Miracle-dz/UniFAR-FTUs huggingface dataset:
Brewpitopes: a pipeline to refine B-cell epitope predictions during public health emergencies

The application of B-cell epitope identification for the development of therapeutic antibodies is well established but consuming in terms of time and resources. For this reason, in the last few years, the immunoinformatic community has developed several computational predictive tools. While relatively successful, most of these tools only use a few properties of the candidate region to determine their likelihood of being a true B-cell epitope. However, this likelihood is influenced by a wide variety of protein features, including the presence of glycosylated residues in the neighbourhood of the candidate epitope, the subcellular location of the protein region or the three-dimensional information about their surface accessibility in the parental protein. In this study we created Brewpitopes, an integrative pipeline to curate computational predictions of B-cell epitopes by accounting for all the aforementioned features. To this end, we implemented a set of rational filters to mimic the conditions for the in vivo antibody recognition to enrich the B-cell epitope predictions in actionable candidates. To validate Brewpitopes, we analyzed the SARS-CoV-2 proteome. In the S protein, Brewpitopes enriched the initial predictions in 5-fold on epitopes with neutralizing potential (p-value < 2e-4). Other than S protein, 4 out of 16 proteins in the proteome contain curated B-cell epitopes and hence, have also potential interest for viral neutralization, since mutational escape mainly affects the S protein. Our results demonstrate that Brewpitopes is a powerful pipeline for the rapid prediction of refined B-cell epitopes during public health emergencies. Statement of significance We have created Brewpitopes, a new pipeline that integrates additional important features such as glycosylation or structural accessibility, to curate B-cell epitope more likely to be functional in vivo. We have also validated Brewpitopes against SARS-CoV-2 not only for S protein but also for the entire viral proteome demonstrating that is a rapid and reliable epitope predictive tool to be implemented in present or future public health emergencies. Brewpitopes has identified 7 SARS-CoV-2 epitopes in S and epitopes allocated in 4 other proteins. Overall, offering an accurate selection of epitopes that might be scaled up to the production of new antibodies.
Zebrafish embryos are more efficient and robust than zebrafish larvae in evaluating human norovirus infectivity

This study reports an essential improvement of the method for replication of human norovirus (hNoV) with the use of zebrafish (Danio rerio) embryos. With three globally prevalent hNoV genotypes and P-types GII.2[P16], GII.4[P16], and GII.17[P31], we demonstrated that this tool had high efficiency and robustness, and enabled continuous virus passaging. This tool is versatile in being applied in hNoV related research. In pathogenesis study, the zebrafish embryo generated hNoVs showed clear binding patterns to human histo-blood group antigens (HBGAs) in human saliva by a simple saliva-binding reverse transcription-quantitative polymerase chain reaction (RT-qPCR). In disinfection study, it was shown that a dose of 6 mJ/cm2 UV254 was able induce > 2-log reduction in hNoV infectivity for all three hNoV strains tested, suggesting that hNoVs were more UV susceptible than multiple enteric viruses and commonly used hNoV surrogates as tested before. IMPORTANCE HNoVs are a leading cause of gastroenteritis outbreaks worldwide. The zebrafish embryo tool as developed in this study serves as an efficient way to generate viruses with high titers and clean background and a straightforward platform to evaluate hNoV inactivation efficacies. It is expected that this tool will not only benefit epidemiological research of hNoV but also be used to generate hNoV inactivation parameters which are highly needed by the water treatment and food industry.
The functional role of oscillatory dynamics in neocortical circuits: a computational perspective

Biological neuronal networks exhibit hallmark features such as oscillatory dynamics, heterogeneity, modularity, and conduction delays. To investigate which of these features support computations or are epiphenomena, we simulated recurrent networks and analyzed the effects of implementing these features on performance in benchmark tests for pattern classification. Configuring the network nodes as damped harmonic oscillators reproduced essential features of cortical dynamics and led to networks that vastly outperformed non-oscillating RNN architectures in learning speed, task performance, parameter efficiency, and noise tolerance. Implementation of additional biological features further improved performance. Analyses of network dynamics uncovered a novel, powerful computational principle and provided plausible a posteriori explanations for features of natural networks whose computational role has remained elusive for a long time. It is discussed how the computational principle realized in the model could be implemented in analog computing devices capable of unsupervised learning. One-Sentence Summary Recurrent networks of damped harmonic oscillators have powerful computational abilities and reproduce biological phenomena.
Polyphenols, antioxidant activity, and functional properties of baobab (Adansonia digitata L) seeds soaked in monovalent ion salts

ABSTRACT Baobab (Adansonia digitata L.) seeds are underutilized and native to Savannah regions of Africa. The problem of the hard-to-cook (HTC) phenomenon with antinutrients exists. The application of monovalent ion salt solutions becomes important. This study analyzed the effect of soaking in deionized water, 0.5% w/v monovalent ion salts (NaCl, NaHCO3), sodium salt of a divalent ion (Na2S2O5) on the polyphenyl, antioxidant activity, and functional properties. The salts caused protein, crude fiber, vitamin C, and dry matter contents of 40.2–44.6 g/100 g, 7.78–9.46%, 3.0–3.4 mg/100 g, and 80.4–86.2%, respectively. Seed thickness, weight, and color were influenced by soaking in monovalent salt solutions. The total phenolic content (TPC), total flavonoid content (TFC), and proanthocyanidins range was 251–326 mg GAE/100 g, 236–288 mg TE/100 g, and 59–70.4 mg LE/100 g respectively. The Ferric Reducing Antioxidant Power (FRAP), DPPH (2,2-diphenyl-1-picrylhydrazyl) free radical scavenging, and ABTS+ (2,2’-azinobis-3-ethyl benzothiazoline-6-sulfonate) ranged between 208.4–291.3 mg EA/g, 86.0–104 mg TE/g, and 98.3–110 µmol AEAC/100 g respectively. Bulk density, phytates, and oxalates were reduced significantly (p < 0.05), and gelatinization temperature increased. Monovalent salts reduce antinutrients, promote solubilization of polyphenols, modify the seed properties, and contribute to softening of the seeds.
RNA- and DNA-binding proteins generally exhibit direct transfer of polynucleotides: Implications for target site search

We previously demonstrated that the PRC2 chromatin-modifying enzyme exhibits the ability to directly transfer between RNA and DNA without a free-enzyme intermediate state. Simulations suggested that such a direct transfer mechanism may be generally necessary for RNA to recruit proteins to chromatin, but the prevalence of direct transfer capability is unknown. Herein, we used fluorescence polarization assays and observed direct transfer for several well-characterized nucleic acid-binding proteins: three-prime repair exonuclease 1 (TREX1), heterogeneous nuclear ribonucleoprotein U, Fem-3-binding factor 2, and MS2 bacteriophage coat protein. For TREX1, the direct transfer mechanism was additionally interrogated by single molecule assays, and the data suggest that direct transfer occurs through an unstable ternary intermediate with partially associated ligands. Generally, direct transfer could allow many DNA- and RNA-binding proteins to conduct a one-dimensional search for their target sites. Furthermore, presumably long-lived protein-polynucleotide complexes might instead be readily replaced by other protein-polynucleotide complexes in vivo. Significance Classically, the lifetime of a protein-ligand complex is presumed to be an intrinsic property, unaffected by competitor molecules in free solution. By contrast, a few oligomeric nucleic acid binding proteins have been observed to exchange competing ligands in their binding sites, and consequently their lifetimes decrease with competitor concentration. Our findings indicate that this “direct transfer” is a more general property of nucleic acid binding proteins. This suggests that many DNA- and RNA-binding proteins can reduce the dimensionality of their search for their target sites by intramolecular direct transfer to nucleosome DNA, instead of relying entirely on three-dimensional diffusion, and it suggests that their mean complex lifetimes in vivo can be regulated by the concentration of free ligand molecules.
Generalization in Sensorimotor Networks Configured with Natural Language Instructions

One of humans’ most fundamental cognitive feats is the ability to interpret linguistic instructions in order to perform novel tasks without any explicit experience with the task. Yet, the computations that the brain might use to accomplish such a feat remains poorly understood. Here we use the latest advances in Natural Language Processing to create a neural model of generalization based on linguistic instructions. Models are trained on a set of commonly studied psychophysical tasks, and receive instructions embedded by a pre-trained language model. Our best models can perform a previously unseen task with a performance of 83% correct on average based solely on linguistic instructions (i.e. 0-shot learning). We found that language scaffolds sensorimotor representations such that activity for interrelated tasks share a common geometry with the semantic representations of instructions, allowing language to cue the proper composition of practiced skills in unseen settings. Finally, we show how this model can generate a linguistic description of a novel task it has identified using only motor feedback, which can subsequently guide a partner model to perform the task. Our models offer several experimentally testable predictions outlining how linguistic information must be represented in order to facilitate flexible and general cognition in the human brain.
Spot modelling of the flare M4.5 dwarf YZ CMi

We report on a photometric study of the flareM4.5 dwarf YZ CMi as based on photoelectric observations from the seasons 1972/73, 1979/80 and 1996/97. We suggest spot activity to explain the light and colour curves. Spots are generally 500K cooler than the surrounding photosphere and there are basically two solutions available for the observations: high latitude spot changing slightly basic properties such as radius and latitude or active near-equatorial (belt-like) centers represented by three spots. However, the activity centers changed in longitudes (∼180°). The typical spot coverage (inclination i = 60°) is 10-15% and 5% for the season 1996/97 or ∼25% for the stellar inclination i = 75°. As a by-product, V curve and (V-I) and (V-K) indexes turn out to be most promising in modelling of M-type stars as far as present calibrations are concerned. (© 2003 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)
Residents’ perception of privacy in selected public housing estates in Ibadan, Nigeria

ABSTRACT The study assessed the residents’ perception of privacy and their privacy regulating mechanisms with a view to providing information that could improve public housing design. The study used quantitative and qualitative approach. A sample size of 565 household heads was selected for questionnaire administration using systematic random sampling, representing 50% of the sampling frame. In-depth interviews were conducted on twelve (12) key informants from among the executive of neighbourhood associations. Descriptive and inferential statistics were used to analyse quantitative data while content analysis was used for the qualitative data. About half of the residents (50.38%) perceived privacy as low or very low, with visual privacy being rated least (Privacy Perception Index, PPI = 2.34), followed by family (2.22), olfactory (2.12), aural (2.00), neighbourhood (1.79) and personal privacy (1.64). Positioning of spaces, orientation of openings, and absence of dedicated guest room, contributed to low perception of visual and family privacy. About 92% of the respondents agreed or strongly agreed to the use of privacy regulating mechanisms, with personal space and territorial behaviour being more adopted, while non-verbal behaviour was least adopted. The study concluded that perception of privacy was influenced more by housing characteristics than by residents’ socio-economic and cultural characteristics.
Wave equation migration with the phase-shift method

Accurate methods for the solution of the migration of zero‐offset seismic records have been developed. The numerical operations are defined in the frequency domain. The source and recorder positions are lowered by means of a phase shift, or a rotation of the phase angle of the Fourier coefficients. For applications with laterally invariant velocities, the equations governing the migration process are solved very accurately by the phase‐shift method. The partial differential equations considered include the 15 degree equation, as well as higher order approximations to the exact migration process. The most accurate migration is accomplished by using the asymptotic equation, whose dispersion relation is the same as that of the full wave equation for downward propagating waves. These equations, however, do not account for the reflection and transmission effects, multiples, or evanescent waves. For comparable accuracy, the present approach to migration is expected to be computationally more efficient than fini.
Towards lower bounds on locally testable codes

1 Abbreviations and Notations 3 1 General Introduction 4 1.1 PCP theorem . 4 1.2 Property Testing . 5 1.3 Locally Testable Codes . 6 1.3.1 Random locally testable codes . 6 1.3.2 Algebraic Construction of LTCs . 7 1.3.3 Combinatorial Construction of LTCs . 7 1.3.4 Constructions of LTCs based on PCPs of proximity . 9 1.4 Locally Decodable Codes . 10 2 Summary of results 11 3 Global Definitions and Preliminaries 14 3.1 General Notations . 14 3.2 Codes invariant under groups . 15 3.3 Locally Testable Codes . 15 3.4 Locally Decodable (Correctable) Codes . 18 4 Locally Testable Codes Require Redundant Testers 20 4.
Consumer Multiattribute Judgments under Attribute-Weight Uncertainty

This article examines how multiattribute impressions are formed in riskless choice and judgment when there is uncertainty or ambiguity associated with attribute-importance weights. Building on previous results in the modeling of ambiguity in probabilities, a mathematical theory of multiattribute judgments under weight uncertainty is developed. The theory incorporates framing effects for ambiguous weights in multiattribute judgments, similar to the gain-loss framing effects found in studies of preferences for lotteries. Specifically, it is shown that the importance of an attribute depends on whether it is seen as enhancing or preserving an expected level of utility in a category. The results of three experiments provide support for the predicted dependency of the effects of weight uncertainty on an attribute's framing. The data also suggest that, within frames, the effects of increasing uncertainty may not be additive across attributes. In particular, given pairs of uncertain attributes with different frames, subjects acted as if they were applying a single frame to both attributes, resulting in a common direction for the weight-uncertainty effect.
Simulated optical images of galaxies at z about 1 using ultraviolet images of nearby galaxies

Ultraviolet sounding rocket images of several nearby galaxies are used to simulate the appearance in optical bandpasses of similar systems at redshifts z = 0.5-2.67, as observed by the WFPC on HST and by ground-based instruments. Since the morphology of galaxies is a strong function of the wavelength, the appearance of galaxies at large redshifts is subjected to a large k-correction effect. The strong dependence of monochromatic surface brightness on redshift also implies that observed morphology of distant systems will be crucially dependent on the limiting surface brightness set by the sky background. Although the angle subtended by sources depends only weakly on z, the fraction of a galaxy whose surface brightness is above the detection threshold varies strongly with z. Morphological distinctions of spiral from elliptical, spiral from irregular, and barred from unbarred types become more difficult, as does accurate evaluation of interactions or of the local environment. 32 refs.
Spaces and maps of idempotent measures

We prove that the weak* topologization of the set of all idempotent measures (Maslov measures) on compact Hausdorff spaces defines a functor on the category of compact Hausdorff spaces, and this functor is normal in the sense of E. V. Shchepin; in particular, it has many properties in common with the probability measure functor and the hyperspace functor. Moreover, we establish that this functor defines a monad in the category , and prove that the idempotent measure monad contains the hyperspace monad as a submonad. For the space of idempotent measures there is an analogue of the Milyutin map (that is, of a continuous map of compact Hausdorff spaces which admits a regular averaging operator for spaces of continuous functions). Using the assertion of the existence of Milyutin maps for idempotent measures, we prove that the idempotent measure functor is open, that is, it preserves the class of open surjective maps. We also prove that, in contrast to the case of probability measure spaces, the correspondence assigning to any pair of idempotent measures the set of measures on their product which have the given marginals is not continuous.
Fundamental problems in the theory of multi-agent robotics

1 Symbols and Abbreviations . 3
Multiplicity and nondegeneracy of positive solutions to quasilinear equations on compact Riemannian manifolds

We consider a compact, connected, orientable, boundaryless Riemannian manifold (M, g) of class C∞ where g denotes the metric tensor. Let n = dim M ≥ 3. Using Morse techniques, we prove the existence of nonconstant solutions u ∈ H1,p(M) to the quasilinear problem for e > 0 small enough, where 2 ≤ p < n, p < q < p*, p* = np/(n - p) and is the p-laplacian associated to g of u (note that Δ2,g = Δg) and denotes the Poincare polynomial of M. We also establish results of genericity of nondegenerate solutions for the quasilinear elliptic problem (Pe).
Impedance of antennas in a warm isotropic plasma - A comparison of different models

The impedance of a sphere in a plasma is calculated for four different models. There are important differences between the four results. In particular, the real part of the impedance is shown to vanish at several frequencies above the plasma frequency for a spherical grid if the plasma is described by hydrodynamic equations. If the kinetic (Vlasov) equation is used, the nulls are changed into minima that are only noticeable if the radius is much greater than the Debye length and the frequency is not too far above the plasma frequency. If the hydrodynamic equations are used but the normal component of the fluid velocity is assumed to vanish on the (solid) sphere, there are no nulls or minima. The relationship of these results to previous work on antennas in plasmas is considered.
Overcomplete dictionaries for sparse representation of signals

In recent years there has been a growing interest in the study of sparse representation of signals. Using an overcomplete dictionary that contains prototype signal-atoms, signals are described as linear combinations of a few of these atoms. Applications that use sparse representation are many and include compression, regularization in inverse problems, feature extraction, and more. Roughly speaking, the activity in this field concentrates around two main problems: (i) algorithms for performing sparse decomposition and their performance analysis, and (ii) dictionary composition methods. The ‘sparse decomposition’ activity deals with the pursuit problem given a signal and an overcomplete dictionary, the goal is to find the smallest set of atoms from the dictionary to represent it. As this problem is known to be NP-hard, several approximation algorithms have been suggested, such as the matching pursuit, the basis pursuit, FOCUSS, and their variants. Recent work has been also directed at the study of these algorithms’ performance and prospects of success. The construction of appropriate dictionaries that lead to the existence of sparse representations for a family of signals in mind is the second challenge addressed in recent years in this field. Among the various contributions on this problem, dictionary learning from examples is especially appealing as it can tune the found dictionary to specific and narrow families of signals. In this work we concentrate on this dictionary learning process. Starting with a wide literature survey of pursuit techniques and existing dictionary learning
Imaging of the Compact Dust Disk around DG Tauri with 1'' Resolution

We have made aperture synthesis observations of 147 GHz continuum emission from the dust around the young star DG Tau with the Nobeyama Millimeter Array. Using the sparsest AB configuration of the array, we attained a small synthesized beam of 1. ″48 × 1. ″08 with P.A. = 117°. As a result, a disklike structure of the dust has been successfully resolved. The size of the dust disk is estimated to be 1. ″56 × 0. ″54 (218 AU × 76 AU) with P.A. = 99°, which is corrected for the synthesized beam pattern and atmospheric seeing. The disk size of the seeing was estimated to be 0. ″42 from observations of a pointlike calibrator. Assuming a geometrically thin disk, the radius and inclination angle of the dust disk are calculated to be 109 ± 22 AU and 70° ± 10°, respectively. The total flux density emitted from the dust disk is 186 ± 17 mJy, and the disk mass is calculated to be 0.01-0.06 M☉, using the dust opacity coefficient κν = 0.05-0.02 cm2 g-1. The resolved dust disk is quite consistent with the spectral energy distribution of DG Tau, although the disk radius of 109 AU is slightly larger than the radius of 75 AU derived by Adams, Emerson, & Fuller. Our results, however, do not agree with the infalling envelope model proposed by Calvet and coworkers, where the major part of the flux density in the millimeter to mid-infrared range comes from the large envelope.
IRROTATIONAL FLOW ABOUT SHIP FORMS

A method of computing the potential flow about a ship model in terms of a source distribution on the hull surface is described. After a formulation and discussion of the flow with wavemaking, the zero-froude number, double-ship-model case is treated in detail. The Fredholm singular integral equation of the second kind for the source distribution is solved numerically by removing the singularity, replacing the integral by a quadrature formula, and solving the resulting high-order set of linear equations by an iteration formula for which convergence is proved. The corresponding velocity potential on the hull surface, the evaluation of which from the source distribution also requires the calculation of a singular integral, is obtained by first solving the equipotential problem for the hull form (which employs the same kernel as the original integral equation). The solution of this Dirichlet problem is then used to remove the singularity from the velocity-potential integral, and then the latter is computed by means of a quadrature formula. The method is applied to an ellipsoid, results from which are compared with the exact solution. A fortran program is included. (Author)