scholarly journals Unified Nanotechnology Format: One Way to Store Them All

Molecules ◽  
2021 ◽  
Vol 27 (1) ◽  
pp. 63
Author(s):  
David Kuťák ◽  
Erik Poppleton ◽  
Haichao Miao ◽  
Petr Šulc ◽  
Ivan Barišić
Keyword(s):  
Free Form ◽  
File Format ◽  
Dna Structures ◽  
Rna Nanotechnology ◽  
Dna And Rna ◽  
File Formats ◽  
Computer Based ◽  
Wet Lab ◽  
The Many ◽  
Future Work

The domains of DNA and RNA nanotechnology are steadily gaining in popularity while proving their value with various successful results, including biosensing robots and drug delivery cages. Nowadays, the nanotechnology design pipeline usually relies on computer-based design (CAD) approaches to design and simulate the desired structure before the wet lab assembly. To aid with these tasks, various software tools exist and are often used in conjunction. However, their interoperability is hindered by a lack of a common file format that is fully descriptive of the many design paradigms. Therefore, in this paper, we propose a Unified Nanotechnology Format (UNF) designed specifically for the biomimetic nanotechnology field. UNF allows storage of both design and simulation data in a single file, including free-form and lattice-based DNA structures. By defining a logical and versatile format, we hope it will become a widely accepted and used file format for the nucleic acid nanotechnology community, facilitating the future work of researchers and software developers. Together with the format description and publicly available documentation, we provide a set of converters from existing file formats to simplify the transition. Finally, we present several use cases visualizing example structures stored in UNF, showcasing the various types of data UNF can handle.

scholarly journals Deep Learning of Sea Surface Temperature Patterns to Identify Ocean Extremes

2021 ◽  
Vol 13 (4) ◽  
pp. 744
Author(s):  
J. Xavier Prochaska ◽  
Peter C. Cornillon ◽  
David M. Reiman
Keyword(s):  
Deep Learning ◽  
Surface Temperature ◽  
Sea Surface Temperature ◽  
Sea Surface ◽  
Space Distribution ◽  
Western Boundary ◽  
Learning Modules ◽  
Ocean Science ◽  
The Many ◽  
Future Work

We performed an out-of-distribution (OOD) analysis of ∼12,000,000 semi-independent 128 × 128 pixel2 sea surface temperature (SST) regions, which we define as cutouts, from all nighttime granules in the MODIS R2019 Level-2 public dataset to discover the most complex or extreme phenomena at the ocean’s surface. Our algorithm (ULMO) is a probabilistic autoencoder (PAE), which combines two deep learning modules: (1) an autoencoder, trained on ∼150,000 random cutouts from 2010, to represent any input cutout with a 512-dimensional latent vector akin to a (non-linear) Empirical Orthogonal Function (EOF) analysis; and (2) a normalizing flow, which maps the autoencoder’s latent space distribution onto an isotropic Gaussian manifold. From the latter, we calculated a log-likelihood (LL) value for each cutout and defined outlier cutouts to be those in the lowest 0.1% of the distribution. These exhibit large gradients and patterns characteristic of a highly dynamic ocean surface, and many are located within larger complexes whose unique dynamics warrant future analysis. Without guidance, ULMO consistently locates the outliers where the major western boundary currents separate from the continental margin. Prompted by these results, we began the process of exploring the fundamental patterns learned by ULMO thereby identifying several compelling examples. Future work may find that algorithms such as ULMO hold significant potential/promise to learn and derive other, not-yet-identified behaviors in the ocean from the many archives of satellite-derived SST fields. We see no impediment to applying them to other large remote-sensing datasets for ocean science (e.g., SSH and ocean color).

Research on the Three-Dimensional Displaying of STL ASCII and Binary File

2014 ◽  
Vol 940 ◽  
pp. 433-436 ◽  
Author(s):  
Ying Zhang ◽  
Xin Shi
Keyword(s):  
Detailed Analysis ◽  
Programming Language ◽  
Coordinate Transformation ◽  
Graphical Representation ◽  
Three Dimensional ◽  
File Format ◽  
Binary File ◽  
Stl File ◽  
File Formats ◽  
Three Dimensional Display

Based on the detailed analysis of the STL file format, VC++ 6.0 programming language was used to extract the STL ASCII and binary file information, at the same time, using the OpenGL triangle drawing technology for graphical representation of the STL file, with rendering functions such as material, coordinate transformation, lighting, et al, finally realizing the loading and three-dimensional display of STL ASCII and binary file formats.

Human RecQ helicases in transcription-associated stress management: bridging the gap between DNA and RNA metabolism

2020 ◽  
Vol 0 (0) ◽  
Author(s):  
Tulika Das ◽  
Surasree Pal ◽  
Agneyo Ganguly
Keyword(s):  
Genome Integrity ◽  
Complex Structures ◽  
Huge Number ◽  
Dna Helicases ◽  
Dna Structures ◽  
Recq Helicases ◽  
Dna And Rna ◽  
Cellular Dna ◽  
Almost All ◽  
Transcription And Replication

Abstract RecQ helicases are a highly conserved class of DNA helicases that play crucial role in almost all DNA metabolic processes including replication, repair and recombination. They are able to unwind a wide variety of complex intermediate DNA structures that may result from cellular DNA transactions and hence assist in maintaining genome integrity. Interestingly, a huge number of recent reports suggest that many of the RecQ family helicases are directly or indirectly involved in regulating transcription and gene expression. On one hand, they can remove complex structures like R-loops, G-quadruplexes or RNA:DNA hybrids formed at the intersection of transcription and replication. On the other hand, emerging evidence suggests that they can also regulate transcription by directly interacting with RNA polymerase or recruiting other protein factors that may regulate transcription. This review summarizes the up to date knowledge on the involvement of three human RecQ family proteins BLM, WRN and RECQL5 in transcription regulation and management of transcription associated stress.

Digital File Formats for Digital Preservation

2018 ◽  
pp. 218-233
Author(s):  
Mayank Yuvaraj
Keyword(s):  
Digital Libraries ◽  
Digital Preservation ◽  
Institutional Repository ◽  
File Format ◽  
Institutional Repositories ◽  
File Formats ◽  
Digital File ◽  
The Common ◽  
Common Understanding

During the course of planning an institutional repository, digital library collections or digital preservation service it is inevitable to draft file format policies in order to ensure long term digital preservation, its accessibility and compatibility. Sincere efforts have been made to encourage the adoption of standard formats yet the digital preservation policies vary from library to library. The present paper is based against this background to present the digital preservation community with a common understanding of the common file formats used in the digital libraries or institutional repositories. The paper discusses both open and proprietary file formats for several media.

Interactive, Flexible, and Adaptable Decision Support Systems

2009 ◽  
pp. 557-562
Author(s):  
John Wang ◽  
James Yao ◽  
Jeffrey Hsu
Keyword(s):  
Information Technology ◽  
Decision Support ◽  
Decision Support Systems ◽  
Support Systems ◽  
Massachusetts Institute Of Technology ◽  
Organizational Decision Making ◽  
History Of ◽  
Computer Based ◽  
Institute Of Technology ◽  
The Many

Over the four decades of its history, decision support systems (DSSs) have moved from a radical movement that changed the way information systems were perceived in business, to a mainstream commercial information technology movement that all organizations engage. This interactive, flexible, and adaptable computer-based information system derives from two main areas of research: the theoretical studies of organizational decision making done at the Carnegie Institute in the 1950s and early 1960s as well as the technical work on interactive computer systems which was mainly performed by the Massachusetts Institute of Technology (Keen & Morton, 1978). DSSs began due to the importance of formalizing a record of ideas, people, systems, and technologies implicated in this sector of applied information technology. But the history of this system is not precise due to the many individuals involved in different stages of DSSs and various industries while claiming to be pioneers of the system (Arnott & Pervan, 2005; Power, 2003). DSSs have become very sophisticated and stylish since these pioneers began their research. Many new systems have expanded the frontiers established by these pioneers yet the core and basis of the system remains the same. Today, DSSs are used in the finance, accounting, marketing, medical, as well as many other fields.

DSS for Web Mining Using Recommendation System

2017 ◽  
pp. 22-34 ◽  
Author(s):  
Varaprasad Rao M ◽  
Vishnu Murthy G
Keyword(s):  
Recommender Systems ◽  
Web Mining ◽  
Recommendation System ◽  
User Behavior ◽  
Web Content ◽  
Web Structure ◽  
Web Structure Mining ◽  
Content Mining ◽  
Computer Based ◽  
The Many

Decision Supports Systems (DSS) are computer-based information systems designed to help managers to select one of the many alternative solutions to a problem. A DSS is an interactive computer based information system with an organized collection of models, people, procedures, software, databases, telecommunication, and devices, which helps decision makers to solve unstructured or semi-structured business problems. Web mining is the application of data mining techniques to discover patterns from the World Wide Web. Web mining can be divided into three different types – Web usage mining, Web content mining and Web structure mining. Recommender systems (RS) aim to capture the user behavior by suggesting/recommending users with relevant items or services that they find interesting in. Recommender systems have gained prominence in the field of information technology, e-commerce, etc., by inferring personalized recommendations by effectively pruning from a universal set of choices that directed users to identify content of interest.

Dynamic Computational Model of the Human Spinal Cord Connectome

2019 ◽  
Vol 31 (2) ◽  
pp. 388-416 ◽  
Author(s):  
Jeffrey E. Arle ◽  
Nicolae Iftimia ◽  
Jay L. Shils ◽  
Longzhi Mei ◽  
Kristen W. Carlson
Keyword(s):  
Spinal Cord ◽  
Computational Model ◽  
Cell Types ◽  
Neural Circuitry ◽  
Simulation Software ◽  
Cross Sectional ◽  
Human Spinal Cord ◽  
Starting Point ◽  
The Many ◽  
Future Work

Connectomes abound, but few for the human spinal cord. Using anatomical data in the literature, we constructed a draft connectivity map of the human spinal cord connectome, providing a template for the many calibrations of specialized behavior to be overlaid on it and the basis for an initial computational model. A thorough literature review gleaned cell types, connectivity, and connection strength indications. Where human data were not available, we selected species that have been studied. Cadaveric spinal cord measurements, cross-sectional histology images, and cytoarchitectural data regarding cell size and density served as the starting point for estimating numbers of neurons. Simulations were run using neural circuitry simulation software. The model contains the neural circuitry in all ten Rexed laminae with intralaminar, interlaminar, and intersegmental connections, as well as ascending and descending brain connections and estimated neuron counts for various cell types in every lamina of all 31 segments. We noted the presence of highly interconnected complex networks exhibiting several orders of recurrence. The model was used to perform a detailed study of spinal cord stimulation for analgesia. This model is a starting point for workers to develop and test hypotheses across an array of biomedical applications focused on the spinal cord. Each such model requires additional calibrations to constrain its output to verifiable predictions. Future work will include simulating additional segments and expanding the research uses of the model.

scholarly journals Teaching Genomic Pathology: Translating Team-Based Learning to a Virtual Environment Using Computer-Based Simulation

2018 ◽  
Vol 143 (4) ◽  
pp. 513-517 ◽  
Author(s):  
Richard L. Haspel ◽  
Asma M. Ali ◽  
Grace C. Huang ◽  
Matt H. Smith ◽  
James B. Atkinson ◽  
...  
Keyword(s):  
Virtual Environment ◽  
Skill Acquisition ◽  
Interactive Simulation ◽  
Residency Programs ◽  
Computer Tools ◽  
Team Based Learning ◽  
Post Test ◽  
Computer Based ◽  
Genomics Education ◽  
Future Work

Context.— Developing skills related to use of computer-based tools is critical for practicing genomic pathology. However, given the relative novelty of genomics education, residency programs may lack faculty members with adequate expertise and/or time to implement training. A virtual team-based learning (TBL) environment would make genomic pathology education available to more trainees. Objective.— To translate an extensively implemented in-person TBL genomic pathology workshop into a virtual environment and to evaluate both knowledge and skill acquisition. Design.— Using a novel interactive simulation approach, online modules were developed translating aspects of the TBL experience into the virtual environment with a goal of acquisition of necessary computer-related skills. The modules were evaluated at 10 postgraduate pathology training programs using a pre-post test design with participants deidentified. A postmodule anonymous survey obtained participant feedback on module quality and efficacy. Results.— There were 147 trainees who received an email request to voluntarily participate in the study. Of these, 43 trainees completed the pretest and 15 (35%) subsequently completed the posttest. Mean overall scores were 45% on the pretest compared with 70% on the posttest (P < .001; effect size = 1.4). Posttest improvement of results was similar for questions testing acquisition of knowledge versus skills. Regarding the 19 participants who took the survey, 18 (95%) would recommend the modules to others and believed they met the stated objectives. Conclusions.— A simulation-based approach allows motivated pathology trainees to acquire computer-related skills for practicing genomic pathology. Future work can explore efficacy in a nonvoluntary setting and adaptation to different specialties, learners, and computer tools.

scholarly journals G-Quadruplexes in the Archaea Domain

Biomolecules ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1349
Author(s):  
Václav Brázda ◽  
Yu Luo ◽  
Martin Bartas ◽  
Patrik Kaura ◽  
Otilia Porubiaková ◽  
...  
Keyword(s):  
Random Distribution ◽  
Dna Structures ◽  
Cellular Processes ◽  
Dna And Rna ◽  
Non Coding Rna ◽  
Archaeal Species ◽  
G Quadruplex ◽  
Potential Part ◽  
Functional Relevance ◽  
Eukaryotic Genomes

The importance of unusual DNA structures in the regulation of basic cellular processes is an emerging field of research. Amongst local non-B DNA structures, G-quadruplexes (G4s) have gained in popularity during the last decade, and their presence and functional relevance at the DNA and RNA level has been demonstrated in a number of viral, bacterial, and eukaryotic genomes, including humans. Here, we performed the first systematic search of G4-forming sequences in all archaeal genomes available in the NCBI database. In this article, we investigate the presence and locations of G-quadruplex forming sequences using the G4Hunter algorithm. G-quadruplex-prone sequences were identified in all archaeal species, with highly significant differences in frequency, from 0.037 to 15.31 potential quadruplex sequences per kb. While G4 forming sequences were extremely abundant in Hadesarchaea archeon (strikingly, more than 50% of the Hadesarchaea archaeon isolate WYZ-LMO6 genome is a potential part of a G4-motif), they were very rare in the Parvarchaeota phylum. The presence of G-quadruplex forming sequences does not follow a random distribution with an over-representation in non-coding RNA, suggesting possible roles for ncRNA regulation. These data illustrate the unique and non-random localization of G-quadruplexes in Archaea.

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