Miracle-dz/UniFAR-FTUs huggingface dataset:
Team UKNLP at TREC 2017 Precision Medicine Track: A Knowledge-Based IR System with Tuned Query-Time Boosting

—This paper describes the system architecture of the University of Kentucky Natural Language Processing (UKNLP) team’s entry for the TREC 2017 Precision Medicine Track. The goal of the challenge is to retrieve useful precision medicine-related information (abstracts, clinical trials) for the given synthetic cancer patient cases, each of which consists of a neoplastic condition, genetic variants, demographic details, and any additional information (e.g., comorbidities). We explored query expansion techniques using well-known broad knowledge sources such as the Uniﬁed Medical Language System (UMLS) and the Medical Subject Headings (MeSH) for each abstract, and additional specialized sources such as the Catalogue Of Somatic Mutations In Cancer (COSMIC) database, which allowed us to construct boosted queries. We conducted several experiments with model averaging techniques and our ﬁnal system architecture placed 6th (in terms of infNDCG and R-prec) among 29 teams that submitted runs to the scientiﬁc abstract retrieval task.
Caught in the act – protein adaptation and the expanding roles of the PACS proteins in tissue homeostasis and disease

ABSTRACT Vertebrate proteins that fulfill multiple and seemingly disparate functions are increasingly recognized as vital solutions to maintaining homeostasis in the face of the complex cell and tissue physiology of higher metazoans. However, the molecular adaptations that underpin this increased functionality remain elusive. In this Commentary, we review the PACS proteins – which first appeared in lower metazoans as protein traffic modulators and evolved in vertebrates to integrate cytoplasmic protein traffic and interorganellar communication with nuclear gene expression – as examples of protein adaptation ‘caught in the act’. Vertebrate PACS-1 and PACS-2 increased their functional density and roles as metabolic switches by acquiring phosphorylation sites and nuclear trafficking signals within disordered regions of the proteins. These findings illustrate one mechanism by which vertebrates accommodate their complex cell physiology with a limited set of proteins. We will also highlight how pathogenic viruses exploit the PACS sorting pathways as well as recent studies on PACS genes with mutations or altered expression that result in diverse diseases. These discoveries suggest that investigation of the evolving PACS protein family provides a rich opportunity for insight into vertebrate cell and organ homeostasis. Summary: We summarize how the vertebrate PACS proteins acquired specific motifs that enabled them to function as metabolic switches that integrate cytoplasmic membrane trafficking and interorganellar communication with nuclear gene expression.
THA-A Hybrid Approach for Rule Induction System using Rough Set Theory, Genetic Algorithm and Boolean algebra

The major process of discovering knowledge in database is the extraction of rules from classes of data. One of the major obstacles in performing rule induction from training data set is the inconsistency of information about a problem domain. In order to deal with this problem, many theories and technology have been developed in recent years. Among them the most successful ones are decision tree, fuzzy set, Dempster-Shafer theory of evidence. Unfortunately, all are referring to either prior or posterior probabilities. The rough set concept proposed by Pawlak is a new mathematical approach to inconsistent, vagueness, imprecision and uncertain data. In this paper we have proposed a hybridized model THA (Training dataset on hybrid approach) which combines rough set theory, genetic algorithm and Boolean algebra for discovering certain rules and also induce probable rules from inconsistent information. The experimental result shows that the projected method induced maximal generalized rules efficiently. The hybridized model was validated using the data obtained from observational study.
Changes in Self-Rated Health During the Transition to Retiring Living Among Medicare Managed-Care Recipients

ABSTRACT Moving into a retirement community may be precipitated by or bring about changes in health status. We hypothesized that moving into a retirement community would be associated with a decline in self-rated health (SRH), but that health-related factors would mitigate this association. We analyzed data from 58,272 participants in Cohort 3 of the Medicare Health Outcome Survey. Individuals answered questions regarding living status in 2000 and 2002. Those who moved into a retirement community were compared with those who did not. The primary outcome was change in SRH. We created adjusted and unadjusted models. A total of 2,520 participants (4.4%) moved into retirement communities between 2000 and 2002. There were no substantial differences in the mean change in SRH between those who moved and those who did not. In adjusted and unadjusted models, moving was not significantly associated with changes in SRH. In an analysis stratified by SRH, only those with the best SRH had a significant decline in SRH during the move. SRH mainly remained stable for most people regardless of moving into a retirement community. These findings argue against environmental context being a main determinant of self-perceived health status among older adults.
A negotiation based dynamic pricing heuristic in cloud computing

Over the years, cloud computing has emerged as a good business platform for IT related services. In cloud, prices of computing resource act as lever to control the utilisation of the resources. That is the reason, when the number of cloud customers started increasing, cloud service providers started offering resources with various pricing schemes to attract customers. This work proposes a negotiation based heuristic for dynamic pricing that considers behaviour of both the service provider and the customer and tries to optimally satisfy both for pricing. Both customer and provider are reluctant to reveal information about their utility to each other. The designed utility function for provider considers payment offered by customer and opinion of the provider about customer. Similarly, utility function for customer considers price offered by the provider and opinion of customer about provider. This will encourage both to offer their true value. Performance study indicates that the proposed method performs well and is a potential candidate for its implementation in a real cloud.
Exploiting Readymades in Linguistic Creativity: A System Demonstration of the Jigsaw Bard

Large lexical resources, such as corpora and databases of Web ngrams, are a rich source of pre-fabricated phrases that can be reused in many different contexts. However, one must be careful in how these resources are used, and noted writers such as George Orwell have argued that the use of canned phrases encourages sloppy thinking and results in poor communication. Nonetheless, while Orwell prized home-made phrases over the readymade variety, there is a vibrant movement in modern art which shifts artistic creation from the production of novel artifacts to the clever reuse of readymades or objets trouves. We describe here a system that makes creative reuse of the linguistic readymades in the Google ngrams. Our system, the Jigsaw Bard, thus owes more to Marcel Duchamp than to George Orwell. We demonstrate how textual readymades can be identified and harvested on a large scale, and used to drive a modest form of linguistic creativity.
Sparse reconstruction algorithms for nonlinear microwave imaging

This paper presents a two-step inverse process which allows sparse recovery of the unknown (complex) dielectric profiles of scatterers for nonlinear microwave imaging. The proposed approach is applied to a nonlinear inverse scattering problem arising in microwave imaging and correlated with joint sparsity which gives multiple sparse solutions that share a common nonzero support. Numerical results demonstrate the potential of the proposed two step inversion approach when compared to existing sparse recovery algorithm for the case of small scatterers.
A V-Band Doherty Power Amplifier Based on Voltage Combination and Balance Compensation Marchand Balun

This paper presents a <inline-formula> <tex-math notation="LaTeX">$V$ </tex-math></inline-formula>-band Doherty power amplifier (PA) which is implemented in a standard 65-nm CMOS technology. The voltage combination technique is used to realize the millimeter-wave Doherty PA without the <inline-formula> <tex-math notation="LaTeX">$\lambda $ </tex-math></inline-formula>/4 transmission lines. A Marchand balun with balance compensation is designed to combine the output power with reduced power loss. Moreover, a nonlinear driver is used to drive the peaking amplifier to enhance the output power and the turn-on speed of it. The power-added efficiency (PAE) of this PA at the 6-dB power back-off point is 8.7% and the peak PAE reaches 16.8%. The small signal power gain is 18 dB, and the maximum output power is 14.9 dBm. The core circuit only costs 0.195 mm<sup>2</sup> chip area as no <inline-formula> <tex-math notation="LaTeX">$\lambda $ </tex-math></inline-formula>/4 transmission lines.
Estimating and Measuring Methods of Residual Stresses Using Inherent strain Distribution Described as Functions. (Report 4). Function Expression for Inherent Strains in Fillet Welds and Its Accuracy.

In this paper, three dimensional residual stresses due to single pass and multipass fillet welding are analysed by thermal elastic-plastic Finite Element Method. Then, inherent strain distributions produced in fillet welds are expressed by series function with good accuracy. Based on the results of series function, a very simple distribution pattern of inherent strains is proposed and described as functions which only has a few unknown parameters. To determine these parameters by experiments, required measurements will be greatly reduced.
Measuring the charge density along the radius in concentric cylinders configuration by sensing system

The measurement of space charge density caused by the corona discharge around the overhead transmission line is a tough problem till nowadays. For this problem, a system for measuring the one-dimensional (1D) distribution of space charge density in a coaxial cylinder model under negative corona discharge in ambient air is developed. This system is a scale model which can provide research basis for actual overhead line measurement. The system consists of acoustic emission, space charge generation, and signal-receiving systems. The sound wave of an ultrasonic transducer is used to stimulate space charge generated by a small corona cage, and the applied voltage ranges from −34 kV to −38 kV. Charge vibration produces an electrical field (E-field) that can be measured with an E-field antenna. After obtaining the E-field signal, the adaptive noise cancellation method is adopted to eliminate noise interference so that the accuracy of charge density can be improved. The Townsend's analysis solution is used to calculate the theoretical value of space charge density. Experimental results are consistent with the simulation value and thus confirm the validity of the proposed adaptive noise cancellation method and sensing system.
Understanding and sharing intentions: The origins of cultural cognition

We propose that the crucial difference between human cognition and that of other species is the ability to participate with others in collaborative activities with shared goals and intentions: shared intentionality. Participation in such activities requires not only especially powerful forms of intention reading and cultural learning, but also a unique motivation to share psychological states with others and unique forms of cognitive representation for doing so. The result of participating in these activities is species-unique forms of cultural cognition and evolution, enabling everything from the creation and use of linguistic symbols to the construction of social norms and individual beliefs to the establishment of social institutions. In support of this proposal we argue and present evidence that great apes (and some children with autism) understand the basics of intentional action, but they still do not participate in activities involving joint intentions and attention (shared intentionality). Human children's skills of shared intentionality develop gradually during the first 14 months of life as two ontogenetic pathways intertwine: (1) the general ape line of understanding others as animate, goal-directed, and intentional agents; and (2) a species-unique motivation to share emotions, experience, and activities with other persons. The developmental outcome is children's ability to construct dialogic cognitive representations, which enable them to participate in earnest in the collectivity that is human cognition.
Transmission Systems Open-loop analysis and self-noise performance of an NDA synchroniser for carrier-independent symbol timing recovery at baud rate

Feedback loops for symbol timing recovery are an attractive solution for continuous transmission of data, where rapid acquisition is not so important as in burst-mode systems. In this context, carrier-independent non-data-aided (NDA) timing error detectors, operated at only one sample per symbol, can be a most interesting option. Assuming M-ary PSK signals and focusing on a linearised loop model for analytical work, such an algorithm has been discussed already in the technical literature. On the other hand, the linear approach does not apply for larger deviations from the stable equilibrium point as they are encountered during initial acquisition. In this case, the detector characteristic (S-curve) must be known. Since not available from the open literature, it is derived in this paper not only for PSK but for linear modulation schemes in general. The slope in the stable equilibrium point is given in closed form such that the linearised tracker can be specified immediately. Furthermore, it turned out that the complexity of the detector, but also the computation of both S-curve and slope, is most simple for a special value of the additional design parameter characterizing the algorithm. Based on this, the self-noise variance is derived in closed form. For M-PSK schemes, it is proved that they experience no jitter floor due to pattern (data) noise. On the other hand, for non-constant modulus signals, like QAM or APSK constellations, it is shown that the performance is proportional to the loop bandwidth. Finally, a detailed comparison with NDA maximum-likelihood and Gardner algorithm, as standard method for carrier-blind NDA tracking, is presented. Copyright © 2009 John Wiley & Sons, Ltd.
Calcium sensor regulation of the CaV2.1 Ca2+ channel contributes to long-term potentiation and spatial learning

Significance Learning and memory are caused by changes in strength of communication between neurons at synapses. Both brief changes (short-term plasticity) and long-lasting changes (long-term plasticity) are important. Synaptic transmission is initiated by calcium channels, which are regulated by calcium-sensor proteins that induce short-term synaptic plasticity. We studied genetically modified mice with a mutation in the binding site for calcium-sensor proteins on calcium channels, which alters short-term synaptic plasticity. Surprisingly, we found that synapses in the hippocampus of these mice also have impaired long-term potentiation. In addition, these mutant mice have impaired spatial learning and memory. Our results show that disruption of calcium-channel regulation by calcium-sensor proteins alters both short-term and long-term plasticity, and these changes impair spatial learning and memory. Many forms of short-term synaptic plasticity rely on regulation of presynaptic voltage-gated Ca2+ type 2.1 (CaV2.1) channels. However, the contribution of regulation of CaV2.1 channels to other forms of neuroplasticity and to learning and memory are not known. Here we have studied mice with a mutation (IM-AA) that disrupts regulation of CaV2.1 channels by calmodulin and related calcium sensor proteins. Surprisingly, we find that long-term potentiation (LTP) of synaptic transmission at the Schaffer collateral-CA1 synapse in the hippocampus is substantially weakened, even though this form of synaptic plasticity is thought to be primarily generated postsynaptically. LTP in response to θ-burst stimulation and to 100-Hz tetanic stimulation is much reduced. However, a normal level of LTP can be generated by repetitive 100-Hz stimulation or by depolarization of the postsynaptic cell to prevent block of NMDA-specific glutamate receptors by Mg2+. The ratio of postsynaptic responses of NMDA-specific glutamate receptors to those of AMPA-specific glutamate receptors is decreased, but the postsynaptic current from activation of NMDA-specific glutamate receptors is progressively increased during trains of stimuli and exceeds WT by the end of 1-s trains. Strikingly, these impairments in long-term synaptic plasticity and the previously documented impairments in short-term synaptic plasticity in IM-AA mice are associated with pronounced deficits in spatial learning and memory in context-dependent fear conditioning and in the Barnes circular maze. Thus, regulation of CaV2.1 channels by calcium sensor proteins is required for normal short-term synaptic plasticity, LTP, and spatial learning and memory in mice.
Centre Stage: How Social Network Position Shapes Linguistic Coordination

In conversation, speakers tend to echo the linguistic style of the person they are interacting with. This paper contributes to a body of work that addresses how this linguistic style coordination is affected by the social context in which the interaction occurs. In particular, we investigate the effect that an agent’s social network centrality has on the coordination exhibited in replies to their utterances. We find that linguistic coordination is positively correlated with social network centrality and that this effect is greater than previous results showing a similar connection between statusbased power and linguistic coordination. We conjecture that the social value of coordination may reside in the wish to conform to the linguistic norms of a community.
Early Childhood Education to Promote Health Equity: A Community Guide Systematic Review.

CONTEXT Children in low-income and racial and ethnic minority families often experience delays in development by 3 years of age and may benefit from center-based early childhood education. DESIGN A meta-analysis on the effects of early childhood education by Kay and Pennucci best met Community Guide criteria and forms the basis of this review. RESULTS There were increases in intervention compared with control children in standardized test scores (median = 0.29 SD) and high school graduation (median = 0.20 SD) and decreases in grade retention (median = 0.23 SD) and special education assignment (median = 0.28 SD). There were decreases in crime (median = 0.23 SD) and teen births (median = 0.46 SD) and increases in emotional self-regulation (median = 0.21 SD) and emotional development (median = 0.04 SD). All effects were favorable, but not all were statistically significant. Effects were also long-lasting. CONCLUSIONS Because many programs are designed to increase enrollment for high-risk students and communities, they are likely to advance health equity.
Mutualism Persistence and Abandonment during the Evolution of the Mycorrhizal Symbiosis

Mutualistic symbioses with mycorrhizal fungi are widespread in plants. The majority of plant species associate with arbuscular mycorrhizal (AM) fungi. By contrast, the minority associate with ectomycorrhizal (EM) fungi, have abandoned the symbiosis and are nonmycorrhizal (NM), or engage in an intermediate, weakly AM symbiosis (AMNM). To understand the processes that maintain the mycorrhizal symbiosis or cause its loss, we reconstructed its evolution using a ∼3,000-species seed plant phylogeny integrated with mycorrhizal state information. Reconstruction indicated that the common ancestor of seed plants most likely associated with AM fungi and that the EM, NM, and AMNM states descended from the AM state. Direct transitions from the AM state to the EM and NM states were infrequent and generally irreversible, implying that natural selection or genetic constraint could promote stasis once a particular state evolved. However, the evolution of the NM state was more frequent via an indirect pathway through the AMNM state, suggesting that weakening of the AM symbiosis is a necessary precursor to mutualism abandonment. Nevertheless, reversions from the AMNM state back to the AM state were an order of magnitude more likely than transitions to the NM state, suggesting that natural selection favors the AM symbiosis over mutualism abandonment.
The right insular cortex infarction: a critical factor for mortality?

Sirs, We read the interesting clinical report by Hanne et al. [1], who found a relationship between right insular cortex (Ic) infarction and mortality after ischaemic stroke. However, data on cause of death were not collected prospectively in the underlying database. Several studies have shown that the cardiovascular system is regulated by a central cortical autonomic network consisting of the Ic, anterior cingulate gyrus and amygdala [2]. Because the Ic is located in the region of the middle cerebral arteries, its structure tends to be exposed to a higher risk of stroke [2]. Many studies have shown the relationship between Ic infarction and autonomic nervous system abnormality. Tokgozoglu et al. [3] evaluated the differential impacts of stroke localization on heart rate variability measures in 62 patients with ischaemic stroke and 62 controls matched for age and gender. Stroke patients had significantly decreased low frequency (LF), high frequency (HF) and standard deviation of all normal-to-normal (SDNN) R wave to R wave (RR) intervals. Specifically, patients with right Ic lesion had significantly lower values of LF, HF and SDNN than those with other localizations [3]. In addition, Colivicchi et al. [4] performed 24-h Holter electrocardiogram monitoring in 103 consecutive patients with first-ever acute ischaemic stroke. Compared with all other stroke patients, patients with right Ic involvement had significantly lower values of SDNN, standard deviation of the root mean square of differences of adjacent normal-to-normal RR intervals, and higher LF/HF. Right Ic lesion was associated with more premature ventricular contractions and premature supraventricular contractions than left-sided ischaemia and with more non-sustained ventricular tachycardia and supraventricular tachyarrhythmias than all other localizations [4]. During the 1-year follow-up in 208 consecutive patients with first-ever acute ischaemic stroke, right Ic lesion, lower SDNN values and the presence of non-sustained ventricular tachycardia were significant predictors for mortality at 1 year [5]. These results suggest that ischaemia including the right Ic is associated with decreased autonomic nervous system activity. And right insular infarction has led to a decrease in parasympathetic nervous activity and shifted the sympathovagal balance towards predominant sympathetic tone. Thus, it was suggested that ventricular tachycardia due to relatively higher sympathetic nervous system activity is associated with mortality in patients with right Ic infarction. Until now, there have been few reports assessing the Ic and autonomic nervous system activity in relation to hemispheric laterality in a large study population. The data presented in the paper by Hanne et al. [1] would have much more importance if the exact mechanism underlying the relationship between the right Ic infarction and mortality were provided.