CRANKITE: a fast polypeptide backbone conformation sampler

Background: CRANKITE is a suite of programs for simulating backbone conformations of polypeptides and proteins. The core of the suite is an efficient Metropolis Monte Carlo sampler of backbone conformations in continuous three-dimensional space in atomic details. Methods: In contrast to other programs relying on local Metropolis moves in the space of dihedral angles, our sampler utilizes local crankshaft rotations of rigid peptide bonds in Cartesian space. Results: The sampler allows fast simulation and analysis of secondary structure formation and conformational changes for proteins of average length

Combining NLP, speech recognition, and indexing. An AI-based learning assistant for higher education

This paper presents the ongoing development of HAnS (Hochschul-Assistenz-System), an Intelligent Tutoring System (ITS) designed to support self-directed digital learning in higher education. Initiated by twelve collaborating German universities and research institutes, HAnS is developed 2021–2025 with the goal of utilizing artificial intelligence (AI) and Big Data in academic settings to enhance technology-based learning. The system employs AI for speech recognition and the indexing of existing learning resources, enabling users to search and compile these materials based on various parameters. Here, we provide an overview of the project, showcasing how iterative design and development processes contribute to innovative educational research in the evolving field of AI-based ITS in higher education. Notwithstanding the potential of HAnS, we also deliberate upon the challenges associated with ensuring a suitable dataset for training the AI, refining complex algorithms for personalization, and maintaining data privacy. (DIPF/Orig.)In diesem Beitrag wird die laufende Entwicklung von HAnS (Hochschul-Assistenz-System) vorgestellt, einem Intelligenten Tutoring-System (ITS), das selbstgesteuertes digitales Lernen in der Hochschulbildung unterstützen soll. HAnS wurde von zwölf deutschen Hochschulen und Forschungsinstituten initiiert und wird 2021-2025 mit dem Ziel entwickelt, künstliche Intelligenz (KI) und Big Data im akademischen Umfeld zu nutzen, um technologiebasiertes Lernen zu verbessern. Das System nutzt KI für die Spracherkennung und die Indizierung vorhandener Lernressourcen und ermöglicht es den Nutzern, diese Materialien auf der Grundlage verschiedener Parameter zu suchen und zusammenzustellen. Hier geben wir einen Überblick über das Projekt und zeigen, wie iterative Design- und Entwicklungsprozesse zu innovativer Bildungsforschung auf dem sich entwickelnden Gebiet der KI-basierten ITS in der Hochschulbildung beitragen. Ungeachtet des Potenzials von HAnS gehen wir auch auf die Herausforderungen ein, die mit der Sicherstellung eines geeigneten Datensatzes für das Training der KI, der Verfeinerung komplexer Algorithmen für die Personalisierung und der Wahrung des Datenschutzes verbunden sind. (Autor

Protein folding on the ribosome studied using NMR spectroscopy

NMR spectroscopy is a powerful tool for the investigation of protein folding and misfolding, providing a characterization of molecular structure, dynamics and exchange processes, across a very wide range of timescales and with near atomic resolution. In recent years NMR methods have also been developed to study protein folding as it might occur within the cell, in a de novo manner, by observing the folding of nascent polypeptides in the process of emerging from the ribosome during synthesis. Despite the 2.3 MDa molecular weight of the bacterial 70S ribosome, many nascent polypeptides, and some ribosomal proteins, have sufficient local flexibility that sharp resonances may be observed in solution-state NMR spectra. In providing information on dynamic regions of the structure, NMR spectroscopy is therefore highly complementary to alternative methods such as X-ray crystallography and cryo-electron microscopy, which have successfully characterized the rigid core of the ribosome particle. However, the low working concentrations and limited sample stability associated with ribosome-nascent chain complexes means that such studies still present significant technical challenges to the NMR spectroscopist. This review will discuss the progress that has been made in this area, surveying all NMR studies that have been published to date, and with a particular focus on strategies for improving experimental sensitivity

Cyclic Density Functional Theory : A route to the first principles simulation of bending in nanostructures

We formulate and implement Cyclic Density Functional Theory (Cyclic DFT) -- a self-consistent first principles simulation method for nanostructures with cyclic symmetries. Using arguments based on Group Representation Theory, we rigorously demonstrate that the Kohn-Sham eigenvalue problem for such systems can be reduced to a fundamental domain (or cyclic unit cell) augmented with cyclic-Bloch boundary conditions. Analogously, the equations of electrostatics appearing in Kohn-Sham theory can be reduced to the fundamental domain augmented with cyclic boundary conditions. By making use of this symmetry cell reduction, we show that the electronic ground-state energy and the Hellmann-Feynman forces on the atoms can be calculated using quantities defined over the fundamental domain. We develop a symmetry-adapted finite-difference discretization scheme to obtain a fully functional numerical realization of the proposed approach. We verify that our formulation and implementation of Cyclic DFT is both accurate and efficient through selected examples. The connection of cyclic symmetries with uniform bending deformations provides an elegant route to the ab-initio study of bending in nanostructures using Cyclic DFT. As a demonstration of this capability, we simulate the uniform bending of a silicene nanoribbon and obtain its energy-curvature relationship from first principles. A self-consistent ab-initio simulation of this nature is unprecedented and well outside the scope of any other systematic first principles method in existence. Our simulations reveal that the bending stiffness of the silicene nanoribbon is intermediate between that of graphene and molybdenum disulphide. We describe several future avenues and applications of Cyclic DFT, including its extension to the study of non-uniform bending deformations and its possible use in the study of the nanoscale flexoelectric effect.Comment: Version 3 of the manuscript, Accepted for publication in Journal of the Mechanics and Physics of Solids, http://www.sciencedirect.com/science/article/pii/S002250961630368

Atrial Fibrosis Hampers Non-invasive Localization of Atrial Ectopic Foci From Multi-Electrode Signals: A 3D Simulation Study

[EN] Introduction: Focal atrial tachycardia is commonly treated by radio frequency ablation with an acceptable long-term success. Although the location of ectopic foci tends to appear in specific hot-spots, they can be located virtually in any atrial region. Multi-electrode surface ECG systems allow acquiring dense body surface potential maps (BSPM) for non-invasive therapy planning of cardiac arrhythmia. However, the activation of the atria could be affected by fibrosis and therefore biomarkers based on BSPM need to take these effects into account. We aim to analyze the effect of fibrosis on a BSPM derived index, and its potential application to predict the location of ectopic foci in the atria. Methodology: We have developed a 3D atrial model that includes 5 distributions of patchy fibrosis in the left atrium at 5 different stages. Each stage corresponds to a different amount of fibrosis that ranges from 2 to 40%. The 25 resulting 3D models were used for simulation of Focal Atrial Tachycardia (FAT), triggered from 19 different locations described in clinical studies. BSPM were obtained for all simulations, and the body surface potential integral maps (BSPiM) were calculated to describe atrial activations. A machine learning (ML) pipeline using a supervised learning model and support vector machine was developed to learn the BSPM patterns of each of the 475 activation sequences and relate them to the origin of the FAT source. Results: Activation maps for stages with more than 15% of fibrosis were greatly affected, producing conduction blocks and delays in propagation. BSPiMs did not always cluster into non-overlapped groups since BSPiMs were highly altered by the conduction blocks. From stage 3 (15% fibrosis) the BSPiMs showed differences for ectopic beats placed around the area of the pulmonary veins. Classification results were mostly above 84% for all the configurations studied when a large enough number of electrodes were used to map the torso. However, the presence of fibrosis increases the area of the ectopic focus location and therefore decreases the utility for the electrophysiologist. Conclusions: The results indicate that the proposed ML pipeline is a promising methodology for non-invasive ectopic foci localization from BSPM signal even when fibrosis is present.This work was partially supported by Ministerio de Economia y Competitividad and Fondo Europeo de Desarrollo Regional (FEDER) DPI2015-69125-R and TIN2014-59932-JIN (MINECO/FEDER, UE).Godoy, EJ.; Lozano, M.; García-Fernández, I.; Ferrer-Albero, A.; Macleod, R.; Saiz, J.; Sebastián, R. (2018). Atrial Fibrosis Hampers Non-invasive Localization of Atrial Ectopic Foci From Multi-Electrode Signals: A 3D Simulation Study. Frontiers in Physiology. 9:1-18. https://doi.org/10.3389/fphys.2018.00404S1189Boyle, P. 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Noninvasive Personalization of a Cardiac Electrophysiology Model From Body Surface Potential Mapping. IEEE Transactions on Biomedical Engineering, 64(9), 2206-2218. doi:10.1109/tbme.2016.2629849Go, A. S., Hylek, E. M., Phillips, K. A., Chang, Y., Henault, L. E., Selby, J. V., & Singer, D. E. (2001). Prevalence of Diagnosed Atrial Fibrillation in Adults. JAMA, 285(18), 2370. doi:10.1001/jama.285.18.2370Guillem, M. S., Climent, A. M., Rodrigo, M., Fernández-Avilés, F., Atienza, F., & Berenfeld, O. (2016). Presence and stability of rotors in atrial fibrillation: evidence and therapeutic implications. Cardiovascular Research, 109(4), 480-492. doi:10.1093/cvr/cvw011Heidenreich, E. A., Ferrero, J. M., Doblaré, M., & Rodríguez, J. F. (2010). Adaptive Macro Finite Elements for the Numerical Solution of Monodomain Equations in Cardiac Electrophysiology. 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P., Haqqani, H., Stevenson, I. H., Vohra, J. K., Morton, J. B., … Kalman, J. M. (2005). Focal Atrial Tachycardia From the Ostium of the Coronary Sinus. Journal of the American College of Cardiology, 45(9), 1488-1493. doi:10.1016/j.jacc.2005.01.042Kistler, P. M., Roberts-Thomson, K. C., Haqqani, H. M., Fynn, S. P., Singarayar, S., Vohra, J. K., … Kalman, J. M. (2006). P-Wave Morphology in Focal Atrial Tachycardia. Journal of the American College of Cardiology, 48(5), 1010-1017. doi:10.1016/j.jacc.2006.03.058Kistler, P. M., Sanders, P., Fynn, S. P., Stevenson, I. H., Hussin, A., Vohra, J. K., … Kalman, J. M. (2003). Electrophysiological and Electrocardiographic Characteristics of Focal Atrial Tachycardia Originating From the Pulmonary Veins. Circulation, 108(16), 1968-1975. doi:10.1161/01.cir.0000095269.36984.75Kistler, P. M., Sanders, P., Hussin, A., Morton, J. B., Vohra, J. K., Sparks, P. B., & Kalman, J. M. (2003). Focal atrial tachycardia arising from the mitral annulus. Journal of the American College of Cardiology, 41(12), 2212-2219. doi:10.1016/s0735-1097(03)00484-4Andrew MacCannell, K., Bazzazi, H., Chilton, L., Shibukawa, Y., Clark, R. B., & Giles, W. R. (2007). A Mathematical Model of Electrotonic Interactions between Ventricular Myocytes and Fibroblasts. Biophysical Journal, 92(11), 4121-4132. doi:10.1529/biophysj.106.101410MacLeod, R. S., Kholmovski, E., DiBella, E. V. R., Oakes, R. S., Blauer, J. E., Fish, E., … Marrouche, N. F. (2008). Integration of MRI in evaluation and ablation of atrial fibrillation. 2008 Computers in Cardiology. doi:10.1109/cic.2008.4748981Maleckar, M. M., Greenstein, J. L., Giles, W. R., & Trayanova, N. A. (2009). Electrotonic Coupling between Human Atrial Myocytes and Fibroblasts Alters Myocyte Excitability and Repolarization. Biophysical Journal, 97(8), 2179-2190. doi:10.1016/j.bpj.2009.07.054Morgan, R., Colman, M. A., Chubb, H., Seemann, G., & Aslanidi, O. V. (2016). Slow Conduction in the Border Zones of Patchy Fibrosis Stabilizes the Drivers for Atrial Fibrillation: Insights from Multi-Scale Human Atrial Modeling. Frontiers in Physiology, 7. doi:10.3389/fphys.2016.00474MORTON, J. B., SANDERS, P., DAS, A., VOHRA, J. K., SPARKS, P. B., & KALMAN, J. M. (2001). Focal Atrial Tachycardia Arising from the Tricuspid Annulus: Electrophysiologic and Electrocardiographic Characteristics. Journal of Cardiovascular Electrophysiology, 12(6), 653-659. doi:10.1046/j.1540-8167.2001.00653.xNiederer, S. A., Kerfoot, E., Benson, A. P., Bernabeu, M. O., Bernus, O., Bradley, C., … Smith, N. P. (2011). Verification of cardiac tissue electrophysiology simulators using an N -version benchmark. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 369(1954), 4331-4351. doi:10.1098/rsta.2011.0139Oakes, R. S., Badger, T. J., Kholmovski, E. G., Akoum, N., Burgon, N. S., Fish, E. N., … Marrouche, N. F. (2009). Detection and Quantification of Left Atrial Structural Remodeling With Delayed-Enhancement Magnetic Resonance Imaging in Patients With Atrial Fibrillation. Circulation, 119(13), 1758-1767. doi:10.1161/circulationaha.108.811877Ramanathan, C., Jia, P., Ghanem, R., Calvetti, D., & Rudy, Y. (2003). Noninvasive Electrocardiographic Imaging (ECGI): Application of the Generalized Minimal Residual (GMRes) Method. Annals of Biomedical Engineering, 31(8), 981-994. doi:10.1114/1.1588655Santangeli, P., & Marchlinski, F. E. (2017). Techniques for the provocation, localization, and ablation of non–pulmonary vein triggers for atrial fibrillation. Heart Rhythm, 14(7), 1087-1096. doi:10.1016/j.hrthm.2017.02.030Santangeli, P., Zado, E. S., Hutchinson, M. D., Riley, M. P., Lin, D., Frankel, D. S., … Marchlinski, F. E. (2016). Prevalence and distribution of focal triggers in persistent and long-standing persistent atrial fibrillation. Heart Rhythm, 13(2), 374-382. doi:10.1016/j.hrthm.2015.10.023Saoudi, N. (2001). A classification of atrial flutter and regular atrial tachycardia according to electrophysiological mechanisms and anatomical bases. A Statement from a Joint Expert Group from the Working Group of Arrhythmias of the European Society of Cardiology and the North American Society of Pacing and Electrophysiology. European Heart Journal, 22(14), 1162-1182. doi:10.1053/euhj.2001.2658Shah, A. J., Hocini, M., Pascale, P., Roten, L., Komatsu, Y., … Daly, M. (2013). Body Surface Electrocardiographic Mapping for Non-invasive Identification of Arrhythmic Sources. Arrhythmia & Electrophysiology Review, 2(1), 16. doi:10.15420/aer.2013.2.1.16SippensGroenewegen, A., Natale, A., Marrouche, N. F., Bash, D., & Cheng, J. (2004). Potential role of body surface ECG mapping for localization of atrial fibrillation trigger sites. 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(2016). Percolation as a mechanism to explain atrial fractionated electrograms and reentry in a fibrosis model based on imaging data. Heart Rhythm, 13(7), 1536-1543. doi:10.1016/j.hrthm.2016.03.019Ward, J. H. (1963). Hierarchical Grouping to Optimize an Objective Function. Journal of the American Statistical Association, 58(301), 236-244. doi:10.1080/01621459.1963.10500845Weber, F. M., Keller, D. U. J., Bauer, S., Seemann, G., Lorenz, C., & Dössel, O. (2011). Predicting Tissue Conductivity Influences on Body Surface Potentials—An Efficient Approach Based on Principal Component Analysis. IEEE Transactions on Biomedical Engineering, 58(2), 265-273. doi:10.1109/tbme.2010.2090151Zhao, J., Kharche, S., Hansen, B., Csepe, T., Wang, Y., Stiles, M., & Fedorov, V. (2015). Optimization of Catheter Ablation of Atrial Fibrillation: Insights Gained from Clinically-Derived Computer Models. International Journal of Molecular Sciences, 16(12), 10834-10854. doi:10.3390/ijms16051083

On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report

A recent paper (Nehrt et al., PLoS Comput. Biol. 7:e1002073, 2011) has proposed a metric for the “functional similarity” between two genes that uses only the Gene Ontology (GO) annotations directly derived from published experimental results. Applying this metric, the authors concluded that paralogous genes within the mouse genome or the human genome are more functionally similar on average than orthologous genes between these genomes, an unexpected result with broad implications if true. We suggest, based on both theoretical and empirical considerations, that this proposed metric should not be interpreted as a functional similarity, and therefore cannot be used to support any conclusions about the “ortholog conjecture” (or, more properly, the “ortholog functional conservation hypothesis”). First, we reexamine the case studies presented by Nehrt et al. as examples of orthologs with divergent functions, and come to a very different conclusion: they actually exemplify how GO annotations for orthologous genes provide complementary information about conserved biological functions. We then show that there is a global ascertainment bias in the experiment-based GO annotations for human and mouse genes: particular types of experiments tend to be performed in different model organisms. We conclude that the reported statistical differences in annotations between pairs of orthologous genes do not reflect differences in biological function, but rather complementarity in experimental approaches. Our results underscore two general considerations for researchers proposing novel types of analysis based on the GO: 1) that GO annotations are often incomplete, potentially in a biased manner, and subject to an “open world assumption” (absence of an annotation does not imply absence of a function), and 2) that conclusions drawn from a novel, large-scale GO analysis should whenever possible be supported by careful, in-depth examination of examples, to help ensure the conclusions have a justifiable biological basis

Magnetism, FeS colloids, and Origins of Life

A number of features of living systems: reversible interactions and weak bonds underlying motor-dynamics; gel-sol transitions; cellular connected fractal organization; asymmetry in interactions and organization; quantum coherent phenomena; to name some, can have a natural accounting via $physical$ interactions, which we therefore seek to incorporate by expanding the horizons of `chemistry-only' approaches to the origins of life. It is suggested that the magnetic 'face' of the minerals from the inorganic world, recognized to have played a pivotal role in initiating Life, may throw light on some of these issues. A magnetic environment in the form of rocks in the Hadean Ocean could have enabled the accretion and therefore an ordered confinement of super-paramagnetic colloids within a structured phase. A moderate H-field can help magnetic nano-particles to not only overcome thermal fluctuations but also harness them. Such controlled dynamics brings in the possibility of accessing quantum effects, which together with frustrations in magnetic ordering and hysteresis (a natural mechanism for a primitive memory) could throw light on the birth of biological information which, as Abel argues, requires a combination of order and complexity. This scenario gains strength from observations of scale-free framboidal forms of the greigite mineral, with a magnetic basis of assembly. And greigite's metabolic potential plays a key role in the mound scenario of Russell and coworkers-an expansion of which is suggested for including magnetism.Comment: 42 pages, 5 figures, to be published in A.R. Memorial volume, Ed Krishnaswami Alladi, Springer 201

X-ray emission from the Sombrero galaxy: discrete sources

We present a study of discrete X-ray sources in and around the bulge-dominated, massive Sa galaxy, Sombrero (M104), based on new and archival Chandra observations with a total exposure of ~200 ks. With a detection limit of L_X = 1E37 erg/s and a field of view covering a galactocentric radius of ~30 kpc (11.5 arcminute), 383 sources are detected. Cross-correlation with Spitler et al.'s catalogue of Sombrero globular clusters (GCs) identified from HST/ACS observations reveals 41 X-rays sources in GCs, presumably low-mass X-ray binaries (LMXBs). We quantify the differential luminosity functions (LFs) for both the detected GC and field LMXBs, whose power-low indices (~1.1 for the GC-LF and ~1.6 for field-LF) are consistent with previous studies for elliptical galaxies. With precise sky positions of the GCs without a detected X-ray source, we further quantify, through a fluctuation analysis, the GC LF at fainter luminosities down to 1E35 erg/s. The derived index rules out a faint-end slope flatter than 1.1 at a 2 sigma significance, contrary to recent findings in several elliptical galaxies and the bulge of M31. On the other hand, the 2-6 keV unresolved emission places a tight constraint on the field LF, implying a flattened index of ~1.0 below 1E37 erg/s. We also detect 101 sources in the halo of Sombrero. The presence of these sources cannot be interpreted as galactic LMXBs whose spatial distribution empirically follows the starlight. Their number is also higher than the expected number of cosmic AGNs (52+/-11 [1 sigma]) whose surface density is constrained by deep X-ray surveys. We suggest that either the cosmic X-ray background is unusually high in the direction of Sombrero, or a distinct population of X-ray sources is present in the halo of Sombrero.Comment: 11 figures, 5 tables, ApJ in pres

Performance of the CMS Cathode Strip Chambers with Cosmic Rays

The Cathode Strip Chambers (CSCs) constitute the primary muon tracking device in the CMS endcaps. Their performance has been evaluated using data taken during a cosmic ray run in fall 2008. Measured noise levels are low, with the number of noisy channels well below 1%. Coordinate resolution was measured for all types of chambers, and fall in the range 47 microns to 243 microns. The efficiencies for local charged track triggers, for hit and for segments reconstruction were measured, and are above 99%. The timing resolution per layer is approximately 5 ns

Azimuthal anisotropy of charged particles at high transverse momenta in PbPb collisions at sqrt(s[NN]) = 2.76 TeV

The azimuthal anisotropy of charged particles in PbPb collisions at nucleon-nucleon center-of-mass energy of 2.76 TeV is measured with the CMS detector at the LHC over an extended transverse momentum (pt) range up to approximately 60 GeV. The data cover both the low-pt region associated with hydrodynamic flow phenomena and the high-pt region where the anisotropies may reflect the path-length dependence of parton energy loss in the created medium. The anisotropy parameter (v2) of the particles is extracted by correlating charged tracks with respect to the event-plane reconstructed by using the energy deposited in forward-angle calorimeters. For the six bins of collision centrality studied, spanning the range of 0-60% most-central events, the observed v2 values are found to first increase with pt, reaching a maximum around pt = 3 GeV, and then to gradually decrease to almost zero, with the decline persisting up to at least pt = 40 GeV over the full centrality range measured.Comment: Replaced with published version. Added journal reference and DO