Miracle-dz/UniFAR-FTUs huggingface dataset:
Structure Determination of the ¢ X 174 Closed Procapsid

The structure of a procapsid of the single-stranded DNA bacteriophage ~pX174 was determined to 3.5 A resolution. The crystal space group was 1213 with a unit-cell length of 774 A. The unit cell contained 16 icosahedral virus particles, each situated on a crystallographic threefold axis. Thus, there are two independent one-thirds of a particle per asymmetric unit, and a total of 40-fold non-crystallographic redundancy. To aid in the interpretation of the packing arrangement, crystals were prepared for thin sectioning and analyzed by electron microscopy. Oscillation X-ray diffraction data was collected on image plates using synchrotron radiation and oscillation° angles of either 0.25 or 0.30:. A lowresolution 6.5 A data set collected from a single frozen crystal was particularly helpful in the structure determination, because of its completeness and internal consistency. The initial particle orientations were determined using self-rotation functions, while the initial position of one particle was determined from a Patterson map. The structure was solved by molecular replacement real-space averaging using a model based on a cryo-clectron microscopy reconstruction as a starting point for the phase determination. The initial structure determination used the data between 20 and 13 ,~ resolution, which was then extended one reciprocal lattice point at a time to 6.5 ,~ resolution. At this point, a 3.5 ,~ resolution data set compiled from a number of crystals collected at 277 K was introduced. Phase extension and averaging continued to 3.5 ,~ resolution after re-determining the particle positions and orientations. The amino-acid sequences of most of the D, F and G proteins and part of the BoPrOtein could be unambiguously built into the 3.5 A electron-density map. Partial crystallographic refinement yielded an R t Present address: Institute of Molecular Agrobiology, The National University of Singapore. Singapore 117604. Present address: Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK. § Present address: Department of Biochemistry, Baylor College of Medicine, Houston, Texas 77030, USA. t Present address: Indiana University School of Medicine, Indianapolis. Indiana 46202, USA. ~" 1998 International Union of Crystallography Printed in Great Britain all rights reserved factor of 31.6%, consistent with the relatively low resolution and lack of completeness of the data.
The Clonal Selection Algorithm with Engineering Applications 1

The clonal selection algorithm is used by the natural immune system to define the basic features of an immune response to an antigenic stimulus. It establishes the idea that only those cells that recognize the antigens are selected to proliferate. The selected cells are subject to an affinity maturation process, which improves their affinity to the selective antigens. In this paper, we propose a powerful computational implementation of the clonal selection principle that explicitly takes into account the affinity maturation of the immune response. The algorithm is shown to be an evolutionary strategy capable of solving complex machinelearning tasks, like pattern recognition and multimodal optimization.
Clipper package ( Version 0 . 99 . 6 )

Different experimental conditions are usually compared in terms of their gene expression mean differences. In the univariate case, if a gene set changes significantly its multivariate mean expression in one condition with respect to the other, it is said to be differentially expressed. However, the difference in mean expression levels does not necessarily result in a change of the interaction strength among genes. In this case, we will have pathways with significant altered mean expression levels but unaltered biological interactions. On the contrary, if transcripts abundances ratios are altered, we expect a significant alteration not only of their mean, but also of the strength of their connections, resulting in pathways with completely corrupted functionality. Therefore, to look for pathways strongly involved in a biological process, we should look at pathways with both mean and variance significantly altered. clipper is based on a two-step approach: 1) it selects pathways with covariance matrices and/or means significantly different between experimental conditions and 2) on such pathways, it identifies the sub-paths mostly associated to the phenotype. This is a very peculiar feature in pathway analysis. To our knowledge this is the first approach able to systematically inspect a pathway deep in its different portions.
The Cognitive Neuroscience of Semantic Memory

Semantic memory refers to general knowledge about the world, including concepts, facts and beliefs (e.g., that a lemon is normally yellow and sour or that Paris is in France). How is this kind of knowledge acquired or lost? How is it stored and retrieved? In this chapter, we review evidence that conceptual knowledge about concrete objects is acquired through experience with them, distributed across brain regions that are involved in perceiving or acting upon them, and impaired via damage to these brain regions. We suggest that these distributed representations result in flexible concepts that can vary depending on the task and context, as well as on individual experience. Further, we discuss the role of brain regions implicated in selective attention in supporting such conceptual flexibility. Finally, we consider the neural bases of other aspects of conceptual knowledge, such as the ability to generalize (e.g., to map lemons and grapes onto the category fruit), and the ability to represent knowledge that does not have a direct sensorimotor correlate (e.g., abstract concepts, such as peace).
Corporate Social Responsibility in Commercial Banking - A Case Study from the Czech Republic

The concept of corporate social responsibility is not new in the banking sector, but nowadays, it becomes highly topical since the crisis has significantly highlighted the need for integration of moral principles in the banking business. Knowledge of business practice indicates the fact that the acceptance of moral principles in business is not integrated into management decisions of companies. It also cannot be accepted that self-regulatory instruments of companies such as CSR will be effective. The existing experience with the implementation of CSR and ethical principles in the banking sector leads to the opinion that the social responsibility of banks and ethics in banking sector are perceived as an appropriate marketing tool for public communication and are not integrated into policies of individual commercial banks. Experience with the crisis demonstrated that there is a lack of moral principles of managers’ decisions. The aim of this article is to introduce theoretical aspects of CSR in commercial banking and measure the level of CSR in selected Czech commercial banks. In the article, the CSR index was calculated for Ceska spořitelna, Ceskoslovenska obchodni banka, Komercni banka and GE Money Bank. Results of our research confirmed that the CSR index of selected Czech commercial banks achieves only an average level. There is a significant lack of transparent information in the context of CSR areas.
Local Stability Analysis for a Delayed Differential-algebraic Biological Economic System with Ratio-dependent Functional Response

Abstract: This paper is concerned with a delayed differential-algebraic biological economic system. Firstly, the differential-algebraic system is transformed into a differential system by employing the local parameterization method of differential-algebraic system, and then the sufficient conditions for the local stability and the existence of Hopf bifurcation are established by regarding the time delay as the bifurcation parameter. Finally, numerical simulations are given to verify the theoretical analysis.
Comparison of Properties of Medial Entorhinal Cortex Layer II Neurons in Two Anatomical Dimensions with and without Cholinergic Activation

Mechanisms underlying grid cell firing in the medial entorhinal cortex (MEC) still remain unknown. Computational modeling studies have suggested that cellular properties such as spike frequency adaptation and persistent firing might underlie the grid cell firing. Recent in vivo studies also suggest that cholinergic activation influences grid cell firing. Here we investigated the anatomical distribution of firing frequency adaptation, the medium spike after hyperpolarization potential (mAHP), subthreshold membrane potential oscillations, sag potential, input resistance and persistent firing, in MEC layer II principal cells using in vitro whole-cell patch clamp recordings in rats. Anatomical distributions of these properties were compared along both the dorso-ventral and medio-lateral axes, both with and without the cholinergic receptor agonist carbachol. We found that spike frequency adaptation is significantly stronger in ventral than in dorsal neurons both with and without carbachol. Spike frequency adaptation was significantly correlated with the duration of the mAHP, which also showed a gradient along the dorso-ventral axis. In carbachol, we found that about 50% of MEC layer II neurons show persistent firing which lasted more than 30 seconds. Persistent firing of MEC layer II neurons might contribute to grid cell firing by providing the excitatory drive. Dorso-ventral differences in spike frequency adaptation we report here are opposite from previous predictions by a computational model. We discuss an alternative mechanism as to how dorso-ventral differences in spike frequency adaptation could contribute to different scales of grid spacing.
Multiple Antioxidants Improve Cardiac Complications and Inhibit Cardiac Cell Death in Streptozotocin-Induced Diabetic Rats

Diabetic cardiomyopathy, a disorder of the heart muscle in diabetic patients, is one of the major causes of heart failure. Since diabetic cardiomyopathy is now known to have a high prevalence in the asymptomatic diabetic patient, prevention at the earliest stage of development by existing molecules would be appropriate in order to prevent the progression of heart failure. In this study, we investigated the protective role of multiple antioxidants (MA), on cardiac dysfunction and cardiac cell apoptosis in streptozotocin (STZ)-induced diabetic rat. Diabetic cardiomyopathy in STZ-treated animals was characterized by declined systolic, diastolic myocardial performance, oxidative stress and apoptosis in cardiac cells. Diabetic rats on supplementation with MA showed decreased oxidative stress evaluated by the content of reduced levels of lipid per-oxidation and decreased activity of catalase with down-regulation of heme-oxygenase-1 mRNA. Supplementation with MA also resulted in a normalized lipid profile and decreased levels of pro-inflammatory transcription factor NF-kappaB as well as cytokines such as TNF-α, IFN-γ, TGF-β, and IL-10. MA was found to decrease the expression of ROS-generating enzymes like xanthine oxidase, monoamine oxidase-A along with 5-Lipoxygenase mRNA and/or protein expression. Further, left ventricular function, measured by a microtip pressure transducer, was re-established as evidenced by increase in ±dp/dtmax, heart rate, decreased blood pressure, systolic and diastolic pressure as well as decrease in the TUNEL positive cardiac cells with increased Bcl-2/Bax ratio. In addition, MA supplementation decreased cell death and activation of NF-kappaB in cardiac H9c2 cells. Based on our results, we conclude that MA supplementation significantly attenuated cardiac dysfunction in diabetic rats; hence MA supplementation may have important clinical implications in terms of prevention and management of diabetic cardiomyopathy.
A Look at Basics of Distributed Computing

This tutorial presents concepts and basics of distributed computing which are important (at least from the author's point of view! ), and should be known and mastered by Master students, researchers, and engineers. Those include: (a) a characterization of distributed computing (which is too much often confused with parallel computing); (b) the notion of a synchronous system and its associated notions of a local algorithm and message adversaries; (c) the notion of an asynchronous shared memory system and its associated notions of universality and progress conditions; and (d) the notion of an asynchronous messagepassing system with its associated broadcast and agreement abstractions, its impossibility results, and approaches to circumvent them. Hence, the tutorial can be seen as a guided tour to key elements that constitute basics of distributed computing.
Human Leucocyte Antigen-G (HLA-G) and Its Murine Functional Homolog Qa2 in the Trypanosoma cruzi Infection

Genetic susceptibility factors, parasite strain, and an adequate modulation of the immune system seem to be crucial for disease progression after Trypanosoma cruzi infection. HLA-G and its murine functional homolog Qa2 have well-recognized immunomodulatory properties. We evaluated the HLA-G 3′ untranslated region (3′UTR) polymorphic sites (associated with mRNA stability and target for microRNA binding) and HLA-G tissue expression (heart, colon, and esophagus) in patients presenting Chagas disease, stratified according to the major clinical variants. Further, we investigated the transcriptional levels of Qa2 and other pro- and anti-inflammatory genes in affected mouse tissues during T. cruzi experimental acute and early chronic infection induced by the CL strain. Chagas disease patients exhibited differential HLA-G 3′UTR susceptibility allele/genotype/haplotype patterns, according to the major clinical variant (digestive/cardiac/mixed/indeterminate). HLA-G constitutive expression on cardiac muscle and colonic cells was decreased in Chagasic tissues; however, no difference was observed for Chagasic and non-Chagasic esophagus tissues. The transcriptional levels of Qa2 and other anti and proinflammatory (CTLA-4, PDCD1, IL-10, INF-γ, and NOS-2) genes were induced only during the acute T. cruzi infection in BALB/c and C57BL/6 mice. We present several lines of evidence indicating the role of immunomodulatory genes and molecules in human and experimental T. cruzi infection.
Tsetse EP Protein Protects the Fly Midgut from Trypanosome Establishment

African trypanosomes undergo a complex developmental process in their tsetse fly vector before transmission back to a vertebrate host. Typically, 90% of fly infections fail, most during initial establishment of the parasite in the fly midgut. The specific mechanism(s) underpinning this failure are unknown. We have previously shown that a Glossina-specific, immunoresponsive molecule, tsetse EP protein, is up regulated by the fly in response to gram-negative microbial challenge. Here we show by knockdown using RNA interference that this tsetse EP protein acts as a powerful antagonist of establishment in the fly midgut for both Trypanosoma brucei brucei and T. congolense. We demonstrate that this phenomenon exists in two species of tsetse, Glossina morsitans morsitans and G. palpalis palpalis, suggesting tsetse EP protein may be a major determinant of vector competence in all Glossina species. Tsetse EP protein levels also decline in response to starvation of the fly, providing a possible explanation for increased susceptibility of starved flies to trypanosome infection. As starvation is a common field event, this fact may be of considerable importance in the epidemiology of African trypanosomiasis.
UMCC_DLSI: Sentiment Analysis in Twitter using Polirity Lexicons and Tweet Similarity

This paper describes a system submitted to SemEval-2014 Task 4B: Sentiment Analysis in Twitter, by the team UMCC DLSI Sem integrated by researchers of the University of Matanzas, Cuba and the University of Alicante, Spain. The system adopts a cascade classification process that uses two classifiers, K-NN using the lexical Levenshtein metric and a Dagging model trained over attributes extracted from annotated corpora and sentiment lexicons. Phrases that fit the distance thresholds were automatically classified by the KNN model, the others, were evaluated with the Dagging model. This system achieved over 52.4% of correctly classified instances in the Twitter message-level subtask.
Fragmentos urbanos después de la burbuja inmobiliaria: el caso de Madrid

The neoliberal logics have a clear and often differentiated impact in the current cities, but it is convenient to contrast empirically the theoretical frameworks coming from the French or North American tradition, in order to understand the differences that exist in the cities of southern Europe. The objective is to apply the theory of the split city (Marcuse and Van Kempen, 2000) through multivariable quantitative analysis, explaining the processes of segregation and differences in social spaces in the Community of Madrid and its possible adaptation to the theoretical model that supports the growth of divisions in urban spaces.
Continuous material identification through tactile sensing

Tactile sensing has recently attracted significant research interest in robotics. Despite the fact that tactile sensors provide temporal sequences of readings, state-of-the-art material recognition approaches are episodic, i.e. a whole sequence of readings is processed to identify the material. Based on vibration frequency response, this work presents an online identification technique using recursive estimation of the probability of identifying a set of materials, i.e. casting the classification problem as a hidden Markov model (HMM) state estimation problem. This allows for faster identification of most materials and does not require several exploratory movements. Our results show that when enough evidence is gathered, the system eventually achieves perfect recognition of our experimental set of 34 materials with an average identification time of ≤ 0.5 seconds. To prove the accuracy of this method, we also conducted a comparative experiment with commonly used machine learning algorithms for material identification such as k-Nearest Neighbour(KNN), an Artificial Neural Network(ANN) and Support Vector Machine(SVM).
Enhanced Authentication Mechanisms for Desktop Platform and Smart Phones

With hundreds of millions using computers and mobile devices all over the globe, these devices have an established position in modern society. Nevertheless, most of these devices use weak authentication techniques with passwords and PINs which can be easily hacked. Thus, stronger identification is needed to ensure data security and privacy. In this paper, we will explain the employment of biometrics to computer and mobile platforms. In addition, the possibility of using keystroke and mouse dynamics for computer authentication is being checked. Finally, we propose an authentication scheme for smart phones that shows positive results.
Drosophila melanogaster Scramblases modulate synaptic transmission

Scramblases are a family of single-pass plasma membrane proteins, identified by their purported ability to scramble phospholipids across the two layers of plasma membrane isolated from platelets and red blood cells. However, their true in vivo role has yet to be elucidated. We report the generation and isolation of null mutants of two Scramblases identified in Drosophila melanogaster. We demonstrate that flies lacking either or both of these Scramblases are not compromised in vivo in processes requiring scrambling of phospholipids. Instead, we show that D. melanogaster lacking both Scramblases have more vesicles and display enhanced recruitment from a reserve pool of vesicles and increased neurotransmitter secretion at the larval neuromuscular synapses. These defects are corrected by the introduction of a genomic copy of the Scramb 1 gene. The lack of phenotypes related to failure of scrambling and the neurophysiological analysis lead us to propose that Scramblases play a modulatory role in the process of neurotransmission.
Image retrieval under very noisy annotations

In recent years, a significant number of tagged images uploaded onto image sharing sites has enabled us to create high-performance image recognition models. However, there are many inaccurate image tags on the Internet, and it is very laborious to investigate the percentage of tags that are incorrect. In this paper, we propose a new method for creating an image recognition model that can be used even when the image data set includes many incorrect tags. Our method has two superior features. First, our method automatically measures the reliability of annotations and does not require any parameter adjustment for the percentage of error tags. This is a very important feature because we usually do not know how many errors are included in the database, especially in actual Internet environments. Second, our method iterates the error modification process. It begins with the modification of simple and obvious errors, gradually deals with much more difficult errors, and finally creates the high-performance recognition model with refined annotations. Using an object recognition image database with many annotation errors, our experiments showed that the proposed method successfully improved the image retrieval performance in approximately 90 percent of the image object categories.
The Influence of Dynamic Bandwidth Adaptation in Metro and Core Networks on Packet Traffic Characteristics

In this paper we present simulation results on how a simple open loop control dynamic bandwidth adaptation algorithm can greatly improve the transport efficiency in metro and core networks. We therefore describe the architecture of a basic control algorithm for the dynamic bandwidth adaptation and elaborate the impact of bandwidth adaptation on the network traffic. By using realistic packet traces for the simulations it is pointed out how basic parameters of a DBA algorithm like the bandwidth adaptation time interval in principle influence the overall achievable performance. Furthermore influences on the traffic characteristics as well as on the network nodes are shown and how certain impairments induced by the dynamic bandwidth adaptation mechanism can be redeemed.
Logical Bell Inequalities

Bell inequalities play a central role in the study of quantum nonlocality and entanglement, with many applications in quantum information. Despite the huge literature on Bell inequalities, it is not easy to find a clear conceptual answer to what a Bell inequality is, or a clear guiding principle as to how they may be derived. In this paper, we introduce a notion of logical Bell inequality which can be used to systematically derive testable inequalities for a very wide variety of situations. There is a single clear conceptual principle, based on purely logical consistency conditions, which underlies our notion of logical Bell inequalities. We show that in a precise sense, all Bell inequalities can be taken to be of this form. Our approach is very general. It applies directly to any family of sets of commuting observables. Thus it covers not only the $n$-partite scenarios to which Bell inequalities are standardly applied, but also Kochen-Specker configurations, and many other examples. There is much current work on experimental tests for contextuality. Our approach directly yields, in a systematic fashion, testable inequalities for a very general notion of contextuality. There has been much work on obtaining proofs of Bell's theorem ``without inequalities'' or ``without probabilities. '' These proofs are seen as being in a sense more definitive and logically robust than the inequality-based proofs. On the hand, they lack the fault-tolerant aspect of inequalities. Our approach reconciles these aspects, and in fact shows how the logical robustness can be converted into systematic, general derivations of inequalities with provable violations. Moreover, the kind of strong non-locality or contextuality exhibited by the GHZ argument or by Kochen-Specker configurations can be shown to lead to maximal violations of the corresponding logical Bell inequalities. Thus the qualitative and the quantitative aspects are combined harmoniously.