scholarly journals Kaleidoscope: A New Bioinformatics Pipeline Web Application for In Silico Hypothesis Exploration of Omics Signatures

2020 ◽  
Author(s):  
Khaled Alganem ◽  
Rammohan Shukla ◽  
Hunter Eby ◽  
Mackenzie Abel ◽  
Xiaolu Zhang ◽  
...  
Keyword(s):  
User Interface ◽  
In Silico ◽  
Web Application ◽  
Single Gene ◽  
Research Question ◽  
Data Exploration ◽  
Easy Access ◽  
Bioinformatics Pipeline ◽  
Medical Disorders ◽  
Research Questions

AbstractBackgroundIn silico data exploration is a key first step of exploring a research question. There are many publicly available databases and tools that offer appealing features to help with such a task. However, many applications lack exposure or are constrained with unfriendly or outdated user interfaces. Thus, it follows that there are many resources that are relevant to investigation of medical disorders that are underutilized.ResultsWe developed an R Shiny web application, called Kaleidoscope, to address this challenge. The application offers access to several omics databases and tools to let users explore research questions in silico. The application is designed to be user- friendly with a unified user interface, while also scalable by offering the option of uploading user-defined datasets. We demonstrate the application features with a starting query of a single gene (Disrupted in schizophrenia 1, DISC1) to assess its protein-protein interactions network. We then explore expression levels of the gene network across tissues and cell types in the brain, as well as across 34 schizophrenia versus control differential gene expression datasets.ConclusionKaleidoscope provides easy access to several databases and tools under a unified user interface to explore research questions in silico. The web application is open-source and freely available at https://kalganem.shinyapps.io/Kaleidoscope/. This application streamlines the process of in silico data exploration for users and expands the efficient use of these tools to stakeholders without specific bioinformatics expertise.

scholarly journals In Silico Structural Modeling and Analysis of Interactions of Tremellomycetes Cytochrome P450 Monooxygenases CYP51s with Substrates and Azoles

2021 ◽  
Vol 22 (15) ◽  
pp. 7811
Author(s):  
Olufunmilayo Olukemi Akapo ◽  
Joanna M. Macnar ◽  
Justyna D. Kryś ◽  
Puleng Rosinah Syed ◽  
Khajamohiddin Syed ◽  
...  
Keyword(s):  
Cytochrome P450 ◽  
Structural Analysis ◽  
In Silico ◽  
Web Application ◽  
Cytochrome P450 Monooxygenases ◽  
Agglomerative Clustering ◽  
Ligand Complex ◽  
P450 Monooxygenase ◽  
Study Results

Cytochrome P450 monooxygenase CYP51 (sterol 14α-demethylase) is a well-known target of the azole drug fluconazole for treating cryptococcosis, a life-threatening fungal infection in immune-compromised patients in poor countries. Studies indicate that mutations in CYP51 confer fluconazole resistance on cryptococcal species. Despite the importance of CYP51 in these species, few studies on the structural analysis of CYP51 and its interactions with different azole drugs have been reported. We therefore performed in silico structural analysis of 11 CYP51s from cryptococcal species and other Tremellomycetes. Interactions of 11 CYP51s with nine ligands (three substrates and six azoles) performed by Rosetta docking using 10,000 combinations for each of the CYP51-ligand complex (11 CYP51s × 9 ligands = 99 complexes) and hierarchical agglomerative clustering were used for selecting the complexes. A web application for visualization of CYP51s’ interactions with ligands was developed (http://bioshell.pl/azoledocking/). The study results indicated that Tremellomycetes CYP51s have a high preference for itraconazole, corroborating the in vitro effectiveness of itraconazole compared to fluconazole. Amino acids interacting with different ligands were found to be conserved across CYP51s, indicating that the procedure employed in this study is accurate and can be automated for studying P450-ligand interactions to cater for the growing number of P450s.

scholarly journals Ecodesign—A Review of Reviews

2020 ◽  
Vol 13 (1) ◽  
pp. 315
Author(s):  
Malte Schäfer ◽  
Manuel Löwer
Keyword(s):  
Success Factors ◽  
Research Question ◽  
Pollution Prevention ◽  
Past Research ◽  
The Past ◽  
Review Articles ◽  
Complete Life Cycle ◽  
Review Of Reviews ◽  
Research Questions ◽  
Over Time

With the intent of summing up the past research on ecodesign and making it more accessible, we gather findings from 106 existing review articles in this field. Five research questions on terminology, evolution, barriers and success factors, methods and tools, and synergies, guide the clustering of the resulting 608 statements extracted from the reference. The quantitative analysis reveals that the number of review articles has been increasing over time. Furthermore, most statements originate from Europe, are published in journals, and address barriers and success factors. For the qualitative analysis, the findings are grouped according to the research question they address. We find that several names for similar concepts exist, with ecodesign being the most popular one. It has evolved from “end-of-pipe” pollution prevention to a more systemic concept, and addresses the complete life cycle. Barriers and success factors extend beyond the product development team to management, customers, policymakers, and educators. The number of ecodesign methods and tools available to address them is large, and more reviewing, testing, validation, and categorization of the existing ones is necessary. Synergies between ecodesign and other research disciplines exist in theory, but require implementation and testing in practice.

scholarly journals Bibliometric Analysis of the Literature on Measuring Techniques for Manipulating Financial Statements

Risks ◽  
2021 ◽  
Vol 9 (7) ◽  
pp. 123
Author(s):  
Ioana Lavinia Safta ◽  
Andrada-Ioana Sabău (Popa) ◽  
Neli Muntean
Keyword(s):  
Bibliometric Analysis ◽  
Web Of Science ◽  
Research Question ◽  
Financial Statements ◽  
Research Papers ◽  
Creative Accounting ◽  
Measuring Techniques ◽  
Research Questions ◽  
Over Time

Creative accounting has its background since early studies in 1975, until the present time. It continues to be a subject of great interest for the companies and interested parties. Thus, the current paper will aim to answer the following proposed research questions: 1. Which are the most used methods for detecting the manipulation of financial statements in the literature? 2. Which are the terms that are most frequently encountered in the literature associated with “creative accounting? 3. Which are the journals that have the highest frequency of articles written on the topic “creative accounting”? 4. Over time, how did research evolve in the field of creative accounting? 5. Which countries are most preoccupied in publishing regarding this topic? To answer the research question 1, the models published in the literature for measuring manipulation techniques through creative accounting were reviewed and analyzed. For the remaining research questions, a bibliometric analysis for the publications in this area was performed. For collecting the sample, articles on this topic were selected from the international Web of Science database. Following this, a bibliometric analysis of the articles was performed, using the VOSviewer program. A total of 4045 publications on creative accounting were identified. Through the bibliometric analysis we have answered research question 2, by identifying the key words that have the closest proximity to creative accounting. To answer the remaining research questions, we identified the journals with the highest frequency of publication and the countries with the highest interest on the topic. It is especially important to evaluate the quality of this many research papers and to obtain valuable information.

E-voting adoption in many countries: A literature review

2021 ◽  
pp. 205789112110405
Author(s):  
Ikhsan Darmawan
Keyword(s):  
United States ◽  
Systematic Review ◽  
Literature Review ◽  
Single Case ◽  
Research Question ◽  
The United States ◽  
Single Case Study ◽  
Academic Publications ◽  
Research Questions

Although the number of countries that have adopted e-voting has decreased lately, the number of academic publications on e-voting adoption has increased in the last two years. To date, there is no coherent narrative in the existing literature that explains the progress of the research on e-voting adoption. This article aims to answer the following research question: “How has research on the topic of e-voting adoption progressed over the last 15 years?” The article provides a semi-systematic review of 78 studies that were conducted from 2005 to 2020. In this article, I argue that although the studies on e-voting adoption are dominated by a single case study, by research in the United States, and by the positivist paradigm, scholars have employed the term “e-voting adoption” diversely and the research on e-voting adoption has evolved to address more specific research questions. Recommendations for the future agenda of research on e-voting adoption are also discussed.

Manifestations of legislative shortcomings in the Iraqi constitution

2021 ◽  
Author(s):  
Yamamah Kashkool ◽  
wael Al-bayati
Keyword(s):  
Prime Minister ◽  
Research Question ◽  
Economic Conditions ◽  
Research Questions ◽  
The Republic ◽  
The Right ◽  
Political Turmoil ◽  
Political Variables ◽  
Transitional Phase ◽  
New Phase

"The period of approving the Constitution of the Republic of Iraq for the year 2005 was surrounded by a state of political turmoil that usually accompanies any transitional phase that carries many political variables through the transition from a phase of dictatorial rule to a new phase bearing the features of democracy. In its approval, the lack of clarity in the political vision and the weakness of the constitutional legal culture of its authors, as well as the way in which it was approved by a popular referendum, which is voted on by yes or no, and does not allow an opportunity to discuss its articles and articles and diagnose its shortcomings. One of the shortcomings in our constitution is that it does not refer to regulating the resignation of the Prime Minister. This position has a political nature, and an administrative nature, and its occupant has the right to decide not to continue with this position and be satisfied with working in this field for any reason, and this must be in accordance with the context Organized legal, which is known as resignation., and this is what we dealt with in this research. For the purpose of researching this topic, we asked a research question that is... How can we address the legislative shortcomings that surrounded the Constitution of the Republic of Iraq for the year 2005 and related to regulating the resignation of the Prime Minister? From this research question, we derived several secondary research questions... 1- What is the limitation of legislative shortcomings? 2- What are the reasons for the legislative deficiencies in the Iraqi constitution? 3- Does the Prime Minister have the right to resign during his tenure? 4- To whom is the resignation submitted? 5- Who is the party that decides whether or not to accept the resignation? 6- What are the procedures that follow the acceptance of the resignation? By discussing these questions, we will try to reach the possibility of developing a legislative text that deals with a complete organization of the resignation of the Prime Minister, especially since the idea of ​​amending the constitution and to this day is still valid and possible, because many political, social and economic conditions in the country have changed from the time of entry into force of this constitution, which makes the idea of ​​the amendment obligatory and necessary"

Of dilemmas and tensions: a qualitative study of palliative care physicians’ positions regarding voluntary active euthanasia in Quebec, Canada

2018 ◽  
Vol 45 (1) ◽  
pp. 48-53 ◽  
Author(s):  
Emmanuelle Bélanger ◽  
Anna Towers ◽  
David Kenneth Wright ◽  
Yuexi Chen ◽  
Golda Tradounsky ◽  
...  
Keyword(s):  
Palliative Care ◽  
End Of Life Care ◽  
Patient Autonomy ◽  
Research Question ◽  
Interpretive Description ◽  
Active Euthanasia ◽  
Semistructured Interviews ◽  
Voluntary Active Euthanasia ◽  
Research Questions ◽  
Insight Into

ObjectivesIn 2015, the Province of Quebec, Canada passed a law that allowed voluntary active euthanasia (VAE). Palliative care stakeholders in Canada have been largely opposed to euthanasia, yet there is little research about their views. The research question guiding this study was the following: How do palliative care physicians in Quebec position themselves regarding the practice of VAE in the context of the new provincial legislation?MethodsWe used interpretive description, an inductive methodology to answer research questions about clinical practice. A total of 18 palliative care physicians participated in semistructured interviews at two university-affiliated hospitals in Quebec.ResultsParticipants positioned themselves in opposition to euthanasia. Their justifications were framed within their professional commitment to not hasten death, which sat in tension with the value of patients’ autonomy to choose how to die. Participants described VAE as unacceptable if it impeded opportunities to evaluate and alleviate suffering. Further, they contested government rhetoric that positioned VAE as a way to improve end-of-life care. Participants felt that VAE would diminish the potential of palliative care to relieve suffering. Dilemmas were apparent in their narratives, about reconciling respect for patient autonomy with broader palliative care values, and the value of accompanying and not abandoning patients who make requests for VAE while being committed to neither prolonging nor hastening death.ConclusionsThis study provides insight into nuanced positions of experienced palliative care physicians in Quebec and confirms expected tensions between an important stakeholder and the practice of VAE as guided by the new legislation.

scholarly journals Homicides and Weapons: Examining the Covariates of Weapon Choice

2018 ◽  
Vol 23 (1) ◽  
pp. 41-63 ◽  
Author(s):  
Karissa R. Pelletier ◽  
Jesenia M. Pizarro
Keyword(s):  
Research Question ◽  
Research Questions

This study examines the covariates of weapon choice in homicide incidents. Two research questions are examined. The first research question is: what variables influence the use of a particular type of weapon in a homicide? The second research question asks: how does the method of weapon retrieval, or lack thereof, affect the choice of weapon? The findings suggest that firearms are more likely to be on the offender’s person and carried to the incident scene relative to other weapon types. In addition, the use of specific types of weapons is conditioned by the demographic and lifestyle characteristics of victims and offenders.

scholarly journals UNDERSTANDING AIRLINE BRAND EQUITY DRIVERS: LESSONS FROM A MULTIPLE CASE STUDY

2017 ◽  
Vol 8 (2) ◽  
pp. 70-93
Author(s):  
Kallol Das ◽  
Karman Khanna ◽  
Surankita Ganguly
Keyword(s):  
Brand Equity ◽  
Emerging Economies ◽  
Research Question ◽  
Consumer Involvement ◽  
Primary Research ◽  
Multiple Case ◽  
Research Questions ◽  
Cross Case Analysis ◽  
Case Design

There is increasing consumer involvement and hence, investor interest in the airlines industry, as far as emerging economies is concerned. A study of the literature by the authors did not produce any research paper on the process drivers of brand equity in the context of airlines. Therefore, the present study makes an attempt to address this gap. The primary research question is: What are the driving factors for building brand equity in the case of airline services? This paper uses a “two-case” multiple-case design employing theoretical replication. The cases are based on two Indian organizations, Indigo Airlines and Go Air. Both these businesses are similar in many aspects but have achieved very contrasting outcomes. The primary research question is broken down into following two secondary research questions. How is Indigo Airlines building its brand? How is Go Air building its brand? Data collection involved use of documents, archives, observations, participant-observations, and surveys. Data analysis involved conducting cross-case analysis. The findings have been used to develop a conceptual framework for building brand equity in airlines.

scholarly journals Nextstrain: real-time tracking of pathogen evolution

2017 ◽  
Author(s):  
James Hadfield ◽  
Colin Megill ◽  
Sidney M. Bell ◽  
John Huddleston ◽  
Barney Potter ◽  
...  
Keyword(s):  
Public Health ◽  
Real Time ◽  
Web Application ◽  
Sequence Data ◽  
Data Types ◽  
Bioinformatics Pipeline ◽  
Public Health Importance ◽  
Viral Genomes ◽  
Effective Public Health ◽  
Interactive Visualisation

AbstractSummaryUnderstanding the spread and evolution of pathogens is important for effective public health measures and surveillance. Nextstrain consists of a database of viral genomes, a bioinformatics pipeline for phylodynamics analysis, and an interactive visualisation platform. Together these present a real-time view into the evolution and spread of a range of viral pathogens of high public health importance. The visualization integrates sequence data with other data types such as geographic information, serology, or host species. Nextstrain compiles our current understanding into a single accessible location, publicly available for use by health professionals, epidemiologists, virologists and the public alike.Availability and implementationAll code (predominantly JavaScript and Python) is freely available from github.com/nextstrain and the web-application is available at nextstrain.org.

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