Miracle-dz/UniFAR-FTUs huggingface dataset:
CluePedia Cytoscape plugin: pathway insights using integrated experimental and in silico data

Summary: The CluePedia Cytoscape plugin is a search tool for new markers potentially associated to pathways. CluePedia calculates linear and non-linear statistical dependencies from experimental data. Genes, proteins and miRNAs can be connected based on in silico and/or experimental information and integrated into a ClueGO network of terms/pathways. Interrelations within each pathway can be investigated, and new potential associations may be revealed through gene/protein/miRNA enrichments. A pathway-like visualization can be created using the Cerebral plugin layout. Combining all these features is essential for data interpretation and the generation of new hypotheses. The CluePedia Cytoscape plugin is user-friendly and has an expressive and intuitive visualization. Availability: http://www.ici. upmc.fr/cluepedia/ and via the Cytoscape plugin manager. The user manual is available at the CluePedia website. Contact: bernhard.mlecnik@crc.jussieu. fr or jerome.galon@crc.jussieu. fr Supplementary information: Supplementary data are available at Bioinformatics online.
A nationwide study of health-related quality of life, stress, pain or discomfort and the use of medicine among problem gamblers

Aim: The aim of this study was to investigate the associations between problem gambling and health-related quality of life, stress, pain or discomfort and the use of analgesics and sleeping pills. Methods: Data derives from the Danish Health and Morbidity Survey 2010. The survey was based on a random sample of 25,000 adult Danes (response rate: 61%), and data were collected via a self-administered questionnaire. The Lie/Bet Questionnaire was used as the screening instrument for problem gambling. Respondents were categorised as current, previous or non-problem gamblers. The questionnaire also included topics such as health-related quality of life (Short Form-12), perceived stress, pain and discomforts within the past two weeks, as well as the use of medication within the past two weeks. Results: Current problem gambling was strongly associated with negative outcomes such as poor mental health, high perception of stress, headache, fatigue and sleeping problems. Furthermore, previous problem gambling was generally associated with poorer health outcomes. Thus, current and previous problem gamblers had 2.36 times (95% confidence interval [CI] 1.44–3.87) and 1.66 times (95% CI 1.07–2.55) higher odds than non-problem gamblers of reporting fair or poor health, respectively. The data revealed no clear association between problem gambling and the use of analgesics. Conclusions: Both current and previous problem gambling were negatively associated with physical and mental-health problems. Health professionals should be alert to any signs of these complicating factors when planning the treatment of problem gamblers.
Malformations of Cortical Development

Background:Malformations of cortical development (MCD) are increasingly recognized as an important cause of epilepsy and developmental delay. MCD encompass a wide spectrum of disorders with various underlying genetic etiologies and clinical manifestations. High resolution imaging has dramatically improved our recognition of MCD. Review Summary:This review will provide a brief overview of the stages of normal cortical development, including neuronal proliferation, neuroblast migration, and neuronal organization. Disruptions at various stages lead to characteristic MCD. Disorders of neurogenesis give rise to microcephaly (small brain) or macrocephaly (large brain). Disorders of early neuroblast migration give rise to periventricular heterotopia (neurons located along the ventricles), whereas abnormalities later in migration lead to lissencephaly (smooth brain) or subcortical band heterotopia (smooth brain with a band of heterotopic neurons under the cortex). Abnormal neuronal migration arrest give rise to over migration of neurons in cobblestone lissencephaly. Lastly, disorders of neuronal organization cause polymicrogyria (abnormally small gyri and sulci). This review will also discuss the known genetic mutations and potential mechanisms that contribute to these syndromes. Conclusion:Identification of various gene mutations has not only given us greater insight into some of the pathophysiologic basis of MCD, but also an understanding of the processes involved in normal cortical development.
Constraint Solving over Semirings

We introduce a general framework for constraint solving where classical CSPs, fuzzy CSPs, weighted CSPs, partial constraint satisfaction , and others can be easily cast. The framework is based on a semiring structure, where the set of the semiring specifies the values to be associated to each tuple of values of the variable domain, and the two semiring operations (+ and x) model constraint projection and combination respectively. Local consistency algorithms, as usually used for classical CSPs, can be exploited in this general framework as well, provided that some conditions on the semiring operations are satisfied. We then show how this framework can be used to model both old and new constraint solving schemes, thus allowing one both to formally justify many informally taken choices in existing schemes, and to prove that the local consistency techniques can be used also in newly defined schemes. 1 Introduction Classical constraint satisfaction problems (CSPs) [Mon-tanari, 1974; Mackworth, 1988] are a very expressive and natural formalism to specify many kinds of real-life problems. In fact, problems ranging from map coloring , vision, robotics, job-shop scheduling, VLSI design , etc., can easily be cast as CSPs and solved using one of the many techniques that have been developed for such problems or subclasses of them However, they also have evident limitations, mainly due to the fact that they are not very flexible when trying to represent real-life scenarios where the knowledge is not completely available nor crisp. In fact, in such situations, the ability of stating whether an instantiation of values to variables is allowed or not is not enough or sometimes not even possible. For these reasons, it is natural to try to extend the CSP formalism in this direction. CSPs have been extended with the ability to associate to each tuple, or to each constraint, a level of preference, and with the possibility of combining constraints using min-max operations. This extended formalism has been called Fuzzy CSPs (FCSPs). Other extensions concern the ability to model incomplete knowledge of the real problem [Fargier and Lang, 1993], to solve overconstrained problems [Freuder and Wallace, 1992], and to represent cost optimization problems. In this paper we define a constraint solving framework where all such extensions, as well as classical CSPs, can be cast. However, we do not relax the assumption of a finite domain for the variables of the constraint problems. The main idea is based …
Blockchain-Based Trusted Electronic Records Preservation in Cloud Storage

Cloud storage represents the trend of intensive, scale and specialization of information technology, which has changed the technical architecture and implementation method of electronic records management. Moreover, it will provide a convenient way to generate more advanced and efficient management of the electronic data records. However, in cloud storage environment, it is difficult to guarantee the trustworthiness of electronic records, which results in a series of severe challenges to electronic records management. Starting from the definition and specification of electronic records, this paper firstly analyzes the requirements of the trustworthiness in cloud storage during their long-term preservation according to the information security theory and subdivides the trustworthiness into the authenticity, integrity, usability, and reliability of electronic records in cloud storage. Moreover, this paper proposes the technology framework of preservation for trusted electronic records. Also, the technology of blockchain, proofs of retrievability, the open archival information system model and erasure code are adopted to protect these four security attributes, to guarantee the credibility of the electronic record.
EEG-based Dominance Level Recognition for Emotion-Enabled Interaction

Emotions recognized from Electroencephalogram (EEG) could reflect the real "inner" feelings of the human. Recently, research on real-time emotion recognition received more attention since it could be applied in games, e-learning systems or even in marketing. EEG signal can be divided into the delta, theta, alpha, beta, and gamma waves based on their frequency bands. Based on the Valence-Arousal-Dominance emotion model, we proposed a subject-dependent algorithm using the beta/alpha ratio to recognize high and low dominance levels of emotions from EEG. Three experiments were designed and carried out to collect the EEG data labeled with emotions. Sound clips from International Affective Digitized Sounds (IADS) database and music pieces were used to evoke emotions in the experiments. Our approach would allow real-time recognition of the emotions defined with different dominance levels in Valence-Arousal-Dominance model.
Persistent Hemodynamic Changes in Ruptured Brain Arteriovenous Malformations

Background and Purpose— Hemodynamic properties of brain arteriovenous malformations (AVMs) with risk factors for a future hemorrhage are essentially unknown. We hypothesized that AVMs with anatomic properties, which are associated with an increased rupture risk, exhibit different hemodynamic characteristics than those without these properties. Methods— Seventy-two consecutive patients with AVMs diagnosed by conventional angiography underwent MRI examination, including time-resolved 3-dimensional MR angiography. Signal-intensity curves derived from the time-resolved 3-dimensional MR angiography datasets were used to calculate relative blood flow transit times through the AVM nidus based on the time-to-peak parameter. For identification of characteristics associated with altered transit times, a multiple normal regression model was fitted with stepwise selection of the following regressors: intracranial hemorrhage, deep nidus location, infratentorial location, deep drainage, associated aneurysm, nidus size, draining venous stenosis, and number of draining veins. Results— A previous intracranial hemorrhage is the only characteristic that was associated with a significant alteration of the relative transit time, leading to an increase of 2.4 seconds (95% CI, 1.2–3.6 seconds;, P<0.001) without adjustment and 2.1 seconds (95% CI, 0.6–3.6 seconds; P=0.007) with adjustment for all other regressors considered. The association was independent of the bleeding age. Conclusion— Hemodynamic parameters do not seem useful for risk assessment of an AVM-related hemorrhage because only a previous AVM rupture leads to a significant and permanent alteration of the hemodynamic situation.
How social influence can undermine the wisdom of crowd effect

Social groups can be remarkably smart and knowledgeable when their averaged judgements are compared with the judgements of individuals. Already Galton [Galton F (1907) Nature 75:7] found evidence that the median estimate of a group can be more accurate than estimates of experts. This wisdom of crowd effect was recently supported by examples from stock markets, political elections, and quiz shows [Surowiecki J (2004) The Wisdom of Crowds]. In contrast, we demonstrate by experimental evidence (N = 144) that even mild social influence can undermine the wisdom of crowd effect in simple estimation tasks. In the experiment, subjects could reconsider their response to factual questions after having received average or full information of the responses of other subjects. We compare subjects’ convergence of estimates and improvements in accuracy over five consecutive estimation periods with a control condition, in which no information about others’ responses was provided. Although groups are initially “wise,” knowledge about estimates of others narrows the diversity of opinions to such an extent that it undermines the wisdom of crowd effect in three different ways. The “social influence effect” diminishes the diversity of the crowd without improvements of its collective error. The “range reduction effect” moves the position of the truth to peripheral regions of the range of estimates so that the crowd becomes less reliable in providing expertise for external observers. The “confidence effect” boosts individuals’ confidence after convergence of their estimates despite lack of improved accuracy. Examples of the revealed mechanism range from misled elites to the recent global financial crisis.
Geolocation for Twitter: Timing Matters

Automated geolocation of social media messages can beneﬁt a variety of downstream applications. However, these geolocation systems are typically evaluated without attention to how changes in time impact geolocation. Since different people, in different locations write messages at different times, these factors can signiﬁcantly vary the performance of a ge-olocation system over time. We demonstrate cyclical temporal effects on geolocation accuracy in Twitter, as well as rapid drops as test data moves beyond the time period of training data. We show that temporal drift can effectively be countered with even modest online model updates.
Mitigating the electron cloud effect in the SuperKEKB positron ring

SuperKEKB is an electron-positron collider with asymmetric energies located at the High Energy Accelerator Research Organization (KEK) in Tsukuba, Japan. After more than five years of upgrading work on KEKB, phase-1 commissioning commenced in February 2016 and ended in June of the same year. Following a 20-month shutdown for the installation of a particle detector, BELLE II, phase-2 commissioning commenced in March 2018 and ended in July of the same year. This paper describes one major issue faced by SuperKEKB: the electron cloud effect (ECE) in the positron ring, which was observed during phase-1 commissioning. In the high-beam-current region, electron clouds, i.e., the source of the ECE, existed in the beam pipes at drift spaces of the ring, which had antechambers and a titanium nitride (TiN) film coating as countermeasures against the ECE. Permanent magnets and solenoids used to generate magnetic fields in the beam direction were attached to the beam pipes as additional countermeasures before the next commissioning phase commenced. Consequently, during phase-2 commissioning, experiments showed that the threshold of the current linear density for exciting the ECE increased by a factor of at least 2 compared to that during phase-1 commissioning. While the countermeasures were strengthened, the effectiveness of the antechambers and TiN film coating of the real beam pipe was reevaluated. Through various simulations and dedicated experiments during phase-2 commissioning, the antechambers were found to be less effective than anticipated with regard to reducing the number of photoelectrons in the beam channel. In contrast, the TiN film coating had a low secondary electron yield, as expected.
Weak variable-length source coding

Given a general source X={X/sup n/}/sub n=1//sup /spl infin//, source coding is characterized by a pair (/spl phi//sub n/, /spl psi//sub n/) of encoder /spl phi//sub n/, and decoder /spl psi//sub n/, together with the probability of error /spl epsi//sub n//spl equiv/Pr{/spl psi//sub n/(/spl phi//sub n/(X/sup n/))/spl ne/X/sup n/}. If the length of the encoder output /spl phi//sub n/(X/sup n/) is fixed, then it is called fixed-length source coding, while if the length of the encoder output /spl phi//sub n/(X/sup n/) is variable, then it is called variable-length source coding. Usually, in the context of fixed-length source coding the probability of error /spl epsi//sub n/ is required to asymptotically vanish (i.e., lim/sub n/spl rarr//spl infin///spl epsi//sub n/=0), whereas in the context of variable-length source coding the probability of error /spl epsi//sub n/ is required to be exactly zero (i.e., /spl epsi//sub n/=0/spl forall/n=1, 2, .). In contrast to these, we consider the problem of variable-length source coding with asymptotically vanishing probability of error (i.e., lim/sub n/spl rarr//spl infin///spl epsi//sub n/=0), and establish several fundamental theorems on this new subject.
Qualitative effects of patchy stomatal conductance distribution features on gas‐exchange calculations

The qualitative influence of patchy stomatal conductance distributions on the values of photosynthesis (A) and intercellular CO 2 concentration (c i ) as determined by gas-exchange measurements were investigated using computer modelling. Gas-exchange measurements were simulated for different conductance distributions by modelling photosynthesis explicitly for each patch, summing these rates, and inferring c i from a diffusion equation. Qualitative relationships are presented between conductance distribution features and the difference between assimilation rates measured for patchy and homogeneous leaves at the same c i (A P and A h , respectively). These data show that, although most conductance distributions have little effect on the value of A measured for a given c i , some distribution features (which we have termed 'bimodality', 'position', 'skewness' and 'range') play a key role in controlling the magnitude of these effects. Distributions that are more nearly bimodal, span regions of lower conductance, are right-skewed, or have broader conductance ranges are associated with larger effects on the A(c i ) relationship. To clarify our mathematical analysis and illustrate some of the trends it predicts, we present conductance distributions and gas-exchange data from leaves of Malus dolgo var. Spring Snow that were treated with ABA. The results are discussed in the light of recent controversy over the effect of patchy stomatal conductance on gas-exchange data.
Error Estimates and Evaluation of Matrix Functions via the Faber Transform

The need to evaluate expressions of the form $f(A)$ or $f(A)b$, where $f$ is a nonlinear function, $A$ is a large sparse $n\times n$ matrix, and $b$ is an $n$-vector, arises in many applications. This paper describes how the Faber transform applied to the field of values of $A$ can be used to determine improved error bounds for popular polynomial approximation methods based on the Arnoldi process. Applications of the Faber transform to rational approximation methods and, in particular, to the rational Arnoldi process also are discussed.
Studies on different concentration of lead (Pb) and sewage water on Pb uptake and growth of Radish (Raphanus sativus)

To investigate the accumulation of lead (Pb) by radish ( Raphanus sativus ) cultivars a study was carried out at Department of Soil and Environmental Sciences, Gomal University, Dera Ismail Khan (Pakistan), during 2012. Two radish varieties i.e., exotic and local, were used. The treatments included sewage water and different concentrations of Pb @ 25, 100, 200 and 400 mg L -1 . The results showed that the total biomass of both the radish varieties were nonsignificantly influenced by the applied Pb concentrations and sewage water, except for root diameter which were significantly greater in the local cultivar (3.261 cm). Pb treatments significantly reduced the growth and yield of both the cultivars. While the Pb uptake by the root and leaf of radish plants was increased by the increasing the applied Pb levels, with the highest value for root (19.008 mg kg -1 ) and leaf (16.134 mg kg -1 ) in the treatment receiving the highest applied Pb concentrations. The total biomass, fresh weight of root and root diameter was found significantly higher except for Pb @ 400 mg L -1 , in the plants receiving sewage water as compared to the control and different levels of Pb. The interaction amongst the varieties and treatments were found significantly different for various parameters. Thus, it can be concluded, that the use of sewage water and Pb contaminated wastewater results in higher metal concentration in the radish root and may lead to different types of health problems to consumers.
Effect of different Cusp Inclinations on the Retention of Cement Retained Implant Supported Prosthesis

Long term durability and high success rate of dental implants made them a proper choice to restore esthetic and function of lost teeth [1-3]. However, complications still widely reported in both screw and cement retained prostheses [4,5]. Majority of the complications reported with dental implants were related to biomechanical factors rather than biological aspects. Mechanical stress is a high risk factor for restored implant under function [6]. Masticatory loading is more complex with a combination of vertical and horizontal directions rather than one direction [7]. The part of the chewing cycle where occlusal contacts occur and the pathways taken by the mandible are determined by the morphology of the teeth [8].
The Role of Efflux Pumps in Schistosoma mansoni Praziquantel Resistant Phenotype

Background Schistosomiasis is a neglected disease caused by a trematode of the genus Schistosoma that is second only to malaria in public health significance in Africa, South America, and Asia. Praziquantel (PZQ) is the drug of choice to treat this disease due to its high cure rates and no significant side effects. However, in the last years increasingly cases of tolerance to PZQ have been reported, which has caused growing concerns regarding the emergency of resistance to this drug. Methodology/Principal Findings Here we describe the selection of a parasitic strain that has a stable resistance phenotype to PZQ. It has been reported that drug resistance in helminths might involve efflux pumps such as members of ATP-binding cassette transport proteins, including P-glycoprotein and multidrug resistance-associated protein families. Here we evaluate the role of efflux pumps in Schistosoma mansoni resistance to PZQ, by comparing the efflux pumps activity in susceptible and resistant strains. The evaluation of the efflux activity was performed by an ethidium bromide accumulation assay in presence and absence of Verapamil. The role of efflux pumps in resistance to PZQ was further investigated comparing the response of susceptible and resistant parasites in the absence and presence of different doses of Verapamil, in an ex vivo assay, and these results were further reinforced through the comparison of the expression levels of SmMDR2 RNA by RT-PCR. Conclusions/Significance This work strongly suggests the involvement of Pgp-like transporters SMDR2 in Praziquantel drug resistance in S. mansoni. Low doses of Verapamil successfully reverted drug resistance. Our results might give an indication that a combination therapy with PZQ and natural or synthetic Pgp modulators can be an effective strategy for the treatment of confirmed cases of resistance to PZQ in S. mansoni.
“Treating” Prejudice

One of the ways in which therapists treat anxiety disorders is to expose patients to a fear-evoking stimulus within a safe environment before encouraging more positive stimulus-related thoughts. In the study reported here, we adapted these psychotherapeutic principles of exposure therapy to test the hypothesis that imagining a positive encounter with a member of a stigmatized group would be more likely to promote positive perceptions when it was preceded by an imagined negative encounter. The results of three experiments targeting a range of stigmatized groups (adults with schizophrenia, gay men, and British Muslims) supported this hypothesis. Compared with purely positive interventions, interventions in which a single negative encounter was imagined just prior to imagining a positive encounter resulted in significantly reduced prejudice. Furthermore, reduced anxiety uniquely derived from the mixed-valence imagery task statistically explained enhanced intentions to engage positively with the previously stigmatized group in the future.