymorphic wild type population. Thecometmutation modified two phenotypic traits known to be under sexual selection in this butterfly: the dorsal forewing eyespot, which is normally round, but became ‘comet’-shaped, and the androconia, the structures producing the male sex pheromone, which were reduced in size. Thecometmutant line remained phenotypically stable for ∼7 seven years, but when outcrossed to the genetically polymorphic wild type population, the outcrossedcometline surprisingly recovered the wild type phenotype within 8 generations. This suggests that mutational robustness against thecometmutation was recovered in thecometoutcrossed line by epistatic interactions with the genetic polymorphism originating from wild types. The extent of wild type phenotype recovery in thecometoutcrossed line was trait- and developmental temperature-dependent, such that mutational robustness was partially recovered at high, but not at low developmental temperatures. We hypothesized that sexual selection through mate choice, which is sex-reversed between developmental temperatures in this butterfly, could produce mutational robustness at a high (but not at a low) temperature. Females are the choosy sex and exert stabilizing or directional selection on male secondary sexual wing traits but only at higher temperatures. Male mating success experiments under semi-natural conditions then revealed that males with the typicalcometmutant phenotype suffered from lower mating success compared to wild type males, while mating success ofcometmales resembling wild types was partially restored. Altogether, we document the roles of cryptic genetic variation and epistasis in restoration of mutational robustness against a spontaneous mutation with known fitness effects, and we provide experimental evidence, for the first time to our knowledge, that sexual selection can produce mutational robustness.