A comparative benchmarking and evaluation framework for heterogeneous network-based drug repositioning methods

Computational drug repositioning, which involves identifying new indications for existing drugs, is an increasingly attractive research area due to its advantages in reducing both overall cost and development time. As a result, a growing number of computational drug repositioning methods have emerged. Heterogeneous network-based drug repositioning methods have been shown to outperform other approaches. However, there is a dearth of systematic evaluation studies of these methods, encompassing performance, scalability and usability, as well as a standardized process for evaluating new methods. Additionally, previous studies have only compared several methods, with conflicting results. In this context, we conducted a systematic benchmarking study of 28 heterogeneous network-based drug repositioning methods on 11 existing datasets. We developed a comprehensive framework to evaluate their performance, scalability and usability. Our study revealed that methods such as HGIMC, ITRPCA and BNNR exhibit the best overall performance, as they rely on matrix completion or factorization. HINGRL, MLMC, ITRPCA and HGIMC demonstrate the best performance, while NMFDR, GROBMC and SCPMF display superior scalability. For usability, HGIMC, DRHGCN and BNNR are the top performers. Building on these findings, we developed an online tool called HN-DREP (http://hn-drep.lyhbio.com/) to facilitate researchers in viewing all the detailed evaluation results and selecting the appropriate method. HN-DREP also provides an external drug repositioning prediction service for a specific disease or drug by integrating predictions from all methods. Furthermore, we have released a Snakemake workflow named HN-DRES (https://github.com/lyhbio/HN-DRES) to facilitate benchmarking and support the extension of new methods into the field.

Web-Based Scaffolds: The Feasibility of a Constructivist Approach to Oncology Fellow Learning

In this 2-institution feasibility pilot, oncology fellows used and updated freely available web-based learning tools (scaffolds) in a constructivist fashion.

NBSTRN Tools to Advance Newborn Screening Research and Support Newborn Screening Stakeholders

Rapid advances in the screening, diagnosis, and treatment of genetic disorders have increased the number of conditions that can be detected through universal newborn screening (NBS). However, the addition of conditions to the Recommended Uniform Screening Panel (RUSP) and the implementation of nationwide screening has been a slow process taking several years to accomplish for individual conditions. Here, we describe web-based tools and resources developed and implemented by the newborn screening translational research network (NBSTRN) to advance newborn screening research and support NBS stakeholders worldwide. The NBSTRN's tools include the Longitudinal Pediatric Data Resource (LPDR), the NBS Condition Resource (NBS-CR), the NBS Virtual Repository (NBS-VR), and the Ethical, Legal, and Social Issues (ELSI) Advantage. Research programs, including the Inborn Errors of Metabolism Information System (IBEM-IS), BabySeq, EarlyCheck, and Family Narratives Use Cases, have utilized NBSTRN's tools and, in turn, contributed research data to further expand and refine these resources. Additionally, we discuss ongoing tool development to facilitate the expansion of genetic disease screening in increasingly diverse populations. In conclusion, NBSTRN's tools and resources provide a trusted platform to enable NBS stakeholders to advance NBS research and improve clinical care for patients and their families.

Biosafety and biosecurity challenges during the COVID-19 pandemic and beyond

As the world continues to battle the SARS-CoV-2 pandemic, it is a stark reminder of the devastation biological threats can cause. In an unprecedented way the global community saw a massive surge in the demand for diagnostic capacities, which had a substantial impact on biosafety and biosecurity. Laboratories had to cope with a surge in laboratory testing capacity, while resources and training possibilities were limited. In addition, the pandemic highlighted the impact biological threats can have, thereby giving rise to new dialogue about biosecurity and new biological threats. This paper aims to highlight some of the most pressing issues regarding biosafety and biosecurity observed during the COVID-19 pandemic with special focus on low and lower middle-income countries. The authors provide lessons learned, tools and recommendations to improve future biosafety and biosecurity and increase preparedness for the next global health crisis.

Online Partner Seeking and Sexual Behaviors Among Men Who Have Sex With Men From Small and Midsized Towns: Cross-sectional Study

BACKGROUND

Men who have sex with men (MSM) residing outside of large urban areas are underrepresented in research on online partner seeking and sexual behaviors related to transmission of HIV.

OBJECTIVE

We aimed to determine associations between the use of the internet or social networking apps (online tools) to meet partners for sex, dating, or for both purposes (online partner seeking) and sexual behaviors among MSM residing in small and midsized towns in Kentucky, United States.

METHODS

Using peer-referral sampling and online self-administered questionnaires, data were collected from 252 men, aged 18 to 34 years, who had recently (past 6 months) engaged in anal sex with another man and resided in Central Kentucky. Using multivariable logistic regression models, we assessed associations of online partner seeking and HIV-related sexual behaviors.

RESULTS

Most (181/252, 71.8%) of the participants reported using online tools for partner seeking. Of these 181 respondents, 166 (91.7%) had used online tools to meet partners for sex (n=45, 27.1% for sex only; and n=121, 72.9% for sex and dating) and 136 (75.1%) had used online tools to meet partners for dating (n=15, 11% for dating only; and n=121, 89% for sex and dating). Adjusted analyses revealed that MSM who had engaged in condomless insertive and receptive anal intercourse were less likely to report online partner seeking (adjusted odds ratio [aOR] 0.22, 95% CI 0.07-0.68; P=.009 and aOR 0.25, 95% CI 0.10-0.66; P=.005, respectively). Increased number of insertive and receptive anal sex partners and substance use before or during sex were associated with higher odds of online partner seeking (aOR 1.31, 95% CI 1.11-1.55; P=.001; aOR 1.20, 95% CI 1.05-1.39; P=.008; and aOR 2.50, 95% CI 1.41-4.44; P=.002, respectively).

CONCLUSIONS

Among MSM who reside outside of large urban areas and practice online partner seeking, HIV risk-reduction interventions should address safer sex practices, including the risks for HIV transmission associated with alcohol or drug use before or during sex. MSM who do not practice online partner seeking are in need of continued outreach to reduce condomless anal sex.

Austrian College Students' Experiences With Digital Media Learning During the First COVID-19 Lockdown

In 2020, the COVID-19 pandemic forced many nations to shut-down schools and universities, catapulting teachers and students into a new, challenging situation of 100% distance learning. To explore how the shift to full distance learning represented a break with previous teaching, we asked Austrian students (n = 874, 65% female, 34% male) which digital media they used before and during the first Corona lockdown, as well as which tools they wanted to use in the future. Students additionally reported on their attitudes and experiences with online learning. Results showed that students used certain tools, such as video, audio, e-assessments, and web conferencing systems, much more often during lockdown than they had before. Their use of classic digital media, such as e-mail, social communication tools, such as chat or online forums, and other interactive tools, such as wikis or educational games, hardly changed at all. Their attitudes toward multimedia learning were positively related to their media use. In their open responses (n = 137), students identified advantages of online learning (flexibility and self-directed learning), as well as disadvantages (limited social interaction) and challenges (motivation and self-discipline). As a group, they also expressed a clear preference for a balanced combination of online- and offline teaching in the future. However, individual students did prefer fully online or offline learning modes, depending on their personal circumstances and educational goals. We view this as a call to researchers and educators alike to explore ways in which the advantages of online and face-to-face learning can best be combined to meet the changed needs and expectations of organizations, students, and teachers in a future “after Corona.”

LINT-Web: A Web-Based Lipidomic Data Mining Tool Using Intra-Omic Integrative Correlation Strategy

Lipidomics is a younger member of the "omics" family. It aims to profile lipidome alterations occurring in biological systems. Similar to the other "omics", lipidomic data is highly dimensional and contains a massive amount of information awaiting deciphering and data mining. Currently, the available bioinformatic tools targeting lipidomic data processing and lipid pathway analysis are limited. A few tools designed for lipidomic analysis perform only basic statistical analyses, and lipid pathway analyses rely heavily on public databases (KEGG, Reactome, and HMDB). Due to the inadequate understanding of lipid signaling and metabolism, the use of public databases for lipid pathway analysis can be biased and misleading. Instead of using public databases to interpret lipidomic ontology, the authors introduce an intra-omic integrative correlation strategy for lipidomic data mining. Such an intra-omic strategy allows researchers to unscramble and predict lipid biological functions from correlated genomic ontological results using statistical approaches. To simplify and improve the lipidomic data processing experience, they designed an interactive web-based tool: LINT-web (http://www.lintwebomics.info/) to perform the intra-omic analysis strategy, and validated the functions of LINT-web using two biological systems. Users without sophisticated statistical experience can easily process lipidomic datasets and predict the potential lipid biological functions using LINT-web.

Music Therapy During COVID-19: Changes to the Practice, Use of Technology, and What to Carry Forward in the Future

In recent years, the field of music therapy (MT) has increasingly embraced the use of technology for conducting therapy sessions and enhancing patient outcomes. Amidst a worldwide pandemic, we sought to examine whether this is now true to an even greater extent, as many music therapists have had to approach and conduct their work differently. The purpose of this survey study is to observe trends in how music therapists from different regions around the world have had to alter their practice, especially in relation to their use of technology during the COVID-19 pandemic, because of limited options to conduct in-person therapy due to social distancing measures. Further, the findings aim to clarify music therapists’ perspectives on the benefits and limitations of technology in MT, as well as online MT. In addition, this survey investigated what changes have been necessary to administer MT during COVID-19, in terms of virtual therapy and online tools, and how the changes made now may affect MT in the future. We also explored music therapists’ views on whether special technology-focused training might be helpful to support the practice of MT in the future. This is the first survey, to our knowledge, to break down opinions of and trends in technology use based on geographical region (North America, Europe, and Asia), and several noteworthy differences were apparent across regions. We hope our findings provide useful information, guidance, and a global reference point for music therapists on effectively continuing the practice of MT during times of crisis, and can encourage reflection and improvement in administering MT.

Interactive pedagogic tools: evaluation of three assessment systems in medical education

Training in biology, pharmacy and medicine are essential in laboratory medicine in faculty and especially with recent residency modifications. Active learning improves critical thinking and is an essential component of health education. Interactive assessment systems for the interactive participation of students have emerged. Recently, many offers of audience response system (ARS) accessible by personal electronic devices such as smartphone, tablet or computer are available. These systems seem to be an effective teaching innovation according to students. We aimed to evaluate three pedagogical tools during real school lectures in order to be able to select them according to the needs: Votar, Socrative and Wooclap. Methods: Three connected participation tools will be tested during teaching at Lille University, faculty of pharmacy by 3 different teachers. 75 fifth-year pharmacy students divided into 2 groups of students will have attended at least one session using each of the systems studied. After lessons, an online questionnaire with 9 questions was submitted to students on their interest in each system. Questions measured student perception using a 1 to 10 scale. Results and discussion: 62 of 75 students completed online surveys and were included in the study. According students, ARS by smartphone or computer improve their education. Favorite application seems to be Socrative and Wooclap. This study provides student perception comparison of ARS. To complete, additional studies are needed to establish their efficacy after several month.

Pain Management in the Cancer Survivor

OBJECTIVES

To describe assessment and interdisciplinary management of pain in the cancer survivor over the continuum of cancer care.

DATA SOURCES

Review of the literature and treatment standards.

CONCLUSION

Pain remains a primary concern throughout the cancer trajectory across all age groups and diagnoses, emphasizing the need to integrate pain assessment and management across the continuum of cancer survivorship and across care settings. Types of pain, pain patterns, assessment of cancer pain in cancer survivors, current strategies and challenges for management, and effective communication and documentation of the process are described. Communication between and among health care clinicians in a way that effectively articulates the individual patient experience, including documentation in the electronic medical record, requires consistent workflows and terminology. The opioid crisis increases the urgency in effective strategies for interdisciplinary pain assessment and management.

IMPLICATIONS FOR NURSING PRACTICE

Oncology clinicians must be able to adequately assess pain, track pain over time, understand and implement a cadre of strategies to manage pain, and effectively pursue any suspicious pain patterns that may indicate recurrence or progression of cancer or other underlying etiologies. The oncology nurse is at the core of patient-clinician communication, critical to effectively describing pain as experienced by the individual patient and continues to play a key role in maintaining consistency of message that is necessary to manage pain over the continuum of cancer survivorship.

A compilation of Web-based research tools for miRNA analysis

Since the discovery of microRNAs (miRNAs), a class of noncoding RNAs that regulate the gene expression posttranscriptionally in sequence-specific manner, there has been a release of number of tools useful for both basic and advanced applications. This is because of the significance of miRNAs in many pathophysiological conditions including cancer. Numerous bioinformatics tools that have been developed for miRNA analysis have their utility for detection, expression, function, target prediction and many other related features. This review provides a comprehensive assessment of web-based tools for the miRNA analysis that does not require prior knowledge of any computing languages.

An evaluation of the behaviour-change techniques used on Canadian cancer centre Web sites to support physical activity behaviour for breast cancer survivors

Background

Cancer centre Web sites can be a useful tool for distributing information about the benefits of physical activity for breast cancer (bca) survivors, and they hold potential for supporting health behaviour change. However, the extent to which cancer centre Web sites use evidence-based behaviour change techniques to foster physical activity behaviour among bca survivors is currently unknown. The aim of our study was to evaluate the presentation of behaviour-change techniques on Canadian cancer centre Web sites to promote physical activity behaviour for bca survivors.

Methods

All Canadian cancer centre Web sites (n = 39) were evaluated by two raters using the Coventry, Aberdeen, and London-Refined (calo-re) taxonomy of behaviour change techniques and the eEurope 2002 Quality Criteria for Health Related Websites. Descriptive statistics were calculated.

Results

The most common behaviour change techniques used on Web sites were providing information about consequences in general (80%), suggesting goal-setting behaviour (56%), and planning social support or social change (46%). Overall, Canadian cancer centre Web sites presented an average of M = 6.31 behaviour change techniques (of 40 that were coded) to help bca survivors increase their physical activity behaviour. Evidence of quality factors ranged from 90% (sites that provided evidence of readability) to 0% (sites that provided an editorial policy).

Conclusions

Our results provide preliminary evidence that, of 40 behaviour-change techniques that were coded, fewer than 20% were used to promote physical activity behaviour to bca survivors on cancer centre Web sites, and that the most effective techniques were inconsistently used. On cancer centre Web sites, health promotion specialists could focus on emphasizing knowledge mobilization efforts using available research into behaviour-change techniques to help bca survivors increase their physical activity.

The Evolution of the Journal Club: From Osler to Twitter

Journal clubs have typically been held within the walls of academic institutions and in medicine have served the dual purpose of fostering critical appraisal of literature and disseminating new findings. In the last decade and especially the last few years, online and virtual journal clubs have been started and are flourishing, especially those harnessing the advantages of social media tools and customs. This article reviews the history and recent innovations of journal clubs. In addition, the authors describe their experience developing and implementing NephJC, an online nephrology journal club conducted on Twitter.

Antitarget Interaction, Acute Toxicity and Protein Binding Studies of Quinazolinedione Sulphonamides as GABA1 Antagonists

Diseases characterized by recurrent seizures are known as epilepsy. One of the most important mechanisms for handling it is GABA₁ receptor mediated inhibition. In the same context while studying the treatment of epilepsy we observed significant effects by derivatives of sulfonamides, which prompted us to design novel derivatives by means of in silico resources with antiepileptic effects. Molecular docking approaches are routinely used in modern drug design to help understand drug–receptor interaction. This study has been performed with the help of Chemdraw Ultra 7.0, GUSAR online tool for IC₅₀ and LD₅₀ predictions, AutoDock Vina (Python Prescription 0.8), and PaDEL software. Results revealed that ligand-protein interaction affinity of all 10 designed molecules ranges from -5.7 Kcal/mol to -5.2 Kcal/mol, which is approximately comparable to pre-existing GABA₁ inhibitor i.e. phenytoin (CID: 1775, ligand-protein interaction affinity is -6.5 Kcal/mol).

A tool to make reporting checklists work

Although the use of reporting guidelines has been demonstrated to increase the completeness and transparency of health research published in journals, there is still a long way to translate their use to the authors at the time where they are needed - during the actual research process and manuscript writing. An online tool for writing methodology section of a randomized controlled trial has been successfully tested in an experimental setting and provides a direction for the development of writing tools for health research. Writing tools should not replace original thinking and the excitement of communicating original discoveries, but make sure that all relevant data are in the manuscript so that research results can be understood, critically evaluated and used in practice. Please see related article: http://www.biomedcentral.com/1741-7015/13/221.

Resources for functional genomics studies in Drosophila melanogaster

Drosophila melanogaster has become a system of choice for functional genomic studies. Many resources, including online databases and software tools, are now available to support design or identification of relevant fly stocks and reagents or analysis and mining of existing functional genomic, transcriptomic, proteomic, etc. datasets. These include large community collections of fly stocks and plasmid clones, "meta" information sites like FlyBase and FlyMine, and an increasing number of more specialized reagents, databases, and online tools. Here, we introduce key resources useful to plan large-scale functional genomics studies in Drosophila and to analyze, integrate, and mine the results of those studies in ways that facilitate identification of highest-confidence results and generation of new hypotheses. We also discuss ways in which existing resources can be used and might be improved and suggest a few areas of future development that would further support large- and small-scale studies in Drosophila and facilitate use of Drosophila information by the research community more generally.