• Computation of parton distributions from the quasi-PDF approach at the physical point

      Alexandrou, C; Bacchio, S; Cichy, K; Constantinou, M; Hadjiyiannakou, K; Jansen, K; Koutsou, G; Scapellato, A; Steffens, F (2018-03-26)
      © The Authors, published by EDP Sciences, 2018. We show the first results for parton distribution functions within the proton at the physical pion mass, employing the method of quasi-distributions. In particular, we present the matrix elements for the iso-vector combination of the unpolarized, helicity and transversity quasi-distributions, obtained with Nf = 2 twisted mass cloverimproved fermions and a proton boosted with momentum p→ = 0.83 GeV. The momentum smearing technique has been applied to improve the overlap with the proton boosted state. Moreover, we present the renormalized helicity matrix elements in the RI' scheme, following the non-perturbative renormalization prescription recently developed by our group.
    • Constraining sea quark distributions through W<sup>±</sup> cross section ratios measured at STAR

      Posik, M (2015-01-01)
      © Copyright owned by the author(s) under the terms of the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC BY-NC-ND 4.0). Over the past several years the STAR experiment at RHIC has been contributing to our understanding of the proton structure. Through its instrumentation, STAR is well equipped to measure W → v + e in √s = 500/510 GeV proton-proton collisions at mid-rapidity (-1.1 ≤ η ≤ 1.1). The W cross section ratio (W+/W-) is sensitive to unpolarized u, d, ū, and d quark distributions. At these kinematics, STAR is able to measure the quark distributions near Bjorken-x values of 0.1. The RHIC runs in 2011, 2012 and 2013 at √s = 500/510 GeV saw a significant increase in delivered luminosity from previous years. This resulted in a total data sample being collected of about 352 pb-1 of integrated luminosity. The increased statistics will lead to a higher precision measurement of the W+/W- cross section ratio than was previously measured by STAR's 2009 run, as well as allow for a measurement of its η dependence at mid-rapidity. Presented here is an update of the W cross section ratio analysis from the STAR 2011, 2012 and 2013 runs.
    • Constraining the sea quark distributions through W<sup>±</sup> cross section ratio measurements at STAR

      Posik, M (2017-01-01)
      © 2017 Copyright owned by the author(s) under the terms of the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC BY-NC-ND 4.0). Over the past several years, parton distribution functions (PDFs) have become more precise. However there are still kinematic regions where more data are needed to help constrain global PDF extractions, such as the sea quark distributions d/ū near the valence region (Bjorken-x ≈ 0.1 - 0.3). Current measurements appear to suggest different high-x behaviors of these distributions, leading to large uncertainties in global fits. The charged W cross section ratio (W+/W-) is sensitive to the unpolarized u; d; ū; and d quark distributions at large Q2 set by theW mass and could help shed light on this discrepancy. The STAR experiment at RHIC is well equipped to measure the leptonic decays of W bosons, in the mid-rapidity range (|η| ≤ 1), produced in proton+proton collisions at √s = 500/510 GeV. At these kinematics STAR is sensitive to quark distributions near Bjorken-x of 0.16. STAR can also measure the W cross section ratio in a more forward bin ranging from 1.1 < η < 2.0, which extends the sea quark sensitivity to higher x. RHIC runs from 2011 through 2013 have collected about 350 pb-1 of integrated luminosity, and a 2017 run is expected to provide an additional 400 pb-1. Presented here are preliminary results for the 2011-2012 charged W cross section ratios (∼100pb-1) and an update on the 2013 charged W cross section analysis (∼250 pb-1).
    • Constraining the sea quark distributions through w<sup>±</sup> cross section ratio measurements at STAR

      Posik, M (2019-01-01)
      © Copyright owned by the author(s) under the terms of the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC BY-NC-ND 4.0). Over the past several years, parton distribution functions (PDFs) have become more precise. However there are still kinematic regions where more data are needed to help constrain global PDF extractions, such as the ratio of the sea quark distributions d¯/ū near the valence region. Furthermore, current measurements appear to suggest different high-x behaviors of this ratio. The W cross section ratio (W+/W−) is sensitive to the unpolarized quark distributions at large Q2 set by the W mass. Such a measurement can be used to help constrain the d¯/ū ratio. The STAR experiment at RHIC is well equipped to measure the leptonic decays of W bosons, in the midpseudorapdity range (|η| ≤ 1), produced in proton-proton collisions at √s = 500/510 GeV. At these kinematics STAR is sensitive to quark distributions near x of 0.16. STAR can also measure W+/W− in a more forward region ranging from 1.0 < η <1.5, which extends the sea quark sensitivity to higher x. RHIC runs from 2011 through 2013 have collected about 350 pb−1 of integrated luminosity, and an additional 350 pb−1 from the 2017 run. These proceedings will present preliminary results of the 2011-2013 W+/W− cross section ratio measurements. Additionally, the W/Z cross section ratio, differential and total W and Z cross sections are presented.
    • Disconnected quark loop contributions to nucleon observables using N<inf>f</inf> = 2 twisted clover fermions at the physical value of the light quark mass

      Abdel-Rehim, A; Alexandrou, C; Constantinou, M; Hadjiyiannakou, K; Jansen, K; Kallidonis, C; Koutsou, G; Avilés-Casco, AV (2015-01-01)
      We compute the disconnected quark loops contributions entering the determination of nucleon observables, by using a Nf = 2 ensemble of twisted mass fermions with a clover term at a pION mass mπ = 133 MeV. We employ exact deflation and implement all calculations in GPUs, enabling us to achieve large statistics and a good signal.
    • Evolution enters the genomic era

      Liberles, DA; Liberles, David A|0000-0003-3487-8826 (2001-12-01)
      A report on the 18th Congress of the European Society for Evolutionary Biology (ESEB), Aarhus, Denmark, 20-25 August, 2001.
    • GIFT: A real-time and scalable 3D shape search engine

      Bai, S; Bai, X; Zhou, Z; Zhang, Z; Latecki, LJ (2016-12-09)
      © 2016 IEEE. Projective analysis is an important solution for 3D shape retrieval, since human visual perceptions of 3D shapes rely on various 2D observations from different view points. Although multiple informative and discriminative views are utilized, most projection-based retrieval systems suffer from heavy computational cost, thus cannot satisfy the basic requirement of scalability for search engines. In this paper, we present a real-time 3D shape search engine based on the projective images of 3D shapes. The real-time property of our search engine results from the following aspects: (1) efficient projection and view feature extraction using GPU acceleration, (2) the first inverted file, referred as F-IF, is utilized to speed up the procedure of multi-view matching, (3) the second inverted file (S-IF), which captures a local distribution of 3D shapes in the feature manifold, is adopted for efficient context-based reranking. As a result, for each query the retrieval task can be finished within one second despite the necessary cost of IO overhead. We name the proposed 3D shape search engine, which combines GPU acceleration and Inverted File (Twice), as GIFT. Besides its high efficiency, GIFT also outperforms the state-of-the-art methods significantly in retrieval accuracy on various shape benchmarks and competitions.
    • Intrinsic disorder in putative protein sequences

      Midic, U; Obradovic, Z (2012-01-01)
      © 2012 Midic and Obradovic; licensee BioMed Central Ltd. Background: Intrinsically disordered proteins (IDPs) and regions (IDRs) perform a variety of crucial biological functions despite lacking stable tertiary structure under physiological conditions in vitro. State-of-the-art sequencebased predictors of intrinsic disorder are achieving per-residue accuracies over 80%. In a genome-wide study of intrinsic disorder in human genome we observed a big difference in predicted disorder content between confirmed and putative human proteins. We investigated a hypothesis that this discrepancy is not correct, and that it is due to incorrectly annotated parts of the putative protein sequences that exhibit some similarities to confirmed IDRs, which lead to high predicted disorder content. Methods: To test this hypothesis we trained a predictor to discriminate sequences of real proteins from synthetic sequences that mimic errors of gene finding algorithms. We developed a procedure to create synthetic peptide sequences by translation of non-coding regions of genomic sequences and translation of coding regions with incorrect codon alignment. Results: Application of the developed predictor to putative human protein sequences showed that they contain a substantial fraction of incorrectly assigned regions. These regions are predicted to have higher levels of disorder content than correctly assigned regions. This partially, albeit not completely, explains the observed discrepancy in predicted disorder content between confirmed and putative human proteins. Conclusions: Our findings provide the first evidence that current practice of predicting disorder content in putative sequences should be reconsidered, as such estimates may be biased.
    • Modeling the mutualistic interactions between tubeworms and microbial consortia

      Cordes, EE; Arthur, MA; Shea, K; Arvidson, RS; Fisher, CR; Cordes, Erik|0000-0002-6989-2348 (2005-03-01)
      The deep-sea vestimentiferan tubeworm Lamellibrachia luymesi forms large aggregations at hydrocarbon seeps in the Gulf of Mexico that may persist for over 250 y. Here, we present the results of a diagenetic model in which tubeworm aggregation persistence is achieved through augmentation of the supply of sulfate to hydrocarbon seep sediments. In the model, L. luymesi releases the sulfate generated by its internal, chemoautotrophic, sulfide-oxidizing symbionts through posterior root-like extensions of its body. The sulfate fuels sulfate reduction, commonly coupled to anaerobic methane oxidation and hydrocarbon degradation by bacterial-archaeal consortia. If sulfate is released by the tubeworms, sulfide generation mainly by hydrocarbon degradation is sufficient to support moderate-sized aggregations of L. luymesi for hundreds of years. The results of this model expand our concept of the potential benefits derived from complex interspecific relationships, in this case involving members of all three domains of life. © 2005 Cordes et al.
    • New Physics Searches from Nucleon Matrix Elements in Lattice QCD

      Constantinou, M (2017-03-22)
      © The Authors, published by EDP Sciences, 2017. In this paper we review recent progress in hadron structure using lattice QCD simulations, with main focus in the evaluation of nucleon matrix elements. We highlight developments that may guide new Physics searches, such as the scalar and tensor charges, as well as, the neutron electric dipole moment.
    • Perturbative Renormalization of Wilson line operators

      Constantinou, M; Panagopoulos, H (2018-03-26)
      © The Authors, published by EDP Sciences, 2018. We present results for the renormalization of gauge invariant nonlocal fermion operators which contain a Wilson line, to one loop level in lattice perturbation theory. Our calculations have been performed for Wilson/clover fermions and a wide class of Symanzik improved gluon actions. The extended nature of such 'long-link' operators results in a nontrivial renormalization, including contributions which diverge linearly as well as logarithmically with the lattice spacing, along with additional finite factors. We present nonperturbative prescriptions to extract the linearly divergent contributions.
    • Progress in computing parton distribution functions from the quasi-PDF approach

      Alexandrou, C; Cichy, K; Constantinou, M; Hadjiyiannakou, K; Jansen, K; Panagopoulos, H; Scapellato, A; Steffens, F (2018-03-26)
      © The Authors, published by EDP Sciences, 2018. We discuss the current developments by the European Twisted Mass Collaboration in extracting parton distribution functions from the quasi-PDF approach. We concentrate on the non-perturbative renormalization prescription recently developed by us, using the RI′ scheme. We show results for the renormalization functions of matrix elements needed for the computation of quasi-PDFs, including the conversion to the MS scheme, and for renormalized matrix elements. We discuss the systematic effects present in the Z-factors and the possible ways of addressing them in the future.
    • Protein disorder in the human diseasome: Unfoldomics of human genetic diseases

      Midic, U; Oldfield, CJ; Keith, AK; Obradovic, Z; Uversky, VN (2009-07-07)
      Background: Intrinsically disordered proteins lack stable structure under physiological conditions, yet carry out many crucial biological functions, especially functions associated with regulation, recognition, signaling and control. Recently, human genetic diseases and related genes were organized into a bipartite graph (Goh KI, Cusick ME, Valle D, Childs B, Vidal M, et al. (2007) The human disease network. Proc Natl Acad Sci U S A 104: 8685-8690). This diseasome network revealed several significant features such as the common genetic origin of many diseases. Methods and findings: We analyzed the abundance of intrinsic disorder in these diseasome network proteins by means of several prediction algorithms, and we analyzed the functional repertoires of these proteins based on prior studies relating disorder to function. Our analyses revealed that (i) Intrinsic disorder is common in proteins associated with many human genetic diseases; (ii) Different disease classes vary in the IDP contents of their associated proteins; (iii) Molecular recognition features, which are relatively short loosely structured protein regions within mostly disordered sequences and which gain structure upon binding to partners, are common in the diseasome, and their abundance correlates with the intrinsic disorder level; (iv) Some disease classes have a significant fraction of genes affected by alternative splicing, and the alternatively spliced regions in the corresponding proteins are predicted to be highly disordered; and (v) Correlations were found among the various diseasome graph-related properties and intrinsic disorder. Conclusion: These observations provide the basis for the construction of the human-genetic-disease-associated unfoldome. © 2009 Midic et al; licensee BioMed Central Ltd.
    • Provably efficient algorithms for joint placement and allocation of virtual network functions

      Sang, Y; Ji, B; Gupta, GR; Du, X; Ye, L; Du, Xiaojiang|0000-0003-4235-9671 (2017-10-02)
      © 2017 IEEE. Network Function Virtualization (NFV) has the potential to significantly reduce the capital and operating expenses, shorten product release cycle, and improve service agility. In this paper, we focus on minimizing the total number of Virtual Network Function (VNF) instances to provide a specific service (possibly at different locations) to all the flows in a network. Certain network security and analytics applications may allow fractional processing of a flow at different nodes (corresponding to datacenters), giving an opportunity for greater optimization of resources. Through a reduction from the set cover problem, we show that this problem is NP-hard and cannot even be approximated within a factor of (1 - o(1))lnm (where m is the number of flows) unless P=NP. Then, we design two simple greedy algorithms and prove that they achieve an approximation ratio of (1 - o(1))ln m + 2, which is asymptotically optimal. For special cases where each node hosts multiple VNF instances (which is typically true in practice), we also show that our greedy algorithms have a constant approximation ratio. Further, for tree topologies we develop an optimal greedy algorithm by exploiting the inherent topological structure. Finally, we conduct extensive numerical experiments to evaluate the performance of our proposed algorithms in various scenarios.
    • Short Linear Motifs recognized by SH2, SH3 and Ser/Thr Kinase domains are conserved in disordered protein regions

      Ren, S; Uversky, VN; Chen, Z; Dunker, AK; Obradovic, Z (2008-09-16)
      Background: Protein interactions are essential for most cellular functions. Interactions mediated by domains that appear in a large number of proteins are of particular interest since they are expected to have an impact on diversities of cellular processes such as signal transduction and immune response. Many well represented domains recognize and bind to primary sequences less than 10 amino acids in length called Short Linear Motifs (SLiMs). Results: In this study, we systematically studied the evolutionary conservation of SLiMs recognized by SH2, SH3 and Ser/Thr Kinase domains in both ordered and disordered protein regions. Disordered protein regions are protein sequences that lack a fixed three-dimensional structure under putatively native conditions. We find that, in all these domains examined, SLiMs are more conserved in disordered regions. This trend is more evident in those protein functional groups that are frequently reported to interact with specific domains. Conclusion: The correlation between SLiM conservation with disorder prediction demonstrates that functional SLiMs recognized by each domain occur more often in disordered as compared to structured regions of proteins. © 2008 Ren et al; licensee BioMed Central Ltd.
    • The salmon genome (and other issues in bioinformatics)

      Milchert, LEF; Liberles, DA; Elofsson, A; Liberles, David A|0000-0003-3487-8826 (2002-10-07)
      A report on the fourth annual conference of the Society for Bioinformatics in the Nordic Countries (SOCBIN), Bioinformatics 2002, Bergen, Norway, 4-7 April 2002.
    • The unfoldomics decade: An update on intrinsically disordered proteins

      Dunker, AK; Oldfield, CJ; Meng, J; Romero, P; Yang, JY; Chen, JW; Vacic, V; Obradovic, Z; Uversky, VN (2008-09-16)
      Background; Our first predictor of protein disorder was published just over a decade ago in the Proceedings of the IEEE International Conference on Neural Networks (Romero P, Obradovic Z, Kissinger C, Villafranca JE, Dunker AK (1997) Identifying disordered regions in proteins from amino acid sequence. Proceedings of the IEEE International Conference on Neural Networks, 1: 90-95). By now more than twenty other laboratory groups have joined the efforts to improve the prediction of protein disorder. While the various prediction methodologies used for protein intrinsic disorder resemble those methodologies used for secondary structure prediction, the two types of structures are entirely different. For example, the two structural classes have very different dynamic properties, with the irregular secondary structure class being much less mobile than the disorder class. The prediction of secondary structure has been useful. On the other hand, the prediction of intrinsic disorder has been revolutionary, leading to major modifications of the more than 100 year-old views relating protein structure and function. Experimentalists have been providing evidence over many decades that some proteins lack fixed structure or are disordered (or unfolded) under physiological conditions. In addition, experimentalists are also showing that, for many proteins, their functions depend on the unstructured rather than structured state; such results are in marked contrast to the greater than hundred year old views such as the lock and key hypothesis. Despite extensive data on many important examples, including disease-associated proteins, the importance of disorder for protein function has been largely ignored. Indeed, to our knowledge, current biochemistry books don't present even one acknowledged example of a disorder-dependent function, even though some reports of disorder-dependent functions are more than 50 years old. The results from genome-wide predictions of intrinsic disorder and the results from other bioinformatics studies of intrinsic disorder are demanding attention for these proteins. Results: Disorder prediction has been important for showing that the relatively few experimentally characterized examples are members of a very large collection of related disordered proteins that are wide-spread over all three domains of life. Many significant biological functions are now known to depend directly on, or are importantly associated with, the unfolded or partially folded state. Here our goal is to review the key discoveries and to weave these discoveries together to support novel approaches for understanding sequence-function relationships. Conclusion: Intrinsically disordered protein is common across the three domains of life, but especially common among the eukaryotic proteomes. Signaling sequences and sites of posttranslational modifications are frequently, or very likely most often, located within regions of intrinsic disorder. Disorder-to-order transitions are coupled with the adoption of different structures with different partners. Also, the flexibility of intrinsic disorder helps different disordered regions to bind to a common binding site on a common partner. Such capacity for binding diversity plays important roles in both protein-protein interaction networks and likely also in gene regulation networks. Such disorder-based signaling is further modulated in multicellular eukaryotes by alternative splicing, for which such splicing events map to regions of disorder much more often than to regions of structure. Associating alternative splicing with disorder rather than structure alleviates theoretical and experimentally observed problems associated with the folding of different length, isomeric amino acid sequences. The combination of disorder and alternative splicing is proposed to provide a mechanism for easily "trying out" different signaling pathways, thereby providing the mechanism for generating signaling diversity and enabling the evolution of cell differentiation and multicellularity. Finally, several recent small molecules of interest as potential drugs have been shown to act by blocking protein-protein interactions based on intrinsic disorder of one of the partners. Study of these examples has led to a new approach for drug discovery, and bioinformatics analysis of the human proteome suggests that various disease-associated proteins are very rich in such disorder-based drug discovery targets. © 2008 Dunker et al; licensee BioMed Central Ltd.
    • Unfoldomics of human diseases: Linking protein intrinsic disorder with diseases

      Uversky, VN; Oldfield, CJ; Midic, U; Xie, H; Xue, B; Vucetic, S; Iakoucheva, LM; Obradovic, Z; Keith, AK (2009-07-07)
      Background: Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) lack stable tertiary and/or secondary structure yet fulfills key biological functions. The recent recognition of IDPs and IDRs is leading to an entire field aimed at their systematic structural characterization and at determination of their mechanisms of action. Bioinformatics studies showed that IDPs and IDRs are highly abundant in different proteomes and carry out mostly regulatory functions related to molecular recognition and signal transduction. These activities complement the functions of structured proteins. IDPs and IDRs were shown to participate in both one-to-many and many-to-one signaling. Alternative splicing and posttranslational modifications are frequently used to tune the IDP functionality. Several individual IDPs were shown to be associated with human diseases, such as cancer, cardiovascular disease, amyloidoses, diabetes, neurodegenerative diseases, and others. This raises questions regarding the involvement of IDPs and IDRs in various diseases. Results: IDPs and IDRs were shown to be highly abundant in proteins associated with various human maladies. As the number of IDPs related to various diseases was found to be very large, the concepts of the disease-related unfoldome and unfoldomics were introduced. Novel bioinformatics tools were proposed to populate and characterize the disease-associated unfoldome. Structural characterization of the members of the disease-related unfoldome requires specialized experimental approaches. IDPs possess a number of unique structural and functional features that determine their broad involvement into the pathogenesis of various diseases. Conclusion: Proteins associated with various human diseases are enriched in intrinsic disorder. These disease-associated IDPs and IDRs are real, abundant, diversified, vital, and dynamic. These proteins and regions comprise the disease-related unfoldome, which covers a significant part of the human proteome. Profound association between intrinsic disorder and various human diseases is determined by a set of unique structural and functional characteristics of IDPs and IDRs. Unfoldomics of human diseases utilizes unrivaled bioinformatics and experimental techniques, paves the road for better understanding of human diseases, their pathogenesis and molecular mechanisms, and helps develop new strategies for the analysis of disease-related proteins. © 2009 Uversky et al; licensee BioMed Central Ltd.