Miracle-dz/UniFAR-FTUs huggingface dataset:
Human VPS34 is required for internal vesicle formation within multivesicular endosomes

After internalization from the plasma membrane, activated EGF receptors (EGFRs) are delivered to multivesicular bodies (MVBs). Within MVBs, EGFRs are removed from the perimeter membrane to internal vesicles, thereby being sorted from transferrin receptors, which recycle back to the plasma membrane. The phosphatidylinositol (PI) 3′-kinase inhibitor, wortmannin, inhibits internal vesicle formation within MVBs and causes EGFRs to remain in clusters on the perimeter membrane. Microinjection of isotype-specific inhibitory antibodies demonstrates that the PI 3′-kinase required for internal vesicle formation is hVPS34. In the presence of wortmannin, EGFRs continue to be delivered to lysosomes, showing that their removal from the recycling pathway and their delivery to lysosomes does not depend on inward vesiculation. We showed previously that tyrosine kinase-negative EGFRs fail to accumulate on internal vesicles of MVBs but are recycled rather than delivered to lysosomes. Therefore, we conclude that selection of EGFRs for inclusion on internal vesicles requires tyrosine kinase but not PI 3′-kinase activity, whereas vesicle formation requires PI 3′-kinase activity. Finally, in wortmannin-treated cells there is increased EGF-stimulated tyrosine phosphorylation when EGFRs are retained on the perimeter membrane of MVBs. Therefore, we suggest that inward vesiculation is involved directly with attenuating signal transduction.
Temporal Gillespie Algorithm: Fast Simulation of Contagion Processes on Time-Varying Networks

Stochastic simulations are one of the cornerstones of the analysis of dynamical processes on complex networks, and are often the only accessible way to explore their behavior. The development of fast algorithms is paramount to allow large-scale simulations. The Gillespie algorithm can be used for fast simulation of stochastic processes, and variants of it have been applied to simulate dynamical processes on static networks. However, its adaptation to temporal networks remains non-trivial. We here present a temporal Gillespie algorithm that solves this problem. Our method is applicable to general Poisson (constant-rate) processes on temporal networks, stochastically exact, and up to multiple orders of magnitude faster than traditional simulation schemes based on rejection sampling. We also show how it can be extended to simulate non-Markovian processes. The algorithm is easily applicable in practice, and as an illustration we detail how to simulate both Poissonian and non-Markovian models of epidemic spreading. Namely, we provide pseudocode and its implementation in C++ for simulating the paradigmatic Susceptible-Infected-Susceptible and Susceptible-Infected-Recovered models and a Susceptible-Infected-Recovered model with non-constant recovery rates. For empirical networks, the temporal Gillespie algorithm is here typically from 10 to 100 times faster than rejection sampling.
The sequence capture by hybridization: a new approach for revealing the potential of mono‐aromatic hydrocarbons bioattenuation in a deep oligotrophic aquifer

The formation water of a deep aquifer (853 m of depth) used for geological storage of natural gas was sampled to assess the mono‐aromatic hydrocarbons attenuation potential of the indigenous microbiota. The study of bacterial diversity suggests that Firmicutes and, in particular, sulphate‐reducing bacteria (Peptococcaceae) predominate in this microbial community. The capacity of the microbial community to biodegrade toluene and m‐ and p‐xylenes was demonstrated using a culture‐based approach after several hundred days of incubation. In order to reveal the potential for biodegradation of these compounds within a shorter time frame, an innovative approach named the solution hybrid selection method, which combines sequence capture by hybridization and next‐generation sequencing, was applied to the same original water sample. The bssA and bssA‐like genes were investigated as they are considered good biomarkers for the potential of toluene and xylene biodegradation. Unlike a PCR approach which failed to detect these genes directly from formation water, this innovative strategy demonstrated the presence of the bssA and bssA‐like genes in this oligotrophic ecosystem, probably harboured by Peptococcaceae. The sequence capture by hybridization shows significant potential to reveal the presence of genes of functional interest which have low‐level representation in the biosphere.
The Effects of Bilingualism and Vocabulary Size on Infants’ Cognitive Control

The Effects of Bilingualism and Vocabulary Size on Infants’ Cognitive Control Sadaf Pour Iliaei There is increasing evidence that bilingualism may lead to cognitive advantages, and some evidence suggests that these may emerge as early as infancy. The present study examined if such advantages could be found in preverbal bilingual infants (7-month-olds), and older bilingual infants who have an emerging vocabulary (20-month-olds). We compared monolinguals and bilinguals in an anticipatory eye movement paradigm. During the training phase, infants learned to use a visual and auditory cue to anticipate a visual reward on one side of a screen. During the test phase, the reward would appear on the opposite side of the screen, necessitating infants to inhibit the previously-learned rule. Results suggest that both 7-month-old and 20-month-old bilingual infants were better able to inhibit their previously learned response than monolinguals. This effect was most apparent in the middle block of test trials. At 20 months, infants with lower vocabulary size were more engaged in the task, showing more total anticipations (both correct and incorrect) than those with higher vocabulary size. Overall, this research provides some evidence that bilingualism may lead to improvements in cognitive control for preverbal and older infants. Keywords: infancy, bilingualism, cognitive control, inhibitory control, eye-tracking
Effect of double-layer composite absorbing coating on shielding effectiveness of electromagnetic shielding fabric

In order to meet the demand for high-performance electromagnetic shielding fabrics, using absorbing coatings to improve the shielding effectiveness has become an research object increasingly. The effect of double-layer mixed material’s absorbing coatings on electromagnetic shielding fabrics has not been clarified currently. At the same time, it is difficult to satisfy the broadband requirement for a single type of absorption layer. Carbon nanotubes, graphene, ferrite and nano-nickel powder are used in this paper. Which made it content at 15%, 25% and 35% respectively. The shielding effectiveness test of the stainless steel electromagnetic shielding fabric coating was carried out by the DR-SO4 electromagnetic shielding test system. Through the experiment, some findings are summarized as followed. Regardless of the same mixed materials, different content of shielding effectiveness comparison experiments, or the comparison of the performance of different kinds of materials mixed with the same content of screen combination, when the content is 15%, the best shielding effectiveness is the double-layer combination of Graphene + Ferrite and Graphene + Nickel. Which peak value is 68 dB respectively. In the analysis of the influence factors of the test coating, the larger the thickness and the corresponding resistance value smaller, the higher the combined shielding effect value. The optimal combination order of shielding effectiveness is: reflective layer + absorbing layer + absorbing layer + reflective layer. This paper revealed the influence of double-layer hybrid coating on the shielding effectiveness of electromagnetic shielding fabrics. It has important academic significance for the design, production and evaluation of high performance electromagnetic shielding fabrics.
Tame decompositions and collisions

A univariate polynomial <i>f</i> over a field is decomposable if <i>f</i> = <i>g</i> o <i>h</i> = <i>g</i>(<i>h</i>) for nonlinear polynomials <i>g</i> and <i>h</i>. It is intuitively clear that the decomposable polynomials form a small minority among all polynomials over a finite field. The tame case, where the characteristic of F<sub><i>q</i></sub> does not divide <i>n</i> = deg <i>f</i>, is fairly well-understood, and we have reasonable bounds on the number of decomposables of degree <i>n</i>. Nevertheless, no exact formula is known if <i>n</i> has more than two prime factors. In order to count the decomposables, one wants to know, under a suitable normalization, the number of collisions, where essentially different components (<i>g, h</i>) yield the same <i>f</i>. In the tame case, Ritt's Second Theorem classifies all collisions of two such pairs. We present a normal form for collisions of any number of decompositions with any number of components and describe exactly the (non)uniqueness of the parameters in the tame case. This yields an exact formula for the number of such collisions over a finite field. We conclude with a fast algorithm for the exact number of decomposable polynomials of degree <i>n</i> over a finite field F<i>q</i> of characteristic coprime to <i>n</i>.
Extracting news text from web pages: an application for the visually impaired

Apart from the actual content, web pages contain several other components (referred to as boilerplate text) that describes how, and in what context the content should be displayed. We show how content bearing text can be efficiently separated from boilerplate text using a random forest classifier. We compare the performance with another state-of-the-art method for boilerplate detection that uses a decision tree classifier and shallow features extracted from the text. The result is a general improvement using the random forest classifier for both classifying problems analyzed, significantly so for the more complex problem. We also show that a small increase in feature set range can lead to even further improved accuracy. The conclusion is that random forest classification can achieve significantly higher accuracy rates than at least one of the current state-of-the-art methods for content extraction. The results can improve content extraction methods for a variety of applications, including search engine optimization and making the web more accessible for the blind or visually impaired.
Noise robustness of heterogeneous features employing minimum classification error feature space transformations

The use of heterogeneous features in automatic speech recognition has been shown to increase clean speech performance. This paper focuses on the noise robustness of systems with heterogeneous features. In particular a system where di(cid:11)erent features are extracted for di(cid:11)erent sets of phon-emes. The employed features are computed by applying a linear transformation, estimated in a data-driven fashion, to standard feature processing methods. The transformed features are tested in a set of experiments employing different system con(cid:12)gurations. Overall the experiments suggests that employing more phoneme speci(cid:12)c features can improve speech recognition. When testing the system on noisy speech with added car or factory noise, this tendency is maintained.
Evolving a Set of Techniques for OO Inspections

Inspecting OO designs is an important way of ensuring the quality of software under development. When high-level design activities are finished, the design documents can be inspected to verify whether they are consistent among themselves and whether the software requirements were correctly and completely captured. This paper discusses some issues regarding the definition and application of reading techniques (i.e. procedural guidelines that can be given to inspectors) to inspect high-level OO design documents. An initial set of OO Reading Techniques and their experimental evaluation is described. A method for evaluating the reading techniques in more detail, i.e. Observational Techniques, is then presented, and experiences with its use are discussed. Through these discussions, we show how the reading techniques have evolved in response to empirical evidence (both qualitative and quantitative) regarding their use in practice. The complete and current set of techniques can be found in the appendices.
Factored Probabilistic Belief Tracking

The problem of belief tracking in the presence of stochastic actions and observations is pervasive and yet computationally intractable. In this work we show however that probabilistic beliefs can be maintained in factored form exactly and efficiently across a number of causally closed beams, when the state variables that appear in more than one beam obey a form of backward determinism. Since computing marginals from the factors is still computationally intractable in general, and variables appearing in several beams are not always backward-deterministic, the basic formulation is extended with two approximations: forms of belief propagation for computing marginals from factors, and sampling of non-backward-deterministic variables for making such variables backward-deterministic given their sampled history. Unlike, Rao-Blackwellized particle-filtering, the sampling is not used for making inference tractable but for making the factorization sound. The resulting algorithm involves sampling and belief propagation or just one of them as determined by the structure of the model.
Challenges in designing trustworthy cryptographic co-processors

Security is becoming ubiquitous in our society. However, the vulnerability of electronic devices that implement the needed cryptographic primitives has become a major issue. This paper starts by presenting a comprehensive overview of the existing attacks to cryptography implementations. Thereafter, the state-of-the-art on some of the most critical aspects of designing cryptographic co-processors are presented. This analysis starts by considering the design of asymmetrical and symmetrical cryptographic primitives, followed by the discussion on the design and online testing of True Random Number Generation. To conclude, techniques for the detection of Hardware Trojans are also discussed.
High-Performance Question Classification Using Semantic Features

A question classification system uses machine learning techniques to classify a question by the type of answer it requires. Recent systems have successfully used syntactic parsing to identify small, highly-informative phrases or words within a question to use as the principle features of a probabilistic model. In this paper, I explore the effectiveness of an alternative feature set that makes use of only semantic features. My system achieves a classification accuracy of 86.6% on the standard UIUC benchmark test set (Li and Roth, 2002), making it superior to all but the most recent classification system (Huang et al., 2008).
The Prognostic Value of Amplitude-Integrated EEG in Full-Term Neonates with Seizures

Neonatal seizures pose a high risk for adverse outcome in survived infants. While the prognostic value of amplitude-integrated electroencephalogram (aEEG) is well established in neonates with encephalopathy and asphyxia, neonatal seizure studies focusing on the direct correlation between early aEEG measurement and subsequent neurologic outcome are scarce. In this study, the prognostic value of aEEG features was systematically analyzed in 143 full-term neonates to identify prognostic indicators of neurodevelopmental outcome. Neonatal aEEG features of background pattern, cyclicity, and seizure activity, as well as the etiology of neonatal seizures, were significantly associated with neurodevelopmental outcome at one year of age. aEEG background pattern was highly associated with neurologic outcomes (χ2 = 116.9), followed by aEEG cyclicity (χ2 = 87.2) and seizure etiology (χ2 = 79.3). Multiple linear regression showed that the four predictors explained 71.2% of the variation in neurological outcome, with standardized β coefficients of 0.44, 0.24, 0.22, and 0.14 for the predictors of aEEG background pattern, cyclicity, etiology, and aEEG seizure activity, respectively. This clinically applicable scoring system based on etiology and three aEEG indices would allow pediatricians to assess the risk for neurodevelopmental impairment and facilitate an early intervention in newborns developing seizures.
Genome Annotation in Plants and Fungi: EuGene as a Model Platform

In this era of whole genome sequencing, reliable genome annotations (identification of functional regions) are the cornerstones for many subsequent analyses. Not only is careful annotation important for studying the gene and gene family content of a genome and its host, but also for wide-scale transcriptome and proteome analyses attempting to de- scribe a certain biological process or to get a global picture of a cell's behavior. Although the number of sequenced ge- nomes is increasing thanks to the application of new technologies, genome-wide analyses will critically depend on the quality of the genome annotations. However, the annotation process is more complicated in the plant field than in the animal field because of the limited funding that leads to much fewer experimental data and less annotation expertise. This situation calls for highly automated annotation platforms that can make the best use of all available data, experimental or not. We discuss how the gene prediction (the process of predicting protein gene structures in genomic sequences) research field increasingly shifts from methods that typically exploited one or two types of data to more integrative approaches that simultaneously deal with various experimental, statistical, or other in silico evidence. We illustrate the importance of inte- grative approaches for producing high-quality automatic annotations of genomes of plants and algae as well as of fungi that live in close association with plants using the platform EuGene as an example.
Neuronal representations of stimulus associations develop in the temporal lobe during learning

Visual stimuli that are frequently seen together become associated in long-term memory, such that the sight of one stimulus readily brings to mind the thought or image of the other. It has been hypothesized that acquisition of such long-term associative memories proceeds via the strengthening of connections between neurons representing the associated stimuli, such that a neuron initially responding only to one stimulus of an associated pair eventually comes to respond to both. Consistent with this hypothesis, studies have demonstrated that individual neurons in the primate inferior temporal cortex tend to exhibit similar responses to pairs of visual stimuli that have become behaviorally associated. In the present study, we investigated the role of these areas in the formation of conditional visual associations by monitoring the responses of individual neurons during the learning of new stimulus pairs. We found that many neurons in both area TE and perirhinal cortex came to elicit more similar neuronal responses to paired stimuli as learning proceeded. Moreover, these neuronal response changes were learning-dependent and proceeded with an average time course that paralleled learning. This experience-dependent plasticity of sensory representations in the cerebral cortex may underlie the learning of associations between objects.
Automating semantics-based reconciliation for mobile databases ⁄

Optimistic replication lets multiple users update local replicas of shared data independently. These replicas may diverge and must be reconciled. In this paper, we present a general-purpose reconciliation system for mobile transactions. The basic reconciliation engine treats reconciliation as an optimization problem. To direct the search, it relies on semantic information and user intents expressed as relations among mobile transactions. Unlike previous semantics-based reconciliation systems, our system includes a module that automatically infers semantic relations from the code of mobile transactions. Thus, it is possible to use semantics-based reconciliation without incurring the overhead of specifying the semantics of the data types or operations.
Proper motions and CCD-photometry of stars in the region of the open cluster Trumpler 2

The results of the complex study of galactic open cluster Trumpler2 are presented.The positions of approximately 3000 stars up to the limit magnitude B ∼ 16.25 mag in the area 80 ′ × 80 ′ around the cluster were measured in order to obtain the proper motions. Measurements of star positions on 6 plates with the maximal epoch difference of 63 years were taken by means of the automated measuring complex ”Fantasy”. The root-mean error of the relative proper motions is 4.2 mas yr −1 . The catalogue of BV magnitudes of all the stars in the investigated area was compiled. Astrometric selection of the cluster members within the region of R < 16 ′ from the center of the cluster was made by means of the W.Sanders method(1971). In that field 192 stars were found to have the individual membership probability greater then 85%, 148 of them are situated within the ±3σB−V band around the main sequence (MS) of the cluster. They are considered to be cluster members by two criteria. The U-B∼B-V diagram plotted for the astrometrical cluster members by the data taken from the Washington catalogue of the UBV photometry in the galactic cluster fields (Hoag et al. 1961) has made it possible to redefine the value of the color excess E(B-V)= 0. m 40 instead of previously published values ranged from 0. m 30 to 0. m 34. The superposition of the MS of the cluster with the ZAMS Schmidt-Kaler (1965) for thus accepted E(B-V) leads to the coincidence at the value of the apparent distance module (V − MV ) = 10.50 which corresponds to the distance r = 725pc. The luminosity and mass functions of the Trumpler2 were constructed and the value of the slope ( = −1.90±0.22) was determined. The cluster age of 8.913×10 7 yr was determined on the base of Girardi et al. (2000) isochrone grid. Correspondent to this age the turn-off
The dynamical formation of LMXBs in dense stellar environments: globular clusters and the inner bulge of M31

The radial distribution of luminous (L x > 10 36 ergs -1 ) X-ray point sources in the bulge of M31 is investigated using archival Chandra observations. We find a significant increase in the specific frequency of X-ray sources, per unit stellar mass, within 1 arcmin from the centre of the galaxy. The radial distribution of surplus sources in this region follows the p2 law, suggesting that they are low-mass X-ray binaries (LMXBs) formed dynamically in the dense inner bulge. We investigate dynamical formation of LMXBs, paying particular attention to the high-velocity regime characteristic for galactic bulges, which has not been explored previously. Our calculations suggest that the majority of the surplus sources are formed in tidal captures of black holes by main-sequence stars of low mass, M*≤ 0.3-0.4 M ⊙ , with some contribution of neutron star (NS) systems of same type. Due to the small size of the accretion discs, a fraction of such systems may be persistent X-ray sources. Some of the sources may be ultracompact X-ray binaries with helium star/white dwarf companions. We also predict a large number of faint transients, both NS and BH systems, within ∼1 arcmin from the M31 galactic centre. Finally, we consider the population of dynamically formed binaries in Galactic globular clusters, emphasizing the differences between these two types of stellar environments.