iTaxoTools 0.1: Kickstarting a specimen-based software toolkit for taxonomists

While powerful and user-friendly software suites exist for phylogenetics, and an impressive cybertaxomic infrastructure of online species databases has been set up in the past two decades, software specifically targeted at facilitating alpha-taxonomic work, i.e., delimiting and diagnosing species, is still in its infancy. Here we present a project to develop a bioinformatic toolkit for taxonomy, based on open-source Python code, including tools focusing on species delimitation and diagnosis and centered around specimen identifiers. At the core of iTaxoTools is user-friendliness, with numerous autocorrect options for data files and with intuitive graphical user interfaces. Assembled standalone executables for all tools or a suite of tools with a launcher window will be distributed for Windows, Linux, and Mac OS systems, and in the future also implemented on a web server. The alpha version (iTaxoTools 0.1) distributed with this paper contains GUI versions of six species delimitation programs (ABGD, ASAP, DELINEATE, GMYC, PTP, tr2) and a simple threshold-clustering delimitation tool. There are also new Python implementations of existing algorithms, including tools to compute pairwise DNA distances, ultrametric time trees based on non-parametric rate smoothing, species-diagnostic nucleotide positions, and standard morphometric analyses. Other utilities convert among different formats of molecular sequences, geographical coordinates, and units; merge, split and prune sequence files and tables; and perform simple statistical tests. As a future perspective, we envisage iTaxoTools to become part of a bioinformatic pipeline for next-generation taxonomy that accelerates the inventory of life while maintaining high-quality species hypotheses.

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iTaxoTools 0.1: Kickstarting a specimen-based software toolkit for taxonomists

Megataxa ◽

10.11646/megataxa.6.2.1 ◽

2021 ◽

Vol 6 (2) ◽

Author(s):

MIGUEL VENCES ◽

AURÉLIEN MIRALLES ◽

SOPHIE BROUILLET ◽

JACQUES DUCASSE ◽

ALEXANDER FEDOSOV ◽

...

Keyword(s):

Open Source ◽

User Interfaces ◽

Species Delimitation ◽

Statistical Tests ◽

Future Perspective ◽

User Friendliness ◽

Morphometric Analyses ◽

Data Files ◽

Set Up ◽

User Friendly

While powerful and user-friendly software suites exist for phylogenetics, and an impressive cybertaxomic infrastructure of online species databases has been set up in the past two decades, software targeted explicitly at facilitating alpha-taxonomic work, i.e., delimiting and diagnosing species, is still in its infancy. Here we present a project to develop a bioinformatic toolkit for taxonomy, based on open-source Python code, including tools focusing on species delimitation and diagnosis and centered around specimen identifiers. At the core of iTaxoTools is user-friendliness, with numerous autocorrect options for data files and with intuitive graphical user interfaces. Assembled standalone executables for all tools or a suite of tools with a launcher window will be distributed for Windows, Linux, and Mac OS systems, and in the future also implemented on a web server. The initial version (iTaxoTools 0.1) distributed with this paper (https://github.com/iTaxoTools/iTaxoTools-Executables) contains graphical user interface (GUI) versions of six species delimitation programs (ABGD, ASAP, DELINEATE, GMYC, PTP, tr2) and a simple threshold-clustering delimitation tool. There are also new Python implementations of existing algorithms, including tools to compute pairwise DNA distances, ultrametric time trees based on non-parametric rate smoothing, species-diagnostic nucleotide positions, and standard morphometric analyses. Other utilities convert among different formats of molecular sequences, geographical coordinates, and units; merge, split and prune sequence files, tables and species partition files; and perform simple statistical tests. As a future perspective, we envisage iTaxoTools to become part of a bioinformatic pipeline for next-generation taxonomy that accelerates the inventory of life while maintaining high-quality species hypotheses. The open source code and binaries of all tools are available from Github (https://github.com/iTaxoTools) and further information from the website (http://itaxotools.org)

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Biofunctional Surfaces for Smart Entrapment of Polysomes

Applied Sciences ◽

10.3390/app11020776 ◽

2021 ◽

Vol 11 (2) ◽

pp. 776

Author(s):

Lorenzo Lunelli ◽

Lorenza Marocchi ◽

Laura Pasquardini ◽

Lia Vanzetti ◽

Gabriella Viero ◽

...

Keyword(s):

Protein Synthesis ◽

Rna Extraction ◽

Future Perspective ◽

Pathological State ◽

Central Process ◽

Force Microscopy ◽

Atomic Force ◽

Surface Functionalizations ◽

Set Up ◽

User Friendly

Protein synthesis is a central process in all cells, crucial for cell development and maintenance. Translational dysregulation, in fact, is associated with cancer or neurodegenerative diseases. Active protein synthesis occurs on a supramolecular complex, named polyribosome or polysome, formed by a mRNA associated with multiple ribosomes. Polysomes therefore can be considered as a privileged molecular platform to obtain information about the physiological or pathological state in cells. The classical methods for purifying the mRNAs associated with polysomes mainly rely on ultracentrifugation in sucrose gradient followed by standard RNA extraction. This method present several drawbacks, among all it is a time-consuming procedure, which requires a fairly large amounts of starting material. New methods offering an efficient, rapid and user-friendly alternative to standard methods are therefore highly desirable. Here, a panel of surfaces and surface functionalizations were screened for their ability to entrap polysomes with the ultimate aim to set up smart biofunctional surfaces for the purification of nonlabelled polysomes and their associated mRNAs. As a proof-of-concept, prepurified ribosomes and polysomes were incubated on multiple functional surfaces and characterized by atomic force microscopy to assess number and morphology of entrapped polysomes. Surfaces able to efficiently capture polysomes were then included in a microdevice with promising results, opening the future perspective of developing protocols and devices based on biofunctional surfaces.

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

Acta Neurochirurgica ◽

10.1007/s00701-021-04967-0 ◽

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.

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Sampo-UI: A full stack JavaScript framework for developing semantic portal user interfaces

Semantic Web ◽

10.3233/sw-210428 ◽

2021 ◽

pp. 1-16

Author(s):

Esko Ikkala ◽

Eero Hyvönen ◽

Heikki Rantala ◽

Mikko Koho

Keyword(s):

User Interfaces ◽

Linked Data ◽

State Of The Art ◽

Software Framework ◽

End User ◽

Faceted Search ◽

Software Developer ◽

Current State ◽

Knowledge Graphs ◽

User Friendly

This paper presents a new software framework, Sampo-UI, for developing user interfaces for semantic portals. The goal is to provide the end-user with multiple application perspectives to Linked Data knowledge graphs, and a two-step usage cycle based on faceted search combined with ready-to-use tooling for data analysis. For the software developer, the Sampo-UI framework makes it possible to create highly customizable, user-friendly, and responsive user interfaces using current state-of-the-art JavaScript libraries and data from SPARQL endpoints, while saving substantial coding effort. Sampo-UI is published on GitHub under the open MIT License and has been utilized in several internal and external projects. The framework has been used thus far in creating six published and five forth-coming portals, mostly related to the Cultural Heritage domain, that have had tens of thousands of end-users on the Web.

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epiTracker: A Framework for Highly Reliable Particle Tracking for the Quantitative Analysis of Fish Movements in Tanks

SLAS TECHNOLOGY Translating Life Sciences Innovation ◽

10.1177/2472630320977454 ◽

2020 ◽

pp. 247263032097745

Author(s):

Roman Bruch ◽

Paul M. Scheikl ◽

Ralf Mikut ◽

Felix Loosli ◽

Markus Reischl

Keyword(s):

Social Interactions ◽

User Interfaces ◽

Particle Tracking ◽

Group Behavior ◽

Correction Method ◽

Graphical User Interfaces ◽

Study Group ◽

Automated Tracking ◽

User Friendly ◽

Track Analysis

Behavioral analysis of moving animals relies on a faithful recording and track analysis to extract relevant parameters of movement. To study group behavior and social interactions, often simultaneous analyses of individuals are required. To detect social interactions, for example to identify the leader of a group as opposed to followers, one needs an error-free segmentation of individual tracks throughout time. While automated tracking algorithms exist that are quick and easy to use, inevitable errors will occur during tracking. To solve this problem, we introduce a robust algorithm called epiTracker for segmentation and tracking of multiple animals in two-dimensional (2D) videos along with an easy-to-use correction method that allows one to obtain error-free segmentation. We have implemented two graphical user interfaces to allow user-friendly control of the functions. Using six labeled 2D datasets, the effort to obtain accurate labels is quantified and compared to alternative available software solutions. Both the labeled datasets and the software are publicly available.

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Research on 3D Reconstruction System for Medical Images

Key Engineering Materials ◽

10.4028/www.scientific.net/kem.464.57 ◽

2011 ◽

Vol 464 ◽

pp. 57-60

Author(s):

Yong Zhang ◽

Jun Fang Ni ◽

Peng Liu

Keyword(s):

User Interfaces ◽

Medical Images ◽

Object Oriented ◽

Graphical User Interfaces ◽

Object Oriented Programming ◽

3D Data ◽

Efficient Data ◽

User Friendly ◽

Process Reconstruction ◽

Display Technique

In accordance with the object-oriented programming, a system for 3D medical images of reconstruction and display has been designed and implemented. The overall software structure is established based on VC++6.0 and display technique of Open Graphics Library. The functional modules, such as acquisition of encoded 3D data, pre-process, reconstruction and display, are achieved by the design and implementation of customized classes. At last the software system provides user-friendly graphical user interfaces, highly efficient data processing and reconstruction, and rapid capability of graphic display.

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ARESIBO HORIZON 2020 EUROPEAN RESEARCH PROJECT – ENRICHED SITUATION AWARENESS FOR BORDER SURVEILLANCE

STRATEGIES XXI - Command and Staff College ◽

10.53477/2668-2028-21-31 ◽

2021 ◽

Vol 17 (1) ◽

pp. 247-255

Author(s):

Konstantinos CHARISI ◽

Andreas TSIGOPOULOS ◽

Spyridon KINTZIOS ◽

Vassilis PAPATAXIARHIS

Keyword(s):

Augmented Reality ◽

Situation Awareness ◽

User Interfaces ◽

Border Security ◽

Multiple Sources ◽

Horizon 2020 ◽

Research And Innovation ◽

Current State ◽

Available Information ◽

User Friendly

Abstract. The paper aims to introduce the ARESIBO project to a greater but targeted audience and outline its main scope and achievements. ARESIBO stands for “Augmented Reality Enriched Situation awareness for Border security”. In the recent years, border security has become one of the highest political priorities in EU and needs the support of every Member State. ARESIBO project is developed under HORIZON 2020 EC Research and Innovation program and it is the joint effort of 20 participant entities from 11 countries. Scientific excellence and technological innovation are top priorities as ARESIBO enhances the current state-of-the-art through technological breakthroughs in Mobile Augmented Reality and Wearables, Robust and Secure Telecommunications, Robots swarming technique and Planning of Context-Aware Autonomous Missions, and Artificial Intelligence (AI), in order to implement user-friendly tools for border and coast guards. The system aims to improve the cognitive capabilities and the perception of border guards through intuitive user interfaces that will help them acquire an improved situation awareness by filtering the huge amount of available information from multiple sources. Ultimately, it will help them respond faster and more effectively when a critical situation occurs.

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High-Throughput Analysis of Selected Urinary Hydroxy Polycyclic Aromatic Hydrocarbons by an Innovative Automated Solid-Phase Microextraction

Molecules ◽

10.3390/molecules23081869 ◽

2018 ◽

Vol 23 (8) ◽

pp. 1869 ◽

Cited By ~ 9

Author(s):

Stefano Dugheri ◽

Alessandro Bonari ◽

Matteo Gentili ◽

Giovanni Cappelli ◽

Ilenia Pompilio ◽

...

Keyword(s):

Polycyclic Aromatic Hydrocarbons ◽

High Throughput ◽

Aromatic Hydrocarbons ◽

High Throughput Screening ◽

Solid Phase Microextraction ◽

Solid Phase ◽

User Friendliness ◽

High Throughput Analysis ◽

Polycyclic Aromatic ◽

User Friendly

High-throughput screening of samples is the strategy of choice to detect occupational exposure biomarkers, yet it requires a user-friendly apparatus that gives relatively prompt results while ensuring high degrees of selectivity, precision, accuracy and automation, particularly in the preparation process. Miniaturization has attracted much attention in analytical chemistry and has driven solvent and sample savings as easier automation, the latter thanks to the introduction on the market of the three axis autosampler. In light of the above, this contribution describes a novel user-friendly solid-phase microextraction (SPME) off- and on-line platform coupled with gas chromatography and triple quadrupole-mass spectrometry to determine urinary metabolites of polycyclic aromatic hydrocarbons 1- and 2-hydroxy-naphthalene, 9-hydroxy-phenanthrene, 1-hydroxy-pyrene, 3- and 9-hydroxy-benzoantracene, and 3-hydroxy-benzo[a]pyrene. In this new procedure, chromatography’s sensitivity is combined with the user-friendliness of N-tert-butyldimethylsilyl-N-methyltrifluoroacetamide on-fiber SPME derivatization using direct immersion sampling; moreover, specific isotope-labelled internal standards provide quantitative accuracy. The detection limits for the seven OH-PAHs ranged from 0.25 to 4.52 ng/L. Intra-(from 2.5 to 3.0%) and inter-session (from 2.4 to 3.9%) repeatability was also evaluated. This method serves to identify suitable risk-control strategies for occupational hygiene conservation programs.

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Virtual Reality Training Applications in Industry - Towards a User-friendly Application Design

10.30844/wgab_2021_4 ◽

2021 ◽

pp. 59-80

Author(s):

Benjamin Knoke ◽

◽

Moritz Quandt ◽

Michael Freitag ◽

Klaus-Dieter Thoben

Keyword(s):

Virtual Reality ◽

Technology Acceptance ◽

User Interfaces ◽

Interface Design ◽

Design Guidelines ◽

Electrical Safety ◽

Industrial Training ◽

Current State ◽

Vr Training ◽

User Friendly

The purpose of this research is to aggregate and discuss the validity of challenges and design guidelines regarding industrial Virtual Reality (VR) training applications. Although VR has seen significant advancements in the last 20 years, the technology still faces multiple research challenges. The challenges towards industrial VR applications are imposed by a limited technological maturity and the need to achieve industrial stakeholders' technology acceptance. Technology acceptance is closely connected with the consideration of individual user requirements for user interfaces in virtual environments. This paper analyses the current state-of-the-art in industrial VR applications and provides a structured overview of the existing challenges and applicable guidelines for user interface design, such as ISO 9241-110. The validity of the identified challenges and guidelines is discussed against an industrial training scenario on electrical safety during maintenance tasks.

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The Impact of Watching Television Sports Channels in Promotion of Sports Activities among the Students of University of Sargodha

Global Mass Communication Review ◽

10.31703/gmcr.2019(iv-i).07 ◽

2019 ◽

Vol IV (I) ◽

pp. 95-107

Author(s):

Sajjad Ali ◽

Muhammad Saqib Ilmas ◽

Shajee Hassan

Keyword(s):

Statistical Tests ◽

Sampling Technique ◽

Chi Square ◽

Uses And Gratification ◽

Uses And Gratification Theory ◽

Chi Square Test ◽

Set Up ◽

The University ◽

The Impact ◽

Sports Activities

This study analyzes the impact of watching television sports channels on the promotion of sports activities among the students of the University of Sargodha. The aim of the study is to explore the impact of sports channels on students. Previous researches are used to set up the concepts of the present study. In this research, a survey technique is used to collect the data. The population of the study consists of male and female students of the University of Sargodha. In this research, the Stratified and Purposive sampling technique is used, through which specification characteristics of the respondent's demographics. The study explores the impact of sports channels in the view of Uses and Gratification Theory. The data for this study is collected through the use of a well-designed questionnaire. Chi-square test and other statistical tests like ANOVA and t-Test are applied to test the hypothesis. The finding shows that more the exposure to TV sports channels more the information level of students of the University of Sargodha.

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