1,985 research outputs found
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 2021â2025 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 unterstĂźtzen soll. HAnS wurde von zwĂślf deutschen Hochschulen und Forschungsinstituten initiiert und wird 2021-2025 mit dem Ziel entwickelt, kĂźnstliche Intelligenz (KI) und Big Data im akademischen Umfeld zu nutzen, um technologiebasiertes Lernen zu verbessern. Das System nutzt KI fĂźr die Spracherkennung und die Indizierung vorhandener Lernressourcen und ermĂśglicht es den Nutzern, diese Materialien auf der Grundlage verschiedener Parameter zu suchen und zusammenzustellen. Hier geben wir einen Ăberblick Ăźber 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 fĂźr das Training der KI, der Verfeinerung komplexer Algorithmen fĂźr 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.; GarcĂa-FernĂĄndez, I.; Ferrer-Albero, A.; Macleod, R.; Saiz, J.; SebastiĂĄn, 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. M., Zahid, S., & Trayanova, N. A. (2016). Towards personalized computational modelling of the fibrotic substrate for atrial arrhythmia. EP Europace, 18(suppl_4), iv136-iv145. doi:10.1093/europace/euw358Courtemanche, M., Ramirez, R. J., & Nattel, S. (1998). 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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. 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N
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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 âfunctional similarityâ 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 âortholog conjectureâ (or, more properly, the âortholog functional conservation hypothesisâ). 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 âopen world assumptionâ (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
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
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