scholarly journals An open-hardware platform for optogenetics and photobiology

2016 ◽  
Author(s):  
Karl P. Gerhardt ◽  
Evan J. Olson ◽  
Sebastian M. Castillo-Hair ◽  
Lucas A. Hartsough ◽  
Brian P. Landry ◽  
...  
Keyword(s):  
Mammalian Cells ◽  
Red Light ◽  
Web Tool ◽  
Entry Barrier ◽  
Open Hardware ◽  
Intensity Control ◽  
Light Signals ◽  
User Friendly ◽  
The Impact ◽  
Plate Apparatus

AbstractIn optogenetics, researchers use light and genetically encoded photoreceptors to control biological processes with unmatched precision. However, outside of neuroscience, the impact of optogenetics has been limited by a lack of user-friendly, flexible, accessible hardware. Here, we engineer the Light Plate Apparatus (LPA), a device that can deliver two independent 310 to 1550 nm light signals to each well of a 24-well plate with intensity control over three orders of magnitude and millisecond resolution. Signals are programmed using an intuitive web tool named Iris. All components can be purchased for under $400 and the device can be assembled and calibrated by a non-expert in one day. We use the LPA to precisely control gene expression from blue, green, and red light responsive optogenetic tools in bacteria, yeast, and mammalian cells and simplify the entrainment of cyanobacterial circadian rhythm. The LPA dramatically reduces the entry barrier to optogenetics and photobiology experiments.

scholarly journals MetaMap, an interactive webtool for the exploration of metatranscriptomic reads in human disease-related RNA-seq data

2018 ◽  
Author(s):  
LM Simon ◽  
G Tsitsiridis ◽  
P Angerer ◽  
FJ Theis
Keyword(s):  
Human Disease ◽  
Expression Patterns ◽  
Heterogeneous Data ◽  
Rna Seq ◽  
Web Tool ◽  
Differential Abundance ◽  
Downstream Analysis ◽  
User Friendly ◽  
Differential Abundance Analysis ◽  
The Impact

AbstractMotivationThe MetaMap resource contains metatranscriptomic expression data from screening >17,000 RNA-seq samples from >400 archived human disease-related studies for viral and microbial reads, so-called “metafeatures”. However, navigating this set of large and heterogeneous data is challenging, especially for researchers without bioinformatic expertise. Therefore, a user-friendly interface is needed that allows users to visualize and statistically analyse the data.ResultsWe developed an interactive frontend to facilitate the exploration of the MetaMap resource. The webtool allows users to query the resource by searching study abstracts for keywords or browsing expression patterns for specific metafeatures. Moreover, users can manually define sample groupings or use the existing annotation for downstream analysis. The web tool provides a large variety of analyses and visualizations including dimension reduction, differential abundance analysis and Krona visualizations. The MetaMap webtool represents a valuable resource for hypothesis generation regarding the impact of the microbiome in human disease.AvailabilityThe presented web tool can be accessed at https://github.com/theislab/MetaMap

The Role of Web Based Accounting Online System 2.0 as the Company's Income and Expense Management

2017 ◽  
Vol 1 (1) ◽  
pp. 44-49
Author(s):  
Nur Azizah ◽  
Dedeh Supriyanti ◽  
Siti Fairuz Aminah Mustapha ◽  
Holly Yang
Keyword(s):  
Financial Management ◽  
Accounting System ◽  
Bank Account ◽  
Web Based ◽  
Online System ◽  
Version 2.0 ◽  
User Friendly ◽  
The Impact ◽  
A Company

In a company, the process of income and expense of money must have a profit-generating goal base. The success of financial management within the company, can be monitored from the ability of the financial management in managing the finances and utilize all the opportunities that exist with as much as possible with the aim to control the company's cash (cash flow) and the impact of generating profits in accordance with expectations. With a web-based online accounting system version 2.0, companies can be given the ease to manage money in and out of the company's cash. It has a user friendly system with navigation that makes it easy for the financial management to use it. Starting from the creation of a company's cash account used as a cash account and corporate bank account on the system, deletion or filing of cash accounts, up to the transfer invoice creation feature, receive and send money. Thus, this system is very effective and efficient in the management of income and corporate cash disbursements.   Keywords:​Accounting Online System, Financial Management, Cash and Bank

scholarly journals Determining the impact of postoperative complications in neurosurgery based on simulated longitudinal smartphone app-based assessment

2021 ◽  
Author(s):  
Lion D. Comfort ◽  
Marian C. Neidert ◽  
Oliver Bozinov ◽  
Luca Regli ◽  
Martin N. Stienen
Keyword(s):  
Postoperative Complications ◽  
Feasibility Study ◽  
Well Being ◽  
Smartphone Application ◽  
Simulated Patients ◽  
Subjective Well Being ◽  
Longitudinal Assessment ◽  
User Friendliness ◽  
User Friendly ◽  
The Impact

Abstract Background Complications after neurosurgical operations can have severe impact on patient well-being, which is poorly reflected by current grading systems. The objective of this work was to develop and conduct a feasibility study of a new smartphone application that allows for the longitudinal assessment of postoperative well-being and complications. Methods We developed a smartphone application “Post OP Tracker” according to requirements from clinical experience and tested it on simulated patients. Participants received regular notifications through the app, inquiring them about their well-being and complications that had to be answered according to their assigned scenarios. After a 12-week period, subjects answered a questionnaire about the app’s functionality, user-friendliness, and acceptability. Results A total of 13 participants (mean age 34.8, range 24–68 years, 4 (30.8%) female) volunteered in this feasibility study. Most of them had a professional background in either health care or software development. All participants downloaded, installed, and applied the app for an average of 12.9 weeks. On a scale of 1 (worst) to 4 (best), the app was rated on average 3.6 in overall satisfaction and 3.8 in acceptance. The design achieved a somewhat favorable score of 3.1. One participant (7.7%) reported major technical issues. The gathered patient data can be used to graphically display the simulated outcome and assess the impact of postoperative complications. Conclusions This study suggests the feasibility to longitudinally gather postoperative data on subjective well-being through a smartphone application. Among potential patients, our application indicated to be functional, user-friendly, and well accepted. Using this app-based approach, further studies will enable us to classify postoperative complications according to their impact on the patient’s well-being.

scholarly journals Baicalin Represses Type Three Secretion System of Pseudomonas aeruginosa through PQS System

Molecules ◽  
2021 ◽  
Vol 26 (6) ◽  
pp. 1497
Author(s):  
Pansong Zhang ◽  
Qiao Guo ◽  
Zhihua Wei ◽  
Qin Yang ◽  
Zisheng Guo ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Virulence Factors ◽  
Mammalian Cells ◽  
Secretion System ◽  
Chinese Herbs ◽  
Infection Model ◽  
Lung Pathology ◽  
Promising Alternative ◽  
The Impact

Therapeutics that target the virulence of pathogens rather than their viability offer a promising alternative for treating infectious diseases and circumventing antibiotic resistance. In this study, we searched for anti-virulence compounds against Pseudomonas aeruginosa from Chinese herbs and investigated baicalin from Scutellariae radix as such an active anti-virulence compound. The effect of baicalin on a range of important virulence factors in P. aeruginosa was assessed using luxCDABE-based reporters and by phenotypical assays. The molecular mechanism of the virulence inhibition by baicalin was investigated using genetic approaches. The impact of baicalin on P. aeruginosa pathogenicity was evaluated by both in vitro assays and in vivo animal models. The results show that baicalin diminished a plenty of important virulence factors in P. aeruginosa, including the Type III secretion system (T3SS). Baicalin treatment reduced the cellular toxicity of P. aeruginosa on the mammalian cells and attenuated in vivo pathogenicity in a Drosophila melanogaster infection model. In a rat pulmonary infection model, baicalin significantly reduced the severity of lung pathology and accelerated lung bacterial clearance. The PqsR of the Pseudomonas quinolone signal (PQS) system was found to be required for baicalin’s impact on T3SS. These findings indicate that baicalin is a promising therapeutic candidate for treating P. aeruginosa infections.

scholarly journals Patient perspectives on tablet-based technology to collect risk factor information in primary care

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Leanne Kosowan ◽  
Alan Katz ◽  
Gayle Halas ◽  
Alexander Singer
Keyword(s):  
Primary Care ◽  
Information Technology ◽  
Risk Factor ◽  
Risk Behaviours ◽  
Patient Risk ◽  
Self Reflection ◽  
Primary Care Clinics ◽  
User Friendly ◽  
The Impact ◽  
Risk Factor Information

Abstract Background Primary care provides an opportunity to introduce prevention strategies and identify risk behaviours. Algorithmic information technology such as the Risk Factor Identification Tool (RFIT) can support primary care counseling. This study explores the integration of the tablet-based RFIT in primary care clinics to support exploration of patient risk factor information. Methods Qualitative study to explore patients’ perspectives of RFIT. RFIT was implemented in two primary care clinics in Manitoba, Canada. There were 207 patients who completed RFIT, offered to them by eight family physicians. We conducted one-on-one patient interviews with 86 patients to capture the patient’s perspective. Responses were coded and categorized into five common themes. Results RFIT had a completion rate of 86%. Clinic staff reported that very few patients declined the use of RFIT or required assistance to use the tablet. Patients reported that the tablet-based RFIT provided a user-friendly interface that enabled self-reflection while in the waiting room. Patients discussed the impact of RFIT on the patient-provider interaction, utility for the clinician, their concerns and suggested improvements for RFIT. Among the patients who used RFIT 12.1% smoked, 21.2% felt their diet could be improved, 9.3% reported high alcohol consumption, 56.4% reported less than 150 min of PA a week, and 8.2% lived in poverty. Conclusion RFIT is a user-friendly tool for the collection of patient risk behaviour information. RFIT is particularly useful for patients lacking continuity in the care they receive. Information technology can promote self-reflection while providing useful information to the primary care clinician. When combined with practical tools and resources RFIT can assist in the reduction of risk behaviours.

scholarly journals m5U54 tRNA Hypomodification by Lack of TRMT2A Drives the Generation of tRNA-Derived Small RNAs

2021 ◽  
Vol 22 (6) ◽  
pp. 2941
Author(s):  
Marisa Pereira ◽  
Diana R. Ribeiro ◽  
Miguel M. Pinheiro ◽  
Margarida Ferreira ◽  
Stefanie Kellner ◽  
...  
Keyword(s):  
Stress Response ◽  
Small Rnas ◽  
Mammalian Cells ◽  
Cellular Stress ◽  
Cellular Stress Response ◽  
Translation Regulation ◽  
Translation Efficiency ◽  
Down Regulation ◽  
Gene Expression Control ◽  
The Impact

Transfer RNA (tRNA) molecules contain various post-transcriptional modifications that are crucial for tRNA stability, translation efficiency, and fidelity. Besides their canonical roles in translation, tRNAs also originate tRNA-derived small RNAs (tsRNAs), a class of small non-coding RNAs with regulatory functions ranging from translation regulation to gene expression control and cellular stress response. Recent evidence indicates that tsRNAs are also modified, however, the impact of tRNA epitranscriptome deregulation on tsRNAs generation is only now beginning to be uncovered. The 5-methyluridine (m5U) modification at position 54 of cytosolic tRNAs is one of the most common and conserved tRNA modifications among species. The tRNA methyltransferase TRMT2A catalyzes this modification, but its biological role remains mostly unexplored. Here, we show that TRMT2A knockdown in human cells induces m5U54 tRNA hypomodification and tsRNA formation. More specifically, m5U54 hypomodification is followed by overexpression of the ribonuclease angiogenin (ANG) that cleaves tRNAs near the anticodon, resulting in accumulation of 5′tRNA-derived stress-induced RNAs (5′tiRNAs), namely 5′tiRNA-GlyGCC and 5′tiRNA-GluCTC, among others. Additionally, transcriptomic analysis confirms that down-regulation of TRMT2A and consequently m5U54 hypomodification impacts the cellular stress response and RNA stability, which is often correlated with tiRNA generation. Accordingly, exposure to oxidative stress conditions induces TRMT2A down-regulation and tiRNA formation in mammalian cells. These results establish a link between tRNA hypomethylation and ANG-dependent tsRNAs formation and unravel m5U54 as a tRNA cleavage protective mark.

scholarly journals A FEM-Based 2D Model for Simulation and Qualitative Assessment of Shot-Peening Processes

Materials ◽  
2021 ◽  
Vol 14 (11) ◽  
pp. 2784
Author(s):  
Georgios Maliaris ◽  
Christos Gakias ◽  
Michail Malikoutsakis ◽  
Georgios Savaidis
Keyword(s):  
Process Parameters ◽  
Material Properties ◽  
Shot Peening ◽  
Qualitative Assessment ◽  
Experimental Investigations ◽  
Elastoplastic Material ◽  
Size Distributions ◽  
User Friendly ◽  
The Impact ◽  
2D Model

Shot peening is one of the most favored surface treatment processes mostly applied on large-scale engineering components to enhance their fatigue performance. Due to the stochastic nature and the mutual interactions of process parameters and the partially contradictory effects caused on the component’s surface (increase in residual stress, work-hardening, and increase in roughness), there is demand for capable and user-friendly simulation models to support the responsible engineers in developing optimal shot-peening processes. The present paper contains a user-friendly Finite Element Method-based 2D model covering all major process parameters. Its novelty and scientific breakthrough lie in its capability to consider various size distributions and elastoplastic material properties of the shots. Therewith, the model is capable to provide insight into the influence of every individual process parameter and their interactions. Despite certain restrictions arising from its 2D nature, the model can be accurately applied for qualitative or comparative studies and processes’ assessments to select the most promising one(s) for the further experimental investigations. The model is applied to a high-strength steel grade used for automotive leaf springs considering real shot size distributions. The results reveal that the increase in shot velocity and the impact angle increase the extent of the residual stresses but also the surface roughness. The usage of elastoplastic material properties for the shots has been proved crucial to obtain physically reasonable results regarding the component’s behavior.

IO/EAM: An Input-Output Economic Assessment Model

1984 ◽  
Vol 16 (2) ◽  
pp. 145-150 ◽  
Author(s):  
Jeffrey L. Jordan ◽  
Rusty Brooks
Keyword(s):  
Research Effort ◽  
Economic Assessment ◽  
Assessment Model ◽  
Input Output ◽  
County Extension Agents ◽  
University Of Georgia ◽  
Microcomputer Software ◽  
The University ◽  
User Friendly ◽  
The Impact

AbstractThis paper describes a microcomputer software package, IO/EAM: An Input-Output Economic Assessment Model, which was developed at the University of Georgia through a joint extension-research effort. The package is a menudriven, user friendly program that is designed to be used by county extension agents, researchers, and other extension personnel to estimate the economic impact of changes in county economies. The program employs an input-output model that provides users with a locally based, easily updated source of economic intelligence. Use of input-output techniques allows users to estimate the impact of changes in county economies on an industry-by-industry basis and to account for the interdependencies among these industries in a county.

scholarly journals Dissection of acute stimulus-inducible nucleosome remodeling in mammalian cells

2019 ◽  
Author(s):  
Federico Comoglio ◽  
Marta Simonatto ◽  
Sara Polletti ◽  
Xin Liu ◽  
Stephen T. Smale ◽  
...  
Keyword(s):  
Mammalian Cells ◽  
Regulatory Elements ◽  
Micrococcal Nuclease ◽  
Nucleosome Remodeling ◽  
Nucleosome Dynamics ◽  
Nucleosome Organization ◽  
Regulatory Information ◽  
Different Types ◽  
Genomic Regions ◽  
The Impact

ABSTRACTAccessibility of the genomic regulatory information is largely controlled by the nucleosome-organizing activity of transcription factors (TFs). Whereas stimulus-induced TFs bind to genomic regions that are maintained accessible by lineage-determining TFs, they also increase accessibility of thousands of cis-regulatory elements. Nucleosome remodeling events underlying such changes and their interplay with basal positioning are unknown. Here, we devised a novel quantitative framework discriminating different types of nucleosome remodeling events in micrococcal nuclease ChIP-seq datasets and used it to analyze nucleosome dynamics at stimulus-regulated cis-regulatory elements. At enhancers, remodeling preferentially affected poorly positioned nucleosomes while sparing well-positioned nucleosomes flanking the enhancer core, indicating that inducible TFs do not suffice to overrule basal nucleosomal organization maintained by lineage-determining TFs. Remodeling events appeared to be combinatorially driven by multiple TFs, with distinct TFs showing however different remodeling efficiencies. Overall, these data provide a systematic view of the impact of stimulation on nucleosome organization and genome accessibility in mammalian cells.

scholarly journals PathScore: a web tool for identifying altered pathways in cancer data

2016 ◽  
Author(s):  
Stephen G. Gaffney ◽  
Jeffrey P. Townsend
Keyword(s):  
Web Application ◽  
Somatic Mutations ◽  
Supplementary Information ◽  
Web Tool ◽  
Cancer Data ◽  
Link Type ◽  
Novel Approach ◽  
Supplementary Material ◽  
User Friendly ◽  
Pathway Effect

ABSTRACTSummaryPathScore quantifies the level of enrichment of somatic mutations within curated pathways, applying a novel approach that identifies pathways enriched across patients. The application provides several user-friendly, interactive graphic interfaces for data exploration, including tools for comparing pathway effect sizes, significance, gene-set overlap and enrichment differences between projects.Availability and ImplementationWeb application available at pathscore.publichealth.yale.edu. Site implemented in Python and MySQL, with all major browsers supported. Source code available at github.com/sggaffney/pathscore with a GPLv3 [email protected] InformationAdditional documentation can be found at http://pathscore.publichealth.yale.edu/faq.

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