Miracle-dz/UniFAR-FTUs huggingface dataset:
Complete sequence and genomic analysis of murine gammaherpesvirus 68

Murine gammaherpesvirus 68 (gammaHV68) infects mice, thus providing a tractable small-animal model for analysis of the acute and chronic pathogenesis of gammaherpesviruses. To facilitate molecular analysis of gammaHV68 pathogenesis, we have sequenced the gammaHV68 genome. The genome contains 118,237 bp of unique sequence flanked by multiple copies of a 1,213-bp terminal repeat. The GC content of the unique portion of the genome is 46%, while the GC content of the terminal repeat is 78%. The unique portion of the genome is estimated to encode at least 80 genes and is largely colinear with the genomes of Kaposi's sarcoma herpesvirus (KSHV; also known as human herpesvirus 8), herpesvirus saimiri (HVS), and Epstein-Barr virus (EBV). We detected 63 open reading frames (ORFs) homologous to HVS and KSHV ORFs and used the HVS/KSHV numbering system to designate these ORFs. gammaHV68 shares with HVS and KSHV ORFs homologous to a complement regulatory protein (ORF 4), a D-type cyclin (ORF 72), and a G-protein-coupled receptor with close homology to the interleukin-8 receptor (ORF 74). One ORF (K3) was identified in gammaHV68 as homologous to both ORFs K3 and K5 of KSHV and contains a domain found in a bovine herpesvirus 4 major immediate-early protein. We also detected 16 methionine-initiated ORFs predicted to encode proteins at least 100 amino acids in length that are unique to gammaHV68 (ORFs M1 to 14). ORF M1 has striking homology to poxvirus serpins, while ORF M11 encodes a potential homolog of Bcl-2-like molecules encoded by other gammaherpesviruses (gene 16 of HVS and KSHV and the BHRF1 gene of EBV). In addition, clustered at the left end of the unique region are eight sequences with significant homology to bacterial tRNAs. The unique region of the genome contains two internal repeats: a 40-bp repeat located between bp 26778 and 28191 in the genome and a 100-bp repeat located between bp 98981 and 101170. Analysis of the gammaHV68, HVS, EBV, and KSHV genomes demonstrated that each of these viruses have large colinear gene blocks interspersed by regions containing virus-specific ORFs. Interestingly, genes associated with EBV cell tropism, latency, and transformation are all contained within these regions encoding virus-specific genes. This finding suggests that pathogenesis-associated genes of gammaherpesviruses, including gammaHV68, may be contained in similarly positioned genome regions. The availability of the gammaHV68 genomic sequence will facilitate analysis of critical issues in gammaherpesvirus biology via integration of molecular and pathogenetic studies in a small-animal model.
Agent-based Players for a First-person Entertainment-based Real-time Artificial Environment

The necessity for improved players and opponents in firstperson entertainment-based real-time artificial environments has inspired our research into artificial game players. We employed the approach of creating agent-based players, one using simple reflex-action based components and another based on a back propagation neural network, to interact in a modified Quake II environment. Our evaluation of these agents utilizes two metrics, a statistical measure and graph similarity based on clustering from player performance traces against interactive feature points in the environments—both comparing the agents to a sample of 20 human players. The reflex-based agent was able to complete 29 of 100 test levels with 73.1% within statistical humanperformance levels and 15.4% similar to the human players, while the BPNN-based agent was unable to complete any levels. These results, including some additional findings that reveal the potential for a combinational approach, are inspiring an architectural vision of a multi-agent system to provide an advanced artificial intelligence engine for the embodiment of advanced artificial characters in gaming and
EMG Working Paper Series WP-EMG-04-2008 ‘ Capital Flight from Central and East European Countries : Estimates and Causes ’

Causes We estimate of capital flight from twelve transition economies of Central and Eastern Europe for the period 1995-2005. Capital flight from these transition economies has been comparable when adjusted for country size to the more highly publicized capital outflows from Russia despite East Europe's seemingly better transition and reform performance and greater political stability. We find that capital flight from the transition economies is mainly an economic phenomenon, driven by differences in interest rates and investors' expectations about future tax rates, inflation, etc. in their countries as well as by the ease with which they are able to transfer their wealth overseas. Our empirical results are thus consistent with the mainstream explanations of capital flight and they mirror results obtained for other countries and time periods.
Genre and Style Based Painting Classification

As the size of digitized painting collections increase, it becomes more difficult to organize and retrieve paintings from these collections. To manage search and other similar operations efficiently, it becomes necessary to organize the painting databases into classes and sub-classes. Manual tagging of these ever-increasing databases would become very costly and time consuming. The above challenging problem has motivated researchers to work in the area of painting analysis, genre and style classification, artist classification and automatic annotation of paintings with these tags. These problems are quite difficult as first the expected human performance for this task for non-expert but reasonably knowledgeable individuals is believed to be well below 100% percent. And second, there is a very big databases of paintings with relatively few painters painting in a single genre and style and many who paint in multiple genres and styles. In this paper, we explore the problem of feature extraction on the paintings and focus on classification of paintings into their genres and styles. We worked with 6 genres and 10 styles. We get an accuracy of 84.56% for genre classification. We achieved an accuracy of 62.37% for classifying the paintings into 10 styles. We include a comparison to existing feature extraction and classification methods as well as an analysis of our own approach across different feature vectors.
LGP2 in Antiviral Innate Immunity DExD/H-Box Helicases RIG-I, MDA5, and Shared and Unique Functions of the

The cellular protein retinoic acid-inducible gene I (RIG-I) senses intracellular viral infection and triggers a signal for innate antiviral responses including the production of type I IFN. RIG-I contains a domain that belongs to a DExD/H-box helicase family and exhibits an N-terminal caspase recruitment domain (CARD) homology. There are three genes encoding RIG-I-related proteins in human and mouse genomes. Melanoma differentiation associated gene 5 (MDA5), which consists of CARD and a helicase domain, functions as a positive regulator, similarly to RIG-I. Both proteins sense viral RNA with a helicase domain and transmit a signal downstream by CARD; thus, these proteins share overlapping functions. Another protein, LGP2, lacks the CARD homology and functions as a negative regulator by interfering with the recognition of viral RNA by RIG-I and MDA5. The nonstructural protein 3/4A protein of hepatitis C virus blocks the signaling by RIG-I and MDA5; however, the V protein of the Sendai virus selectively abrogates the MDA5 function. These results highlight ingenious mechanisms for initiating antiviral innate immune responses and the action of virus-encoded inhibitors. The Journal of Immunology, 2005, 175: 2851–2858. ntracellular antiviral responses, including the activation of type I IFN genes, are initiated by the recognition of dsRNA generated by the replication of infected viruses. Type I IFN plays a critical role in initiating antiviral innate immunity and modulating subsequent adaptive immunity (1, 2). A dsRNA-in-duced
The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013

ChEBI (http://www.ebi.ac.uk/chebi) is a database and ontology of chemical entities of biological interest. Over the past few years, ChEBI has continued to grow steadily in content, and has added several new features. In addition to incorporating all user-requested compounds, our annotation efforts have emphasized immunology, natural products and metabolites in many species. All database entries are now ‘is_a’ classified within the ontology, meaning that all of the chemicals are available to semantic reasoning tools that harness the classification hierarchy. We have completely aligned the ontology with the Open Biomedical Ontologies (OBO) Foundry-recommended upper level Basic Formal Ontology. Furthermore, we have aligned our chemical classification with the classification of chemical-involving processes in the Gene Ontology (GO), and as a result of this effort, the majority of chemical-involving processes in GO are now defined in terms of the ChEBI entities that participate in them. This effort necessitated incorporating many additional biologically relevant compounds. We have incorporated additional data types including reference citations, and the species and component for metabolites. Finally, our website and web services have had several enhancements, most notably the provision of a dynamic new interactive graph-based ontology visualization.
Time-Frequency Analysis of EEG Asymmetry Using Bivariate Empirical Mode Decomposition

A novel method is introduced to determine asymmetry, the lateralization of brain activity, using extension of the algorithm empirical mode decomposition (EMD). The localized and adaptive nature of EMD make it highly suitable for estimating amplitude information across frequency for nonlinear and nonstationary data. Analysis illustrates how bivariate extension of EMD (BEMD) facilitates enhanced spectrum estimation for multichannel recordings that contain similar signal components, a realistic assumption in electroencephalography (EEG). It is shown how this property can be used to obtain a more accurate estimate of the marginalized spectrum, critical for the localized calculation of amplitude asymmetry in frequency. Simulations on synthetic data sets and feature estimation for a brain-computer interface (BCI) application are used to validate the proposed asymmetry estimation methodology.
A Theoretical Integration within Obsessive-Compulsive Disorder (OCD) and Dissociative Spectrums: Obsessional Dissociation

Over the recent three decades, there has been a growing academic interest on significant associations between obsessive compulsive disorder (OCD) and dissociation (Belli, Ural, Vardar, Yesilyurt, & Oncu, 2012; Belli et al., 2013; Fontenelle et al., 2007; Norton, Ross, & Novotny, 1990; Pica, Beere, & Maurer, 1997). In this regard, while the relationships with checking, ordering and symmetry has been widely highlighted from the view of obsessive-compulsive symptoms (Goff, Olin, Jenike, Baer, & Buttolph, 1992; Grabe et al., 1999; Lochner et al., 2004; Rufer, Fricke, Held, Cremer, & Hand, 2006; Watson & Wu, 2002; Watson, Wu, & Cutshall, 2004), the role of absorption / imaginative involvement dimension of dissociative symptoms in the pathophysiology of OCD has been underscored (Aardema & Wu, 2011; Paradisis, Aardema, & Wu, 2015; Soffer-Dudek, 2014; SofferDudek, Lassri, Soffer-Dudek, & Shahar, 2015; Tapancı, Yıldırım, & Boysan, 2018). Nevertheless, to the best of our opinion, a great deal of commonalities and transitions between these two phenomena exist. The overlapping features within these two clinical entities include heterogeneity of symptom structure (Boysan, 2016; Holmes et al., 2005; Mataix-Cols, do Rosario-Campos, & Leckman, 2005; Waller, Putnam, & Carlson, 1996), intrusiveness in nature (Boon, Steele, & van der Hart, 2011; Clark, 2004), ubiquity in general population (Maaranen et al., 2008; Rachman & De Silva, 1978; Ross, Joshi, & Currie, 1990; Salkovskis & Harrison, 1984; Vanderlinden, Van der Hart, & Varga, 1996), serve as defense mechanism in response to heightened stress but become counterproductive in pathological levels (Boysan, 2015; Boysan, Goldsmith, Çavuş, Kayri, & Keskin, 2009; Butler, Duran, Jasiukaitis, Koopman, & Spiegel, 1996), significant linkages to developmental trauma (Chu, 2011; Lochner et al., 2002; Mathews, Kaur, & Stein, 2008; Ogawa, Sroufe, Weinfield, Carlson, & Egeland, 1997; Schimmenti & Caretti, 2016), interpersonal aspects central to the etiological accounts (Aardema et al., 2013; Boysan & Çam, 2016; Doron & Kyrios, 2005; Doron et al., 2012; Guidano & Liotti, 1983; Liotti, 2004), pronounced deficits in memory and attention (Giesbrecht, Lynn, Lilienfeld, & Merckelbach, 2008; Muller & Roberts, 2005), and transdiagnostic characteristics as the hallmark of the psychopathology (Abramowitz, McKay, & Storch, 2017; Dell & O'Neil, 2015; Kadak, Nasiroglu, Boysan, & Aydin, 2013; Lanius et al., 2010). Therefore, more integrative LETTER TO THE EDITOR
Thermal AdS(3), BTZ and competing winding modes condensation

We study the thermal physics of AdS3 and the BTZ black hole when embedded in String theory. The exact calculation of the Hagedorn temperature in TAdS3 is reinterpreted as the appearance of a winding tachyon both in AdS3 and BTZ. We construct a dual framework for analyzing the phases of the system. In this dual framework, tachyon condensation and geometric capping appear on the same footing, bridging the usual gap of connecting tachyon condensation to modifications of geometry. This allows us to construct in a natural way a candidate for the unstable phase, analogous to a small black hole in higher dimensions. Additional peculiar effects associated with the Hagedorn temperature and the Hawking-Page transition, some to do with the asymptotic structure of AdS3 and some with strong curvature effects, are analyzed and explained.
Limits on the Macho Content of the Galactic Halo from the EROS-2 Survey of the Magellanic Clouds

The EROS-2 project was designed to test the hypothesis that massive compact halo objects (the so-called ''machos'') could be a major component of the dark matter halo of the Milky Way galaxy. To this end, EROS-2 monitored millions of stars in the Magellanic clouds for microlensing events caused by such objects. (abridged)
Probabilistic Models for Continuous Ontogenetic Transition Processes

Background Probabilistic reaction norms (PRNs) are an extension of the concept of reaction norms, developed to account for stochasticity in ontogenetic transitions. However, logistic regression based PRNs are restricted to discrete time intervals, whereas previously proposed models for continuous transitions are demanding in terms of modelling effort and data needed. Methodology/Principal Findings Here we introduce two alternative approaches for the probabilistic modelling of continuous ontogenetic transitions. The models are simplified in their description of forces underlying transitions, thus being empirical rather than mechanistic by their nature, but therefore applicable to situations where data and prior knowledge of transitions are limited. The models provide continuous time description of the transition pattern, insights into how it is affected by covariates, at the same time allowing for fine scale transition probability predictions. Performance of the models is demonstrated using empirical data on metamorphosis in common frogs (Rana temporaria) reared in a common garden experiment. Conclusions/Significance As being user-friendly and methodologically easily accessible, the models introduced in this study aid the concept of probabilistic reaction norms becoming as general and applicable tool in the studies of life-history variation as the deterministic reaction norms are today.
Management of Ewing sarcoma family of tumors: Current scenario and unmet need

Ewing sarcoma family tumors (ESFT) are heterogeneous, aggressive group of disease with peak incidence in adolescent and young adults. The outcome has been improved dramatically from 10% with surgery and radiotherapy alone to 65%-70% now, in localized disease, with the introduction of chemotherapy. Chemotherapy regimen evolved from single agent to multiagent with effort of many cooperative clinical trials over decades. The usual treatment protocol include introduction of multi-agent chemotherapy in neoadjuvant setting to eradicate systemic disease with timely incorporation of surgery and/or radiotherapy as local treatment modality and further adjuvant chemotherapy to prevent recurrence. Risk adapted chemotherapy in neoadjuvant and adjuvant setting along with radiotherapy has been used in many international collaborative trials and has resulted in improved outcome, more so in patients with localized disease. The role of high dose chemotherapy with stem cell rescue is still debatable. The outcome of patients with metastatic disease is dismal with long term outcome ranges from 20%-40% depending on the sites of metastasis and intensity of treatment. There is a huge unmet need to improve outcome further, more so in metastatic setting. Novel therapy targeting the molecular pathways and pathogenesis of ESFT is very much required. Here we have discussed the current standard of management in patients with ESFT, investigational targeted or novel therapies along with future promises.
The RNA–Methyltransferase Misu (NSun2) Poises Epidermal Stem Cells to Differentiate

Homeostasis of most adult tissues is maintained by balancing stem cell self-renewal and differentiation, but whether post-transcriptional mechanisms can regulate this process is unknown. Here, we identify that an RNA methyltransferase (Misu/Nsun2) is required to balance stem cell self-renewal and differentiation in skin. In the epidermis, this methyltransferase is found in a defined sub-population of hair follicle stem cells poised to undergo lineage commitment, and its depletion results in enhanced quiescence and aberrant stem cell differentiation. Our results reveal that post-transcriptional RNA methylation can play a previously unappreciated role in controlling stem cell fate.
Vector Disparity Sensor with Vergence Control for Active Vision Systems

This paper presents an architecture for computing vector disparity for active vision systems as used on robotics applications. The control of the vergence angle of a binocular system allows us to efficiently explore dynamic environments, but requires a generalization of the disparity computation with respect to a static camera setup, where the disparity is strictly 1-D after the image rectification. The interaction between vision and motor control allows us to develop an active sensor that achieves high accuracy of the disparity computation around the fixation point, and fast reaction time for the vergence control. In this contribution, we address the development of a real-time architecture for vector disparity computation using an FPGA device. We implement the disparity unit and the control module for vergence, version, and tilt to determine the fixation point. In addition, two on-chip different alternatives for the vector disparity engines are discussed based on the luminance (gradient-based) and phase information of the binocular images. The multiscale versions of these engines are able to estimate the vector disparity up to 32 fps on VGA resolution images with very good accuracy as shown using benchmark sequences with known ground-truth. The performances in terms of frame-rate, resource utilization, and accuracy of the presented approaches are discussed. On the basis of these results, our study indicates that the gradient-based approach leads to the best trade-off choice for the integration with the active vision system.
Single vacancy defect in graphene: insights into its magnetic properties from theoretical modeling

Magnetic properties of a single vacancy in graphene is a relevant and still unsolved problem. The experimental results point to a clearly detectable magnetic defect state at the Fermi energy, while several calculations based on density functional theory (DFT) yield widely varying results for the magnetic moment, in the range of $\mu=1.04-2.0$ $\mu_{B}$. We present a multi-tool \textit{ab initio} theoretical study of the same defect, using two simulation protocols for a defect in a crystal (cluster and periodic boundary conditions) and different DFT functionals - bare and hybrid DFT, mixing a fraction of exact Hartree-Fock exchange (XC). Our main conclusions are two-fold: First, we find that due to the $\pi$-character of the Fermi-energy states of graphene, inclusion of XC is crucial and for a single isolated vacancy we can predict an integer magnetic moment $\mu=2\mu_{B}$. Second, we find that due to the specific symmetry of the graphene lattice, periodic arrays of single vacancies may provide interesting diffuse spin-spin interactions.
Reference-Free Comparative Genomics of 174 Chloroplasts

Direct analysis of unassembled genomic data could greatly increase the power of short read DNA sequencing technologies and allow comparative genomics of organisms without a completed reference available. Here, we compare 174 chloroplasts by analyzing the taxanomic distribution of short kmers across genomes [1]. We then assemble de novo contigs centered on informative variation. The localized de novo contigs can be separated into two major classes: tip = unique to a single genome and group = shared by a subset of genomes. Prior to assembly, we found that ∼18% of the chloroplast was duplicated in the inverted repeat (IR) region across a four-fold difference in genome sizes, from a highly reduced parasitic orchid [2] to a massive algal chloroplast [3], including gnetophytes [4] and cycads [5]. The conservation of this ratio between single copy and duplicated sequence was basal among green plants, independent of photosynthesis and mechanism of genome size change, and different in gymnosperms and lower plants. Major lineages in the angiosperm clade differed in the pattern of shared kmers and de novo contigs. For example, parasitic plants demonstrated an expected accelerated overall rate of evolution, while the hemi-parasitic genomes contained a great deal more novel sequence than holo-parasitic plants, suggesting different mechanisms at different stages of genomic contraction. Additionally, the legumes are diverging more quickly and in different ways than other major families. Small duplicated fragments of the rrn23 genes were deeply conserved among seed plants, including among several species without the IR regions, indicating a crucial functional role of this duplication. Localized de novo assembly of informative kmers greatly reduces the complexity of large comparative analyses by confining the analysis to a small partition of data and genomes relevant to the specific question, allowing direct analysis of next-gen sequence data from previously unstudied genomes and rapid discovery of informative candidate regions.
Combining the glottal mixture model (GLOMM) with UBM for speaker recognition

We present an iterative algorithm to extract the voice source waveform from recordings of speech for speaker identification. The method detects glottal closings, then constructs a speaker-dependent library of glottal pulse waveforms by clustering data windows centered on the linear prediction error time-series at the glottal closures. With the voice source modeled as scaled and shifted glottal pulses, the algorithm iteratively determines the vocal tract parameters in each frame. In experiments, we combine the extracted voice source information with a universal background model (UBM). Using the TIMIT data corpus and a 200-speaker population size, we demonstrate a factor of three speaker recognition error reduction.