On inference of causality for discrete state models in a multiscale context.

Abstract:

:Discrete state models are a common tool of modeling in many areas. E.g., Markov state models as a particular representative of this model family became one of the major instruments for analysis and understanding of processes in molecular dynamics (MD). Here we extend the scope of discrete state models to the case of systematically missing scales, resulting in a nonstationary and nonhomogeneous formulation of the inference problem. We demonstrate how the recently developed tools of nonstationary data analysis and information theory can be used to identify the simultaneously most optimal (in terms of describing the given data) and most simple (in terms of complexity and causality) discrete state models. We apply the resulting formalism to a problem from molecular dynamics and show how the results can be used to understand the spatial and temporal causality information beyond the usual assumptions. We demonstrate that the most optimal explanation for the appropriately discretized/coarse-grained MD torsion angles data in a polypeptide is given by the causality that is localized both in time and in space, opening new possibilities for deploying percolation theory and stochastic subgridscale modeling approaches in the area of MD.

authors

Gerber S,Horenko I

doi

10.1073/pnas.1410404111

subject

Has Abstract

pub_date

2014-10-14 00:00:00

pages

14651-6

issue

41

eissn

0027-8424

issn

1091-6490

pii

1410404111

journal_volume

111

pub_type

杂志文章
  • Fibroblast growth factor (FGF) homologous factors: new members of the FGF family implicated in nervous system development.

    abstract::Four new members of the fibroblast growth factor (FGF) family, referred to as fibroblast growth factor homologous factors (FHFs), have been identified by a combination of random cDNA sequencing, data base searches, and degenerate PCR. Pairwise comparisons between the four FHFs show between 58% and 71% amino acid seque...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.93.18.9850

    authors: Smallwood PM,Munoz-Sanjuan I,Tong P,Macke JP,Hendry SH,Gilbert DJ,Copeland NG,Jenkins NA,Nathans J

    更新日期:1996-09-03 00:00:00

  • Cancer dormancy and cell signaling: induction of p21(waf1) initiated by membrane IgM engagement increases survival of B lymphoma cells.

    abstract::The p21(WAF1) (p21) cyclin-dependent kinase inhibitor plays a major role in regulating cell cycle arrest. It was recently reported that the p53-independent elevation of p21 protein levels is essential in mediating the G(1) arrest resulting from signal transduction events initiated by the crosslinking of membrane IgM o...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.96.15.8711

    authors: Marches R,Hsueh R,Uhr JW

    更新日期:1999-07-20 00:00:00

  • Promoter-regulatory region of the major immediate early gene of human cytomegalovirus.

    abstract::The DNA templates containing immediate early (IE) genes of human cytomegalovirus (CMV) were transcribed in vitro by using a HeLa cell extract. When IE region 1, 2, and 3 were used, transcription was detected qualitatively only from IE region 1. Transcription was detected with DNA representing IE region 2 when the IE r...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.81.3.659

    authors: Thomsen DR,Stenberg RM,Goins WF,Stinski MF

    更新日期:1984-02-01 00:00:00

  • Anticancer peptide PNC-27 adopts an HDM-2-binding conformation and kills cancer cells by binding to HDM-2 in their membranes.

    abstract::The anticancer peptide PNC-27, which contains an HDM-2-binding domain corresponding to residues 12-26 of p53 and a transmembrane-penetrating domain, has been found to kill cancer cells (but not normal cells) by inducing membranolysis. We find that our previously determined 3D structure of the p53 residues of PNC-27 is...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0909364107

    authors: Sarafraz-Yazdi E,Bowne WB,Adler V,Sookraj KA,Wu V,Shteyler V,Patel H,Oxbury W,Brandt-Rauf P,Zenilman ME,Michl J,Pincus MR

    更新日期:2010-02-02 00:00:00

  • Curved DNA: design, synthesis, and circularization.

    abstract::Curved DNA molecules and unusually small circles have been obtained by ligation of synthetic 21-base precursors: (sequence in text). The ligation resulted in the formation of double-stranded oligo-(precursor)s possessing a strong 10.5-base-pair (bp) periodicity of the runs of adenines. Two-dimensional polyacrylamide g...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.83.4.862

    authors: Ulanovsky L,Bodner M,Trifonov EN,Choder M

    更新日期:1986-02-01 00:00:00

  • Kappa opioid receptor contributes to EGF-stimulated neurite extension in development.

    abstract::Epidermal growth factor (EGF), a mitogen, also stimulates neurite extension during development, but the underlying mechanism is elusive. This study reveals a functional role for kappa opioid receptor (KOR) in EGF-stimulated neurite extension, and the underlying mechanism. EGF and activated EGF receptor (EGFR) levels a...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0912367107

    authors: Tsai NP,Tsui YC,Pintar JE,Loh HH,Wei LN

    更新日期:2010-02-16 00:00:00

  • Transient dwarfism of soil fauna during the Paleocene-Eocene Thermal Maximum.

    abstract::Soil organisms, as recorded by trace fossils in paleosols of the Willwood Formation, Wyoming, show significant body-size reductions and increased abundances during the Paleocene-Eocene Thermal Maximum (PETM). Paleobotanical, paleopedologic, and oxygen isotope studies indicate high temperatures during the PETM and shar...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0909674106

    authors: Smith JJ,Hasiotis ST,Kraus MJ,Woody DT

    更新日期:2009-10-20 00:00:00

  • Adenosine diphosphate glucose pyrophosphatase: A plastidial phosphodiesterase that prevents starch biosynthesis.

    abstract::A distinct phosphodiesterasic activity (EC 3.1.4) was found in both mono- and dicotyledonous plants that catalyzes the hydrolytic breakdown of ADPglucose (ADPG) to produce equimolar amounts of glucose-1-phosphate and AMP. The enzyme responsible for this activity, referred to as ADPG pyrophosphatase (AGPPase), was puri...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.120168097

    authors: Rodriguez-López M,Baroja-Fernández E,Zandueta-Criado A,Pozueta-Romero J

    更新日期:2000-07-18 00:00:00

  • Differential transport of protein in axons: comparison between the sciatic nerve and dorsal columns of cats.

    abstract::Fast axoplasmic transport was studied in dorsal root ganglion cells of the cat. Proteins carried in the fast axoplasmic flow were labeled after an intraganglionic injection of (L)-[4,5-(3)H]leucine. The rate of transport was 380 +/- 26 mm/day in both the central and peripheral branches of the bifurcating axons that ar...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.70.5.1521

    authors: Anderson LE,McClure WO

    更新日期:1973-05-01 00:00:00

  • Genetic confirmation for a central role for TNFα in the direct action of thyroid stimulating hormone on the skeleton.

    abstract::Clinical data showing correlations between low thyroid-stimulating hormone (TSH) levels and high bone turnover markers, low bone mineral density, and an increased risk of osteoporosis-related fractures are buttressed by mouse genetic and pharmacological studies identifying a direct action of TSH on the skeleton. Here ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1308336110

    authors: Sun L,Zhu LL,Lu P,Yuen T,Li J,Ma R,Baliram R,Moonga SS,Liu P,Zallone A,New MI,Davies TF,Zaidi M

    更新日期:2013-06-11 00:00:00

  • Structural characteristics of supramolecular assemblies formed by guanidinium-cholesterol reagents for gene transfection.

    abstract::We have recently discovered that cationic cholesterol derivatives characterized by guanidinium polar headgroups are very efficient for gene transfection in vitro and in vivo. In spite of being based on some rationale at the molecular level, the development of these new synthetic vectors was nevertheless empirical. Ind...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.96.6.2621

    authors: Pitard B,Oudrhiri N,Vigneron JP,Hauchecorne M,Aguerre O,Toury R,Airiau M,Ramasawmy R,Scherman D,Crouzet J,Lehn JM,Lehn P

    更新日期:1999-03-16 00:00:00

  • Sleeping Beauty mutagenesis in a mouse medulloblastoma model defines networks that discriminate between human molecular subgroups.

    abstract::The Sleeping Beauty (SB) transposon mutagenesis screen is a powerful tool to facilitate the discovery of cancer genes that drive tumorigenesis in mouse models. In this study, we sought to identify genes that functionally cooperate with sonic hedgehog signaling to initiate medulloblastoma (MB), a tumor of the cerebellu...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1318639110

    authors: Genovesi LA,Ng CG,Davis MJ,Remke M,Taylor MD,Adams DJ,Rust AG,Ward JM,Ban KH,Jenkins NA,Copeland NG,Wainwright BJ

    更新日期:2013-11-12 00:00:00

  • Quaternary structure of the ribosomal 30S subunit: model and its experimental testing.

    abstract::In considering the structure of the 30S subunit of the Escherichia coli ribosome, we have assumed that: (i) all or almost all the proteins within the 30S particle are compact and globular, as recently shown for the isolated proteins S4, S7, S8, S15, and S16 in solution [Serdyuk, I.N., Zaccai, G. & Spirin, A.S. (1978) ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.76.10.4867

    authors: Spirin AS,Serdyuk IN,Shpungin JL,Vasiliev VD

    更新日期:1979-10-01 00:00:00

  • Changing numbers of neuronal and non-neuronal cells underlie postnatal brain growth in the rat.

    abstract::The rat brain increases >6x in mass from birth to adulthood, presumably through the addition of glial cells and increasing neuronal size, without the addition of neurons. To test this hypothesis, here we investigate quantitatively the postnatal changes in the total number of neuronal and non-neuronal cells in the deve...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0804650106

    authors: Bandeira F,Lent R,Herculano-Houzel S

    更新日期:2009-08-18 00:00:00

  • Mechanism of interferon action: structure of the mouse PKR gene encoding the interferon-inducible RNA-dependent protein kinase.

    abstract::The gene for the RNA-dependent eIF-2 alpha protein kinase (PKR) was isolated from mouse genomic DNA and characterized. The mouse PKR gene contains 16 exons and spans about 28 kilobase pairs. Exon 1 is untranslated; the AUG translation initiation site is located early in the second exon. Exon 16 includes the UAG transl...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.91.17.7995

    authors: Tanaka H,Samuel CE

    更新日期:1994-08-16 00:00:00

  • A general method for determining helix packing in membrane proteins in situ: helices I and II are close to helix VII in the lactose permease of Escherichia coli.

    abstract::It was previously shown that coexpression of the lactose permease of Escherichia coli in two contiguous fragments leads to functional complementation. We demonstrate here that site-directed thiol crosslinking of coexpressed permease fragments can be used to determine helix proximity in situ without the necessity of pu...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.93.25.14498

    authors: Wu J,Kaback HR

    更新日期:1996-12-10 00:00:00

  • Binding and biomimetic cleavage of the RNA poly(U) by synthetic polyimidazoles.

    abstract::Four polyimidazoles were used in the binding and cleavage studies with poly(U). The two polydisperse polyvinylimidazoles were previously described by others, while the other two new polymers of polyethyleneimines were prepared by cationic polymerization of oxazolines. The latter had imidazole units attached to each ni...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1210846109

    authors: Cheng L,Abhilash KG,Breslow R

    更新日期:2012-08-07 00:00:00

  • Virstatin inhibits dimerization of the transcriptional activator ToxT.

    abstract::The development of antimicrobials is critical in this time of increasing antibiotic resistance of most clinically relevant bacteria. To date, all current antibiotics focus on inhibiting crucial enzymatic activities of their protein targets (i.e., trimethoprim for dihydrofolate reductase), thus disrupting in vitro esse...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0611643104

    authors: Shakhnovich EA,Hung DT,Pierson E,Lee K,Mekalanos JJ

    更新日期:2007-02-13 00:00:00

  • P2Y2 receptor activates nerve growth factor/TrkA signaling to enhance neuronal differentiation.

    abstract::Neurotrophins are essential for neuronal differentiation, but the onset and the intensity of neurotrophin signaling within the neuronal microenvironment are poorly understood. We tested the hypothesis that extracellular nucleotides and their cognate receptors regulate neurotrophin-mediated differentiation. We found th...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0505913102

    authors: Arthur DB,Akassoglou K,Insel PA

    更新日期:2005-12-27 00:00:00

  • Light-activated protein interaction with high spatial subcellular confinement.

    abstract::Methods to acutely manipulate protein interactions at the subcellular level are powerful tools in cell biology. Several blue-light-dependent optical dimerization tools have been developed. In these systems one protein component of the dimer (the bait) is directed to a specific subcellular location, while the other com...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1713845115

    authors: Benedetti L,Barentine AES,Messa M,Wheeler H,Bewersdorf J,De Camilli P

    更新日期:2018-03-06 00:00:00

  • Interisland and interarchipelago transfer of stone tools in prehistoric Polynesia.

    abstract::Tracing interisland and interarchipelago movements of people and artifacts in prehistoric Polynesia has posed a challenge to archaeologists due to the lack of pottery and obsidian, two materials most readily used in studies of prehistoric trade or exchange. Here we report the application of nondestructive energy-dispe...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 历史文章,杂志文章

    doi:10.1073/pnas.93.4.1381

    authors: Weisler MI,Kirch PV

    更新日期:1996-02-20 00:00:00

  • The Drosophila Trpm channel mediates calcium influx during egg activation.

    abstract::Egg activation is the process in which mature oocytes are released from developmental arrest and gain competency for embryonic development. In Drosophila and other arthropods, eggs are activated by mechanical pressure in the female reproductive tract, whereas in most other species, eggs are activated by fertilization....

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1906967116

    authors: Hu Q,Wolfner MF

    更新日期:2019-09-17 00:00:00

  • Murine isoforms of retinoic acid receptor gamma with specific patterns of expression.

    abstract::We have characterized seven murine retinoic acid receptor gamma cDNA isoforms (mRAR-gamma 1 to -gamma 7) generated by alternative splicing of at least seven exons. These isoforms differ from one another in their 5' untranslated region and in two cases (mRAR-gamma 1 and -gamma 2) differ in their N-terminal A region, wh...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.87.7.2700

    authors: Kastner P,Krust A,Mendelsohn C,Garnier JM,Zelent A,Leroy P,Staub A,Chambon P

    更新日期:1990-04-01 00:00:00

  • Two proto-oncogenes implicated in mammary carcinogenesis, int-1 and int-2, are independently regulated during mouse development.

    abstract::The int-1 and int-2 genes were first isolated as targets for transcriptional activation by proviral insertion mutations in mammary carcinomas induced by the mouse mammary tumor virus (MMTV). Since these proto-oncogenes are not expressed at detectable levels in previously tested normal tissues from adult mice, we sough...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.83.20.7806

    authors: Jakobovits A,Shackleford GM,Varmus HE,Martin GR

    更新日期:1986-10-01 00:00:00

  • Anti-VEGF treatment improves neurological function and augments radiation response in NF2 schwannoma model.

    abstract::Hearing loss is the main limitation of radiation therapy for vestibular schwannoma (VS), and identifying treatment options that minimize hearing loss are urgently needed. Treatment with bevacizumab is associated with tumor control and hearing improvement in neurofibromatosis type 2 (NF2) patients; however, its effect ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1512570112

    authors: Gao X,Zhao Y,Stemmer-Rachamimov AO,Liu H,Huang P,Chin S,Selig MK,Plotkin SR,Jain RK,Xu L

    更新日期:2015-11-24 00:00:00

  • Germ-cell deficient (gcd), an insertional mutation manifested as infertility in transgenic mice.

    abstract::A genetic analysis is necessary to gain a greater understanding of the complex developmental processes in mammals. Toward this end, an insertional transgenic mouse mutant has been isolated that results in abnormal germ-cell development. This recessive mutation manifests as infertility in both males and females and is ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.88.19.8787

    authors: Pellas TC,Ramachandran B,Duncan M,Pan SS,Marone M,Chada K

    更新日期:1991-10-01 00:00:00

  • Menkes disease: a biochemical abnormality in cultured human fibroblasts.

    abstract::Cultured skin fibroblasts from patients with Menkes disease, an X-linked disorder involving a defect in copper metabolism, were analyzed for copper concentration by means of atomic absorption spectrophotometry. These cultures consistently exhibited elevated copper concentrations (mean = 335.5 ng of copper per mg of pr...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.73.2.604

    authors: Goka TJ,Stevenson RE,Hefferan PM,Howell RR

    更新日期:1976-02-01 00:00:00

  • Genome scan for teratogen-induced clefting susceptibility loci in the mouse: evidence of both allelic and locus heterogeneity distinguishing cleft lip and cleft palate.

    abstract::Nonsyndromic clefting of the lip and palate in humans has a highly complex etiology, with both multiple genetic loci and exposure to teratogens influencing susceptibility. Previous studies using mouse models have examined only very small portions of the genome. Here we report the findings of a genome-wide search for s...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.94.10.5231

    authors: Diehl SR,Erickson RP

    更新日期:1997-05-13 00:00:00

  • Rapid evolution of male-biased gene expression in Drosophila.

    abstract::A number of genes associated with sexual traits and reproduction evolve at the sequence level faster than the majority of genes coding for non-sex-related traits. Whole genome analyses allow this observation to be extended beyond the limited set of genes that have been studied thus far. We use cDNA microarrays to demo...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1630690100

    authors: Meiklejohn CD,Parsch J,Ranz JM,Hartl DL

    更新日期:2003-08-19 00:00:00

  • Dynamics of self assembly of magnetized disks rotating at the liquid-air interface.

    abstract::This paper is a theoretical study of dynamic self assembly in a system of millimeter-sized magnetized disks floating at a liquid-air interface and spinning under the influence of a rotating magnetic field. Equations of motions are derived that account for the hydrodynamic and magnetic forces acting in the system. Nume...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.062036699

    authors: Grzybowski BA,Stone HA,Whitesides GM

    更新日期:2002-04-02 00:00:00