Sequential Parameter Estimation for Large-Scale Systems with Multiple Data Sets. 1. Computational Framework

2003 ◽  
Vol 42 (23) ◽  
pp. 5850-5860 ◽  
Author(s):  
Richard Faber ◽  
Pu Li ◽  
Günter Wozny
Keyword(s):  
Parameter Estimation ◽  
Large Scale ◽  
Data Sets ◽  
Computational Framework ◽  
Large Scale Systems ◽  
Multiple Data ◽  
Multiple Data Sets

scholarly journals The Compact Macronuclear Genome of the Ciliate Halteria grandinella: A Transcriptome-Like Genome with 23,000 Nanochromosomes

mBio ◽  
2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Weibo Zheng ◽  
Chundi Wang ◽  
Michael Lynch ◽  
Shan Gao
Keyword(s):  
Large Scale ◽  
Cell Structure ◽  
Unicellular Eukaryote ◽  
Data Sets ◽  
Chromosomal Structure ◽  
Content Type ◽  
Dna And Rna ◽  
Copy Numbers ◽  
Multiple Data ◽  
Multiple Data Sets

ABSTRACT How to achieve protein diversity by genome and transcriptome processing is essential for organismal complexity and adaptation. The present work identifies that the macronuclear genome of Halteria grandinella, a cosmopolitan unicellular eukaryote, is composed almost entirely of gene-sized nanochromosomes with extremely short nongenic regions. This challenges our usual understanding of chromosomal structure and suggests the possibility of novel mechvanisms in transcriptional regulation. Comprehensive analysis of multiple data sets reveals that Halteria transcription dynamics are influenced by: (i) nonuniform nanochromosome copy numbers correlated with gene-expression level; (ii) dynamic alterations at both the DNA and RNA levels, including alternative internal eliminated sequence (IES) deletions during macronucleus formation and large-scale alternative splicing in transcript maturation; and (iii) extremely short 5′ and 3′ untranslated regions (UTRs) and universal TATA box-like motifs in the compact 5′ subtelomeric regions of most chromosomes. This study broadens the view of ciliate biology and the evolution of unicellular eukaryotes, and identifies Halteria as one of the most compact known eukaryotic genomes, indicating that complex cell structure does not require complex gene architecture.

scholarly journals FragMAX: the fragment-screening platform at the MAX IV Laboratory

2020 ◽  
Vol 76 (8) ◽  
pp. 771-777 ◽  
Author(s):  
Gustavo M. A. Lima ◽  
Vladimir O. Talibov ◽  
Elmir Jagudin ◽  
Céleste Sele ◽  
Maria Nyblom ◽  
...  
Keyword(s):  
Large Scale ◽  
Structure Refinement ◽  
Fourth Generation ◽  
Data Sets ◽  
Fragment Screening ◽  
Efficient Management ◽  
Multiple Data ◽  
Crystal Fragment ◽  
Multiple Data Sets ◽  
Screening Platform

Advances in synchrotron storage rings and beamline automation have pushed data-collection rates to thousands of data sets per week. With this increase in throughput, massive projects such as in-crystal fragment screening have become accessible to a larger number of research groups. The quality of support offered at large-scale facilities allows medicinal chemistry-focused or biochemistry-focused groups to supplement their research with structural biology. Preparing the experiment, analysing multiple data sets and prospecting for interesting complexes of protein and fragments require, for both newcomers and experienced users, efficient management of the project and extensive computational power for data processing and structure refinement. Here, FragMAX, a new complete platform for fragment screening at the BioMAX beamline of the MAX IV Laboratory, is described. The ways in which users are assisted in X-ray-based fragment screenings and in which the fourth-generation storage ring available at the facility is best exploited are also described.

scholarly journals TheXChemExplorergraphical workflow tool for routine or large-scale protein–ligand structure determination

2017 ◽  
Vol 73 (3) ◽  
pp. 267-278 ◽  
Author(s):  
Tobias Krojer ◽  
Romain Talon ◽  
Nicholas Pearce ◽  
Patrick Collins ◽  
Alice Douangamath ◽  
...  
Keyword(s):  
User Interfaces ◽  
Large Scale ◽  
Data Dissemination ◽  
Data Sets ◽  
Acta Cryst ◽  
Multiple Data ◽  
Entry Points ◽  
Ligand Discovery ◽  
Ligand Identification ◽  
Multiple Data Sets

XChemExplorer(XCE) is a data-management and workflow tool to support large-scale simultaneous analysis of protein–ligand complexes during structure-based ligand discovery (SBLD). The user interfaces of established crystallographic software packages such asCCP4 [Winnet al.(2011),Acta Cryst.D67, 235–242] orPHENIX[Adamset al.(2010),Acta Cryst.D66, 213–221] have entrenched the paradigm that a `project' is concerned with solving one structure. This does not hold for SBLD, where many almost identical structures need to be solved and analysed quickly in one batch of work. Functionality to track progress and annotate structures is essential.XCEprovides an intuitive graphical user interface which guides the user from data processing, initial map calculation, ligand identification and refinement up until data dissemination. It provides multiple entry points depending on the need of each project, enables batch processing of multiple data sets and records metadata, progress and annotations in an SQLite database.XCEis freely available and works on any Linux and Mac OS X system, and the only dependency is to have the latest version ofCCP4 installed. The design and usage of this tool are described here, and its usefulness is demonstrated in the context of fragment-screening campaigns at the Diamond Light Source. It is routinely used to analyse projects comprising 1000 data sets or more, and therefore scales well to even very large ligand-design projects.

The development of nurses’ foundational values

2021 ◽  
pp. 096973302110032
Author(s):  
Sastrawan Sastrawan ◽  
Jennifer Weller-Newton ◽  
Gabrielle Brand ◽  
Gulzar Malik
Keyword(s):  
Professional Training ◽  
Reference Points ◽  
Constructivist Grounded Theory ◽  
Professional Values ◽  
Data Sets ◽  
Value System ◽  
Institutional Values ◽  
Multiple Data ◽  
Human Ethics ◽  
Multiple Data Sets

Background: In the ever-changing and complex healthcare environment, nurses encounter challenging situations that may involve a clash between their personal and professional values resulting in a profound impact on their practice. Nevertheless, there is a dearth of literature on how nurses develop their personal–professional values. Aim: The aim of this study was to understand how nurses develop their foundational values as the base for their value system. Research design: A constructivist grounded theory methodology was employed to collect multiple data sets, including face-to-face focus group and individual interviews, along with anecdote and reflective stories. Participants and research context: Fifty-four nurses working across various nursing settings in Indonesia were recruited to participate. Ethical considerations: Ethics approval was obtained from the Monash University Human Ethics Committee, project approval number 1553. Findings: Foundational values acquisition was achieved through family upbringing, professional nurse education and organisational/institutional values reinforcement. These values are framed through three reference points: religious lens, humanity perspective and professionalism. This framing results in a unique combination of personal–professional values that comprise nurses’ values system. Values are transferred to other nurses either in a formal or informal way as part of one’s professional responsibility and customary social interaction via telling and sharing in person or through social media. Discussion: Values and ethics are inherently interweaved during nursing practice. Ethical and moral values are part of professional training, but other values are often buried in a hidden curriculum, and attained and activated through interactions during nurses’ training. Conclusion: Developing a value system is a complex undertaking that involves basic social processes of attaining, enacting and socialising values. These processes encompass several intertwined entities such as the sources of values, the pool of foundational values, value perspectives and framings, initial value structures, and methods of value transference.

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