11,951 research outputs found
Author response
No full textTranscription regulation in metazoans often involves promoter-proximal pausing of RNA polymerase (Pol) II, which requires the 4-subunit negative elongation factor (NELF). Here we discern the functional architecture of human NELF through X-ray crystallography, protein crosslinking, biochemical assays, and RNA crosslinking in cells. We identify a NELF core subcomplex formed by conserved regions in subunits NELF-A and NELF-C, and resolve its crystal structure. The NELF-AC subcomplex binds single-stranded nucleic acids in vitro, and NELF-C associates with RNA in vivo. A positively charged face of NELF-AC is involved in RNA binding, whereas the opposite face of the NELF-AC subcomplex binds NELF-B. NELF-B is predicted to form a HEAT repeat fold, also binds RNA in vivo, and anchors the subunit NELF-E, which is confirmed to bind RNA in vivo. These results reveal the three-dimensional architecture and three RNA-binding faces of NELF
Minnesota Solvation Database (MNSOL) version 2012
No full textThe Minnesota Solvation Database and User Manual is available for download as a .zip file named MNSolDatabase-v2012.The Minnesota Solvation Database consists of a collection of 3037 experimental free energies of solvation or transfer free energies for 790 unique solutes in 92 solvents (including water) and gas-phase M06-2X/MG3S optimized molecular geometries in Cartesian coordinates for the corresponding solutes. All of the 790 solutes in this database (541 neutrals and 249 singly-charged ions) contain at most the following elements: H, C, N, O, F, Si, P, S, Cl, Br, and I.Office of Naval Research (N00014-05-1-0538)National Science Foundation (CHE07-04974)Minnesota Supercomputing InstituteMarenich, Aleksandr V; Kelly, Casey P; Thompson, Jason D; Hawkins, Gregory D; Chambers, Candee C; Giesen, David J; Winget, Paul; Cramer, Christopher J; Truhlar, Donald G. (2020). Minnesota Solvation Database (MNSOL) version 2012. Retrieved from the University Digital Conservancy, https://doi.org/10.13020/3eks-j059
Supplementary_material_NNR20190506c – Supplemental material for Neural Correlates of Passive Position Finger Sense After Stroke
No full textSupplemental material, Supplementary_material_NNR20190506c for Neural Correlates of Passive Position Finger Sense After Stroke by Morgan L. Ingemanson, Justin R. Rowe, Vicky Chan, Jeff Riley, Eric T. Wolbrecht, David J. Reinkensmeyer and Steven C. Cramer in Neurorehabilitation and Neural Repair</p
Panel C: Author-Meets-Readers Session
No full textAuthor David Webber discusses his book The Rise of the Working Class Shareholder: Labor\u27s Last Best Weapon published on Harvard University Press
Cult: A Composite Novel
No full textCult (redacted)
The first component of the thesis is a composite novel called Cult which falls into two parts with seven narratives in each. Part 1 tracks the protagonist, Ellen, from her first involvement with the cult through to her eventually leaving it. Although fiction, the first half of the book answers the kinds of questions the author is asked when people discover that she was once a sannyasin (a follower of the guru Bhagwan Shree Rajneesh). While the experiences of meditation, group therapy and communal living are all faithfully rendered within the stories, the need for strong characters, narrative drive and a lightness of touch takes precedence.
Part 2 picks up Ellen’s story some twenty or so years later and explores what becomes of her in middle age. It also looks at other groups in society, such as academia, the law and the internet dating community which each have their own jargon, hierarchies, rituals and rules but are not considered to be cults.
The book examines the question raised in the Epigraph, ‘how do we be together when we feel so alone’ with a focus on relationships other than the familial and the romantic.
Collisions, Chasms and Connections: a Performative Exploration of the Composite Novel Form
The second part of the thesis is both a critical and creative response to three contemporary American books: Olive Kitteridge by Elizabeth Strout; A Visit from the Goon Squad by Jennifer Egan; and Legend of a Suicide by David Vann. The critical element comprises a close reading of the three books; a chronological reconstruction of their overarching storylines; and a consideration of what their authors have said about writing the books. It concludes that, in the composite novel, the simultaneous presentation of multiple views and storylines operate much like a 3D image to give the impression of depth to the characters and situations rendered. The creative element of the essay is a playful and personal response to the texts
Analysis of a File System Using the Verifying C Compiler
No full textTitle: Analysis of a File System Using the Verifying C Compiler Author: Bc. David Škorvaga Department: Department of Distributed and Dependable Systems Supervisor: RNDr. Jan Kofroň, Ph.D. Abstract: Formal verification is a way to improve reliability of software systems. One approach of formal verification is focused on proving correctness of annotat- ed source code of an established programming language. Verifying C Compiler (VCC) is a verifier for concurrent C that accepts an annotated code in C language and automatically verifies its correctness with respect to the given annotation. There have been successful attempts to verify some critical systems, including the operating system kernel. Another critical part of operating system is its file system. In the thesis, we choose FatFs file system, a simple device-independent implementation of the FAT file system. We specify a part of it using the VCC annotation and successfully verify its correctness. Keywords: Formal Verification, File System, VC
Supplemental material for Study protocol for a pivotal randomised study assessing vagus nerve stimulation during rehabilitation for improved upper limb motor function after stroke
No full textSupplemental Material for Study protocol for a pivotal randomised study assessing vagus nerve stimulation during rehabilitation for improved upper limb motor function after stroke by Teresa J Kimberley, Cecília N Prudente, Navzer D Engineer, David Pierce, Brent Tarver, Steven C Cramer, David Alexander Dickie and Jesse Dawson in European Stroke Journal</p
Analýza souborového systému pomocí Verifying C Compiler
No full textNázev práce: Analýza souborového systému pomocí Verifying C Compiler Autor: Bc. David Škorvaga Katedra: Katedra distribuovaných a spolehlivých systémů Vedoucí diplomové práce: RNDr. Jan Kofroň, Ph.D. Abstrakt: Formální verifikace je jeden ze způsobů, jak zlepšit spolehlivost soft- warových systémů. Jeden z přístupů formální verifikace se zaměřuje na dokazo- vaní správnosti anotovaného zdrojového kódu v široce používaném programovacím jazyce. Verifier C Compiler (VCC) je verifikátor pro concurrent C, který přijímá anotovaný kód v jazyce C a automaticky ověřuje jeho správnost s ohledem na tuto anotaci. Už se objevily úspěšné pokusy o ověření některých kritických systémů, včetně jádra operačního systému. Další důležitou součástí operačního systému je jeho systém souborů. V diplomové práci jsme si vybrali souborový systém FatFs, odlehčenou implementaci souborového systému FAT, nezávislou na zařízení. V této práci vytvoříme specifikaci jeho části pomocí anotace VCC a úspěšně ověříme jeho korektnost. Klíčová slova: Formal Verification, File System, VCCTitle: Analysis of a File System Using the Verifying C Compiler Author: Bc. David Škorvaga Department: Department of Distributed and Dependable Systems Supervisor: RNDr. Jan Kofroň, Ph.D. Abstract: Formal verification is a way to improve reliability of software systems. One approach of formal verification is focused on proving correctness of annotat- ed source code of an established programming language. Verifying C Compiler (VCC) is a verifier for concurrent C that accepts an annotated code in C language and automatically verifies its correctness with respect to the given annotation. There have been successful attempts to verify some critical systems, including the operating system kernel. Another critical part of operating system is its file system. In the thesis, we choose FatFs file system, a simple device-independent implementation of the FAT file system. We specify a part of it using the VCC annotation and successfully verify its correctness. Keywords: Formal Verification, File System, VCCDepartment of Distributed and Dependable SystemsKatedra distribuovaných a spolehlivých systémůMatematicko-fyzikální fakultaFaculty of Mathematics and Physic
The phosphatidylserine receptor from <it>Hydra </it>is a nuclear protein with potential Fe(II) dependent oxygenase activity
No full textAbstract Background Apoptotic cell death plays an essential part in embryogenesis, development and maintenance of tissue homeostasis in metazoan animals. The culmination of apoptosis in vivo is the phagocytosis of cellular corpses. One morphological characteristic of cells undergoing apoptosis is loss of plasma membrane phospholipid asymmetry and exposure of phosphatidylserine on the outer leaflet. Surface exposure of phosphatidylserine is recognised by a specific receptor (phosphatidylserine receptor, PSR) and is required for phagocytosis of apoptotic cells by macrophages and fibroblasts. Results We have cloned the PSR receptor from Hydra in order to investigate its function in this early metazoan. Bioinformatic analysis of the Hydra PSR protein structure revealed the presence of three nuclear localisation signals, an AT-hook like DNA binding motif and a putative 2-oxoglutarate (2OG)-and Fe(II)-dependent oxygenase activity. All of these features are conserved from human PSR to Hydra PSR. Expression of GFP tagged Hydra PSR in hydra cells revealed clear nuclear localisation. Deletion of one of the three NLS sequences strongly diminished nuclear localisation of the protein. Membrane localisation was never detected. Conclusions Our results suggest that Hydra PSR is a nuclear 2-oxoglutarate (2OG)-and Fe(II)-dependent oxygenase. This is in contrast with the proposed function of Hydra PSR as a cell surface receptor involved in the recognition of apoptotic cells displaying phosphatidylserine on their surface. The conservation of the protein from Hydra to human infers that our results also apply to PSR from higher animals.</p
Protein Free Energy Landscapes Remodeled by Ligand Binding
No full textAbstractGlucose/galactose binding protein (GGBP) functions in two different larger systems of proteins used by enteric bacteria for molecular recognition and signaling. Here we report on the thermodynamics of conformational equilibrium distributions of GGBP. Three fluorescence components appear at zero glucose concentration and systematically transition to three components at high glucose concentration. Fluorescence anisotropy correlations, fluorescent lifetimes, thermodynamics, computational structure minimization, and literature work were used to assign the three components as open, closed, and twisted conformations of the protein. The existence of three states at all glucose concentrations indicates that the protein continuously fluctuates about its conformational state space via thermally driven state transitions; glucose biases the populations by reorganizing the free energy profile. These results and their implications are discussed in terms of the two types of specific and nonspecific interactions GGBP has with cytoplasmic membrane proteins
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