The Digital World of Cytogenetic and Cytogenomic Web Resources.

The dynamic growth of technological capabilities at the cellular and molecular level has led to a rapid increase in the amount of data on the genes and genomes of organisms. In order to store, access, compare, validate, classify, and understand the massive data generated by different researchers, and to promote effective communication among research communities, various genome and cytogenetic online databases have been established. These data platforms/resources are essential not only for computational analyses and theoretical syntheses but also for helping researchers select future research topics and prioritize molecular targets. Furthermore, they are valuable for identifying shared recurrent genomic patterns related to human diseases and for avoiding unnecessary duplications among different researchers. The website interface, menu, graphics, animations, text layout, and data from databases are displayed by a front end on the screen of a monitor or smartphone. A database front-end refers to the user interface or application that enables accessing tabular, structured, or raw data stored in the database. The Internet makes it possible to reach a greater number of users around the world and gives them quick access to information stored in databases. The number of ways of presenting this data by front-ends increases as well. This requires unifying the ways of operating and presenting information by front-ends and ensuring contextual switching between front-ends of different databases. This chapter aims to present selected cytogenetic and cytogenomic Internet resources in terms of obtaining the needed information and to indicate how to increase the efficiency of access to stored information. Through a brief introduction of these databases and by providing examples of their usage in cytogenetic analyses, we aim to bridge the gap between cytogenetics and molecular genomics by encouraging their utilization.

Current Quality of Videos on Colorectal Cancer Screening for General Public.

BACKGROUND: One-third of American adults encompassed by current colorectal cancer screening guidelines fail to obtain recommended screening evaluations. Educational videos are a valuable medium through which to educate and encourage recommended health behaviors in patients. METHODS: A cross-sectional study reviewing the quality of patient education videos addressing colorectal cancer screening. Video quality was assessed in 3 domains: accountability, content, and production. RESULTS: Forty-four videos met inclusion criteria. Out of 33 possible points, videos scored a median of 15.0 (interquartile range 12.9-16.6). Videos scored 1.0 (interquartile range .8-1.0) out of 4.0 for accountability, 6.0 (interquartile range 4.4-8.0) out of 20 for content, and 8.0 (interquartile range 7.4-8.0) out of 9.0 for production. Colonoscopy was the most frequently discussed method of screening (38, 86%). While 13 (34%) videos discussed the risk of colorectal cancer in the general population and 15 (32%) discussed the risk in those with a family history, few videos addressed those with other risk factors. Most (31, 70%) videos discussed the medical consequences of not receiving screening, but only 1 (2%) video discussed the social consequences. Similarly, medical benefits were discussed in 34 (77%) videos while other benefits were not discussed by any video. Only one-fifth of the videos address three or more barriers to screening. CONCLUSIONS: Videos on colorectal cancer screening have excellent production quality but need improvement in the domains of accountability and content. The videos included in this analysis did not adequately address the concerns of viewers nor the benefits of colorectal cancer screening.

Quality of YouTube® videos on thrombolysis and thrombectomy for deep venous thrombosis.

OBJECTIVE: YouTube® has gained popularity as an unofficial educational resource for surgical trainees, but its content's quality and educational value remain to be evaluated. The aim of this study is to analyze the current content on these techniques for lower extremity DVT (LEDVT) on YouTube®. METHODS: A search was performed on YouTube® using 13 search terms in August 2022 on a clear-cached browser. Open-access videos focusing on the surgical techniques of venous thrombolysis or thrombectomy for LEDVT were included. Quality and educational value were assessed and graded based on metrics for accountability (4 items), content (13 items), and production (9 items). RESULTS: Out of 138 videos regarding LEDVT oriented towards medical professionals, only 14 met inclusion criteria. Videos ran for a median of 3.4 min (range 0.37-35.6 min) with a median of 941 views (range 106-54624). Videos scored a median of 5.5 (range 1.0-8.0) out of 11 for content, a median of 2.0 out of 6.0 (range 0.0-2.0) for accountability, and a median of 5.5 out of 9.0 (range 3.0-9.0) for production. CONCLUSION: Few YouTube® videos focus on the technical aspects of DVT thrombolysis/thrombectomy, and they vary significantly in content with overall poor accountability and production quality.

Qualitative assessment of available online patient resources for pulmonary embolism and deep vein thrombosis.

OBJECTIVE: This study seeks to evaluate the quality and readability of freely available online patient information resources for deep vein thrombosis (DVT) and pulmonary embolism (PE). METHODS: Internet searches were performed for five DVT and PE search terms in July 2020 across three search engines and two metasearch engines. Qualitative content analysis was performed. Readability was assessed using four validated instruments. RESULTS: Two hundred fifty websites were identified of which 62 websites met inclusion criteria.Website structure and content were satisfactory (>50% overall score), accountability was mixed between DVT (47%) and PE (56%) sites, while interactivity was poor (<30%). On qualitative content analysis, anticoagulation (95.2%) was the most discussed treatment while the most discussed procedures were IVC filter placement for DVT and thrombolysis for PE. Overall readability was difficult with median level suitable for ages 14-18 years. CONCLUSION: Freely available online DVT and PE patient information resources publish appropriate content but have very variable accountability and poor readability for the average patient.

Viral Disease Goes Viral: Characterizing How Cancer Patients Use Internet Resources for COVID-19 Information.

This study aims to evaluate the usage of Internet resources for COVID-19 information among cancer patients. Specifically, to understand where patients are seeking information, what topics are most frequently searched, and how physicians and web developers can improve clinical conversations and digital resources, respectively, to support cancer patients' needs. From May to June 2021, cancer patients who were attending follow-up at a tertiary cancer center completed a survey consisting of 28 closed and open-ended questions. Quantitative results were evaluated using descriptive statistics and qualitative responses were evaluated using a grounded-theory approach. Fifty-seven surveys were distributed, and fifty-two surveys were received (91% response rate). The majority of respondents (96%) were Internet users. Seventy percent used the Internet as a source of information about COVID-19 and cancer personally, with another 15% reporting that friends and family accessed online information on their behalf. The vast majority used Google as their choice of search engine, with COVID-19 rates and vaccine information being the most frequently searched topics. Three quarters (74%) considered Internet information easy to understand, and 90% stated that the Internet increased their understanding of COVID-19 and cancer. Only 15% of patients had been recommended online resource(s) by a physician, yet 100% of those patients found the physician-recommended sites useful. Most cancer patients use the Internet to search for COVID-19 information. Healthcare professionals (HCPs) should help guide patients towards credible online sources and address knowledge gaps to improve physician-patient communication and support educational needs.

An Evaluation of the Quality of COVID-19 Internet Resources for Cancer Patients.

Cancer patients may face difficulty evaluating web-based COVID-19 resources in context with their cancer diagnosis. The purpose of this study is to systematically evaluate educational resources available for cancer patients seeking online information on COVID-19 and cancer. The term "COVID-19 and Cancer" was searched in Google and metasearch engines Yippy and Dogpile. After applying inclusion and exclusion criteria, the results from the 3 lists were systematically combined for a final ranked list. This list was analyzed using a validated structured rating tool with respect to accountability, interactivity, organization, readability, and content coverage and accuracy. Three hundred ninety-eight websites were identified, and 37 websites were included for analysis. Only 43% of sites disclosed authorship, 24% cited sources, and 32% were updated within 3 months of the search date. Fifty-four percent of websites had high school readability (8.0-12.0), 43% were at university level or above, and no websites demonstrated the recommended reading level for health information for the public (< 6.0). Topics most discussed were special considerations for cancer patients during COVID-19 (84%) and COVID-19 risk factors (73%). Topics least covered were COVID-19 incidence/prevalence (5%) and prognosis (8%). There is some COVID-19 information for cancer patients available online, but quality is variable. Healthcare professionals may direct cancer patients to the most reliable COVID-19 and cancer websites shown in this study and results may be helpful when designing future online health information resources.

Databases and Tools to Investigate Protein-Metabolite Interactions.

Protein-metabolite interactions (PMIs) are directly responsible for the regulation of numerous processes. From the direct regulation of enzymes to complex developmental processes intermediated by hormones, PMIs are central to understanding the molecular mechanisms of important physiological phenomena. Still, proving such interactions experimentally has proven an arduous task. We discuss here some of the current technologies contributing to expand our knowledge on PMIs, with particular emphasis on platforms and databases to explore the highly heterogenous nature of characterized PMIs, which is likely to be an essential resource on the development of new computational approaches to predict and validate interactions based on large-scale PMI screenings.

Potential Use of Microbial Community Genomes in Various Dimensions of Agriculture Productivity and Its Management: A Review.

Agricultural productivity is highly influenced by its associated microbial community. With advancements in omics technology, metagenomics is known to play a vital role in microbial world studies by unlocking the uncultured microbial populations present in the environment. Metagenomics is a diagnostic tool to target unique signature loci of plant and animal pathogens as well as beneficial microorganisms from samples. Here, we reviewed various aspects of metagenomics from experimental methods to techniques used for sequencing, as well as diversified computational resources, including databases and software tools. Exhaustive focus and study are conducted on the application of metagenomics in agriculture, deciphering various areas, including pathogen and plant disease identification, disease resistance breeding, plant pest control, weed management, abiotic stress management, post-harvest management, discoveries in agriculture, source of novel molecules/compounds, biosurfactants and natural product, identification of biosynthetic molecules, use in genetically modified crops, and antibiotic-resistant genes. Metagenomics-wide association studies study in agriculture on crop productivity rates, intercropping analysis, and agronomic field is analyzed. This article is the first of its comprehensive study and prospects from an agriculture perspective, focusing on a wider range of applications of metagenomics and its association studies.

Analysis of Internet-Based Search Patterns Utilized by Glioma Patients as Information Source.

The aim of this study is to assess the Internet usage pattern amongst glioma patients and to characterize its impact in their decision-making and clinical interactions. Glioma patients attending a tertiary cancer center between June and December 2019 were invited to participate in this study. A 26-item survey consisting of closed and open-ended questions was distributed with a unique identifier. Quantitative data were analyzed with descriptive statistics using SPSS Statistical package, and qualitative data with grounded theory approach. Thirty-two patients completed the survey. Demographics varied in age, time since diagnosis, glioma type, and level of education. Eighty-one percent were identified as "Internet users" who sought online glioma information. Google was the most popular search engine (96%), with "glioma" being the most frequent search term. The selection of websites often relied on perceived credibility and top search hits. The most searched topic was prognosis (73%). The majority of patients found that online information was easy to understand, and this did not vary significantly amongst age groups. Website quality was always assessed by 60% of patients. Only 62% patients found the Internet a useful resource, and 70% patients found it facilitated their understanding. Most patients discussed their Internet findings with a physician, largely regarding concerns about reliability. There is variable glioma information available online. Patients with glioma use the Internet as a resource, with variable impact on their interactions and decision-making. This information can be used by physicians, educators, and website developers to support glioma patients' needs.

Web-Based Quantitative Structure-Activity Relationship Resources Facilitate Effective Drug Discovery.

Traditional drug discovery effectively contributes to the treatment of many diseases but is limited by high costs and long cycles. Quantitative structure-activity relationship (QSAR) methods were introduced to evaluate the activity of compounds virtually, which saves the significant cost of determining the activities of the compounds experimentally. Over the past two decades, many web tools for QSAR modeling with various features have been developed to facilitate the usage of QSAR methods. These web tools significantly reduce the difficulty of using QSAR and indirectly promote drug discovery. However, there are few comprehensive summaries of these QSAR tools, and researchers may have difficulty determining which tool to use. Hence, we systematically surveyed the mainstream web tools for QSAR modeling. This work may guide researchers in choosing appropriate web tools for developing QSAR models, and may also help develop more bioinformatics tools based on these existing resources. For nonprofessionals, we also hope to make more people aware of QSAR methods and expand their use.

Structural dynamics bridge the gap between the genetic and functional levels of GPCRs.

G protein-coupled receptors (GPCRs) are implicated in nearly all physiological processes in the human body and represent an important drug targeting class. The genes encoding the different GPCR (sub)types determine their specific functionality, which can be altered by natural genetic variants and isoforms. Deciphering the molecular link between sequence diversity and its functional consequences is a current challenge and critical for the comprehension of the physiological response of GPCRs. It requires a global understanding of how protein sequence translates into protein structure, how this impacts the structural motions of the protein, and, finally, how all these factors determine the receptor functionality. Here, we discuss available resources and state-of-the-art computational approaches to address this question.

Critical analysis of the quality of internet resources for patients with varicose veins.

OBJECTIVE: Patients increasingly seek information on their medical conditions from the internet. The present study evaluated the quality and readability of readily available online patient resources for varicose veins. METHODS: An internet search for "varicose veins" was conducted using the meta-search engines Yippy and Dogpile and the general search engines Google, Yahoo, and Bing with a cleared-cache web browser in July 2019. Two trained raters scored the websites separately on the dimensions of accessibility, accountability, interactivity, structure, and content. Any discrepancies were discussed, and a consensus was reached. Readability was calculated using four readability metric systems. Rater consistency was evaluated using kappa, weighted kappa, and interrater correlation coefficient, as indicated. RESULTS: A total of 189 websites met the inclusion criteria. The total median quality score was 15.6 (interquartile range [IQR], 13.1-20.5; range, 7.4-31.3) of 38. The websites scored a median of 4 (IQR, 1-8) of 15 for accountability, 2 (IQR, 2-2) of 5 for interactivity, 4 (IQR, 2-4) of 4 for organization, and 6.4 (IQR, 3.9-7.9) of 14 for weighted content. Most websites (81.5%) were accessible. However, the overall readability was poor. The median Flesch-Kincaid reading ease score was 55.1 (IQR, 49.4-6.7), indicating that the text was fairly difficult to read. The median grade level was 10th grade using both the Flesch-Kincaid grade level and simple measure of the Gobbledygook index and 11th to 12th grade using the new Dale-Chall readability formula. Government websites were the most accountable, featured the best content, and were the most readable. The website traffic had a positive, nonlinear correlation with the total score and a negative, nonlinear correlation with the website rank (or position on the search result page). Website rank correlated negatively with the total score, although the correlation was weak. CONCLUSIONS: The quality of the online patient resources on varicose veins varies greatly, and the readability for most sites is poor. Government-sponsored websites had the highest quality and were the most readable. Physicians are advised to consider providing a list of appropriate websites to their patients to better inform them, avoid confusion, and ensure appropriate delivery of accurate and readable information.

Analysis of the quality of meningioma education resources available on the Internet.

BACKGROUND: Meningiomas are the most common primary central nervous system tumors and patients face difficulty evaluating resources available online. The purpose of this study is to systematically evaluate the educational resources available for patients seeking meningioma information on the Internet. METHODS: A total of 127 meningioma websites were identified by inputting the term "meningioma" on Google and two meta-search engines. A structured rating tool developed by our research group was applied to top 100 websites to evaluate with respect to accountability, interactivity, readability, and content quality. Responses to general and personal patient questions were evaluated for promptness, accuracy, and completeness. The frequency of various social media account types was analyzed. RESULTS: Of 100 websites, only 38% disclosed authorship, and 32% cited sources. Sixty-two percent did not state date of creation or modification, and 32% provided last update less than 2 years ago. Websites most often discussed the definition (99%), symptoms (97%), and treatment (96%). Prevention (8%) and prognosis (47%) were most often not covered. Only 3% of websites demonstrated recommended reading level for general population. Of 84 websites contacted, 42 responded, 32 within 1 day. CONCLUSIONS: Meningioma information is readily available online, but quality varies. Sites often lack markers for accountability, and content may be difficult to comprehend. Information on specific topics are often not available for patients. Physicians can direct meningioma patients to appropriate reliable online resources depicted in this study. Furthermore, future web developers can address the current gaps to design reliable online resources.

Evaluation of Neuroanatomy Web Resources for Undergraduate Education: Educators' and Students' Perspectives.

Despite the development of novel teaching strategies and the abundance of adjunct teaching web resources, students and early career physicians have continuously reported difficulties in learning and clinically applying neuroanatomy. Differences in instructional design of these resources, the lack of assessment of their capacity to meet intended educational goals, and a poor understanding of the user's perspective may have hindered their success in increasing understanding and retention of neuroanatomical knowledge. To decipher the limitations of existing web resources, an online search for neuroanatomy web resources was performed and distilled through a strict filtration rubric. A selection of resources were analyzed by a panel of educators and rated using Likert scales, focusing on the identification of features influencing their usefulness in learning the anatomy of the spinal pathways. The top three ranked web resources were subsequently evaluated by a panel of medical and neuroscience students to assess how specific features aided in their learning of the subject. This detailed analysis has identified features of neuroanatomy web resources that are valued by both educators and users with regard to instructional design. One resource was rated highest by end users and educators on a series of Likert scale questions in terms of clarity of explanation, step-wise teaching design, summarization of information, control of instructional-pace, integration with neurophysiology, neuroradiology and clinical correlates, deployment of a wide array of pedagogical tools, and factors for visualizing neuroanatomical inter-relationships. These results have provided a novel user perspective on the influence of specific elements of neuroanatomy web resources to improve instructional design and enhance learner performance.

Databases and Web Sites for Neurogenetics.

The goal of neurogenetics is an understanding of the genetic basis of brain structure and function. Neurogenetics deals with multiple areas of investigation, including the genetic basis of neural induction, patterning, cell fate specification, neuron maturation, axonal and dendritic organization, synapse function, neural information processing, and learning and behavior. This appendix provides links to databases and other Web sites used by neurobiologists for discovery of information about genes and cellular networks involved in neural development and neuron function. Special care has been taken to curate sites involving model organisms, since great strides have been made using Drosophila and C. elegans for understanding neural development and function. Published 2019. U.S. Government.

BPG: Seamless, automated and interactive visualization of scientific data.

BACKGROUND: We introduce BPG, a framework for generating publication-quality, highly-customizable plots in the R statistical environment. RESULTS: This open-source package includes multiple methods of displaying high-dimensional datasets and facilitates generation of complex multi-panel figures, making it suitable for complex datasets. A web-based interactive tool allows online figure customization, from which R code can be downloaded for integration with computational pipelines. CONCLUSION: BPG provides a new approach for linking interactive and scripted data visualization and is available at http://labs.oicr.on.ca/boutros-lab/software/bpg or via CRAN at https://cran.r-project.org/web/packages/BoutrosLab.plotting.general.

Talk CPR - a technology project to improve communication in do not attempt cardiopulmonary resuscitation decisions in palliative illness.

BACKGROUND: A national Do Not Attempt Cardiopulmonary Resuscitation policy was rolled out for the National Health Service in Wales in 2015. A national steering group led on producing information videos and a website for patients, carers and healthcare professionals, forming part of a quality improvement program. Videos were planned, scripted and produced with healthcare professionals and patient/carer representatives, and were completed with both English and Welsh language versions. The TalkCPR videos encourage and promote open discussion about Cardiopulmonary Resuscitation (CPR) and DNACPR in palliative care situations. METHODS: We worked with patient/carer groups to evaluate whether video resources to convey the salient facts involved in CPR and DNACPR decisions for people with palliative and life-limiting illness were acceptable or not. We conducted a mixed-method design service review in five phases to evaluate whether this technological resource could help. After creating video and website materials, they were evaluated by doctors, nurses and a patient/carer group. We also sent out one lightweight TalkCPR video media pad to each practice in Wales. These rechargeable electronic video media pads had communication videos pre-loaded for easy viewing, especially in areas with poor roaming data coverage. RESULTS: Videos were demonstrably acceptable to both patient and carer groups, and improved healthcare professional confidence and understanding. Videos went live on the TalkCPR website, in all Welsh Health Boards and on Youtube, and are now used in routine practice throughout Wales. CONCLUSION: This is the first time that DNACPR information videos are aimed directly at palliative care patients and carers, to explore this sensitive subject with them, and to encourage them to approach their doctor or nurse about it. The website, app and video media pads were developed by patients, the Digital Legacy Association, Welsh NHS IT services, Welsh Government, the Bevan Commission and the Dying Matters Charity in Wales 'Byw Nawr'. The GMC, the Royal College of General Practitioners and NICE have listed TalkCPR as a learning resource. There has also been a collaboration with Falmouth University Art College, who helped produce graphic designs to facilitate and encourage discussions about CPR and end of life care.

Understanding neurophobia: Reasons behind impaired understanding and learning of neuroanatomy in cross-disciplinary healthcare students.

Recent studies have highlighted a fear or difficulty with the study and understanding of neuroanatomy among medical and healthcare students. This has been linked with a diminished confidence of clinical practitioners and students to manage patients with neurological conditions. The underlying reasons for this difficulty have been queried among a broad cohort of medical, dental, occupational therapy, and speech and language sciences students. Direct evidence of the students' perception regarding specific difficulties associated with learning neuroanatomy has been provided and some of the measures required to address these issues have been identified. Neuroanatomy is perceived as a more difficult subject compared to other anatomy topics (e.g., reproductive/pelvic anatomy) and not all components of the neuroanatomy curriculum are viewed as equally challenging. The difficulty in understanding neuroanatomical concepts is linked to intrinsic factors such as the inherent complex nature of the topic rather than outside influences (e.g., lecture duration). Participants reporting high levels of interest in the subject reported higher levels of knowledge, suggesting that teaching tools aimed at increasing interest, such as case-based scenarios, could facilitate acquisition of knowledge. Newer pedagogies, including web-resources and computer assisted learning (CAL) are considered important tools to improve neuroanatomy learning, whereas traditional tools such as lecture slides and notes were considered less important. In conclusion, it is suggested that understanding of neuroanatomy could be enhanced and neurophobia be decreased by purposefully designed CAL resources. This data could help curricular designers to refocus attention and guide educators to develop improved neuroanatomy web-resources in future. Anat Sci Educ 11: 81-93. © 2017 American Association of Anatomists.

Useful Web Resources.

An increasing number of web resources are available for aiding in proteomics research. Databases contain repositories of proteins and associated information. A recent article by Chen et al. (Genomics Proteomics Bioinformatics 13(1):36-39, 2015) evaluates a number of MS-based proteomics repositories containing MS and expression data, including repositories devoted to cataloguing high confidence post-translational modifications. Many sites have tools developed by research labs that are shared with the community and online tutorials and videos for learning how to use the tools. This chapter contains a selection of web sites useful for proteomics analyses but is by no means comprehensive. Using a search engine such as Google is the easiest way to find the sites using the name given below.