Miracle-dz/UniFAR-FTUs huggingface dataset:
Incorporating antigen processing into CD4+ T cell epitope prediction with integer linear programming

CD4+ T-cell receptors recognize peptide-MHCII complexes displayed on the surface of antigen-presenting cells to induce an immune response. A fundamental problem in immunology is to characterize which peptides (i.e., epitopes) in an antigen induce such a response; this is the problem of computational epitope prediction. To be presented in the form of peptide-MHCII complex, peptides must satisfy two important criteria: they should be processed from an antigen to be available in the pool of peptides to which MHCII can bind and should have a sufficiently high binding affinity to MHCII molecules to form stable complexes. This latter phenomenon has been studied widely and used almost exclusively for epitope prediction. In prior work we have developed methods for modeling antigen processing and have shown that it has significant predictive power in predicting epitopes. In this paper, we propose an integer linear programming (ILP) approach to combine the contributions of antigen processing and peptide binding that provides a holistic and flexible framework for epitope prediction. We validate our results on data sets comprising of antigens associated with tumors and pathogens and show consistent enrichment and improvement in accuracy over other methods.
Haplotype-aware variant selection for genome graphs

Graph-based genome representations have proven to be a powerful tool in genomic analysis due to their ability to encode variations found in multiple haplotypes and capture population genetic diversity. Such graphs also unavoidably contain paths which switch between haplotypes (i.e., recombinant paths) and thus do not fully match any of the constituent haplotypes. The number of such recombinant paths increases combinatorially with path length and cause inefficiencies and false positives when mapping reads. In this paper, we study the problem of finding reduced haplotype-aware genome graphs that incorporate only a selected subset of variants, yet contain paths corresponding to all α-long substrings of the input haplotypes (i.e., non-recombinant paths) with at most δ mismatches. Solving this problem optimally, i.e., minimizing the number of variants selected, is previously known to be NP-hard [14]. Here, we first establish several inapproximability results regarding finding haplotype-aware reduced variation graphs of optimal size. We then present an integer linear programming (ILP) formulation for solving the problem, and experimentally demonstrate this is a computationally feasible approach for real-world problems and provides far superior reduction compared to prior approaches.
ArcheGEO: towards improving relevance of gene expression omnibus search results

Transciptomic data stored in the Gene Expression Omnibus (GEO) serves thousands of queries per day, but a lack of standardized machine-readable metadata causes many searches to return irrelevant hits, which impede convenient access to useful data in the GEO repository. Here, we describe ArcheGEO, a novel end-to-end framework that improves results from the GEO Browser by automatically determining the relevance of these results. Unlike existing tools, ArcheGEO reports on the irrelevant results and provides reasoning for their exclusion. Such reasoning can be leveraged to improve annotations of metadata.
Neighborhood embedding and re-ranking of disease genes with ADAGIO

We present ADAGIO, a new method for network-based disease gene prioritization that balances network interconnection structure with an embedding measure of network similarity. We show ADAGIO performs better than previous methods for recovering known disease genes in a recent benchmark set encompassing disease-associated genes for 22 polygenic diseases. We find ADAGIO discovers some interesting new disease gene candidates in both Alzheimer's and Parkinson's diseases. Code, ranked lists of disease genes, and supplementary figures and tables appear at https://github.com/merterden98/ADAGIO.
Connectome transformer with anatomically inspired attention for Parkinson's diagnosis

Parkinson's disease (PD) is the second most prevalent neurodegenerative disease in the United States. The structural or functional connectivity between regions of interest (ROIs) in the brain and their changes captured in brain connectomes could be potential biomarkers for PD. To effectively model the complex non-linear characteristic connectomic patterns related to PD and exploit the long-range feature interactions between ROIs, we propose a connectome transformer model for PD patient classification and biomarker identification. The proposed connectome transformer learns the key connectomic patterns by leveraging the global scope of the attention mechanism guided by an additional skip-connection from the input connectome and the local level focus of the CNN techniques. Our proposed model significantly outperformed the benchmarking models in the classification task and was able to visualize key feature interactions between ROIs in the brain.
The historical approach to marketing and consumption: Contributions and research programmes

The historical approach is too rarely used in our discipline, while it offers many advantages for marketing and consumer research. In particular, the historical approach offers the following contributions: (1) to grasp the density and discontinuities of consumption phenomena, which is necessary for the mobilisation of certain theoretical perspectives; (2) to challenge new theoretical proposals and instituted chronologies and (3) to feed managerial thought through the historicising of marketing and consumption issues and strategies. Based on these reflections and a review of the work in our discipline, we propose research programmes that deserve to be developed and enriched by the historical approach.
MEASUREMENT OF TEMPORAL COHERENCE OF VISIBLE CW LASER SOURCES USING INTERFEROMETRIC METHODS

The use o f Mi chel son interfero met er to measure the coheren ce function for the determin ation o f temporal coherence o f visi ble continuous wave Nd:YA G and Diode laser sources is present ed. The application o f this method is i mport ant in particul ar wh en dealin g wi th weak coherent li ght sources wh ere in formation about their coherence properti es may be useful. Frin ge pat terns were formed, modulated and measured b y point detection and obser vation on an oscilloscope were used to obtain the fringe visibilit y as a funct ion of the length diffe rence bet ween interfero met er arms. The visibilit y function indicativel y measured the modulus of the t emporal coherence function of laser sources. By Fourier transforming th e sq uare o f th e modulus o f t h e t emporal coherence function , the auto-correl atio n of th e frequency di stributi on of the laser sources were obtained. Thei r mode structures, coh eren ce lengths and coherence ti mes were then esti mat ed fro m this distribution. The result also shows a stead y decrease o f visibilit y as the len gth di fference bet ween the arms o f the interfero met er was made very large for both sources, which is consist ent with th e theo ry.
Gakushuin Natural Radiocarbon Measurements II

This date list covers many of the datings done from November 1961 to October 1962. Technique described in Gakushuin I (Gakushuin I) is virtually unchanged, using 900-ml acetylene-filled proportional counter (Counter 1) with multiple-anode anti-coincidence ring counter.
A periodic adaptive controller for the torque loop of variable speed brushless DC motor drives with non-ideal back-electromotive force

In this paper, an adaptive current controller is proposed for variable speed brushless direct current (BLDC) motor drives to minimize the output torque ripples caused by parametric and periodically varying uncertainties. Phase-to-phase non-ideal back-electromotive force (back-EMF) in BLDC motor changes periodically with respect to the shaft angle, and hence the period of these signals alters depending on the rotor frequency. To address these problems, the uncertain current dynamics of the BLDC motor is reformulated by transforming the time variable, then the periodic adaptive controller employing the instantaneous estimation values of the unknown periodic signal is developed to achieve the torque ripple reduction. The periodic estimation of the non-ideal back-EMF waveform is achieved considering the switching between conduction and commutation periods. Also, the update rules based on direct adaptation for parametric uncertainties are derived, and thus, hybrid differential-periodic adaptation rules are obtained considering the switching phenomenon. Asymptotic convergence of the phase currents to the reference values is proven by an appropriate Lyapunov–Krasovskii function depending on the angular position. Comprehensive numerical simulation studies have been successfully carried out to verify the performance and the effectiveness of the proposed controller for variable speed applications.
MAKOY (SOLANUM NIGRUM) - A REVIEW ON A UNANI DRUG

A Unani medicine has been practiced traditionally in Indian subcontinent since a very long time. A Unani drug Makoy or blacknight shade, botanically named as Solanum nigrum Linn. belongs to family Solanaceae cultivated throughout the country in dry parts, quite common in cultivated lands, road sides and gardens. The drug has two varieties, one is bearing black color fruit, and other one has reddish brown color fruit. In both varieties, black color fruits are toxic in nature. It is recommended that the root bark should not to be given to pregnant women. The Unani physicians have prescribed Makoy in various ailments like ascites, piles and chronic cirrhosis of the liver, gonorrhoea, inflammatory swellings and chronic cirrhosis of the liver and spleen, rheumatic and gouty joints and various skin disorders. This drug has been used extensively for its various therapeutic purposes such that astringent, carminative, diuretic, anti inflammatory, anti microbial, hepatoprotective and analgesic. In this review, an effort has been made to provide information on medicinal properties of Makoy (Solanum nigrum) mentioned in Unani classical literature as well as in recent scientific studies. and The results of the study indicated that aqueous extracts of leaf and fruit significant effect in dose dependent manner, by extracts. It was observed the stem extract of no [27] antidiabetic
QCD Phase Transition in Dgp Brane Cosmology

In the standard picture of cosmology it is predicted that a phase transition, associated with chiral symmetry breaking after the electroweak transition, has occurred at approximately 10μ seconds after the Big Bang to convert a plasma of free quarks and gluons into hadrons. We consider the quark-hadron phase transition in a Dvali, Gabadadze and Porrati (DGP) brane world scenario within an effective model of QCD. We study the evolution of the physical quantities useful for the study of the early universe, namely, the energy density, temperature and the scale factor before, during and after the phase transition. Also, due to the high energy density in the early universe, we consider the quadratic energy density term that appears in the Friedmann equation. In DGP brane models such a term corresponds to the negative branch (ϵ = -1) of the Friedmann equation when the Hubble radius is much smaller than the crossover length in 4D and 5D regimes. We show that for different values of the cosmological constant on a brane, λ, phase transition occurs and results in decreasing the effective temperature of the quark-gluon plasma and of the hadronic fluid. We then consider the quark-hadron transition in the smooth crossover regime at high and low temperatures and show that such a transition occurs along with decreasing the effective temperature of the quark-gluon plasma during the process of the phase transition.
SAT-Based Leximax Optimisation Algorithms

In several real-world problems, it is often the case that the goal is to optimise several objective functions. However, usually there is not a single optimal objective vector. Instead, there are many optimal objective vectors known as Pareto-optima. Finding all Pareto-optima is computationally expensive and the number of Pareto-optima can be too large for a user to analyse. A compromise can be made by defining an optimisation criterion that integrates all objective functions. In this paper we propose several SAT-based algorithms to solve multi-objective optimisation problems using the leximax criterion. The leximax criterion is used to obtain a Pareto-optimal solution with a small trade-off between the objective functions, which is suitable in problems where there is an absence of priorities between the objective functions. Experimental results on the Multi-Objective Package Upgradeability Optimisation problem show that the SAT-based algorithms are able to outperform the Integer Linear Programming (ILP) approach when using non-commercial ILP solvers. Additionally, experimental results on selected instances from the MaxSAT evaluation adapted to the multi-objective domain show that our approach outperforms the ILP approach using commercial solvers.
On the origin of high-energy cosmic neutrinos

Recently, the IceCube collaboration made a big announcement of the first discovery of high-energy cosmic neutrinos. Their origin is a new interesting mystery in astroparticle physics, but the present data may give us hints of connection to cosmic-ray and/or gamma-ray sources. We will look over possible scenarios for the cosmic neutrino signal, and emphasize the importance of multimessenger approaches in order to identify the PeV neutrino sources and get crucial clues to the cosmic-ray origin. We also discuss some possibilities to study neutrino properties and probe new physics.
Local aspects in distributed algorithms

Dans cette these, nous etudions differents aspects lies a la localite des algorithmes distribues. D'abord, dans le modele avec echange de messages, nous donnons des algortithmes deterministes sous lineaires en temps pour la construction de decompositions peu denses de graphes et des applications sou-jacentes. Nous donnons aussi des algortithmes ayant une complexite en temps mieux que ous lineaire pour la construction de sous graphes couvrants ayalnt peu d'aretes et un petit facteur d'etirement. Ensuite, nous etudions le probleme de la poignee de main distribuee (ou calcul de couplage en temps constant) dans le modele avec agents mobiles ainsi que deux autres extentions de ce probleme. Parmis nos resultats, nous obtenons de nouvelles idees pour ameliorer les algortithmes existants dans le modele avec echange de messages. Dans une approche plus formelle, nous montrons a travers plusieurs exemples comment on peut coder des algorthmes distribues complexes en utilisant le formalisme des systemes de reetiquetage. Dans une approche plus pratique, nous exposons nos contributiond dans le developpement de la plateforme logicielle ViSiDiA pour la simulation et la visualisation d'algorithmes distribues.
Distributed control of linear time‐varying systems interconnected over arbitrary graphs

In this paper, we focus on designing distributed controllers for interconnected systems in situations where the controller sensing and actuation topology is inherited from that of the plant. The distributed systems considered are composed of discrete‐time linear time‐varying subsystems interconnected over arbitrary graph structures. The main contribution of this paper is to provide results on general graph interconnection structures in which the graphs have potentially an infinite number of vertices. This is accomplished by first extending previous machinery developed for systems with spatial dynamics on the lattice Zn . We derive convex analysis and synthesis conditions for design in this setting. These conditions reduce to finite sequences of LMIs in the case of eventually periodic subsystems interconnected over finite graphs. The paper also provides results on distributed systems with communication latency and gives an illustrative example on the distributed control of hovercrafts along eventually periodic trajectories. The methodology developed here provides a unifying viewpoint for our previous and related work on distributed control. Copyright © 2013 John Wiley & Sons, Ltd.
Infinite Loop Spaces

The theory of infinite loop spaces has been the center of much recent activity in algebraic topology. Frank Adams surveys this extensive work for researchers and students. Among the major topics covered are generalized cohomology theories and spectra; infinite-loop space machines in the sense of Boadman-Vogt, May, and Segal; localization and group completion; the transfer; the Adams conjecture and several proofs of it; and the recent theories of Adams and Priddy and of Madsen, Snaith, and Tornehave.
Large-Scale Geographic Size Variability of Cyprideis torosa (Ostracoda) and Its Taxonomic and Ecologic Implications

Body-size variability results from a variety of extrinsic and intrinsic factors (environmental and biological influences) underpinned by phylogeny. In ostracodes it is assumed that body size is predominantly controlled by ecological conditions, but investigations have mostly focused on local or regional study areas. In this study, we investigate the geographical size variability (length, height, and width) of Holocene and Recent valves of the salinity-tolerant ostracode species Cyprideis torosa within a large geographical area (31°–51° latitude, and 12°–96° longitude). It is shown that distant local size clusters of Cyprideis torosa are framed within two large-scale geographical patterns. One pattern describes the separation of two different size classes (i.e., morphotypes) at around ∼42° N. The co-occurrence of both size morphotypes in the same habitats excludes an environmental control on the distribution of the morphotypes but rather could point to the existence of two differentiated lineages. Generally, correlations between valve size and environmental parameters (salinity, geographical positions) strongly depend on the taxonomic resolution. While latitude explains the overall size variability of C. torosa sensu lato (i.e., undifferentiated for morphotypes), salinity-size correlations are restricted to the morphotype scale. Another large-scale pattern represents a continuous increase in valve size of C. torosa with latitude according to the macroecological pattern referred as Bergmann trend. Existing explanations for Bergmann trends insufficiently clarify the size cline of C. torosa which might be because these models are restricted to intraspecific levels. The observed size-latitude relationship of C. torosa may, therefore, result from interspecific divergence (i.e., size ordered spatially may result from interspecific divergence sorting) while environmental influence is of minor importance. Our results imply that geographical body-size patterns of ostracodes are not straightforward and are probably not caused by universal mechanisms. Consideration of phylogenetic relationships of ostracodes is therefore necessary before attempting to identify the role of environmental controls on body size variability.
Sensory neuroecology and multimodal evolution across the genus Drosophila

The neural basis and genetic mechanisms for sensory evolution are increasingly being explored in depth across many closely related members of the Drosophila genus. This has, in part, been achieved due to the immense efforts toward adapting gene-editing technologies for additional, non-model species. Studies targeting both peripheral sensory variations, as well as interspecies divergence in coding or neural connectivity, have generated numerous, tangible examples of how and where the evolution of sensory-driven animal behavior has occurred. Here, we review and discuss studies that each aim to identify the neurobiological and genetic components of sensory system evolution to provide a comparative overview of the types of functional variations observed across both perceptual input and behavioral output. In addition, we examined the roles neuroecology and neuroevolution play in speciation events, such as courtship and intraspecies communication, as well as those aspects related to behavioral divergence in host navigation or egg-laying preferences. Through the investigation of comparative, large-scale trends and correlations across diverse, yet closely related species within this highly ecologically variable genus of flies, we can begin to describe the underlying pressures, mechanisms, and constraints that have guided sensory and nervous system evolution within the natural environments of these organisms.
Transcriptome and association mapping revealed functional genes respond to drought stress in Populus

Drought frequency and severity are exacerbated by global climate change, which could compromise forest ecosystems. However, there have been minimal efforts to systematically investigate the genetic basis of the response to drought stress in perennial trees. Here, we implemented a systems genetics approach that combines co-expression analysis, association genetics, and expression quantitative trait nucleotide (eQTN) mapping to construct an allelic genetic regulatory network comprising four key regulators (PtoeIF-2B, PtoABF3, PtoPSB33, and PtoLHCA4) under drought stress conditions. Furthermore, Hap_01PtoeIF-2B, a superior haplotype associated with the net photosynthesis, was revealed through allelic frequency and haplotype analysis. In total, 75 candidate genes related to drought stress were identified through transcriptome analyses of five Populus cultivars (P. tremula × P. alba, P. nigra, P. simonii, P. trichocarpa, and P. tomentosa). Through association mapping, we detected 92 unique SNPs from 38 genes and 104 epistatic gene pairs that were associated with six drought-related traits by association mapping. eQTN mapping unravels drought stress-related gene loci that were significantly associated with the expression levels of candidate genes for drought stress. In summary, we have developed an integrated strategy for dissecting a complex genetic network, which facilitates an integrated population genomics approach that can assess the effects of environmental threats.