Abstract
Pathway Commons (https://www.pathwaycommons.org) is an integrated resource of publicly available information about biological pathways including biochemical reactions, assembly of ...biomolecular complexes, transport and catalysis events and physical interactions involving proteins, DNA, RNA, and small molecules (e.g. metabolites and drug compounds). Data is collected from multiple providers in standard formats, including the Biological Pathway Exchange (BioPAX) language and the Proteomics Standards Initiative Molecular Interactions format, and then integrated. Pathway Commons provides biologists with (i) tools to search this comprehensive resource, (ii) a download site offering integrated bulk sets of pathway data (e.g. tables of interactions and gene sets), (iii) reusable software libraries for working with pathway information in several programming languages (Java, R, Python and Javascript) and (iv) a web service for programmatically querying the entire dataset. Visualization of pathways is supported using the Systems Biological Graphical Notation (SBGN). Pathway Commons currently contains data from 22 databases with 4794 detailed human biochemical processes (i.e. pathways) and ∼2.3 million interactions. To enhance the usability of this large resource for end-users, we develop and maintain interactive web applications and training materials that enable pathway exploration and advanced analysis.
Abstract
Summary
Cytoscape.js is an open-source JavaScript-based graph library. Its most common use case is as a visualization software component, so it can be used to render interactive graphs in a ...web browser. It also can be used in a headless manner, useful for graph operations on a server, such as Node.js. This update describes new features and enhancements introduced over many new versions from 2015 to 2022.
Availability and implementation
Cytoscape.js is implemented in JavaScript. Documentation, downloads and source code are available at http://js.cytoscape.org.
Supplementary information
Supplementary data are available at Bioinformatics online.
This paper describes an ongoing multi-scale visual analytics approach for exploring and analyzing biomedical knowledge at scale. We utilize global and local views, hierarchical and flow-based graph ...layouts, multi-faceted search, neighborhood recommendations, and document visualizations to help researchers interactively explore, query, and analyze biological graphs against the backdrop of biomedical knowledge. The generality of our approach - insofar as it requires only knowledge graphs linked to documents - means it can support a range of therapeutic use cases across different domains, from disease propagation to drug discovery. Early interactions with domain experts support our approach for use cases with graphs with over 40,000 nodes and 350,000 edges.
This paper describes an ongoing multi-scale visual analytics approach for exploring and analyzing biomedical knowledge at scale.We utilize global and local views, hierarchical and flow-based graph ...layouts, multi-faceted search, neighborhood recommendations, and document visualizations to help researchers interactively explore, query, and analyze biological graphs against the backdrop of biomedical knowledge. The generality of our approach - insofar as it re-quires only knowledge graphs linked to documents - means it can support a range of therapeutic use cases across different domains, from disease propagation to drug discovery. Early interactions with domain experts support our approach for use cases with graphs with over 40,000 nodes and 350,000 edges.
This paper presents a study on the evaluation of hybrid learning and teaching practices by academics. A mixed research method involving a questionnaire survey and a focus group interview was employed ...to gather academics’ feedback on their experience in delivering hybrid instruction in a synchronous manner in which on-site and remote students attended classes simultaneously, their students’ hybrid learning effectiveness, and their suggestions for improvement. The questionnaire was administered to 76 academics from a university in Hong Kong where hybrid learning and teaching were implemented, and the focus group interview involved 10 academics. The findings reveal that the participating academics perceived themselves as having an overall high degree of readiness to handle technical issues. They expressed that the students from their hybrid classes had lower levels of interaction, engagement, and motivation than those from traditional face-to-face classes. The participants also reported their challenges regarding hybrid learning and teaching, including heavy workload for lesson preparation and face-to-face and online classroom management, unfamiliarity with interactive teaching design suitable for hybrid classes, and difficulties in monitoring students’ learning process. They provided suggestions for the improvement of hybrid classes, ranging from the provision of technological support to professional development for enhancing students’ online interaction and engagement. These findings contribute to revealing academics’ experience in practising hybrid learning and teaching and identifying ways to address their challenges.
Normal mammary morphogenesis involves transitions between simple and multilayered epithelial organizations. We used electron microscopy and molecular markers to determine whether intercellular ...junctions and apico-basal polarity were maintained in the multilayered epithelium. We found that multilayered elongating ducts had polarized apical and basal tissue surfaces both in three-dimensional culture and in vivo. However, individual cells were only polarized on surfaces in contact with the lumen or extracellular matrix. The basolateral marker scribble and the apical marker atypical protein kinase C zeta localized to all interior cell membranes, whereas PAR3 displayed a cytoplasmic localization, suggesting that the apico-basal polarity was incomplete. Despite membrane localization of E-cadherin and β-catenin, we did not observe a defined zonula adherens connecting interior cells. Instead, interior cells were connected through desmosomes and exhibited complex interdigitating membrane protrusions. Single-cell labeling revealed that individual cells were both protrusive and migratory within the epithelial multilayer. Inhibition of Rho kinase (ROCK) further reduced intercellular adhesion on apical and lateral surfaces but did not disrupt basal tissue organization. Following morphogenesis, segregated membrane domains were re-established and junctional complexes re-formed. We observed similar epithelial organization during mammary morphogenesis in organotypic culture and in vivo. We conclude that mammary epithelial morphogenesis involves a reversible, spatially limited, reduction in polarity and intercellular junctions and active individualistic cell migration. Our data suggest that reductions in polarity and adhesion during breast cancer progression might reflect partial recapitulation of a normal developmental program.
Young people recovering from drug addiction often face challenges in returning to the job market and in maintaining their jobs. Many of them feel they have no choice but to do entry-level work, and ...they are often unsure about their work ability and vocational choice.
In collaboration with a youth outreach service, this study aims to provide a package of vocational assessment, guidance, and support for these clients.
Using a strength-based case management framework, we conducted a comprehensive vocational evaluation for each participant (N = 17), which covered self-perception of abilities, work and occupational interests, work readiness, work-related self-efficacy, and work aptitudes. We presented assessment results to each client and provided guidance on their education, training, or vocational choice.
The results of aptitude tests indicate that most participants can cope with an entry-level job. Many participants are strong in jobs that require quick decision-making, sorting, assembly, and clerical tasks, but many are weak in fine manual dexterity and eye-hand-foot coordination. Many participants preferred jobs that are creative, indefinite, and autonomous in nature.
Longer-term vocational counseling and coaching is needed to help clients make vocational choices and extend their job tenure. Many clients will also need training in job seeking and job maintenance skills.
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IZUM, KILJ, NUK, OILJ, PILJ, SAZU, UL, UM, UPUK, VSZLJ
Host genetic variations play a significant role in conferring predisposition to infection. In this study, we examined the immune mechanisms underlying the host genetic predisposition to severe ...Staphylococcus aureus infection in different mouse strains. Whereas C57BL/6 mice were the most resistant in terms of control of bacterial growth and survival, A/J, DBA/2, and BALB/c mice were highly susceptible and succumbed to infection shortly after bacterial inoculation. Other strains (C3H/HeN, CBA, and C57BL/10) exhibited intermediate susceptibility levels. Susceptibility of mice to S. aureus was associated with an inability to limit bacterial growth in the kidneys and development of pathology. Resistance to S. aureus in C57BL/6 mice was dependent on innate immune mechanisms because Rag2-IL2Rγ−/− C57BL/6 mice, which are deficient in B, T, and NK cells, were also resistant to infection. Indeed, neutrophil depletion or inhibition of neutrophil recruitment rendered C57BL/6 mice completely susceptible to S. aureus , indicating that neutrophils are essential for the observed resistance. Although neutrophil function is not inhibited in A/J mice, expression of neutrophil chemoattractants KC and MIP-2 peaked earlier in the kidneys of C57BL/6 mice than in A/J mice, indicating that a delay in neutrophil recruitment to the site of infection may underlie the increased susceptibility of A/J mice to S. aureus.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
We detail the development of the ancestry informative single nucleotide polymorphisms (SNPs) panel forming part of the VISAGE Basic Tool (BT), which combines 41 appearance predictive SNPs and 112 ...ancestry predictive SNPs (three SNPs shared between sets) in one massively parallel sequencing (MPS) multiplex, whereas blood-based age analysis using methylation markers is run in a parallel MPS analysis pipeline. The selection of SNPs for the BT ancestry panel focused on established forensic markers that already have a proven track record of good sequencing performance in MPS, and the overall SNP multiplex scale closely matched that of existing forensic MPS assays. SNPs were chosen to differentiate individuals from the five main continental population groups of Africa, Europe, East Asia, America, and Oceania, extended to include differentiation of individuals from South Asia. From analysis of 1000 Genomes and HGDP-CEPH samples from these six population groups, the BT ancestry panel was shown to have no classification error using the Bayes likelihood calculators of the
online analysis portal. The differentiation power of the component ancestry SNPs of BT was balanced as far as possible to avoid bias in the estimation of co-ancestry proportions in individuals with admixed backgrounds. The balancing process led to very similar cumulative population-specific divergence values for Africa, Europe, America, and Oceania, with East Asia being slightly below average, and South Asia an outlier from the other groups. Comparisons were made of the African, European, and Native American estimated co-ancestry proportions in the six admixed 1000 Genomes populations, using the BT ancestry panel SNPs and 572,000 Affymetrix Human Origins array SNPs. Very similar co-ancestry proportions were observed down to a minimum value of 10%, below which, low-level co-ancestry was not always reliably detected by BT SNPs. The
analysis portal provides a comprehensive population dataset for the BT ancestry panel SNPs, comprising a 520-sample standardised reference dataset; 3445 additional samples from 1000 Genomes, HGDP-CEPH, Simons Foundation and Estonian Biocentre genome diversity projects; and 167 samples of six populations from in-house genotyping of individuals from Middle East, North and East African regions complementing those of the sampling regimes of the other diversity projects.
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