KNIME-CDK: Workflow-driven cheminformatics

BACKGROUND: Cheminformaticians have to routinely process and analyse libraries of small molecules. Among other things, that includes the standardization of molecules, calculation of various descriptors, visualisation of molecular structures, and downstream analysis. For this purpose, scientific workflow platforms such as the Konstanz Information Miner can be used if provided with the right plug-in. A workflow-based cheminformatics tool provides the advantage of ease-of-use and interoperability between complementary cheminformatics packages within the same framework, hence facilitating the analysis process. RESULTS: KNIME-CDK comprises functions for molecule conversion to/from common formats, generation of signatures, fingerprints, and molecular properties. It is based on the Chemistry Development Toolkit and uses the Chemical Markup Language for persistence. A comparison with the cheminformatics plug-in RDKit shows that KNIME-CDK supports a similar range of chemical classes and adds new functionality to the framework. We describe the design and integration of the plug-in, and demonstrate the usage of the nodes on ChEBI, a library of small molecules of biological interest. CONCLUSIONS: KNIME-CDK is an open-source plug-in for the Konstanz Information Miner, a free workflow platform. KNIME-CDK is build on top of the open-source Chemistry Development Toolkit and allows for efficient cross-vendor structural cheminformatics. Its ease-of-use and modularity enables researchers to automate routine tasks and data analysis, bringing complimentary cheminformatics functionality to the workflow environment

Somatically ill persons’ self-nominated quality of life domains: review of the literature and guidelines for future studies

OBJECTIVE: To review which domains somatically ill persons nominate as constituting their QoL. Specific objective is to examine whether the method of enquiry affect these domains. METHODS: We conducted two literature searches in the databases PubMed/Medline, CINAHL and Psychinfo for qualitative studies examining patients' self-defined QoL domains using (1) SEIQoL and (2) study-specific questions. For each database, two researchers independently assessed the eligibility of the retrieved abstracts and three researchers subsequently classified all QoL domains. RESULTS: Thirty-six eligible papers were identified: 27 studies using the SEIQoL, and nine presenting data derived from study-specific questions. The influence of the method of enquiry on patients' self-nominated QoL domains appears limited: most domains were presented in both types of studies, albeit with different frequencies. CONCLUSIONS: This review provides a comprehensive overview of somatically ill persons' self-nominated QoL domains. However, limitations inherent to reviewing qualitative studies (e.g., the varying level of abstraction of patients' self-defined QoL domains), limitations of the included studies and limitations inherent to the review process, hinder cross-study comparisons. Therefore, we provide guidelines to address shortcomings of qualitative reports amenable to improvement and to stimulate further improvement of conducting and reporting qualitative research aimed at exploring respondents' self-nominated QoL domains

Structure-based drug discovery for combating influenza virus by targeting the PA?PB1 interaction

Influenza virus infections are serious public health concerns throughout the world. The development of compounds with novel mechanisms of action is urgently required due to the emergence of viruses with resistance to the currently-approved anti-influenza viral drugs. We performed in silico screening using a structure-based drug discovery algorithm called Nagasaki University Docking Engine (NUDE), which is optimised for a GPU-based supercomputer (DEstination for Gpu Intensive MAchine; DEGIMA), by targeting influenza viral PA protein. The compounds selected by NUDE were tested for anti-influenza virus activity using a cell-based assay. The most potent compound, designated as PA-49, is a medium-sized quinolinone derivative bearing a tetrazole moiety, and it inhibited the replication of influenza virus A/WSN/33 at a half maximal inhibitory concentration of 0.47?μM. PA-49 has the ability to bind PA and its anti-influenza activity was promising against various influenza strains, including a clinical isolate of A(H1N1)pdm09 and type B viruses. The docking simulation suggested that PA-49 interrupts the PA?PB1 interface where important amino acids are mostly conserved in the virus strains tested, suggesting the strain independent utility. Because our NUDE/DEGIMA system is rapid and efficient, it may help effective drug discovery against the influenza virus and other emerging viruses

Research On and Activities For Mathematically Gifted Students

This Topical Survey offers a brief overview of the current state of research on and activities for mathematically gifted students around the world. This is of interest to a broad readership, including educational researchers, research mathematicians, mathematics teachers, teacher educators, curriculum designers, doctoral students, and other stakeholders. It first discusses research concerning the nature of mathematical giftedness, including theoretical frameworks and methodologies that are helpful in identifying and/or creating mathematically gifted students, which is described in this section. It also focuses on research on and the development of mathematical talent and innovation in students, including connections between cognitive, social and affective aspects of mathematically gifted students. Exemplary teaching and learning practices, curricula and a variety of programs that contribute to the development of mathematical talent, gifts, and passion are described as well as the pedagogy and mathematics content suitable for educating pre-service and in-service teachers of mathematically gifted students. The final section provides a brief summary of the paper along with suggestions for the research, activities, and resources that should be available to support mathematically gifted students and their teachers, parents, and other stakeholders

The Heidelberg Milestones Communication Approach (MCA) for patients with prognosis <12 months: protocol for a mixed-methods study including a randomized controlled trial

Background: The care needs of patients with a limited prognosis (<12 months median) are complex and dynamic. Patients and caregivers must cope with many challenges, including physical symptoms and disabilities, uncertainty. and compromised self-efficacy. Healthcare is often characterized by disruptions in the transition between healthcare providers. The Milestones Communication Approach (MCA) is a structured, proactive, interprofessional concept that involves physicians and nurses and is aimed at providing coherent care across the disease trajectory. This study aims to evaluate these aspects of MCA: (1) the training of healthcare professionals, (2) implementation context and outcomes, (3) patient outcomes, and (4) effects on interprofessional collaboration. Methods/design: A multiphase mixed-methods design will be used for the study. A total of 100 patients and 120 healthcare professionals in a specialized oncology hospital will be involved. The training outcomes will be documented using a questionnaire. Implementation context and outcomes will be explored through semi-structured interviews and written questionnaires with healthcare professionals and with the training participants and through a content analysis of patient files. Patient outcomes will be assessed in a pragmatic non-blinded randomized controlled trial and in qualitative interviews with patients and caregivers. Trial outcomes are supportive care needs (SCNS-SF34-G), quality of life (SeiQol and Fact-L), depression and anxiety symptoms (PHQ-4), and distress (Distress Thermometer). Qualitative semi-structured interviews on patients’ views will focus on shared decision-making, communication needs, feeling empathy, and further utilization of healthcare services. Interprofessional collaboration will be explored using the UWE-IP-D before the implementation of MCA (t0) and after 3 (t1), 9 (t2), and 12 (t3) months. Discussion: Using guideline-concordant early palliative care, MCA aims to foster patient-centered communication with shared decision-making and facilitation of advance care planning including end-of-life decisions, thus increasing patient quality of life and decreasing aggressive medical care at the end of life. It is assumed that the communication skills training and interprofessional coaching will improve the communication behavior of healthcare providers and influence team communications and team processes. Trial registration German Clinical Trials Register, DRKS00013649 and DRKS00013469. Registered on 22 December 2017

Assessing subjective change in chronic illness: an examination of response shift in health-related and goal-oriented subjective status

This study examined changes over time on scales from the Short Form 36 (SF-36) and a new measure of goal-oriented subjective status (the GOSS) which assessed perceived rate of goal approach. Our aim was to determine whether adaptation to a moderately disabling chronic illness was associated with response shift. We also investigated predictors of response shift. At baseline, 301 members of a self-help group for people with Ménière's disease completed the GOSS and SF-36 scales, and potential predictors of response shift. At 10-month follow-up, respondents completed the GOSS and SF-36 again in the conventional manner, and as a Then-test. The GOSS was the only scale that indicated subjective improvement between baseline and follow-up. Then-test results suggested substantial response shift on the SF-36. Severe symptoms and social comparison predicted greater response shift. Less response shift was seen in those with a longer time since diagnosis, longer membership of the self-help group and higher baseline levels of self-esteem and optimism. <br/