Miracle-dz/UniFAR-FTUs huggingface dataset:
Discovery of pan-VEGF inhibitory peptides directed to the extracellular ligand-binding domains of the VEGF receptors

Extracellular ligand-binding inhibitors of receptor tyrosine kinases (eTKIs) in angiogenesis. Receptor tyrosine kinases (RTKs) are key molecules in numerous cellular processes, the inhibitors of which play an important role in the clinic. Among them are the vascular endothelial growth factor (VEGF) family members and their receptors (VEGFR), which are essential in the formation of new blood vessels by angiogenesis. Anti-VEGF therapy has already shown promising results in oncology and ophthalmology, but one of the challenges in the field is the design of specific small-molecule inhibitors for these receptors. We show the identification and characterization of small 6-mer peptides that target the extracellular ligand-binding domain of all three VEGF receptors. These peptides specifically prevent the binding of VEGF family members to all three receptors and downstream signaling but do not affect other angiogenic RTKs and their ligands. One of the selected peptides was also very effective at preventing pathological angiogenesis in a mouse model of retinopathy, normalizing the vasculature to levels similar to those of a normal developing retina. Collectively, our results suggest that these peptides are pan-VEGF inhibitors directed at a common binding pocket shared by all three VEGFRs. These peptides and the druggable binding site they target might be important for the development of novel and selective small-molecule, extracellular ligand-binding inhibitors of RTKs (eTKIs) for angiogenic-dependent diseases.
Diagrams for symmetric product orbifolds

We develop a diagrammatic language for symmetric product orbifolds of two-dimensional conformal field theories. Correlation functions of twist operators are written as sums of diagrams: each diagram corresponds to a branched covering map from a surface where the fields are single-valued to the base sphere where twist operators are inserted. This diagrammatic language facilitates the study of the large N limit and makes more transparent the analogy between symmetric product orbifolds and free non-abelian gauge theories. We give a general algorithm to calculate the leading large N contribution to four-point correlators of twist fields.
The Strategy of Mining Association Rule Based on Cloud Computing

Cloud computing provides cheap and efficient solutions of storing and analyzing mass data. It is very important to research the data mining strategy based on cloud computing from the theoretical view and practical view. In this paper, the strategy of mining association rules in cloud computing environment is focused on. Firstly, cloud computing, Hadoop, MapReduce programming model, Apriori algorithm and parallel association rule mining algorithm are introduced. Then, a parallel association rule mining strategy adapting to the cloud computing environment is designed. It includes data set division method, data set allocation method, improved Apriori algorithm, and the implementation procedure of the improved Apriori algorithm on MapReduce. Finally, the Hadoop platform is built and the experiment for testing performance of the strategy as well as the improved algorithm has been done. The results show that the strategy designed in this paper can archive higher efficiency when doing frequent item set mining in cloud computing environment.
Océ at TREC 2003

This report describes the work done at Oce Research for the TREC 2003. This first participation consists of ad hoc experiments for the Robust track. We used the BM25 model and our new probabilistic model to rank documents. Knowledge Concepts’ Content Enabler semantic network was used for stemming and query expansion. Our main goal was to compare the BM25 model and the probabilistic model implemented with and/or without query expansion. The developed generic probabilistic model does not use global statistics of a document collection to rank documents. The relevance of the document to a given query is calculated using term frequencies of the query terms in the document and the length of the document. Furthermore, some theoretical research has been done. We have constructed a model that uses relevance judgements of previous years. However, we did not implement it due to the time constraints.
The phase diagram of random threshold networks

Threshold networks are used as models for neural or gene regulatory networks. They show rich dynamical behaviour with a transition between a frozen phase and a chaotic phase. We investigate the phase diagram of randomly connected threshold networks with real-valued thresholds h and a fixed number of inputs per node. The nodes are updated according to the same rules as in a model of the cell-cycle network of Saccharomyces cereviseae (Li et al 2004 Proc. Natl Acad. Sci. USA 101 4781–6). Using the annealed approximation, we derive expressions for the time evolution of the proportion of nodes in the ‘on’ and ‘off’ states, and for the sensitivity λ. The results are compared with simulations of quenched networks. We find that for integer values of h the simulations show marked deviations from the annealed approximation even for large networks. This can be attributed to the particular choice of the updating rule.
Signal transduction during Fc receptor‐mediated phagocytosis

Phagocytosis is the process whereby cells engulf large particles, usually over 0.5 μm in diameter. Phagocytosis is triggered by the interaction of opsonins that cover the particle to be internalized with specific receptors on the surface of the phagocyte. The best‐studied phagocytic receptors include the Fc receptors (FcR) that bind to the Fc portion of immunoglobulins. Cross‐linking of FcR on the phagocyte initiates a variety of signals, which lead through the reorganization of the actin cytoskeleton, and membrane remodeling, to the formation of the phagosome. From recent data, it is becoming clear that FcR‐mediated phagocytosis occurs as a series of steps that are regulated in a nonlinear manner and that signaling for phagocytosis does not terminate when the phagosome is formed. Several lipid molecules localize around the nascent phagosome and function as initiators of important signaling pathways for the late stages of phagolysosome formation. In addition, the use of particular signaling molecules may change for different receptors and may also vary depending on the activation or differentiation state of the cell. This review focuses on this new information and presents a model of our present understanding of the signal transduction events that regulate phagocytosis mediated by FcR.
Talking about quantities in space: Vague quantifiers, context and similarity

Abstract In this paper we examine how vague quantifiers, such as few, several, lots of, map onto non-linguistic number systems. In particular our focus is to examine how judgements about vague quantifiers are affected by the presence of objects in visual scenes other than those being referred to. An experiment is presented that manipulated the number of objects in a visual scene (men playing golf; the ‘focus’ objects) together with the number of other objects in those scenes and their similarity — in terms of form (women or crocodiles) and function (playing golf, not playing golf) — to the focus objects. We show that the number of other objects in a scene impacts upon quantifiers judgements even when those objects are in a different category to the focus objects. We discuss the results in terms of the mapping between the large approximate number (estimation) system and language.
Localized nuclear and perinuclear Ca2+ signals in intact mouse skeletal muscle fibers

Nuclear Ca2+ is important for the regulation of several nuclear processes such as gene expression. Localized Ca2+ signals (LCSs) in skeletal muscle fibers of mice have been mainly studied as Ca2+ release events from the sarcoplasmic reticulum. Their location with regard to cell nuclei has not been investigated. Our study is based on the hypothesis that LCSs associated with nuclei are present in skeletal muscle fibers of adult mice. Therefore, we carried out experiments addressing this question and we found novel Ca2+ signals associated with nuclei of skeletal muscle fibers (with possibly attached satellite cells). We measured localized nuclear and perinuclear Ca2+ signals (NLCSs and PLCSs) alongside cytosolic localized Ca2+ signals (CLCSs) during a hypertonic treatment. We also observed NLCSs under isotonic conditions. The NLCSs and PLCSs are Ca2+ signals in the range of micrometer [FWHM (full width at half maximum): 2.75 ± 0.27 μm (NLCSs) and 2.55 ± 0.17 μm (PLCSs), S.E. M. ]. Additionally, global nuclear Ca2+ signals (NGCSs) were observed. To investigate which type of Ca2+ channels contribute to the Ca2+ signals associated with nuclei in skeletal muscle fibers, we performed measurements with the RyR blocker dantrolene, the DHPR blocker nifedipine or the IP3R blocker Xestospongin C. We observed Ca2+ signals associated with nuclei in the presence of each blocker. Nifedipine and dantrolene had an inhibitory effect on the fraction of fibers with PLCSs. The situation for the fraction of fibers with NLCSs is more complex indicating that RyR is less important for the generation of NLCSs compared to the generation of PLCSs. The fraction of fibers with NLCSs and PLCSs is not reduced in the presence of Xestospongin C. The localized perinuclear and intranuclear Ca2+ signals may be a powerful tool for the cell to regulate adaptive processes as gene expression. The intranuclear Ca2+ signals may be particularly interesting in this respect.
Error probabilities of noncoherent and coherent FSK in the presence of frequency and phase offsets for two-hop relay networks

We analyze the error performance of two-hop relay networks adopting frequency shift keying (FSK) over frequency flat Rayleigh fading channels. It is assumed that relay networks consist of a source, a relay, and a destination without a direct path signal from the source to the destination and the relay adopts the amplify-and-forward protocol with a fixed gain. Firstly, considering imperfect frequency and phase synchronization, we obtain the exact error probability expressions for noncoherent and coherent binary FSK (BFSK). Secondly, assuming perfect frequency and phase synchronization, we derive a closed-form error probability approximation for coherent M-ary FSK (MFSK). The proposed methods can also be used for the error performance analysis of classical one-hop FSK systems with perfect/imperfect frequency and phase synchronization. The obtained error probability expressions will help the design of two-hop relay networks adopting FSK in determining the system parameters such as the transmission power at the source, the amplifying coefficient at the relay, and the maximum affordable frequency and phase offsets to satisfy the required error performance.
On the Defensibility and Believability of Moral Error Theory: Reply to Evers, Streumer, and Toppinen

This article is a response to critical articles by Daan Evers, Bart Streumer, and Teemu Toppinen on my book Moral Error Theory: History, Critique, Defence (Oxford: Oxford University Press, 2014). I will be concerned with four main topics. I shall first try to illuminate the claim that moral facts are queer, and its role in the argument for moral error theory. In section 2, I discuss the relative merits of moral error theory and moral contextualism. In section 3, I explain why I still find the queerness argument concerning supervenience an unpromising argument against non-naturalistic moral realism. In section 4, finally, I reconsider the question whether I, or anyone, can believe the error theory.
Conditions for propagation and block of excitation in atrial tissue

Detailed ionic models of cardiac cells are difficult for numerical simulations because they consist of a large number of equations and contain small parameters. The presence of small parameters, however, may be used for asymptotic reduction of the models. Earlier results have shown that the asymptotics of cardiac equations are non-standard. Here we apply such a novel asymptotic method to an ionic model of human atrial tissue in order to obtain a reduced but accurate model for the description of excitation fronts. Numerical simulations of spiral waves in atrial tissue show that wave fronts of propagating action potentials break-up and self-terminate. Our model, in particular, yields a simple analytical criterion of propagation block, which is similar in purpose but completely different in nature to the `Maxwell rule' in the FitzHugh-Nagumo type models. Our new criterion agrees with direct numerical simulations of break-up of re-entrant waves.
DEVELOPMENT OF A SOFTWARE SYSTEM FOR COMPUTER AIDED DECISION SUPPORT IN TOOL DESIGN

The paper describes the development of a software for Computer Aided Decision Support, which supports the tool designer on the way from part design to the final tool design. The software is connected to a CAD/CAM system. Within the European Community funded GROWTH project GRD1 –200010866 Directool BIBA is developing this software in co-operation with partners from the castings industry. A large variety of tool designs from sand casting to gravity die casting have been analysed with regard to the relevant characteristics. The results have been used to develop a reference model which is capable of mapping tool designs concerning their relevant features. The paper describes, how this reference model has been used for the software implementation. Furthermore the 2-step-decision-support consisting of Case Based Reasoning (CBR) and interactive design support is presented. In the first step the CBR enables the retrieval of a best match tooling design solution for the new part design out of a database. In the second step the designer can adapt this solution to the current part design and is fully supported by the software through interactive formulae, pictures, tables and charts, which allow a detailed methoding and storage of the results. The paper presents this approach in a case study. The software system constitutes a new approach to support tool designers.
L30 Cognitive training improves disease symptoms in a mouse model of huntington’s disease

Background Huntington’s disease (HD) can cause cognitive disturbances, including problems with attention, which can significantly affect the ability to manage independently and quality of life. Cognitive training interventions therefore offer a potential therapeutic intervention. Aim To determine if cognitive training, that is focused on attention, can alter HD signs in a mouse model of HD. Methods HdhQ111 heterozygous mice were given cognitive training in the 5-choice serial reaction time task (5-CSRTT) of attention, for 20 days at 4 months of age. Two age matched control groups were also used. One control group received training in a similar task with no attentional component for a comparable number of days, and the other group were cage controls. All animals were then tested in the 5-CSRTT at 12 months of age. Results All cognitive training regimes had a positive effect on task performance in comparison to cage controls. Attentional cognitive training, improved attentional performance in all animals and specifically improved motor performance in HD animals. In the control group who received comparable training in a non-attentional task, a positive effect of training was seen, although, this type of training did not confer any specific advantage to HD animals in comparison to wildtype animals. Conclusion The results demonstrate that attentional cognitive training implemented at a young age improves attentional performance at an older age in both wildtype and HD mice. Attentional cognitive training also specifically improved motor performance in HD mice. This leads to the exciting possibility that specific cognitive training may improve HD related disease symptoms later in life.
Retina enhanced SIFT descriptors for video indexing

This paper investigates how the detection of diverse high-level semantic concepts (objects, actions, scene types, persons etc.) in videos can be improved by applying a model of the human retina. A large part of the current approaches for Content-Based Image/Video Retrieval (CBIR/CBVR) relies on the Bag-of-Words (BoW) model, which has shown to perform well especially for object recognition in static images. Nevertheless, the current state-of-the-art framework shows its limits when applied to videos because of the added temporal information. In this paper, we enhance a BoW model based on the classical SIFT local spatial descriptor, by preprocessing videos with a model of the human retina. This retinal preprocessing allows the SIFT descriptor to become aware of temporal information. Our proposed descriptors extend the SIFT genericity to spatio-temporal content, making them interesting for generic video indexing. They also benefit from the retinal spatio-temporal “robustness” to various disturbances such as noise, compression artifacts, luminance variations or shadows. The proposed approaches are evaluated on the TRECVID 2012 Semantic Indexing task dataset.
De- and repolarization mechanism of flagellar morphogenesis during a bacterial cell cycle

In this study, Viollier and colleagues identify a cyclic nucleotide pathway that signals the synthesis and loss of the polar flagellum in Caulobacter. The authors show that the second messenger, cyclic-di-GMP, controls the activation, polarization, and stabilization of the flagellar regulator TipF. This study not only elucidates how small nucleotide signaling is used to implement a polarity pathway during the cell cycle, but also uncovers a mechanism for its elimination.
Lyα Resonant Scattering in Young Galaxies: Predictions from Cosmological Simulations

We present results obtained with a three-dimensional, Lyα radiative transfer code applied to a fully cosmological galaxy formation simulation. The developed Monte Carlo code is capable of treating an arbitrary distribution of source Lyα emission, neutral hydrogen density, temperature, and peculiar velocity of the interstellar medium. We investigate the influence of resonant scattering on the appearance and properties of young galaxies by applying the code to a simulated "Lyman break galaxy" at redshift z = 3.6, star formation rate 22 M☉ yr-1, and total Lyα luminosity 2.0 × 1043 ergs s-1. It is found that resonant scattering of Lyα radiation can explain that young galaxies are frequently observed to be more extended on the sky in Lyα than in the optical. Moreover, it is shown that, for the system investigated, due to the anisotropic escape of the photons, the observed maximum surface brightness can differ by more than an order of magnitude, and the total derived luminosity by a factor of ~4, depending on the orientation of the system relative to the observer.
Extraction automatique de modèles de processus pour l'étude de la résolution collective de problèmes dans les communautés du logiciel libre

Les auteurs du present article presentent une methode d'analyse des aspects socio-techniques de la gestion de problemes logiciels dans les communautes du logiciel libre (F/OSS: Free/Open-Source Software); analyse effectuee a partir de bases de donnees de rapports de problemes telles que celles du systeme de gestion de defauts Bugzilla. Les auteurs donnent quelques resultats preliminaires obtenus en appliquant cette methode. Etant donnee la quantite de donnees disponibles, il est necessaire de recourir a des techniques automatisees pour extraire les informations requises par les analyses et pour modeliser le comportement des collectifs etudies. Differentes techniques associant des analyses qualitatives manuelles et des techniques automatiques d'extraction et de modelisation sont utilisees pour caracteriser et etudier les processus impliques dans la gestion de problemes logiciels.
Single Market Nonparametric Identification of Multi-Attribute Hedonic Equilibrium Models

This paper derives conditions under which preferences and technology are nonparametrically identified in hedonic equilibrium models, where products are differentiated along more than one dimension and agents are characterized by several dimensions of unobserved heterogeneity. With products differentiated along a quality index and agents characterized by scalar unobserved heterogeneity, single crossing conditions on preferences and technology provide identifying restrictions. We develop similar shape restrictions in the multi-attribute case and we provide identification results from the observation of a single market. We thereby extend identification results in Matzkin (2003) and Heckman, Matzkin, and Nesheim (2010) to accommodate multiple dimensions of unobserved heterogeneity.
A trust based cooperative model for congestion in ad hoc networks

Ad hoc network is flexibly formed by a group of peer nodes and depends on the irresponsible cooperation among them, so it is vulnerable to various attacks. Thus, trust is introduced to promote nodes to transmit messages. Nodes with higher trust values are more easily selected for transmission which results in unbalanced load distribution. Therefore, packets from different sources are more likely to meet others at the same nodes. Consequently, congestion forms and trust values of congestion nodes decrease. Learning from social life, trust values decrease fast and increase slowly. Then congestion nodes encounter false trust fluctuation, resulting in that source nodes lose the best candidates to transmit packets and the performance of the whole network degrades. Thus, a trust based cooperative model for congestion is proposed to prevent false trust fluctuation and improve successful transmission rate. Simulation results show that congestion easily happens in busy networks and is largely alleviated by our method.
Efficient Prediction of Marsaglia-Zaman Random Number Generators

We show that the random number generator of Marsaglia and Zaman (1991) produces the successive digits of a rational b-adic number. (The b-adic number system generalizes p-adic numbers to an arbitrary integer base b.) Using continued fractions, we derive an efficient prediction algorithm for this generator.
A Graph Based Approach to Word Sense Disambiguation for Hindi Language

Hindi is the official language of the Republic of India. Hindi is the third most widely spoken language in the world (after English and Mandarin) an estimated 500600 million peoples speaks the language. But, the language is making hindrances in the advantages of Information Technology revolution in India. So, there is the need of the adequate measures to perform natural language processing (NLP) through computer processing so that computer based system can be interacted by users through natural language like Hindi and handled by users who have knowledge of regional language. In computational linguistics, word sense disambiguation (WSD) is an open problem of natural language processing, which governs the process of identifying which sense of a word (i.e. meaning) is used in a sentence, when the word has multiple meanings. In this paper, we are concerned with graph-based algorithm for word sense disambiguation for Hindi language and finding the correct sense for given Hindi word. We introduce the graph based WSD algorithm which has few parameters using this algorithm we measures of graph connectivity the aim of identifying those best suited for WSD. We explore the multiple meanings of Hindi word with the help of Hindi Word net prepared by