Miracle-dz/UniFAR-FTUs huggingface dataset:
Adverse Drug Event Detection in Tweets with Semi-Supervised Convolutional Neural Networks

Current Adverse Drug Events (ADE) surveillance systems are often associated with a sizable time lag before such events are published. Online social media such as Twitter could describe adverse drug events in real-time, prior to official reporting. Deep learning has significantly improved text classification performance in recent years and can potentially enhance ADE classification in tweets. However, these models typically require large corpora with human expert-derived labels, and such resources are very expensive to generate and are hardly available. Semi-supervised deep learning models, which offer a plausible alternative to fully supervised models, involve the use of a small set of labeled data and a relatively larger collection of unlabeled data for training. Traditionally, these models are trained on labeled and unlabeled data from similar topics or domains. In reality, millions of tweets generated daily often focus on disparate topics, and this could present a challenge for building deep learning models for ADE classification with random Twitter stream as unlabeled training data. In this work, we build several semi-supervised convolutional neural network (CNN) models for ADE classification in tweets, specifically leveraging different types of unlabeled data in developing the models to address the problem. We demonstrate that, with the selective use of a variety of unlabeled data, our semi-supervised CNN models outperform a strong state-of-the-art supervised classification model by +9.9% F1-score. We evaluated our models on the Twitter data set used in the PSB 2016 Social Media Shared Task. Our results present the new state-of-the-art for this data set.
Agonist-specific conformational changes in the yeast alpha-factor pheromone receptor

The yeast alpha-factor pheromone receptor is a member of the G-protein-coupled receptor family. Limited trypsin digestion of yeast membranes was used to investigate ligand-induced conformational changes in this receptor. The agonist, alpha-factor, accelerated cleavage in the third intracellular loop, whereas the antagonist, desTrp1,Ala3-alpha-factor, reduced the cleavage rate. Thus, the enhanced accessibility of the third intracellular loop is specific to the agonist. alpha-Factor inhibited cleavage weakly at a second site near the cytoplasmic terminus of the seventh transmembrane helix, whereas the antagonist showed a stronger inhibition of cleavage at this site and at another site in the C-terminal domain of the receptor. The alpha-factor-induced conformational changes appeared to be inherent properties of the receptor, as they were retained in G-protein-deficient mutants. Moreover, a mutant receptor (ste2-L236H) that affects the third loop and is defective for G-protein coupling retained the ability to undergo the agonist-induced conformational changes. These results are consistent with a model in which G-protein activation is limited by the availability of specific contacts between the G protein and the third intracellular loop of the receptor. The antagonist appears to promote a distinct conformational state that differs from either the unoccupied or the agonist-occupied state.
Comparison of computational methods for high dimensional item factor analysis

In this article we conduct a simulation study to compare several methods for estimating conrmatory and exploratory item factor analysis using the software programs Mplus and IRTPRO. When the number of factors is bigger than three or four the standard numerical integration methodology used for computing the maximum-likelihood estimates is intractable due to the exponentially large number of integration points needed to compute the likelihood. Several methods have been developed recently to overcome these computational problems however they have not been directly compared previously. In this paper we present a simulation study to compare maximum likelihood estimation based on Montecarlo integration, maximum likelihood estimation based on Metropolis-Hastings Robbins-Monro algorithm, maximum likelihood estimation based on two-tier integration, Bayesian estimation and the weighted least square estimation.
O ct 1 99 9 Freezing of Simple Liquid Metals

Freezing of simple liquid metals and the relative stabilities of competing crystalline solids are investigated using thermodynamic perturbation theory, the interactions between ions being modeled by effective pair potentials derived from pseudopotential theory. The ionic free energy of the solid phase is calculated, to first order in the perturbation potential, using classical density-functional theory and an accurate approximation to the hard-sphere radial distribution function. Free energy calculations for Na, Mg, and Al yield well-defined freezing transitions and structural free energy differences for bcc, fcc, and hcp crystals in qualitative agreement with experiment.
Pharmacological properties of the potent epileptogenic amino acid dysiherbaine, a novel glutamate receptor agonist isolated from the marine sponge Dysidea herbacea.

Dysiherbaine (DH) is a marine sponge-derived amino acid that causes seizures upon injection into mice. In this report we investigate the behavioral effects and characterize the pharmacological activity of DH. DH induced convulsive behaviors in mice with ED(50) values of 13 pmol/mouse, i.c. v. and 0.97 mg/kg, i.p. In rat brain synaptic membranes DH displaced binding of [3H]kainic acid (KA) and [3H]alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) with K(i) values of 26 and 153 nM, respectively; in contrast, DH did not displace the N-methyl-D-aspartic acid (NMDA) receptor ligand [3H]CGS-19755. DH displaced [3H]KA from recombinant GluR5 and GluR6 kainate receptor subunits expressed in HEK293 cells with K(i) values of 0.74 and 1.2 nM, respectively. In whole-cell voltage-clamp recordings from cultured rat hippocampal neurons, DH evoked inward currents from both AMPA and KA receptors with EC(50) values of 9.7 microM and 210 nM, respectively. AMPA receptor currents were blocked by GYKI 53655, whereas KA receptor currents were blocked by 6-cyano-7-nitroquinoxaline-2,3-dione (CNQX). Surprisingly, in calcium imaging experiments we found that DH also activated recombinant mGluR5 receptors but did not activate mGluR1 receptors. DH did not activate glutamate transporters or gamma-aminobutyric acid A (GABA(A)) receptors. These results indicate that DH is a potent non-NMDA-type agonist with very high affinity for KA receptors, as well as a subtype-selective mGluR agonist. DH possesses the most potent epileptogenic activity among the amino acids yet identified. This novel excitatory amino acid may prove useful for evaluating the physiological and pathological roles of non-NMDA receptors, especially KA receptors, in the central nervous system.
Simultaneous partitioning and frequency assignment for on-chip bus architectures

We provide a methodology to perform both bus partitioning and bus frequency assignment to each of the bus segments simultaneously while optimizing both the power consumption and performance of the system. We use a genetic algorithm and design an appropriate cost function which optimizes the solution on the basis of its power consumption and performance. The evaluation of our approach using a set of multiprocessor applications shows an average reduction of the energy consumption by 60% over a single shared bus architecture. Our results also show that it is beneficial to assign bus frequencies and perform bus partitioning simultaneously, instead of performing them sequentially.
Injection therapy for subacute and chronic low-back pain.

BACKGROUND The effectiveness of injection therapy for low-back pain is still debatable. Heterogeneity of target tissue, pharmacological agent and dosage generally found in randomized controlled trials (RCTs) points to the need for clinically valid comparisons in a literature synthesis. OBJECTIVES To determine if injection therapy is more effective than placebo or other treatments for patients with subacute or chronic low-back pain. SEARCH STRATEGY We updated the search of the earlier systematic review and searched the Cochrane Central Register of Controlled Trials, MEDLINE and EMBASE databases from January 1999 to March 2007 for relevant trials reported in English, French, German, Dutch and Nordic languages. We also screened references from trials identified. SELECTION CRITERIA RCTs on the effects of injection therapy involving epidural, facet or local sites for subacute or chronic low-back pain were included. Studies which compared the effects of intradiscal injections, prolotherapy or Ozone therapy with other treatments, were excluded unless injection therapy with another pharmaceutical agent (no placebo treatment) was part of one of the treatment arms. Studies about injections in sacroiliac joints and studies evaluating the effects of epidural steroids for radicular pain were also excluded. DATA COLLECTION AND ANALYSIS Two review authors independently assessed the quality of the trials. If study data were clinically and statistically too heterogeneous to perform a meta-analysis, we used a best evidence synthesis to summarize the results. The evidence was classified into five levels (strong, moderate, limited, conflicting or no evidence), taking into account the methodological quality of the studies. MAIN RESULTS 18 trials (1179 participants) were included in this updated review. The injection sites varied from epidural sites and facet joints (i.e. intra-articular injections, peri-articular injections and nerve blocks) to local sites (i.e. tender- and trigger points). The drugs that were studied consisted of corticosteroids, local anesthetics and a variety of other drugs. The methodological quality of the trials was limited with 10 out of 18 trials rated as having a high methodological quality. Statistical pooling was not possible due to clinical heterogeneity in the trials. Overall, the results indicated that there is no strong evidence for or against the use of any type of injection therapy. AUTHORS' CONCLUSIONS There is insufficient evidence to support the use of injection therapy in subacute and chronic low-back pain. However, it cannot be ruled out that specific subgroups of patients may respond to a specific type of injection therapy.
The Prevention of Gastric Inflation — A Neglected Benefit of Cricoid Pressure

The ability of cricoid pressure to prevent inflation of the stomach during mask ventilation of a patient was studied. Fifty patients were randomly allocated to either have or not have cricoid pressure applied during a three-minute period of standardised mask ventilation. Patients who had had cricoid pressure applied had less gas in the stomach after mask ventilation (P< 0.001). However, in a subgroup of patients considered difficult to ventilate, cricoid pressure seemed less successful in preventing gastric inflation. Cricoid pressure is a useful technique for reducing gastric inflation during mask ventilation, particularly in patients who are relatively easy to ventilate.
Bandwidth Efficiency Maximization for Single-Cell Massive Spatial Modulation MIMO: An Adaptive Power Allocation Perspective

The concept of massive spatial modulation aided multiple-input multiple-output (SM-MIMO) systems, where the base station (BS) is equipped with a large number of antennas and simultaneously serves several multi-antenna users that employ SM for their uplink transmission, has recently attracted substantial research interest. In this paper, we investigate the uplink bandwidth efficiency (BE) of single-cell massive SM-MIMO systems, and derive a new BE lower bound when the BS employs maximum ratio combining for uplink user detection. The proposed BE bound takes into account the impact of spatial correlations at the transmitter, of imperfect channel estimation, and of non-uniform power allocation among each user’s antennas (i.e., different antennas are allocated with different levels of transmit power). These bounds are shown to be tight even when a moderate number of antennas is used by the BS. Based on this bound, a gradient ascent method-based optimization is carried out to find the optimal power allocation among the transmit antennas (TAs) of each user, so that the uplink BE can be maximized. More specifically, the optimal power allocation is found to be typically dependent both on the TAs’ spatial correlation and on the large-scale attenuation of each user. Aided by this new power allocation scheme, a substantial BE gain can be achieved over the conventional uniform power allocation schemes, which is substantiated by our simulation results.
You and your kin: Neural signatures of family-based group perception in the subgenual cortex

Attachment to one’s kin as an in-group emerges from a fundamental human motivation and is vital for human survival. Despite important recent advances in the field of social neuroscience, the neural mechanisms underlying family-related in-group perception remain obscure. To examine the neural basis of perceiving family-related in-group boundaries in response to written kinship scenarios, we used functional magnetic resonance imaging in 27 healthy adults and obtained self-report ratings of family-related entitativity, which measures to what degree participants perceive their family as a coherent and distinct group in society. We expected that activity in the subgenual cingulate cortex and septo-hypothalamic region would track individual differences in entitativity. Perceiving one’s family as a distinct and cohesive group (high entitativity) was associated with increased subgenual cortex response to kinship scenarios. The subgenual cingulate cortex may represent a key link between kin-related emotional attachment and group perception, providing a neurobiological basis for group belongingness.
Pharmacological Analysis of the Anti-epileptic Mechanisms of Fenfluramine in scn1a Mutant Zebrafish

Dravet syndrome (DS) is a genetic encephalopathy that is characterized by severe seizures and prominent co-morbidities (e.g., physical, intellectual disabilities). More than 85% of the DS patients carry an SCN1A mutation (sodium channel, voltage gated, type I alpha subunit). Although numerous anti-epileptic drugs have entered the market since 1990, these drugs often fail to adequately control seizures in DS patients. Nonetheless, current clinical data shows significant seizure reduction in DS patients treated with the serotonergic (5-hydroxytryptamine, 5-HT) drug fenfluramine (FA). Recent preclinical research confirmed the anti-epileptiform activity of FA in homozygous scn1a mutant zebrafish larvae that mimic DS well. Here we explored the anti-epileptiform mechanisms of FA by investigating whether selective agonists/antagonists of specific receptor subtypes were able to counteract the FA-induced inhibition of seizures and abnormal brain discharges observed in the scn1a mutants. We show that antagonists of 5-HT1D and 5-HT2C receptor subtypes were able to do so (LY 310762 and SB 242084, respectively), but notably, a 5-HT2A-antagonist (ketanserin) was not. In addition, exploring further the mechanism of action of FA beyond its serotonergic profile, we found that the anti-epileptiform brain activity of FA was significantly abolished when it was administered in combination with a σ1-agonist (PRE 084). Our study therefore provides the first evidence of an involvement of the σ1 receptor in the mechanism of FA. We further show that the level of some neurotransmitters [i.e., dopamine and noradrenaline (NAD)] in head homogenates was altered after FA treatment, whereas γ-aminobutyric acid (GABA) and glutamate levels were not. Of interest, NAD-decreasing drugs have been employed successfully in the treatment of neurological diseases; including epilepsy and this effect could contribute to the therapeutic effect of the compound. In summary, we hypothesize that the anti-epileptiform activity of FA not only originates from its 5-HT1D- and 5-HT2C-agonism, but likely also from its ability to block σ1 receptors. These findings will help in better understanding the pharmacological profile of compounds that is critical for their applicability in the treatment of DS and possibly also other drug-resistant epilepsies.
The Art and Science of Modeling Decision-Making Under Severe Uncertainty

For obvious reasons, models for decision-making under severe uncertainty are austere. Simply put, there is precious little to work with under these conditions. This fact highlights the great importance of utilizing in such cases the ingredients of the mathematical model to the fullest extent, which in turn brings under the spotlight the art of mathematical modeling. In this discussion we examine some of the subtle considerations that are called for in the mathematical modeling of decision-making under severe uncertainty in general, and worst-case analysis in particular. As a case study we discuss the lessons learnt on this front from the Info-Gap experience.
Influence of Fires on Desert Plant Communities at the Chernye Zemli (SW Russia)

Understanding the rate and direction of pyrogenic succession in arid ecosystems, which depends on many factors, including the intensity of grazing and the frequency of pyrogenic expo-sure, will allow for more accurate predictions of the consequences of fire onplant communities, and will assist with better fire management. We studied the vegetation on 55 sites in and near the “Chernye Zemli” Natural Biosphere Reserve that burned at different times or were not affected by fires over the past 35 years and characterized the changes in vegetation cover associated with the impact of wildfire and grazing. The descriptions were grouped into chronological stages according to the time elapsed since the last fire, or into groups according to the frequency of fires. In pairwise comparison of the projective cover of plant species between chronological stages, it correlated most strongly between successive initial stages (for stages 1 and 2, p = 0.003, r = 0.73; for stages 2 and 3, p < 0.001, r = 0.78). Species with an initially higher projective cover were more likely to grow on plots in the first year after the fire: p < 0.03. Plots with rare and frequent fires had similar projective cover of individual species (r = 0.64, p < 0.001). We conclude that in the course of pyrogenic succession, communities are gradually replaced over at least ten years. At the same time, the composition of a plant community at the initial point of succession depends on the prevalence of species in the community before the fire. No fundamental effect of the frequency of fires on the composition of plant communities has been revealed.
γ-Tubulin 2 Nucleates Microtubules and Is Downregulated in Mouse Early Embryogenesis

γ-Tubulin is the key protein for microtubule nucleation. Duplication of the γ-tubulin gene occurred several times during evolution, and in mammals γ-tubulin genes encode proteins which share ∼97% sequence identity. Previous analysis of Tubg1 and Tubg2 knock-out mice has suggested that γ-tubulins are not functionally equivalent. Tubg1 knock-out mice died at the blastocyst stage, whereas Tubg2 knock-out mice developed normally and were fertile. It was proposed that γ-tubulin 1 represents ubiquitous γ-tubulin, while γ-tubulin 2 may have some specific functions and cannot substitute for γ-tubulin 1 deficiency in blastocysts. The molecular basis of the suggested functional difference between γ-tubulins remains unknown. Here we show that exogenous γ-tubulin 2 is targeted to centrosomes and interacts with γ-tubulin complex proteins 2 and 4. Depletion of γ-tubulin 1 by RNAi in U2OS cells causes impaired microtubule nucleation and metaphase arrest. Wild-type phenotype in γ-tubulin 1-depleted cells is restored by expression of exogenous mouse or human γ-tubulin 2. Further, we show at both mRNA and protein levels using RT-qPCR and 2D-PAGE, respectively, that in contrast to Tubg1, the Tubg2 expression is dramatically reduced in mouse blastocysts. This indicates that γ-tubulin 2 cannot rescue γ-tubulin 1 deficiency in knock-out blastocysts, owing to its very low amount. The combined data suggest that γ-tubulin 2 is able to nucleate microtubules and substitute for γ-tubulin 1. We propose that mammalian γ-tubulins are functionally redundant with respect to the nucleation activity.
Sound source separation in monaural music signals using excitation-filter model and em algorithm

This paper proposes a method for separating the signals of individual musical instruments from monaural musical audio. The mixture signal is modeled as a sum of the spectra of individual musical sounds which are further represented as a product of excitations and filters. The excitations are restricted to harmonic spectra and their fundamental frequencies are estimated in advance using a multipitch estimator, whereas the filters are restricted to have smooth frequency responses by modeling them as a sum of elementary functions on Mel-frequency scale. A novel expectation-maximization (EM) algorithm is proposed which jointly learns the filter responses and organizes the excitations (musical notes) to filters (instruments). In simulations, the method achieved over 5 dB SNR improvement compared to the mixture signals when separating two or three musical instruments from each other. A slight further improvement was achieved by utilizing musical properties in the initialization of the algorithm.
Sustaining Young People's Enrolment Intentions in Relation to Physics: Development and Validation of a Tool.

Currently there is a need for measures to examine the issue of sustaining students’ enrolment intentions over an extended period of study in physics, a subject which is generally perceived as hard and demanding by students. This paper addresses this gap in research by describing the development and the assessment of psychometric properties of the Physics Motivation Questionnaire, which examines the predictive relations among senior secondary physics students’ achievement motivation, sustained engagement and sustained enrolment intentions. The theoretical framework of the instrument largely draws on the Expectancy-Value theory of achievement motivation and the latent variables are assessed through six measures. Data shows that the Physics Motivation Questionnaire is a theoretically sound and psychometrically valid instrument which has utility in examining physics at a topic-specific level. The questionnaire makes a unique contribution to the physics enrolment literature and has significant implications for educational practitioners. These implications are discussed in the context of the findings.
Puzzles and peculiarities: How scientists attend to and process anomalies during data analysis

We used an "in vivo" methodology to investigate how scientists working alone or with a single colleague in informal data analysis sessions deal with anomalous data. We focused on the extent to which several scientists paid attention to anomalies, both immediately and over time, and the processes by which they addressed them. We found that the scientists paid more immediate attention to anomalies than to expected phenomena and also that they continued to devote more attention to anomalies, in some cases over considerable periods of time. We further identified a pattern of response to anomalies that differed from the response to expected phenomena. This pattern included identifying specific features of the phenomenon, proposing a hypothesis to account for it, elaborating that hypothesis by reference to the visual display, and considering the anomaly in the context of the surrounding dataset. We consider how our results mesh with those of previous work and propose some possible explanations for the differences.