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Regularity and Conformity

Yingzi Wang, Nicholas Jing Yuan, Defu Lian, Linli Xu, Xing Xie, Enhong Chen, Yong Rui
2015 Proceedings of the 21th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining - KDD '15  
However, existing approaches for location prediction fail to organically combine both the regularity and conformity of human mobility in a unified model, and lack the capacity to incorporate heterogeneous  ...  We evaluate the proposed model using several city-scale mobility datasets including location check-ins, GPS trajectories of taxis, and public transit data.  ...  In this paper, we tackle the above challenges by proposing a hybrid model called RCH, combining both Regularity and Conformity, and employing Heterogeneous mobility data for location prediction.  ... 
doi:10.1145/2783258.2783350 dblp:conf/kdd/WangYLXXCR15 fatcat:er7kf2hiv5etncxlq4xzq23spi

DNA, RNA Structure & Conformation

2008 Biophysical Journal  
We also discovered dependencies between the average structural changes of the RNA structural elements within a cluster and their  ...  Board B137 We recently developed the RNAJunction database, which contains more than thirteen thousand RNA junctions, bulges, internal loops and loop-loop interactions (http://rnajunction.abcc.ncifcrf.gov  ...  We use experimental data to predict the twist-stretch coupling for DNA and compare our simulations to published results of single-molecule experiments on DNA supercoiling. 302-Pos Systematic Design  ... 
doi:10.1016/s0006-3495(08)79009-x fatcat:5wslivpqbndt7gs4y6lpiytt5y

Water and globular proteins

John A. Rupley, Enrico Gratton, Giorgio Careri
1983 TIBS -Trends in Biochemical Sciences. Regular ed  
Acknowledgements We are grateful to NATO for a Research Grant that supported the travel that this collaboration was based upon and to the National Institutes of Health and the National Science Foundation  ...  Thermodynamic differences at full hydration are excess values per mole ol water, with sorption data 2:~ having been integrated to estimate AG and AH. Data for ovalbumin 2~` were used to estimate AV.  ...  Hill's theory predicts two phase transitions.  ... 
doi:10.1016/0968-0004(83)90063-4 fatcat:t3kdppt4qvdbrcjq7lpbvdpvte

Conformation of receptor-bound visual arrestin

M. Kim, S. A. Vishnivetskiy, N. Van Eps, N. S. Alexander, W. M. Cleghorn, X. Zhan, S. M. Hanson, T. Morizumi, O. P. Ernst, J. Meiler, V. V. Gurevich, W. L. Hubbell
2012 Proceedings of the National Academy of Sciences of the United States of America  
To map conformational changes upon binding to the receptor, pairs of spin labels were introduced in arrestin-1 and double electron-electron resonance was used to monitor interspin distance changes upon  ...  conformation.  ...  Christian Altenbach for his help with distance data analysis.  ... 
doi:10.1073/pnas.1216304109 pmid:23091036 pmcid:PMC3494953 fatcat:ype5hrve7bbdvk6epkwuj53elm

Double electron–electron resonance reveals cAMP-induced conformational change in HCN channels

Michael C. Puljung, Hannah A. DeBerg, William N. Zagotta, Stefan Stoll
2014 Proceedings of the National Academy of Sciences of the United States of America  
We thank Shellee Cunnington and Stacey Camp for technical assistance, Ellen Hayes for help with the EPR and DEER experiments, and Christopher Miller for helpful comments on the manuscript.  ...  (S.S.), and by a fellowship from the Sackler Scholars Program in Integrative Biophysics (to H.A.D.).  ...  Both DEER and CW EPR predict a decrease in the conformational heterogeneity of the C-helix upon binding to cAMP, particularly at the distal end.  ... 
doi:10.1073/pnas.1405371111 pmid:24958877 pmcid:PMC4103371 fatcat:ku7le2uxx5dexkmkyze7vkushm

Quaternary structure and function of transport proteins

Liesbeth M Veenhoff, Esther H.M.L Heuberger, Bert Poolman
2002 TIBS -Trends in Biochemical Sciences. Regular ed  
and the rigorousness of the published data.  ...  The motional time scales of measurements using saturation-transfer electron-spin resonance (ST-ESR) and phosphorescence anisotropy (10 −6 -10 −3 s) are appropriate to observe the rotational mobility of  ... 
doi:10.1016/s0968-0004(02)02077-7 pmid:12076536 fatcat:me363w2gbfdldik4awi7xpxpuy

Cyberspace Security Using Adversarial Learning and Conformal Prediction

Harry Wechsler
2015 Intelligent Information Management  
Conformal prediction leverages apparent relationships between immunity and intrusion detection using non-conformity measures characteristic of affinity, a typicality, and surprise, to recognize patterns  ...  Conformal prediction is the principled and unified adaptive and learning framework used to design, develop, and deploy a multi-faceted self-managing defensive shield to detect, disrupt, and deny intrusive  ...  Additional goals would include investigating integration issues ranging from fusing multiple information channels (e.g., appearance, behavior, location, and profiles) using conformal prediction, best ways  ... 
doi:10.4236/iim.2015.74016 fatcat:wqiu3pkl6zeurlr3mizdahhgd4

Conformational flexibility of the protein insertase BamA in the native asymmetric bilayer elucidated with ESR spectroscopy

Aathira Gopinath, Benesh Joseph
2021 Angewandte Chemie  
In the detergent micelles,the data is consistent with mainly an inward-open conformation of BamA.  ...  af avorable environment for occupying multiple conformational states independent of the lipoproteins.Our results reveal ahighly dynamic behavior of the lateral gate and other key structural elements and  ...  We are grateful to Sebastian Hiller for providing the JCM166 cells lines and Marc Baldus for inputs on protein expression and purification. Open Access funding enabled and organized by Projekt DEAL.  ... 
doi:10.1002/ange.202113448 fatcat:yxukopleije7xmacrocgpp5gua

Linkage-specific conformational ensembles of non-canonical polyubiquitin chains

Carlos A. Castañeda, Apurva Chaturvedi, Christina M. Camara, Joseph E. Curtis, Susan Krueger, David Fushman
2016 Physical Chemistry, Chemical Physics - PCCP  
Ensemble analysis using NMR and SANS revealed conformational heterogeneity of polyubiquitin chains, suggesting unique as well as overlapping functions.  ...  DMR-0944772, and benefited from CCP-SAS software developed through a joint EPSRC (EP/K039121/1) and NSF (CHE-1265821) grant.  ...  We thank Emma Dixon for assistance in assembly and purification of some Ub 2 proteins, and Konstantin Berlin for helpful discussions regarding SES.  ... 
doi:10.1039/c5cp04601g pmid:26422168 pmcid:PMC4758893 fatcat:mabvthtg2nab3fiuqxqfgn7vfe

Visualisation of xanthan conformation by atomic force microscopy

Jonathan Moffat, Victor J. Morris, Saphwan Al-Assaf, A. Patrick Gunning
2016 Carbohydrate Polymers  
Direct visual evidence obtained by atomic force microscopy demonstrates that when xanthan is adsorbed from aqueous solution onto the heterogeneously charged substrate mica, its helical conformation is  ...  Once the helix state reforms, the AFM images obtained showed clear resolution of the periodicity with a value of 4.7 nm consistent with the previously predicted models.  ...  The AFM data suggests that xanthan's predominant equilibrium structural conformation is a double helix.  ... 
doi:10.1016/j.carbpol.2016.04.078 pmid:27185152 pmcid:PMC4879867 fatcat:rlvubhemabafddzllco2qpa2v4

Conformational flexibility of the protein insertase BamA in the native asymmetric bilayer elucidated with ESR spectroscopy

Aathira Gopinath, Benesh Joseph
2021 Angewandte Chemie International Edition  
In the detergent micelles, the data is consistent with mainly an inward-open conformation of BamA. The native membrane considerably enhanced the conformational heterogeneity.  ...  The lateral gate and the extracellular loop 3 exist in an equilibrium between different conformations.  ...  We are grateful to Sebastian Hiller for providing the JCM166 cells lines and Marc Baldus for inputs on protein expression and purification. Open Access funding enabled and organized by Projekt DEAL.  ... 
doi:10.1002/anie.202113448 pmid:34761852 pmcid:PMC9299766 fatcat:yh26gfcjrjdp5oa62ufpvo2yd4

Conformational properties of cardiolipin-bound cytochrome c

J. Hanske, J. R. Toffey, A. M. Morenz, A. J. Bonilla, K. H. Schiavoni, E. V. Pletneva
2011 Proceedings of the National Academy of Sciences of the United States of America  
The heterogeneous CL-bound cyt c ensemble is difficult to characterize with traditional structural methods and ensemble-averaged probes.  ...  The Dns decay curves and extracted Dns-to-heme distance distributions PðrÞ reveal a conformational diversity of the CL-bound cyt c ensemble with distinct populations of the polypeptide structures that  ...  Winkler for sharing his MATLAB codes, Kenneth Tichauer and Frederic Leblond for their help with IRF deconvolution, Kara L.  ... 
doi:10.1073/pnas.1112312108 pmid:22190488 pmcid:PMC3252944 fatcat:brzg5kyg3je5lg4nu6czqkpkg4

Parameter estimation of subsurface flow models using iterative regularized ensemble Kalman filter

A. H. ELSheikh, C. C. Pain, F. Fang, J. L. M. A. Gomes, I. M. Navon
2012 Stochastic environmental research and risk assessment (Print)  
The EnKF Kalman gain matrix is regularized using truncated SVD to filter out noisy correlations.  ...  The inverse problem is formulated as a sequential data integration problem. Gaussian Process Regression (GRP) is used to integrate the prior knowledge (static data).  ...  Making predictions using a Gaussian process is equivalent to estimating p( y| x, D), where y is the new function value at the location x.  ... 
doi:10.1007/s00477-012-0613-x fatcat:xetaxtduyncqtlylax2koerkxe

Current Status of Conformal Radiotherapy

Olav Dahl, Dimitris Kardamakis, Bengt Lind, Jean Claude Rosenwald
1996 Acta Oncologica  
Such information is necessary to define in which patient groups (curative or palliative, tumour locations, etc.) the use of conformal therapy is worthwhile.  ...  For reproducible positioning of the patients the current use of plastic casts for head and neck tumours must also be used for tumours in other locations: for instance, casts are part of the routine set-up  ... 
doi:10.3109/02841869609098520 pmid:9073048 fatcat:6z23vs6jdfeedhctxkkreyvq6i

Conformational Selection Underlies Recognition of a Molybdoenzyme by Its Dedicated Chaperone

Magali Lorenzi, Léa Sylvi, Guillaume Gerbaud, Elisabetta Mileo, Frédéric Halgand, Anne Walburger, Hervé Vezin, Valérie Belle, Bruno Guigliarelli, Axel Magalon, Hendrik W. van Veen
2012 PLoS ONE  
The combination of two techniques ie site-directed spin labeling followed by EPR spectroscopy and ion mobility mass spectrometry, was used to get information about the structure and conformational dynamics  ...  Additionally, ion mobility mass spectrometry experiments fully support these findings by revealing the existence of several conformers in equilibrium through the distinction of different drift time curves  ...  Mure and W. Kaaki for technical support. Author Contributions  ... 
doi:10.1371/journal.pone.0049523 pmid:23185350 pmcid:PMC3501500 fatcat:zuqzfodgobddzojbqooyin25li
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