Miracle-dz/UniFAR-FTUs huggingface dataset:
Tumor Antigens and Proteomics from the Point of View of the Major Histocompatibility Complex Peptides*

The major histocompatibility complex (MHC) peptide repertoire of cancer cells serves both as a source for new tumor antigens for development of cancer immunotherapy and as a rich information resource about the protein content of the cancer cells (their proteome). Thousands of different MHC peptides are normally displayed by each cell, where most of them are derived from different proteins and thus represent most of the cellular proteome. However, in contrast to standard proteomics, which surveys the cellular protein contents, analyses of the MHC peptide repertoire correspond more to the rapidly degrading proteins in the cells (i.e. the transient proteome). MHC peptides can be efficiently purified by affinity chromatography from membranal MHC molecules, or preferably following transfection of vectors for expression of recombinant soluble MHC molecules. The purified peptides are resolved and analyzed by capillary high-pressure liquid chromatography-electrospray ionization-tandem mass spectrometry, and the data are deciphered with new software tools enabling the creation of large databanks of MHC peptides displayed by different cell types and by different MHC haplotypes. These lists of identified MHC peptides can now be used for searching new tumor antigens, and for identification of proteins whose rapid degradation is significant to cancer progression and metastasis. These lists can also be used for identification of new proteins of yet unknown function that are not detected by standard proteomics approaches. This review focuses on the presentation, identification and analysis of MHC peptides significant for cancer immunotherapy. It is also concerned with the aspects of human proteomics observed through large-scale analyses of MHC peptides.
Multi-application profile updates propagation: a semantic layer to improve mapping between applications

In the field of multi-application personalization, several techniques have been proposed to support user modeling for user data management across different applications. Many of them are based on data reconciliation techniques often implying the concepts of static ontologies and generic user data models. None of them have sufficiently investigated two main issues related to user modeling: (1) profile definition in order to allow every application to build their own view of users while promoting the sharing of these profiles and (2) profile evolution over time in order to avoid data inconsistency and the subsequent loss of income for web-site users and companies. In this paper, we conduct work and propose separated solutions for every issue. We propose a flexible user modeling system, not imposing any fixed user model whom different applications should conform to, but based on the concept of mapping among applications (and mapping functions among their user attributes). We focus in particular on the management of user profile data propagation, as a way to reduce the amount of inconsistent user profile information over several applications. A second goal of this paper is to illustrate, in this context, the benefit obtained by the integration of a Semantic Layer that can help application designers to automatically identify potential user attribute mappings between applications. This paper so illustrates a work-in-progress work where two complementary approaches are integrated to improve a main goal: managing multi-application user profiles in a semi-automatic manner.
Structure of matrix elements in the quantum Toda chain

We consider the quantum Toda chain using the method of separation of variables. We show that the matrix elements of operators in the model are written in terms of a finite number of `deformed Abelian integrals'. The properties of these integrals are discussed. We explain that these properties are necessary in order to provide the correct number of independent operators. A comparison with the classical theory is made.
Race and differences in breast cancer survival in a managed care population.

BACKGROUND African-American women with breast cancer have poorer survival than European-American women. After adjustment for socioeconomic variables, survival differences diminish but do not disappear, possibly because of residual differences in health care access, biology, or behavior. This study compared breast cancer survival in African-American and European-American women with similar health care access. METHODS We measured survival in women with breast cancer who are served by a large medical group and a metropolitan Detroit health maintenance organization where screening, diagnosis, treatment, and follow-up are based on standard practices and mammography is a covered benefit. We abstracted data on African-American and European-American women who had been diagnosed with breast cancer from January 1986 through April 1996 (n = 886) and followed these women for survival through April 1997 (137 deaths). RESULTS African-American women were diagnosed at a later stage than were European-American women. Median follow-up was 50 months. Five-year survival was 77% for African-American and 84% for European-American women. The crude hazard ratio for African-American women relative to European-American women was 1.6 (95% confidence interval [CI] = 1.1-2.2). Adjusting only for stage, the hazard ratio was 1.3 (95% CI = 0.9-1.9). Adjusting only for sociodemographic factors (age, marital status, and income), the hazard ratio was 1.2 (95% CI = 0.8-1.9). After adjusting for age, marital status, income, and stage, the hazard ratio was 1.0 (95% CI = 0.7-1.5). CONCLUSION Among women with similar medical care access since before their diagnoses, we found ethnic differences in stage of breast cancer at diagnosis. Adjustment for this difference and for income, age, and marital status resulted in a negligible effect of race on survival.
Deep Tracking: Visual Tracking Using Deep Convolutional Networks

In this paper, we study a discriminatively trained deep convolutional network for the task of visual tracking. Our tracker utilizes both motion and appearance features that are extracted from a pre-trained dual stream deep convolution network. We show that the features extracted from our dual-stream network can provide rich information about the target and this leads to competitive performance against state of the art tracking methods on a visual tracking benchmark.
Object category pose estimation based on sparse representation and rank minimization

This paper presents a novel framework for object category pose estimation. The novelty of our approach consists in combining the low rank and sparse representation with the PCA-HOG feature[1] so as to estimate the object pose quickly and accurately. Moreover, the refinement mechanism formed by discriminant method is integrated to improve the performance of the classification between the opposite pose. We evaluate our approach for the class car on 3D categories dataset and the EPFL car dataset. Experimental results show that our method outperforms the state-of-the-art.
Turbulent drag reduction by constant near-wall forcing

Computational experiments based on the direct numerical simulation of turbulent channel flow reveal that the skin friction can be reduced as much as 70% by the action of a localized steady force acting against the flow close to the wall. In addition, the excessive shear stresses observed during the laminar-to-turbulence transition can be substantially reduced. For a sustained reduction in the skin friction, the control force has to act within a distance of 20 wall units (scaling with the location of the maximum Reynolds stress gradient); otherwise a transient drag reduction is observed or even an increase in drag. The forcing leads to the formation of a shear layer close to the wall that reduces the skin friction and limits the development of the Reynolds shear stresses. As the amplitude of the forcing is increased, the shear layer breaks down and generates its own turbulence, setting an upper limit to the level of drag reduction. This transition of the shear layer is correlated with a Reynolds number based on the forcing amplitude and length scale.
Lidar profiling of aerosol optical properties from Paris to Lake Baikal (Siberia)

Abstract. In June 2013, a ground-based mobile lidar performed the ~10 000 km ride from Paris to Ulan-Ude, near Lake Baikal, profiling for the first time aerosol optical properties all the way from western Europe to central Siberia. The instrument was equipped with N2-Raman and depolarization channels that enabled an optical speciation of aerosols in the low and middle troposphere. The extinction-to-backscatter ratio (also called lidar ratio or LR) and particle depolarization ratio (PDR) at 355 nm have been retrieved. The LR in the lower boundary layer (300–700 m) was found to be 63 ± 17 sr on average during the campaign with a distribution slightly skewed toward higher values that peaks between 50 and 55 sr. Although the difference is small, PDR values observed in Russian cities (>2%, except after rain) are systematically higher than the ones measured in Europe (
Resilient Big Data Monetization

Resilient Big Data monetization is devised as k-dominance and m-connectivity problems, such that common-interests are connected by k-ways to measurement tools, which are tied within each other in m-ways. Consequently, a greedy approximation algorithm Plutus (i.e resembling Greek god of wealth) is proposed, which isolates measurement tools to ac-quire domination over common-interests, establishes synergy from common-interests to measurement tools and then acquires divergence and sustains it within measurement tools
Duality, Vector advection and the Navier-Stokes equations

In this article we show that three dimensional vector advection equation is self dual in certain sense defined below. As a consequence, we infer classical result of Serrin of existence of strong solution of Navier-Stokes equation. Also we deduce Feynman-Kac type formula for solution of the vector advection equation and show that the formula is not unique i.e. there exist flows which differ from standard flow along which vorticity is conserved.
Good continuation of general 2D visual features: dual harmonic models and computational inference

Good continuation is a fundamental principle of perceptual organization that guides the grouping of parts based on how they should succeed one another within coherent wholes. Despite the general language that was used by the Gestalt psychologists in phrasing this principle, computational work has focused almost exclusively on the study of curve-like structures. Here we offer for the first time, a rigorous generalization of good continuation to arbitrary visual structures that can be abstracted as scalar functions over the image plane. The differential geometry of these structures dictates that their good continuation should be based both on their value and on the geometry of their level sets, which yield a coupled system of equations solvable for a formal model. We exhibit the resulting computation on shading and intensity functions, demonstrating how it eliminates spurious measurements while preserving both regular structure and singularities. Related implementations could be applied to color channels, motion magnitude, and disparity signals
PSS: Provably Secure Encoding Method for Digital Signatures

We describe two encoding methods: EMSA-PSS, for signing with appendix, and EMSR-PSS, for signing with message recovery. These encodings are appropriate for signatures based on the RSA or Rabin/Williams primitive. The methods are as simple and e cient as the methods in the current P1363 draft (based on X9.31 and ISO 9796), but they have better demonstrated security. In particular, treating the underlying hash function as ideal, EMSA-PSS and EMSR-PSS give rise to provably-secure schemes: the ability to forge implies the ability to invert the underlying trapdoor permutation. In fact, when the underlying primitive is RSA, the schemes are not only provably secure, but are so in a tight way: the ability to forge with a certain amount of computational resources implies the ability to invert RSA (on the same size modulus) with essentially the same computational resources. Additional bene ts are described in the body of this paper. The methods described in this contribution are from our Eurocrypt '96 paper, The exact security of digital signatures| How to sign with RSA and Rabin [3]. Department of Computer Science & Engineering, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093. E-Mail: mihir@cs.ucsd. edu. URL: http://www-cse.ucsd. edu/users/mihir. Supported by NSF CAREER Award CCR-9624439 and a 1996 Packard Foundation Fellowship in Science and Engineering. y Department of Computer Science, University of California at Davis, Davis, California 95616. Email: rogaway@cs.ucdavis.edu. URL: http://www.cs.ucdavis.edu/~rogaway. Supported by NSF CAREER Award CCR-9624560, and RSA Data Security { MICRO Grant 97-150.
RECONCILING BEHAVIOURAL AND NEOCLASSICAL ECONOMICS

The representation of the individual in economics as a rational homo oeconomicus had been seriously questioned by the development of behavioural economics. Some authors nevertheless argue that economists do not need to produce complex models of human behaviour, since such investigation does not fall within the scope of economic analysis. We show that the mere definition of the scope of economic analysis is quite ambiguous, between on the one hand a conception of economics as a science of individual choice and on the other hand as a science of social institutions: this duality finds its origins during the marginalist revolution with Jevons, Menger and Walras, whose theories seem to be in conflict concerning the scope of economic analysis and the definition of the "economic man". Economists then produced two distinct models of this economic man, one as the simplification of a real individual, and the other as a representative agent. The figure of the homo oeconomicus developed later by Pareto homogenized these two traditions, leading to the indeterminacy of the scope of economic analysis and in fine to the development of behavioural economics. Since behavioural and neoclassical economics are the continuation of these two distinct traditions, we stress that they should be considered as complementary rather than substitute approaches to economic analysis.
Probabilistic Fusion of $\hbox{K}_{\rm u}$ - and C-band Scatterometer Data for Determining the Freeze/Thaw State

A novel sensor fusion algorithm for retrieving the freeze/thaw (f/t) state from scatterometer data is presented: It is based on a probabilistic model, which is a variant of the Hidden Markov model, and it computes the probability that the landscape is frozen, thawed, or thawing for each day. By combining Ku- and C-band scatterometer data, the distinct backscattering properties of snow, soil, and vegetation at the two radar bands are exploited. The parameters that are necessary for inferring the f/t state are estimated in an unsupervised fashion, i.e., no training data are required. Comparison with model and in situ temperature data in a test area in Siberia/northern China indicates that the approach yields promising results (typical accuracies exceeding 90%); difficulties are encountered over bare rock and areas where large fluctuations in soil moisture are common. These limitations turn out to be closely linked to the inherent assumptions of the probabilistic model.
Melanocortin 4 Receptor-Mediated Hyperphagia and Activation of Neuropeptide Y Expression in the Dorsomedial Hypothalamus during Lactation

In several hyperphagic models, including lactation, in which hypothalamic melanocortin signaling is reduced, a novel expression of NPY mRNA in the dorsomedial hypothalamus (DMH) has been observed, suggesting that melanocortin signaling and the induced NPY in the DMH may constitute unique neurocircuitry in mediating energy balance. Using lactating rats as a model, the present study first showed that in the DMH abundant α-MSH and agouti-related protein fibers are in close apposition to NPY-positive cells. However, no NPY and MC4R (a melanocortin receptor) double-labeled neurons were observed. These data suggested that melanocortin input may synapse on presynaptic terminals that then synapse on DMH NPY cells. To study the function of DMH MC4Rs in energy balance, an MC3/4R-selective agonist, melanotan II (MTII), was injected bilaterally into the DMH. MTII injection significantly suppressed feeding induced by 24 hr fasting or suckling-induced hyperphagia. Furthermore, MTII treatment greatly attenuated suckling-induced NPY expression in the DMH. MTII treatment also stimulated uncoupling protein 1 activity in the brown adipose tissue of suckling female rats, indicative of increased sympathetic outflow. In summary, the present study demonstrated that the melanocortin system in the DMH not only plays an important role in inducing NPY expression in the DMH of lactating rats but also in regulating energy homeostasis, at least in part, by modulating appetite and energy expenditure.
Properties of

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Context and Content in Dialogue Systems

Abstract The paper outlines our dialogue model which com-prises utterance analysis, processing and generationin a DRT framework. We present and discuss in de-tail an example from the EMBASSI domain 1 . 1 Introduction The challenges for speech dialogue systems aremanifold: spontaneous speech phenomena at tele-phone quality, robustness at the language and in-teraction levels, partial interpretation, etc. Thereare also requirements for cooperative behaviourand negotiation abilities. Nearly all working sys-tems, including the Erlangen System EVAR (see[Gallwitz et al.1998]), use a structural approach,i.e.the dialogue is modelled by some kind of ﬁnite statemachine. An evaluation of more than 1000 traintimetable dialogues with EVAR showed that out of31.5% of incomplete dialogues, 83.1% failed be-cause of a failure to integrate utterances into thecontext! There is an obvious lack of ﬂexibilityfor dynamic tasks with a high degree of context-dependency. Furthermore, it is an open questionhow meta-discourse,which occursfrequentlyin dia-logue corpora, can be accommodated for. And thereare further limitations: The dialogue models are tai-loredto a certain applicationtypewhich makes port-ing and scaling up nearly impossible. So, a lot ofwork has concentrated on analysing communicativeplans to overcome these shortcomings. In the fol-lowing, we show the advantages of plan-based di-alogue modelling for rational dialogues, stressingthe usefulness of distinguishing between properdia-loguefeaturesandtask-speciﬁcones. Forthesystemarchitecture, our dialogue model enables, orthogo-
Comparative Polygenic Analysis of Maximal Ethanol Accumulation Capacity and Tolerance to High Ethanol Levels of Cell Proliferation in Yeast

The yeast Saccharomyces cerevisiae is able to accumulate ≥17% ethanol (v/v) by fermentation in the absence of cell proliferation. The genetic basis of this unique capacity is unknown. Up to now, all research has focused on tolerance of yeast cell proliferation to high ethanol levels. Comparison of maximal ethanol accumulation capacity and ethanol tolerance of cell proliferation in 68 yeast strains showed a poor correlation, but higher ethanol tolerance of cell proliferation clearly increased the likelihood of superior maximal ethanol accumulation capacity. We have applied pooled-segregant whole-genome sequence analysis to identify the polygenic basis of these two complex traits using segregants from a cross of a haploid derivative of the sake strain CBS1585 and the lab strain BY. From a total of 301 segregants, 22 superior segregants accumulating ≥17% ethanol in small-scale fermentations and 32 superior segregants growing in the presence of 18% ethanol, were separately pooled and sequenced. Plotting SNP variant frequency against chromosomal position revealed eleven and eight Quantitative Trait Loci (QTLs) for the two traits, respectively, and showed that the genetic basis of the two traits is partially different. Fine-mapping and Reciprocal Hemizygosity Analysis identified ADE1, URA3, and KIN3, encoding a protein kinase involved in DNA damage repair, as specific causative genes for maximal ethanol accumulation capacity. These genes, as well as the previously identified MKT1 gene, were not linked in this genetic background to tolerance of cell proliferation to high ethanol levels. The superior KIN3 allele contained two SNPs, which are absent in all yeast strains sequenced up to now. This work provides the first insight in the genetic basis of maximal ethanol accumulation capacity in yeast and reveals for the first time the importance of DNA damage repair in yeast ethanol tolerance.
Social login privacy alert: Does it improve privacy awareness of facebook users?

Social login (SL) allows web application providers to obtain authentication service from social network providers for users who own the social network accounts. By approving a consent dialogue, users are granted access to the web applications when login using the SL. It also allows web application providers to access personal information that is associated with the users' social network credentials (SNC). This can be a source to privacy leakage if the users simply approve the consent dialogue without understanding the contents. Therefore, this research intends to explore users' privacy awareness when they login to web applications using SL for the first time particularly using Facebook SNC. An experimental study was conducted to evaluate the effects of SL permission messages on users' privacy awareness. The results suggested that the permission message with privacy alert has significantly increased the participants' awareness on the privacy of their personal information obtained through SNC. The outcome of this study provides an opportunity as a guide to increase users' awareness on the privacy of their personal information obtained from SNC.
Fair Computation with Tit-for-Tat Strategy

Complete fairness means that either all parties learn the output of the function or none of them does. It was deemed as an impossible task in general in secure two party computation by Cleve (STOC 1986). However, a seminal result of complete fairness between two parties was achieved by Gordorn et al. (STOC 2008). Recently Groce and Katz (Euro crypt 2012) corrected the insufficient assumptions and gave some positive results of fairness. Here we revisit this problem and introduce the Tit-for-Tat (TFT) strategy into rational two-party computation. To the best of our knowledge, it is the first secure two-party computation protocol with constant rounds that allows both parties to know the terminal round.