Miracle-dz/UniFAR-FTUs huggingface dataset:
Site‐specific basal body duplication in Chlamydomonas

Correct centriole/basal body positioning is required for numerous biological processes, yet how the cell establishes this positioning is poorly understood. Analysis of centriolar/basal body duplication provides a key to understanding basal body positioning and function. Chlamydomonas basal bodies contain structural features that enable specific triplet microtubules to be specified. Electron tomography of cultures enriched in mitotic cells allowed us to follow basal body duplication and identify a specific triplet at which duplication occurs. Probasal bodies elongate in prophase, assemble transitional fibers (TF) and are segregated with a mature basal body near the poles of the mitotic spindle. A ring of nine‐singlet microtubules is initiated at metaphase, orthogonal to triplet eight. At telophase/cytokinesis, triplet microtubule blades assemble first at the distal end, rather than at the proximal cartwheel. The cartwheel undergoes significant changes in length during duplication, which provides further support for its scaffolding role. The uni1‐1 mutant contains short basal bodies with reduced or absent TF and defective transition zones, suggesting that the UNI1 gene product is important for coordinated probasal body elongation and maturation. We suggest that this site‐specific basal body duplication ensures the correct positioning of the basal body to generate landmarks for intracellular patterning in the next generation. © 2013 Wiley Periodicals, Inc.
Adaptation to the Primary User CSI in Cognitive Radio Sensing and Access

In Cognitive Radio (CR) networks, multiple secondary network users (SUs) attempt to communicate over wide potential spectrum without causing significant interference to the Primary Users (PUs). A spectrum sensing algorithm is a critical component of any sensing strategy. Performance of conventional spectrum detection methods is severely limited when the average SNR of the fading channel between the PU transmitter and the SU sensor is low. Cooperative sensing and advanced detection techniques only partially remedy this problem. A key limitation of conventional approaches is that the sensing threshold is determined from the miss detection rate averaged over the fading distribution. In this paper, the threshold is adapted to the instantaneous PU-to-SU Channel State Information (CSI) under the prescribed collision probability constraint, and a novel sensing strategy design is proposed for overlay CR network where the instantaneous false alarm probability is incorporated into the belief update and the reward computation. It is demonstrated that the proposed sensing approach improves SU confidence, randomizes sensing decisions, and significantly improves SU network throughput while satisfying the collision probability constraint to the PUs in the low average PU-to-SU SNR region. Moreover, the proposed adaptive sensing strategy is robust to mismatched and correlated fading CSI and improves significantly on conventional cooperative sensing techniques. Finally, joint adaptation to PU channel gain and SU link CSI is explored to further improve CR throughput and reduce SU collisions.
Field Estimates of Attraction of Ceratitis capitata to Trimedlure and Bactrocera dorsalis (Diptera: Tephritidae) to Methyl Eugenol in Varying Environments

ABSTRACT Measuring and modeling the attractiveness of semiochemical-baited traps is of significant importance to detection, delimitation, and control of invasive pests. Here, we describe the results of field mark—release—recapture experiments with Ceratitis capitata (Wiedemann) and Bactrocera dorsalis (Hendel) to estimate the relationship between distance from a trap baited with trimedlure and methyl eugenol, respectively, and probability of capture for a receptive male insect. Experiments were conducted using a grid of traps with a central release point at two sites on Hawaii Island, a Macadamia orchard on the East side of the island and a lava field on theWest side.We found that for B. dorsalis and methyl eugenol there is a 65% probability of capture at ∼36m from a single trap, regardless of habitat. For C. capitata, we found a 65% probability of capture at a distance of ∼14m from a single trap in the orchard and 7 m in the lava field. We also present results on the spatial and temporal pattern of recaptures. The attraction data are analyzed via a hyperbolic secant-based capture probability model.
Japanese encephalitis

Japanese encephalitis (JE) is an infectious disease of the central nervous system caused by Japanese encephalitis virus (JEV), a zoonotic mosquito-borne flavivirus. JEV is prevalent in much of Asia and the Western Pacific, with over 4 billion people living at risk of infection. In the absence of antiviral intervention, vaccination is the only strategy to develop long-term sustainable protection against JEV infection. Over the past half-century, a mouse brain-derived inactivated vaccine has been used internationally for active immunization. To date, however, JEV is still a clinically important, emerging, and re-emerging human pathogen of global significance. In recent years, production of the mouse brain-derived vaccine has been discontinued, but 3 new cell culture-derived vaccines are available in various parts of the world. Here we review current aspects of JEV biology, summarize the 4 types of JEV vaccine, and discuss the potential of an infectious JEV cDNA technology for future vaccine development.
Application of Associative Neural Networks for Prediction of Lipophilicity in ALOGPS 2.1 Program

This article provides a systematic study of several important parameters of the Associative Neural Network (ASNN), such as the number of networks in the ensemble, distance measures, neighbor functions, selection of smoothing parameters, and strategies for the user-training feature of the algorithm. The performance of the different methods is assessed with several training/test sets used to predict lipophilicity of chemical compounds. The Spearman rank-order correlation coefficient and Parzen-window regression methods provide the best performance of the algorithm. If additional user data is available, an improved prediction of lipophilicity of chemicals up to 2-5 times can be calculated when the appropriate smoothing parameters for the neural network are selected. The detected best combinations of parameters and strategies are implemented in the ALOGPS 2.1 program that is publicly available at http://www.vcclab. org/lab/alogps.
Microwave Assisted Extraction of Phenolic Compounds from Four Different Spices

Spices and herbs are known not only for their taste, aroma and flavour, but also for their medical properties and value. Both spices and herbs have been used for centuries in traditional medical systems to cure various kinds of illnesses such as common cold, diabetes, cough and cancers. The aim of this work was the comparison between two different extractive techniques in order to get qualitative and quantitative data regarding bioactive compounds of four different spices (Cinnamomum zeylanicum, Coriandrum sativum, Cuminum cyminum, Crocus sativus). The plants were extracted employing ultrasonication and microwave-assisted extractions. The efficiency of extraction of bioactive compounds obtained with the microwave extraction process was in general about four times higher than that resulting from sonication extraction. The various extracts obtained were analyzed for their antioxidant activity using ABTS, DPPH and FRAP assays and for their total polyphenolic content. It can be concluded that microwave-assisted extractions provide significant advantages in terms of extraction efficiency and time savings.
Magnetically induced deep brain stimulation of neuronal firing for pain relief

Pain, either acute pain or chronic pain, is usually treated/relieved by chemical means, in which nociceptive signals are blocked from transmitting into the pain registration sites in the brain. However, besides their side effects, chemical means of pain relief are not always effective, causing some serious clinical incidents like anesthesia awareness and chronic pains that are not treatable. A physical means of pain relief that physically modifies pain perception at the brain sites responsible for pain registration could be more effective, for both acute pain and chronic pain. In this paper a novel approach of magnetically induced deep brain modulation of neuronal firing is proposed for pain treatment/relief, in which pain treatment/relief is bioelectronics based and is non-invasive and free of side effects. A novel pulse magnetic field projector has been developed for pain relief through modulation of neuronal firing at the anterior cingulate cortex (ACC). It is based on the neuroscience findings that pain registration in the brain is closely related to the excitation of nociceptive neurons at the ACC, in which the nociceptive neuronal firing rate increases as pain gets more intense. The mechanism of pain relief in the proposed approach is to modify the nociceptive neuronal firing rate at the ACC by magnetically inducing a pulse electric field applying on the neurons in the ACC, hyperpolarizing the neurons that are firing at high frequency during pain perception, resulting in a low level firing rate associated to no pain. A parametric study has been carried out to determine the physical and technical parameters of the proposed approach. The feasibility of the approach has been verified by simulation with the modulation implemented on a reconstructed ACC LV pyramidal cell using Hodgkin-Huxley style model. Action potentials recorded in the soma indicated that the firing frequency can be modulated by the applied pulse electric field.
Spatial simulations of the Kelvin-Helmholtz instability in astrophysical jets. A partial stabilizati

Aims. The long term magnetohydrodynamic stability of magnetized transonic/supersonic jets is numerically investigated using a spatial approach. We focus on two-dimensional linearly-unstable slab configurations where the jet is embedded in a flow-aligned uniform magnetic field of weak amplitude. We compare our results with previous studies using a temporal approach where longitudinally periodic domains were adopted. Methods. The finite-volume based versatile advection code is used to solve the full set of ideal compressible MHD equations. We follow the development of Kelvin-Helmholtz modes that are driven by a white noise perturbation continuously introduced at the jet inlet. Results. No noticeable difference is observed in spatial simulations versus analogous temporal ones during the linear and early non-linear evolution of the configuration. However, in the case of transonic flows, a different long-term scenario occurs in our spatial runs. Indeed, after the large-scale disruption of the flow, a sheath region of enhanced magnetic field encompassing the jet core forms along the whole flow. This provides a partial stabilization mechanism leading to enhanced stability for later times, which is almost independent of the initial magnitude of the magnetic field. The implication of this mechanism for the stability of astrophysical jets is discussed.
Risk in Dynamic Arbitrage: The Price Effects of Convergence Trading

This paper studies the adverse price effects of convergence trading. I assume two assets with identical cash flows traded in segmented markets. Initially, there is gap between the prices of the assets, because local traders’ face asymmetric temporary shocks. In the absence of arbitrageurs, the gap remains constant until a random time when the difference across local markets disappears. While arbitrageurs’ activity reduces the price gap, it also generates potential losses: the price gap widens with positive probability at each time instant. With the increase of arbitrage capital on the market, the predictability of the dynamics of the gap decreases, and the arbitrage opportunity turns into a risky speculative bet. In a calibrated example we show that the endogenously created losses alone can explain episodes when arbitrageurs lose most of their capital in a relatively short time.
Magneto-Nanofluid Dynamics in Convergent-Divergent Channel and its Inherent Irreversibility

The effects of Cu-nanoparticles on the entropy generation of steady magnetohydrodynamic incompressible flow with viscous dissipation and Joule heating through convergent-divergent channel are analysed in this paper. The basic nonlinear partial differential equations are transformed into a system of coupled ordinary differential equations using suitable transformations which are then solved using power series with Hermite- Padé approximation technique. The velocity profiles, temperature distributions, entropy generation rates, Bejan number as well as the rate of heat transfer at the wall are presented in convergent-divergent channels for various values of nanoparticles solid volume fraction, Eckert number, Reynolds number and channel angle. A stability analysis has been performed for the shear stress which signifies that the lower solution branch is stable and physically realizable, whereas the upper solution branch is unstable. It is interesting to remark that the entropy generation of the system increases at the two walls as well as the heat transfer irreversibility is dominant there whereas the fluid friction irreversibility is dominant along the centreline of the channel.
Turing at SemEval-2017 Task 8: Sequential Approach to Rumour Stance Classification with Branch-LSTM

This paper describes team Turing’s submission to SemEval 2017 RumourEval: Determining rumour veracity and support for rumours (SemEval 2017 Task 8, Subtask A). Subtask A addresses the challenge of rumour stance classification, which involves identifying the attitude of Twitter users towards the truthfulness of the rumour they are discussing. Stance classification is considered to be an important step towards rumour verification, therefore performing well in this task is expected to be useful in debunking false rumours. In this work we classify a set of Twitter posts discussing rumours into either supporting, denying, questioning or commenting on the underlying rumours. We propose a LSTM-based sequential model that, through modelling the conversational structure of tweets, which achieves an accuracy of 0.784 on the RumourEval test set outperforming all other systems in Subtask A.
Planform, aero-structural and flight control optimization for tailless morphing aircraft

Tailless swept wing airplanes rely on variations of the spanwise lift distribution to achieve controllability in all axes. As every flight condition requires different control moments, the conventional discrete control surfaces will be practically continuously deflected, leading to drag penalties. Shape adaptation base on chordwise morphing can achieve continuous deformations of the wing profile, leading to local lift variations with minimum drag penalties. As the shape is varied continuously along the wingspan, the lift distribution can be tailored to each flight condition. Tailless aircraft appear therefore as prime candidates for morphing, as the attainable benefits are potentially significant. This work presents a methodology to determine the optimal planform, profile shape, and morphing structure for a tailless aircraft. The employed morphing concept is based on a distributed compliance structure, actuated by piezoelectric elements. The multidisciplinary optimization considers the static and dynamic aeroelastic behavior of the structure and aims to maximize the aerodynamic efficiency of the plane while guaranteeing its controllability by means of morphing. The potential of the resulting wing design is fully exploited by means of a second optimization process, which identifies the actuation configuration resulting in the highest aerodynamic efficiency for a wide variety of control moments.
Phylogenetic Analysis of a Human Isolate from the 2000 Israel West Nile virus Epidemic

Specimens from a patient of the 2000 Israel West Nile virus epidemic were analyzed by reverse transcription-polymerase chain reaction. Products corresponding to E, NS3, and NS5 sequences were amplified from cerebellar but not from cortical samples. Phylogenetic analyses indicated a closer relationship of this isolate to 1996 Romanian and 1999 Russian than to 1998-99 Israeli or 1999 New York isolates.
Selective Binding of FKBP12.6 by the Cardiac Ryanodine Receptor*

The calcium release channels (CRC)/ryanodine receptors of skeletal (Sk) and cardiac (C) muscle sarcoplasmic reticulum (SR) are hetero-oligomeric complexes with the structural formulas (ryanodine recepter (RyR)1 protomer)4(FKBP12)4 and (RyR2 protomer)4(FKBP12.6)4, respectively, where FKBP12 and FKBP12.6 are isoforms of the 12-kDa receptor for the immunosuppressant drug FK506. The sequence similarity between the RyR protomers and FKBP12 isoforms is 63 and 85%, respectively. Using 35S-labeled FKBP12 and 35S-labeled FKBP12.6 as probes to study the interaction with CRC, we find that: 1) analogous to its action in skeletal muscle sarcoplasmic reticulum (SkMSR), FK506 (or analog FK590) dissociates FKBP12.6 from CSR; 2) both FKBP isoforms bind to FKBP-stripped SkMSR and exchange with endogenously bound FKBP12 of SkMSR; and 3) by contrast, only FKBP12.6 exchanges with endogenously bound FKBP12.6 or rebinds to FKBP-stripped CSR. This selective binding appears to explain why the cardiac CRC is isolated as a complex with FKBP12.6, whereas the skeletal muscle CRC is isolated as a complex with FKBP12, although only FKBP12 is detectable in the myoplasm of both muscle types. Also, in contrast to the activation of the channel by removal of FKBP from skeletal muscle, no activation is detected in CRC activity in FKBP-stripped CSR. This differential action of FKBP may reflect a fundamental difference in the modulation of excitation-contraction coupling in heart versus skeletal muscle.
Schistosoma japonicum infection induces macrophage polarization

Abstract The role of macrophages (Mφ) as the first line of host defense is well accepted. These cells play a central role in orchestrating crucial functions during schistosomal infection. Thus, understanding the functional diversity of these cells in the process of infection as well as the mechanisms underlying these events is crucial for developing disease control strategies. In this study, we adopted a Mφ polarization recognition system. M1 macrophage was characterized by expressing CD16/32, IL-12 and iNOS. M2 macrophage was characterized by expressing CD206, IL-10 and arg-1. In vivo (mouse peritoneal macrophages of different infection stages were obtained) and in vitro (different S. japonicum antigens were used to stimulate RAW264.7) were characterized by using the above mentioned system. NCA and ACA stimulated RAW264.7 express significantly higher levels of IL-12 while significantly higher levels of IL-10 were detected after soluble egg antigen (SEA) stimulation. The results showed that dramatic changes of antigen in the microenvironment before and after egg production led to macrophage polarization. Furthermore, through TLR blocking experiments, the TLR4 signaling pathway was found to play a role in the process of macrophage polarization toward M1. Our data suggest that macrophage polarization during S. japonicum infection had significant effects on host immune responses to S. japonicum.
The Toronto Hospital Alertness Test scale: relationship to daytime sleepiness, fatigue, and symptoms of depression and anxiety

Objective The Toronto Hospital Alertness Test (THAT) scale was designed to measure alertness, defined as the capacity of the mind to respond appropriately to external and internal stimuli. The present study’s aim is to determine normative values of alertness on the THAT and to explore the relationship among excessive daytime sleepiness, fatigue, depressive symptoms, and alertness. Methods Normative data were collected from 60 healthy males and females. To explore the relationship among alertness, daytime sleepiness, fatigue, depression, and anxiety, data were collected from charts of sleep clinic patients. All study subjects completed measures for fatigue, sleepiness, depressive symptoms, and anxiety. Results The average score on the THAT was 34.9±7.2 (range 22–50) for the control group. The cutoff score for the THAT, indicative of clinically significant reduced alertness, was determined to be ≤20.5 (mean −2 SD). THAT alertness scores were found to be modestly, significantly, and negatively correlated with fatigue levels (r=−0.39, P<0.001), depressive symptoms (r=−0.53, P<0.001), and anxiety symptoms (r=−0.41, P<0.001). No correlations were found between alertness levels and daytime sleepiness. Regression analyses revealed a significant model (F=19.9, P<0.001, adjusted R2=0.35) with depressive symptoms (P<0.001) and fatigue (P=0.006) emerging as the only significant predictors of scores on the THAT. Conclusion The findings of this study support that sleepiness is not the same as poor alertness. Depressive symptoms and fatigue, but not sleepiness, were found to have a strong and significant impact on levels of alertness. This is the first study to link poor alertness to depressive symptoms.
Expert-Built and Collaboratively Constructed Lexical Semantic Resources

Knowledge about words, their meanings, and their relations to other words contained in lexical semantic resources is of particular interest for the automatic processing of human language. In the last decades, expert-built lexical semantic resources such as WordNet have been utilized in a vast number of natural language processing (NLP) tasks. Recently, collaboratively constructed resources such as the online encyclopedia Wikipedia with its exceptional scale and Wiktionary, a combination of dictionary and thesaurus, have been discovered as valuable substitutes for expert-built resources. In this study, we first introduce diverse types of lexical semantic resources with respect to their content and structure. We identify the differences between expert-built and collaboratively constructed resources and compare WordNet, Wiktionary, and Wikipedia. We provide a comprehensive overview of the lexical semantic knowledge therein and discuss their assets and drawbacks. Finally, we review work on orchestrating different resources in order to combine their strengths and explore their use in major NLP applications.