Systematic investigation of machine learning on limited data: A study on predicting protein-protein binding strength

The application of machine learning techniques in biological research, especially when dealing with limited data availability, poses significant challenges. In this study, we leveraged advancements in method development for predicting protein-protein binding strength to conduct a systematic investigation into the application of machine learning on limited data. The binding strength, quantitatively measured as binding affinity, is vital for understanding the processes of recognition, association, and dysfunction that occur within protein complexes. By incorporating transfer learning, integrating domain knowledge, and employing both deep learning and traditional machine learning algorithms, we mitigated the impact of data limitations and made significant advancements in predicting protein-protein binding affinity. In particular, we developed over 20 models, ultimately selecting three representative best-performing ones that belong to distinct categories. The first model is structure-based, consisting of a random forest regression and thirteen handcrafted features. The second model is sequence-based, employing an architecture that combines transferred embedding features with a multilayer perceptron. Finally, we created an ensemble model by averaging the predictions of the two aforementioned models. The comparison with other predictors on three independent datasets confirms the significant improvements achieved by our models in predicting protein-protein binding affinity. The programs for running these three models are available at https://github.com/minghuilab/BindPPI.

Hemispheric asymmetry of hand and tool perception in left- and right-handers with known language dominance

Regions in the brain that are selective for images of hands and tools have been suggested to be lateralised to the left hemisphere of right-handed individuals. In left-handers, many functions related to tool use or tool pantomime may also depend more on the left hemisphere. This result seems surprising, given that the dominant hand of these individuals is controlled by the right hemisphere. One explanation is that the left hemisphere is dominant for speech and language in the majority of left-handers, suggesting a supraordinate control system for complex motor sequencing that is required for skilled tool use, as well as for speech. In the present study, we examine if this left-hemispheric specialisation extends to perception of hands and tools in left- and right-handed individuals. We, crucially, also include a group of left-handers with right-hemispheric language dominance to examine their asymmetry biases. The results suggest that tools lateralise to the left hemisphere in most right-handed individuals with left-hemispheric language dominance. Tools also lateralise to the language dominant hemisphere in right-hemispheric language dominant left-handers, but the result for left-hemispheric language dominant left-handers are more varied, and no clear bias towards one hemisphere is found. Hands did not show a group-level asymmetry pattern in any of the groups. These results suggest a more complex picture regarding hemispheric overlap of hand and tool representations, and that visual appearance of tools may be driven in part by both language dominance and the hemisphere which controls the motor-dominant hand.

Development of a core set of outcome measures to be applied toward breast cancer-related lymphedema core outcome domains

PURPOSE

For breast cancer survivors (BCS) living with breast cancer-related lymphedema (BCRL), what outcome measures (OMs) are recommended to be used to measure standardized outcome domains to fully assess the burden of the disease and efficacy of interventions? An integral component of a standardized core outcome set (COS) are the OMs used to measure the COS.

METHODS

A supplemental online survey was linked to a Delphi study investigating a COS for BCRL. OMs were limited to a maximum of 10 options for each outcome domain (OD). There were 14 ODs corresponding to the International Classification of Functioning, Disability, and Health (ICF) framework and respondents rated the OMs with a Likert level of recommendation. The feasibility of the listed OMs was also investigated for most outpatient, inpatient, and research settings.

RESULTS

This study identified 27 standardized OMs with a few ODs having 2-3 highly recommended OMs for proper measurement. A few of the recommended OMs have limitations with reliability due to being semi-quantitative measures requiring the interpretation of the rater.

CONCLUSION

Narrowing the choices of OMs to 27 highly recommended by BCRL experts may reduce selective reporting, inconsistency in clinical use, and variability of reporting across interdisciplinary healthcare fields which manage or research BCRL. There is a need for valid, reliable, and feasible OMs that measure tissue consistency. Measures of upper extremity activity and motor control need further research in the BCS with BCRL population.

Development and evaluation of shared decision-making tools in rheumatology: A scoping review

INTRODUCTION

Shared decision-making (SDM) tools are facilitators of decision-making through a collaborative process between patients/caregivers and clinicians. These tools help clinicians understand patient's perspectives and help patients in making informed decisions based on their preferences. Despite their usefulness for both patients and clinicians, SDM tools are not widely implemented in everyday practice. One barrier is the lack of clarity on the development and evaluation processes of these tools. Such processes have not been previously described in the field of rheumatology.

OBJECTIVE

To describe the development and evaluation processes of shared decision-making (SDM) tools used in rheumatology.

METHODS

Bibliographic databases (e.g., EMBASE and CINAHL) were searched for relevant articles. Guidelines for the PRISMA extension for scoping reviews were followed. Studies included were: addressing SDM among adults in rheumatology, focusing on development and/or evaluation of SDM tool, full texts, empirical research, and in the English language.

RESULTS

Of the 2030 records screened, forty-six reports addressing 36 SDM tools were included. Development basis and evaluation measures varied across the studies. The most commonly reported development basis was the International Patient Decision Aids Standards (IPDAS) criteria (19/36, 53 %). Other developmental foundations reported were: The Ottawa Decision Support Framework (ODSF) (6/36, 16 %), Informed Medical Decision Foundation elements (3/36, 8 %), edutainment principles (2/36, 5.5 %), and others (e.g. DISCERN and MARKOV Model) (9/31,29 %). The most commonly used evaluation measures were the Decisional Conflict Scale (18/46, 39 %), acceptability and knowledge (7/46, 15 %), and the preparation for decision-making scale (5/46,11 %).

CONCLUSION

For better quality and wider implementation of such tools, there is a need for detailed, transparent, systematic, and consistent reporting of development methods and evaluation measures. Using established checklists for reporting development and evaluation is encouraged.

Quality of life tools among patients on dialysis: A systematic review

Introduction

 The universal increase in obesity and diabetes has increased the chronic kidney disease (CKD) rate. In 2017, almost 800 million individuals suffered from CKD worldwide. Kidney dialysis becomes necessary as the disease progresses. Dialysis negatively impacts CKD patients' quality of life (QoL). It causes several complications that affect patients' physical, social, psychological, and spiritual aspects of life. This systematic review aims to identify condition-specific tools used to assess CKD patients' quality of life on dialysis.

Material and Methods

A systematic literature search was conducted to investigate studies using QoL tools among patients on dialysis from February 2000 to June 2023. The search was conducted in several databases and followed the PRISMA guidelines. The focus was to identify tools that capture intrinsic factors, such as spiritual subdomains, rather than extrinsic factors, such as environmental subdomains.

Results

The review identified five studies and seven dialysis-specific tools for assessing the QoL of CKD patients on dialysis. The physical domain was the most assessed, followed by the psychological and social domains. Fatigue, muscle weakness, sleep disorders, and pain were identified as the most common concerns in the physical domain.

Conclusion

Dialysis negatively impacts all aspects of QoL in CKD patients. This review can guide clinicians in understanding the disease and treatment burden by identifying the most appropriate tools for assessing the QoL of adult CKD patients undergoing dialysis. There is a need for further studies to explore the detrimental effects of CKD treatment and better understand its impact on patients' QoL.

Lessons learned about development and assessment of feasibility of tools for health and rehabilitation services

BACKGROUND

Given the dire need for health and rehabilitation services internationally, exacerbated during the COVID-19 pandemic, there is a critical need to develop tools to support service delivery. This need is palpable in the Global South where tools developed in Eurocentric contexts are not always adaptable, applicable, or relevant. It is for this reason that the researchers present three case studies of tool development using pilot and feasibility studies in South Africa and share the lessons learned from these studies.

OBJECTIVES

To describe three case studies that developed new tools for health and rehabilitation services using pilot and feasibility studies. To synthesize lessons learned from these case studies on the development of tools.

METHOD

The researchers describe three case studies that were developed. The case studies are summarized as follows: aims and objectives, context, problem, study design, findings, and what happened after the study. Thereafter, a qualitative cross-case analysis was conducted by the researchers to generate themes.

FINDINGS

The case studies are described individually and followed by themes identified through cross-case analysis.

DISCUSSION

The lessons learned are discussed. It is essential to develop new tools and protocols, motivated by the need for equitable and contextually relevant practices. Partnerships and collaboration with end-users are critical for success. A critical, scientific process is essential in developing new tools. Pilot and feasibility studies are invaluable in developing tools and assessing the feasibility of tools and implementation. The goal is to develop practical, usable tools and protocols.

CONCLUSION

Through the lessons learned, the researchers are hopeful that the international health and rehabilitation professions will continue to strengthen the scientific development of contextually relevant tools and resources.

Informational resources used by farmers with ruminants and monogastrics for animal health monitoring: importance of sensory indicators

Managers of health in livestock systems are asked to shift from a curative approach to a more preventive approach. This change requires sociological and technical reconfiguration and raises the issue of how changes are implemented by farmers and their technical support ecosystem (advisors, trainers, veterinarians). Here, we report work conducted in western France by an Agricultural European Innovation Partnership Operational Group bringing together animal scientists and sociologists to advance knowledge on animal health in a range of livestock sectors, i.e. dairy cattle, beef cattle, small ruminants (sheep, goats), poultry and pigs. In this study, our aim was to answer this question: what are the Informational Resources (I.R.) that farmers use to promote animal health of their herds? First, we used a survey to characterize 129 I.R. used by advisors, then, we used statistical analysis to classify these I.R. into six clusters. Second, we organized eight focus-group sessions that involved a total of 50 farmers from across all livestock sectors to find out how they mobilize the I.R. and what they see as important for animal health monitoring practice. Finally, we performed individual interviews with 42 farmers to expand the data captured in the collective focus groups. Results showed that farmers and advisors have a broad and diverse range of I.R. to help monitor animal health. We identified six clusters of I.R.: regulatory tools, periodic reports, tools for farmer-led monitoring, tools and indicators for national reference datasets, slaughterhouse and laboratory indicators, and training delivered to farmers. During focus group, livestock farmers identified some of their I.R. within these clusters but they also cited other daily routines that help them monitor animal health that were not cited by advisors. We found that farmers mainly use sensory indicators (typically smell, sight, touch) in their daily practice whereas advisors mainly use relatively sophisticated retrospective monitoring tools. Farmers also cited the importance of indicators that can rapidly objectify any change in animal condition, behavior, or health. This work finds a split in the distribution of animal health management roles, with farmers implementing daily checks whereas advisors run periodic health surveillance, thus revealing differentiated roles and needs between farmers and their advisors.

A scoping review reveals candidate quality indicators of knowledge translation and implementation science practice tools

OBJECTIVES

To identify candidate quality indicators from existing tools that provide guidance on how to practice knowledge translation and implemenation science (KT practice tools) across KT domains (dissemination, implementation, sustainability, and scalability).

STUDY DESIGN AND SETTING

We conducted a scoping review using the Joanna Briggs Institute Manual for Evidence Synthesis. We systematically searched multiple electronic databases and the gray literature. Documents were independently screened, selected, and extracted by pairs of reviewers. Data about the included articles, KT practice tools, and candidate quality indicators were analyzed, categorized, and summarized descriptively.

RESULTS

Of 43,060 titles and abstracts that were screened from electronic databases and gray literature, 850 potentially relevant full-text articles were identified, and 253 articles were included in the scoping review. Of these, we identified 232 unique KT practice tools from which 27 unique candidate quality indicators were generated. The identified candidate quality indicators were categorized according to the development (n = 17), evaluation (n = 5) and adaptation (n = 3) of the tools, and engagement of knowledge users (n = 2). No tools were identified that appraised the quality of KT practice tools.

CONCLUSIONS

The development of a quality appraisal instrument of KT practice tools is needed. The results will be further refined and finalized in order to develop a quality appraisal instrument for KT practice tools.

The functional organization of skilled actions in the adextral and atypical brain

When planning functional grasps of tools, right-handed individuals (dextrals) show mostly left-lateralized neural activity in the praxis representation network (PRN), regardless of the used hand. Here we studied whether or not similar cerebral asymmetries are evident in non-righthanded individuals (adextrals). Sixty two participants, 28 righthanders and 34 non-righthanders (21 lefthanders, 13 mixedhanders), planned functional grasps of tools vs. grasps of control objects, and subsequently performed their pantomimed executions, in an event-related functional magnetic resonance imaging (fMRI) project. Both hands were tested, separately in two different sessions, counterbalanced across participants. After accounting for non-functional components of the prospective grasp, planning functional grasps of tools was associated with greater engagement of the same, left-hemisphere occipito-temporal, parietal and frontal areas of PRN, regardless of hand and handedness. Only when the analyses involved signal changes referenced to resting baseline intervals, differences between adextrals and dextrals emerged. Whereas in the left hemisphere the neural activity was equivalent in both groups (except for the occipito-temporo-parietal junction), its increases in the right occipito-temporal cortex, medial intraparietal sulcus (area MIP), the supramarginal gyrus (area PFt/PF), and middle frontal gyrus (area p9-46v) were significantly greater in adextrals. The inverse contrast was empty. Notably, when individuals with atypical and typical hemispheric phenotypes were directly compared, planning functional (vs. control) grasps invoked, instead, significant clusters located nearly exclusively in the left hemisphere of the typical phenotype. Previous studies interpret similar right-sided vs. left-sided increases in neural activity for skilled actions as handedness dependent, i.e., located in the hemisphere dominant for manual skills. Yet, none of the effects observed here can be purely handedness dependent because there were mixed-handed individuals among adextrals, and numerous mixed-handed and left-handed individuals possess the typical phenotype. Thus, our results clearly show that hand dominance has limited power in driving the cerebral organization of motor cognitive functions.

Tools, frameworks and resources to guide global action on strengthening rural health systems: a mapping review

BACKGROUND

Inequities of health outcomes persist in rural populations globally. This is strongly associated with there being less health coverage in rural and underserviced areas. Increasing health care coverage in rural area requires rural health system strengthening, which subsequently necessitates having tools to guide action.

OBJECTIVE

This mapping review aimed to describe the range of tools, frameworks and resources (hereafter called tools) available globally for rural health system capacity building.

METHODS

This study collected peer-reviewed materials published in 15-year period (2005-2020). A systematic mapping review process identified 149 articles for inclusion, related to 144 tools that had been developed, implemented, and/or evaluated (some tools reported over multiple articles) which were mapped against the World Health Organization's (WHO's) six health system building blocks (agreed as the elements that need to be addressed to strengthen health systems).

RESULTS

The majority of tools were from high- and middle-income countries (n = 85, 59% and n = 43, 29%, respectively), and only 17 tools (12%) from low-income countries. Most tools related to the health service building block (n = 57, 39%), or workforce (n = 33, 23%). There were a few tools related to information and leadership and governance (n = 8, 5% each). Very few tools related to infrastructure (n = 3, 2%) and financing (n = 4, 3%). This mapping review also provided broad quality appraisal, showing that the majority of the tools had been evaluated or validated, or both (n = 106, 74%).

CONCLUSION

This mapping review provides evidence that there is a breadth of tools available for health system strengthening globally along with some gaps where no tools were identified for specific health system building blocks. Furthermore, most tools were developed and applied in HIC/MIC and it is important to consider factors that influence their utility in LMIC settings. It may be important to develop new tools related to infrastructure and financing. Tools that have been positively evaluated should be made available to all rural communities, to ensure comprehensive global action on rural health system strengthening.

Psychometric properties of trust in trauma care in an emergency department tool

BACKGROUND

In emergency cases, lack of other treatment alternatives may affect a person's decision, but it does not render that decision involuntary. Being able to make choices is a crucial (but not necessary) element of trust. We aimed to develop a tool to evaluate the Trust in Trauma Care in an Emergency Department (TTC-ED) among traumatic patients.

METHODS

This psychometric study was carried out on 498 trauma patients who referred to the Imam Reza hospital in Tabriz, Iran, 2022. Patient-focused interviews, expert/key informants' opinions, and literature reviews were used to generate the items. Several statistical techniques were used to evaluate the TTC-ED trust tool's content validity, reliability, and construct validity, including the modified Kappa (k*), the Intra-Class Correlation (ICC) coefficient, and Exploratory Factor Analysis (EFA). Data were analyzed using SPSS version 26.0 and STATA 14 statistical software packages.

RESULTS

A tool with 22 items was developed. As a measure of content validity assessment, the k* coefficient was 0.97. Regarding the evaluation of reliability, a good level of internal consistency was noted with a Cronbach's α 0.93, and the scale's test-retest reliability (as measured by ICC) was 0.96. The results of exploratory factor analysis indicated that the TTC-ED had a two-component tool fitted the data. Factor 1 includes 13 items covered 43.0% of the variance (eigenvalue = 9.47) and factor 2 consisted of nine items which accounted for 5.64% of the variance (eigenvalue: 1.24).

CONCLUSION

The Trust in TTC-ED has been shown to be a valid and reliable test for assessing patients' trust in emergency room settings delivering trauma care. Future research may examine the validity in other contexts and create a TTC-ED instrument with a shorter version.

Transformer-based tool recommendation system in Galaxy

BACKGROUND

Galaxy is a web-based open-source platform for scientific analyses. Researchers use thousands of high-quality tools and workflows for their respective analyses in Galaxy. Tool recommender system predicts a collection of tools that can be used to extend an analysis. In this work, a tool recommender system is developed by training a transformer on workflows available on Galaxy Europe and its performance is compared to other neural networks such as recurrent, convolutional and dense neural networks.

RESULTS

The transformer neural network achieves two times faster convergence, has significantly lower model usage (model reconstruction and prediction) time and shows a better generalisation that goes beyond training workflows than the older tool recommender system created using RNN in Galaxy. In addition, the transformer also outperforms CNN and DNN on several key indicators. It achieves a faster convergence time, lower model usage time, and higher quality tool recommendations than CNN. Compared to DNN, it converges faster to a higher precision@k metric (approximately 0.98 by transformer compared to approximately 0.9 by DNN) and shows higher quality tool recommendations.

CONCLUSION

Our work shows a novel usage of transformers to recommend tools for extending scientific workflows. A more robust tool recommendation model, created using a transformer, having significantly lower usage time than RNN and CNN, higher precision@k than DNN, and higher quality tool recommendations than all three neural networks, will benefit researchers in creating scientifically significant workflows and exploratory data analysis in Galaxy. Additionally, the ability to train faster than all three neural networks imparts more scalability for training on larger datasets consisting of millions of tool sequences. Open-source scripts to create the recommendation model are available under MIT licence at https://github.com/anuprulez/galaxy_tool_recommendation_transformers.

Sepsis triggers and tools to support early identification in healthcare settings: An integrative review

BACKGROUND

There is no universal trigger or tool to aid sepsis diagnosis.

OBJECTIVES

The objective of this study was to identify triggers and tools to assist the early detection of sepsis that can be readily implemented across various health care settings.

METHODS

A systematic integrative review was conducted using MEDLINE, CINAHL, EMBASE, Scopus, and the Cochrane Database of Systematic Reviews. Relevant grey literature and subject-matter expert consultation also informed the review. Study types included systematic reviews, randomised controlled trials, and cohort studies. All patient populations across prehospital, emergency department, and acute hospital inpatient settings, excluding the intensive care unit, were included. Sepsis triggers and tools were evaluated for efficacy in detecting sepsis and association with process measures and patient outcomes. Methodological quality was appraised using Joanna Briggs Institute tools.

RESULTS

Of the 124 included studies, most were retrospective cohort (49.2%) in adults (83.9%) within the emergency department (44.4%). The most commonly evaluated sepsis tools were qSOFA (12 studies) and SIRS (11 studies) with a median sensitivity of 28.0% versus 51.0% and a specificity of 98.0% versus 82.0%, respectively, for sepsis diagnosis. Lactate plus qSOFA (two studies) had a sensitivity between 57.0 and 65.5%, whereas the National Early Warning Score (four studies) demonstrated median sensitivity and specificity >80%, but the latter was considered difficult to implement. Amongst triggers, lactate (18 studies) at the threshold of ≥2.0 mmol/L showed higher sensitivity for predicting sepsis-related clinical deterioration than <2.0 mmol/L. Automated sepsis alerts and algorithms (35 studies) showed median sensitivity between 58.0 and 80.0% and specificity between 60.0 and 93.1%. There were limited data for other sepsis tools and maternal, paediatric, and neonatal populations. Overall methodological quality was high.

CONCLUSION

No single sepsis tool or trigger is applicable across various settings and populations, but considering efficacy and ease of implementation, there is evidence to use lactate plus qSOFA for adult patients. More research is needed in maternal, paediatric, and neonatal populations.

Identification of appropriate tools to gauge brain functions in a clinical setup of a developing country: A pilot study

Objective

To identify the most appropriate tools to measure functions of the brain that can be utilized in the clinical setups of developing countries.

Methods

This qualitative research with a three-step approach was carried out from January 2022 to May 2022 at the Institute of Basic Medical Sciences, Khyber Medical University, Pakistan. Firstly, literature was searched to identify main brain faculties, then interviews were conducted with regional field experts to identify appropriate scales for the selected functions. Lastly a rubric was filled using interview transcripts and literature.

Results

The identified functions were vision, hearing, cognition, motor and emotions. Based on the rubric the best tests were visual fields (17/24), pure tone audiometry (16/24), Mini-Mental State Exam (20/24), Trait Emotional Intelligence Questionnaire (18/24), Romberg's test (19/24) and Manual Muscle Testing (18/24).

Conclusion

The clinicians in developing countries can utilize the visual fields, pure tone audiometry, Mini-Mental State Exam, Trait Emotional Intelligence Questionnaire, Romberg's test and Manual Muscle Testing for most efficient, feasible, accurate and cost-effective measurement of brain functions.

Patient Expectations and Satisfaction in Pediatric Orthopedics

PURPOSE OF REVIEW

The purpose of the current review is to analyze the current literature regarding the tools available to evaluate patient expectations and satisfaction. There have been an increasing number of tools that have been developed and validated for various orthopedic procedures. Despite the growing number of tools, there are a limited number of tools available for pediatric patients.

RECENT FINDINGS

Several tools have been developed in orthopedics to evaluate patient expectations. However, there are no tools that have been validated in the pediatric population. In addition, pediatric patient expectations should be collected in conjunction with parent/caregiver expectations. Although not specifically validated for pediatric patients, there are several tools available that may pertain to pediatric patients including the HSS ACL Expectations Survey, HSS Shoulder Expectations Survey, HSS Knee Surgery Expectations Survey, HSS Foot and Ankle Surgery Expectation Survey, Sunnybrook Surgery Expectations Survey, Musculoskeletal Outcomes Data Evaluation and Management System (MODEMS) Instruments, Quick DASH, and DASH. In terms of patient satisfaction, there are even fewer tools available. Several tools have been developed to evaluate patient satisfaction and five additional tools within orthopedics. Of these tools, there are two that have been validated for pediatric patients: The Swedish Parents Satisfaction Questionnaire and the Scoliosis Research Society-22. There are a growing number of tools to evaluate patient's expectations and satisfaction in the orthopedic literature. Given most of these tools pertain to adult patients, there is a need for further development of tools specifically validated for pediatric patients and their parents/caregivers. Through the measurement of expectations and satisfaction, medical professionals can hope to improve satisfaction and outcomes.

Social vulnerability indices: a scoping review

BACKGROUND

Social vulnerability occurs when the disadvantage conveyed by poor social conditions determines the degree to which one's life and livelihood are at risk from a particular and identifiable event in health, nature, or society. A common way to estimate social vulnerability is through an index aggregating social factors. This scoping review broadly aimed to map the literature on social vulnerability indices. Our main objectives were to characterize social vulnerability indices, understand the composition of social vulnerability indices, and describe how these indices are utilized in the literature.

METHODS

A scoping review was conducted in six electronic databases to identify original research, published in English, French, Dutch, Spanish or Portuguese, and which addressed the development or use of a social vulnerability index (SVI). Titles, abstracts, and full texts were screened and assessed for eligibility. Data were extracted on the indices and simple descriptive statistics and counts were used to produce a narrative summary.

RESULTS

In total, 292 studies were included, of which 126 studies came from environmental, climate change or disaster planning fields of study and 156 studies were from the fields of health or medicine. The mean number of items per index was 19 (SD 10.5) and the most common source of data was from censuses. There were 122 distinct items in the composition of these indices, categorized into 29 domains. The top three domains included in the SVIs were: at risk populations (e.g., % older adults, children or dependents), education, and socioeconomic status. SVIs were used to predict outcomes in 47.9% of studies, and rate of Covid-19 infection or mortality was the most common outcome measured.

CONCLUSIONS

We provide an overview of SVIs in the literature up to December 2021, providing a novel summary of commonly used variables for social vulnerability indices. We also demonstrate that SVIs are commonly used in several fields of research, especially since 2010. Whether in the field of disaster planning, environmental science or health sciences, the SVIs are composed of similar items and domains. SVIs can be used to predict diverse outcomes, with implications for future use as tools in interdisciplinary collaborations.

Learning does not just happen: establishing learning principles for tools to translate resilience into practice, based on a participatory approach

BACKGROUND

Theories of learning are of clear importance to resilience in healthcare since the ability to successfully adapt and improve patient care is closely linked to the ability to understand what happens and why. Learning from both positive and negative events is crucial. While several tools and approaches for learning from adverse events have been developed, tools for learning from successful events are scarce. Theoretical anchoring, understanding of learning mechanisms, and establishing foundational principles for learning in resilience are pivotal strategies when designing interventions to develop or strengthen resilient performance. The resilient healthcare literature has called for resilience interventions, and new tools to translate resilience into practice have emerged but without necessarily stipulating foundational learning principles. Unless learning principles are anchored in the literature and based on research evidence, successful innovation in the field is unlikely to occur. The aim of this paper is to explore: What are key learning principles for developing learning tools to help translate resilience into practice?

METHODS

This paper reports on a two-phased mixed methods study which took place over a 3-year period. A range of data collection and development activities were conducted including a participatory approach which involved iterative workshops with multiple stakeholders in the Norwegian healthcare system.

RESULTS

In total, eight learning principles were generated which can be used to help develop learning tools to translate resilience into practice. The principles are grounded in stakeholder needs and experiences and in the literature. The principles are divided into three groups: collaborative, practical, and content elements.

CONCLUSIONS

The establishment of eight learning principles that aim to help develop tools to translate resilience into practice. In turn, this may support the adoption of collaborative learning approaches and the establishment of reflexive spaces which acknowledge system complexity across contexts. They demonstrate easy usability and relevance to practice.

Family-Reflections.com: Creating a parent-to-parent web-based tool regarding pediatric home ventilation

BACKGROUND

The decision to initiate pediatric mechanical ventilation via tracheostomy ("home ventilation") is complex and parents often desire information from other parents who have faced this decision. However, parent-to-parent communication is challenging as it is difficult to connect new families to experienced families in ways that optimize informed, balanced decision-making.

OBJECTIVE

Create a parent-to-parent web-based tool to support decision-making about pediatric home ventilation.

PATIENT INVOLVEMENT

The tool was created based on interviews and feedback from parents.

METHODS

We interviewed parents who previously chose for, or against, home ventilation for their child. Interview themes and family comments guided website development. Viewer feedback was solicited via an embedded survey in the tool.

RESULTS

We created 6 composite character families to communicate 6 themes about home ventilation: 1) Considering treatment options, 2) Talking with medical team, 3) Impact on life at home, 4) Impact on relationships, 5) Experience for the child, and 6) If the child's life is short. Nine families who reviewed the draft tool felt it would have helped with their decision about home ventilation. Specifically, it supported families in thinking through what was "most important about their child's breathing problems" (7 of 9 parents) and feeling "more at peace with the decision" (8 of 9 parents). Between 6/1/20-12/31/22, nearly 5500 viewers have accessed the tool and 56 viewers completed the survey (including 13 families and 39 clinicians). Feedback from experienced families and clinicians reported the tool taught them something new.

DISCUSSION

This novel parent-to-parent tool shows promise for expanding access to balanced, family-centered information about pediatric home ventilation.

PRACTICAL VALUE

The diverse stories and decisions let parents access multiple family perspectives. The tool's focus is on family-centric information that parents reported was usually missing from clinician counseling.

FUNDING

This work was supported by the National Palliative Care Research Center.

A Systematic Review of Methodological Tools for Evaluating the Water, Energy, Food, and One Health Nexus in Transboundary Water Basins

Water plays a vital role in human socioeconomic development and overall well-being, making its effective management essential in achieving the Sustainable Development Goals. The close interlinkage between water, other environmental resources, and socioeconomic development have prompted the emergence and adoption of holistic and trans-sectoral concepts such as integrated water resources management and, more recently, the resource nexus. However, even such holistic approaches often exclude the one health approach, particularly at the transboundary water basins (TWBs), which not only dominate 40% of the earth but are vital in environmental and human sustainability. This review aimed to understand, evaluate, and compare assessment tools for water, energy, food, and one health (WEF + H) nexus management in TWBs. The review applied the systematic review guidelines for articles published in the Scopus database. The inclusion criteria encompassed English-language articles featuring case studies, meta-studies, or review articles with no less than three nexus resources. The review categorized the article based on criteria that focused on identifying tools capable of analyzing scenarios and policies for WEF + H in TWBs and their accessibility and easiness of implementation in case studies. Of the eighteen analyzed tools, 13 (72%) had limitations in their application at various geographical scales. Additionally, they could not integrate one health into the nexus or analyze policies through running scenarios. On the contrary, the Bayesian networks, system dynamics, agent-based models, life-cycle assessments, and input-output tools were highly accessible for efficiently conducting scenario-based WEF + H nexus assessments in TWBs.

Turning the tide on inequity through systematic equity action-analysis

BACKGROUND

Collective agreement about the importance of centering equity in health research, practice, and policy is growing. Yet, responsibility for advancing equity is often situated as belonging to a vague group of 'others', or delegated to the leadership of 'equity-seeking' or 'equity-deserving' groups who are tasked to lead systems transformation while simultaneously navigating the violence and harms of oppression within those same systems. Equity efforts also often overlook the breadth of equity scholarship. Harnessing the potential of current interests in advancing equity requires systematic, evidence-guided, theoretically rigorous ways for people to embrace their own agency and influence over the systems in which they are situated. ln this article, we introduce and describe the Systematic Equity Action-Analysis (SEA) Framework as a tool that translates equity scholarship and evidence into a structured process that leaders, teams, and communities can use to advance equity in their own settings.

METHODS

This framework was derived through a dialogic, critically reflective and scholarly process of integrating methodological insights garnered over years of equity-centred research and practice. Each author, in a variety of ways, brought engaged equity perspectives to the dialogue, bringing practical and lived experience to conversation and writing. Our scholarly dialogue was grounded in critical and relational lenses, and involved synthesis of theory and practice from a broad range of applications and cases.

RESULTS

The SEA Framework balances practices of agency, humility, critically reflective dialogue, and systems thinking. The framework guides users through four elements of analysis (worldview, coherence, potential, and accountability) to systematically interrogate how and where equity is integrated in a setting or object of action-analysis. Because equity issues are present in virtually all aspects of society, the kinds of 'things' the framework could be applied to is only limited by the imagination of its users. It can inform retrospective or prospective work, by groups external to a policy or practice setting (e.g., using public documents to assess a research funding policy landscape); or internal to a system, policy, or practice setting (e.g., faculty engaging in a critically reflective examination of equity in the undergraduate program they deliver).

CONCLUSIONS

While not a panacea, this unique contribution to the science of health equity equips people to explicitly recognize and interrupt their own entanglements in the intersecting systems of oppression and injustice that produce and uphold inequities.

MDSi: Multi-omics Database for Setaria italica

BACKGROUND

Foxtail millet (Setaria italica) harbors the small diploid genome (~ 450 Mb) and shows the high inbreeding rate and close relationship to several major foods, feed, fuel and bioenergy grasses. Previously, we created a mini foxtail millet, xiaomi, with an Arabidopsis-like life cycle. The de novo assembled genome data with high-quality and an efficient Agrobacterium-mediated genetic transformation system made xiaomi an ideal C₄ model system. The mini foxtail millet has been widely shared in the research community and as a result there is a growing need for a user-friendly portal and intuitive interface to perform exploratory analysis of the data.

RESULTS

Here, we built a Multi-omics Database for Setaria italica (MDSi, http://sky.sxau.edu.cn/MDSi.htm ), that contains xiaomi genome of 161,844 annotations, 34,436 protein-coding genes and their expression information in 29 different tissues of xiaomi (6) and JG21 (23) samples that can be showed as an Electronic Fluorescent Pictograph (xEFP) in-situ. Moreover, the whole-genome resequencing (WGS) data of 398 germplasms, including 360 foxtail millets and 38 green foxtails and the corresponding metabolic data were available in MDSi. The SNPs and Indels of these germplasms were called in advance and can be searched and compared in an interactive manner. Common tools including BLAST, GBrowse, JBrowse, map viewer, and data downloads were implemented in MDSi.

CONCLUSION

The MDSi constructed in this study integrated and visualized data from three levels of genomics, transcriptomics and metabolomics, and also provides information on the variation of hundreds of germplasm resources that can satisfies the mainstream requirements and supports the corresponding research community.

Bridging Big Data: Procedures for Combining Non-equivalent Cognitive Measures from the ENIGMA Consortium

Investigators in neuroscience have turned to Big Data to address replication and reliability issues by increasing sample sizes, statistical power, and representativeness of data. These efforts unveil new questions about integrating data arising from distinct sources and instruments. We focus on the most frequently assessed cognitive domain - memory testing - and demonstrate a process for reliable data harmonization across three common measures. We aggregated global raw data from 53 studies totaling N = 10,505 individuals. A mega-analysis was conducted using empirical bayes harmonization to remove site effects, followed by linear models adjusting for common covariates. A continuous item response theory (IRT) model estimated each individual's latent verbal learning ability while accounting for item difficulties. Harmonization significantly reduced inter-site variance while preserving covariate effects, and our conversion tool is freely available online. This demonstrates that large-scale data sharing and harmonization initiatives can address reproducibility and integration challenges across the behavioral sciences.

Tools for measuring client experiences and satisfaction with healthcare in low- and middle-income countries: a systematic review of measurement properties

BACKGROUND

Perspectives of patients as clients on healthcare offer unique insights into the process and outcomes of care and can facilitate improvements in the quality of services. Differences in the tools used to measure these perspectives often reflect differences in the conceptualization of quality of care and personal experiences. This systematic review assesses the validity and reliability of instruments measuring client experiences and satisfaction with healthcare in low- and middle-income countries (LMICs).

METHODS

We performed a systematic search of studies published in PubMed, SCOPUS, and CINAHL. This review was reported according to the Preferred Reporting Items for Systematic Review and Meta-analysis (PRISMA) guidelines. Studies describing the development and psychometric properties of client experience and satisfaction with general health care were included in the review. Critical appraisal of study design was undertaken using the Appraisal tool for Cross-Sectional Studies (AXIS). The Consensus-based Standards for the Selection of Health Measurement Instruments (COSMIN) checklist and Terwee's criteria were used to appraise the psychometric properties of the included studies. A narrative synthesis approach was used in the interpretation of the findings.

RESULTS

Of the 7470 records identified, 12 studies with 14 corresponding instruments met the inclusion criteria and were included in the final review. No study assessed all the psychometric properties highlighted by the COSMIN criteria. In most instruments, we found evidence that initial development work incorporated client participation. The most evaluated measurement properties were content validity, internal consistency, and structural validity. Measurement error and responsiveness were not reported in any study.

CONCLUSION

Reliability and validity should be considered important elements when choosing or developing an instrument for professionals seeking an effective instrument for use within the population. Our review identified limitations in the psychometric properties of patient experience and satisfaction instruments, and none met all methodological quality standards. Future studies should focus on further developing and testing available measures for their effectiveness in clinical practice. Furthermore, the development of new instruments should incorporate clients' views and be rigorously tested or validated in studies with high methodological quality.

TRIAL REGISTRATION

CRD42020150438.

The burdock database: a multi-omic database for Arctium lappa, a food and medicinal plant

BACKGROUND

Burdock is a biennial herb of Asteraceae found in Northern Europe, Eurasia, Siberia, and China. Its mature dry fruits, called Niu Bang Zi, are recorded in various traditional Chinese medicine books. With the development of sequencing technology, the mitochondrial, chloroplast, and nuclear genomes, transcriptome, and sequence-related amplified polymorphism (SRAP) fingerprints of burdock have all been reported. To make better use of this data for further research and analysis, a burdock database was constructed.

RESULTS

This burdock multi-omics database contains two burdock genome datasets, two transcriptome datasets, eight burdock chloroplast genomes, one burdock mitochondrial genome, one A. tomentosum chloroplast genome, one A. tomentosum mitochondrial genome, 26 phenotypes of burdock varieties, burdock rhizosphere-associated microorganisms, and chemical constituents of burdock fruit, pericarp, and kernel at different growth stages (using UPLC-Q-TOF-MS). The wild and cultivation distribution of burdock in China was summarized, and the main active components and pharmacological effects of burdock currently reported were concluded. The database contains ten central functional modules: Home, Genome, Transcriptome, Jbrowse, Search, Tools, SRAP fingerprints, Associated microorganisms, Chemical, and Publications. Among these, the "Tools" module can be used to perform sequence homology alignment (Blast), multiple sequence alignment analysis (Muscle), homologous protein prediction (Genewise), primer design (Primer), large-scale genome analysis (Lastz), and GO and KEGG enrichment analyses (GO Enrichment and KEGG Enrichment).

CONCLUSIONS

The database URL is http://210.22.121.250:41352/ . This burdock database integrates molecular and chemical data to provide a comprehensive information and analysis platform for interested researchers and can be of immense help to the cultivation, breeding, and molecular pharmacognosy research of burdock.

The Systematic Review Toolbox: keeping up to date with tools to support evidence synthesis

BACKGROUND

The Systematic Review (SR) Toolbox was developed in 2014 to collate tools that can be used to support the systematic review process. Since its inception, the breadth of evidence synthesis methodologies has expanded greatly. This work describes the process of updating the SR Toolbox in 2022 to reflect these changes in evidence synthesis methodology. We also briefly analysed included tools and guidance to identify any potential gaps in what is currently available to researchers.

METHODS

We manually extracted all guidance and software tools contained within the SR Toolbox in February 2022. A single reviewer, with a second checking a proportion, extracted and analysed information from records contained within the SR Toolbox using Microsoft Excel. Using this spreadsheet and Microsoft Access, the SR Toolbox was updated to reflect expansion of evidence synthesis methodologies and brief analysis conducted.

RESULTS

The updated version of the SR Toolbox was launched on 13 May 2022, with 235 software tools and 112 guidance documents included. Regarding review families, most software tools (N = 223) and guidance documents (N = 78) were applicable to systematic reviews. However, there were fewer tools and guidance documents applicable to reviews of reviews (N = 66 and N = 22, respectively), while qualitative reviews were less served by guidance documents (N = 19). In terms of review production stages, most guidance documents surrounded quality assessment (N = 70), while software tools related to searching and synthesis (N = 84 and N = 82, respectively). There appears to be a paucity of tools and guidance relating to stakeholder engagement (N = 2 and N = 3, respectively).

CONCLUSIONS

The SR Toolbox provides a platform for those undertaking evidence syntheses to locate guidance and software tools to support different aspects of the review process across multiple review types. However, this work has also identified potential gaps in guidance and software that could inform future research.

Disentangling hand and tool processing: Distal effects of neuromodulation

Neural processing within a local brain region that responds to more than one object category (e.g., hands and tools) nonetheless have different functional connectivity patterns with other distal brain areas, which suggests that local processing can affect and/or be affected by processing in distal areas, in a category-specific way. Here we wanted to test whether administering either a hand- or tool-related training task in tandem with transcranial direct current stimulation (tDCS) to a region that responds both to hands and tools (posterior middle temporal gyrus; pMTG), modulated local and distal neural processing more for the trained than the untrained category in a subsequent fMRI task. After each combined tDCS/training session, participants viewed images of tools, hands, and animals, in an fMRI scanner. Using multivoxel pattern analysis, we found that tDCS stimulation to pMTG indeed improved the classification accuracy between tools vs. animals, but only when combined with a tool and not a hand training task. Surprisingly, tDCS stimulation to pMTG also improved classification accuracy between hands vs. animals when combined with a tool but not a hand training task. Our findings suggest that overlapping but functionally-specific networks may be engaged separately by using a category-specific training task together with tDCS - a strategy that can be applied more broadly to other cognitive domains using tDCS. By hypothesis, these effects on local processing are a direct result of within-domain connectivity constraints from domain-specific networks that are at play in the processing and organization of object representations.

Developing communication tools on rotavirus vaccination to support family paediatricians in Italy

BACKGROUND

Universal rotavirus (RV) vaccination for newborns was introduced in Italy in 2018, but national vaccination coverage is still suboptimal. Effective communication between the family paediatrician (FP) and parents/caregivers is essential to promote vaccination acceptance. This project aimed to support FPs in communicating RV vaccination to parents/caregivers through the development and implementation of demonstrative videos and training modules.

METHODS

A working group composed of two FPs, two communication professionals, a medical expert from GSK and a clinical psychologist, was formed to establish the key scientific information to be communicated to parents/caregivers and develop the demonstrative videos. Four videos depicting four communication styles (I to IV) were developed based on the Social Styles Theory. Thirty FPs were then asked to pilot test the videos and provide feedback. In addition, two training modules with scientific information were developed to learn how to respond to parents'/caregivers' objections.

RESULTS

A total of 23 FPs provided feedback after using one or more videos at least five times. Twenty FPs (87.0 %) used mostly-one style, and most (60.0 %) used Style IV. Overall, the feedback was positive, as the majority of FPs (82.6 %, n = 19/23) indicated that the proposed videos were 'useful' or 'extremely useful' for introducing the RV vaccination to parents/caregivers in their actual practice. Based on this feedback, shorter versions of each video were also produced, and two training modules were developed to support FPs in responding to parental objections. Most FPs 75 % (n = 9/12) found Module 1 'very useful', and all found Module 2 'very useful' (100 %, n = 12/12).

CONCLUSIONS

The communication tools developed were well appreciated by the FPs and are expected to support FPs in communicating RV vaccination thereby increasing its coverage. Practicing RV communication may also prove beneficial for FPs to communicate other critical topics to parents/caregivers.

Prevalence of Bacterial Burden on Macroscopic Contaminants of Orthopaedic Surgical Instruments Following Sterilization

BACKGROUND

Macroscopic contamination of orthopaedic instruments with particulates, including cortical bone and polymethyl methacrylate (PMMA) cement, having previously undergone preoperative sterilization, is frequently encountered peri- or intraoperatively, calling into question the sterility of such instruments.

AIM

The purpose of this study is to determine if macroscopic contaminants of orthopaedic surgical instrumentation maintain a bacterial burden following sterile processing. Additionally, this manuscript looks to determine the most commonly contaminated instruments and what the most common contaminants are.

METHODS

At a single tertiary referral centre, we prospectively collected available macroscopic contaminants in orthopaedic instrument trays over a six month period from August 2021 to May 2022. When identified, these specimens were swabbed and plated on sheep blood agar. All specimens were incubated at 37°C for 14 days, and visually inspected for colony formation. When bacterial colony formation was identified, samples were sent for species identification.

RESULTS

A total of 33 contaminants were tested, with only one contaminant growing bacterial colonies which was found to be Corynebacterium. The items most commonly found to have macroscopic contamination were surgical trays (9) and cannulated drills. The identifiable contaminants were bone (10), PMMA bone cement (4), and hair (4). There were 11 macroscopic contaminants that were not identifiable.

CONCLUSION

This study found that 97% of macroscopic orthopaedic surgical instrument contaminants that underwent sterile processing did not possess a bacterial burden. Contaminants discovered during a procedure are likely to be sterile and do not pose a substantially increased risk of infection to a patient.

Design and validation of a preparedness evaluation tool of pre-hospital emergency medical services for terrorist attacks: a mixed method study

INTRODUCTION

Terrorist attacks are one of the human problems that affect many countries, leaving behind a huge toll of disabilities and deaths. The aim of this study was to use a mixed-method analysis to design and validate an evaluation tool for pre-hospital emergency medical services for terrorist attacks.

METHODS

The present study is a mixed-method (qualitative and quantitative) study that was conducted in two phases. In the qualitative phase (item generation), semi-structured interviews were conducted with 34 Iranian emergency medical technicians who were selected through a purposive sampling method and a scoping literature review was conducted to generate an item pool for the preparedness evaluation of Emergency Medical Services (EMS) in terrorist attacks. In the quantitative phase (item reduction), for validity of tool face, content and construct validity, were performed; for tool reliability, the test and retest and intra-class correlation coefficient were evaluated.

RESULTS

At the first stage, 7 main categories and 16 subcategories were extracted from the data, the main categories including "Policy and Planning", "Education and Exercise "," Surge Capacity", "Safety and Security", "Command, Control and Coordination", "Information and Communication Management "and "Response Operations Management". The initial item pool included 160 items that were reduced to 110 after assessment of validity (face, content and construct). intra-class correlation coefficient (ICC = 0.71) examination and Pearson correlation test (r = 0.81) indicated that the tool was also reliable.

CONCLUSION

The research findings provide a new perspective to understand the preparedness of pre-hospital emergency medical services for terrorist attacks. The existing 110-item tool can evaluate preparedness of pre-hospital emergency medical services for terrorist attacks through collecting data with appropriate validity and reliability.

Advances in database systems education: Methods, tools, curricula, and way forward

Fundamentals of Database Systems is a core course in computing disciplines as almost all small, medium, large, or enterprise systems essentially require data storage component. Database System Education (DSE) provides the foundation as well as advanced concepts in the area of data modeling and its implementation. The first course in DSE holds a pivotal role in developing students' interest in this area. Over the years, the researchers have devised several different tools and methods to teach this course effectively, and have also been revisiting the curricula for database systems education. In this study a Systematic Literature Review (SLR) is presented that distills the existing literature pertaining to the DSE to discuss these three perspectives for the first course in database systems. Whereby, this SLR also discusses how the developed teaching and learning assistant tools, teaching and assessment methods and database curricula have evolved over the years due to rapid change in database technology. To this end, more than 65 articles related to DSE published between 1995 and 2022 have been shortlisted through a structured mechanism and have been reviewed to find the answers of the aforementioned objectives. The article also provides useful guidelines to the instructors, and discusses ideas to extend this research from several perspectives. To the best of our knowledge, this is the first research work that presents a broader review about the research conducted in the area of DSE.

Development of the Arabic Health Measures database: a bibliometric analysis of Arabic health-related measures

Background

To develop an open-access database of Arabic health measures intended for use by researchers and healthcare providers, along with a bibliometric analysis of the measures included in the database.

Methods

A search was conducted up to 31 December 2021 in PubMed, Embase, CINAHL, SAGE, Springer and Elsevier for published articles or abstracts with keywords “Arabic” AND “translation”, “adaptation” OR “validation”. Information on the measure and the methodology used in the study was then entered into a database. An open-access platform was developed to allow users to search for measures according to their needs. A bibliometric analysis of the articles and measures was then conducted.

Results

A total of 894 publications met the inclusion criteria. The articles discussed 716 measures that were developed using participants from at least 38 countries. The number of measures for adults was five times that for children. Mental health was the most frequent construct assessed (11.5%), followed by “function/disability” measures (10.6%). The majority of measures (54%) required 5 minutes or less to complete. Approximately 17% of the tools were available directly from the article. Saudi Arabia and Lebanon had the greatest number of publications, with 217 (23%) and 114 (12%), respectively. The majority of the publications included reporting of the validation and reliability of the instruments (64% and 56%, respectively).

Conclusions

There is a paucity of research on the quantity and quality of Arabic health measures. Similar to previous reviews, we found the number of publications on Arabic measures to be limited in comparison to those in English; however, it is encouraging that the number of publications appears to have increased steadily over the past decade. While we found the majority of publications reported on psychometric testing, we are unable to comment on the quality of the methodology used, and further investigation into this area is recommended. As the Arabic Health Measures database will facilitate the search for health instruments that have published data on their development, this will increase their visibility and use in research and clinical settings.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12961-022-00890-7.

FAIR assessment tools: evaluating use and performance

Publishing research data using a findable, accessible, interoperable, and reusable (FAIR) approach is paramount to further innovation in many areas of research. In particular in developing innovative approaches to predict (eco)toxicological risks in (nano or advanced) material design where efficient use of existing data is essential. The use of tools assessing the FAIRness of data helps the future improvement of data FAIRness and therefore their re-use. This paper reviews ten FAIR assessment tools that have been evaluated and characterized using two datasets from the nanomaterials and microplastics risk assessment domain. The tools were grouped into four categories: online and offline self-assessment survey based, online (semi-) automated and other tools. We found that the online self-assessment tools can be used for a quick scan of a user's dataset due to their ease of use, little need for experience and short time investment. When a user is looking to assess full databases, and not just datasets, for their FAIRness, (semi-)automated tools are more practical. The offline assessment tools were found to be limited and unreliable due to a lack of guidance and an under-developed state. To further characterize the usability, two datasets were run through all tools to check the similarity in the tools' results. As most of the tools differ in their implementation of the FAIR principles, a large variety in outcomes was obtained. Furthermore, it was observed that only one tool gives recommendations to the user on how to improve the FAIRness of the evaluated dataset. This paper gives clear recommendations for both the user and the developer of FAIR assessment tools.

Implementing shared decision-making in UK: Progress 2017-2022

Shared decision making has been on the policy agenda in the UK for at least twelve years, but it lacked a comprehensive approach to delivery. That has changed over the past five years, and we can now see significant progress across all aspects of a comprehensive approach, including leadership at policy, professional and patient levels; infrastructure developments, including the provision of training, tools and campaigns; and practice improvements, such as demonstrations, measurement and coordination. All these initiatives were necessary, but the last, central coordination, would appear to be key to success.

Evidence for a Shared Instrument Prototype from English, Dutch, and German

At conceptual and linguistic levels of cognition, events are said to be represented in terms of abstract categories, for example, the sentence Jackie cut the bagel with a knife encodes the categories Agent (i.e., Jackie) and Patient (i.e., the bagel). In this paper, we ask whether entities such as the knife are also represented in terms of such a category (often labeled “Instrument”) and, if so, whether this category has a prototype structure. We hypothesized the Proto‐instrument is a tool: a physical object manipulated by an intentional agent to affect a change in another individual or object. To test this, we asked speakers of English, Dutch, and German to complete an event description task and a sentence acceptability judgment task in which events were viewed with more or less prototypical instruments. We found broad similarities in how English, Dutch, and German partition the semantic space of instrumental events, suggesting there is a shared concept of the Instrument category. However, there was no evidence to support the specific hypothesis that tools are the core of the Instrument category—instead, our results suggest the most prototypical Instrument is the direct extension of an intentional agent. This paper supports theoretical frameworks where thematic roles are analyzed in terms of prototypes and suggests new avenues of research on how instrumental category structure differs across linguistic and conceptual domains.

Enthesitis-related arthritis: monitoring and specific tools

OBJECTIVES

In this article, the authors aimed to review the different tools used in the monitoring of enthesitis-related arthritis.

SOURCES

The authors performed a literature review on PubMed, Google Scholar, and Scopus databases. The dataset included the original research and the reviews including patients with enthesitis-related arthritis or juvenile spondylarthritis up to October 2020.

SUMMARY OF FINDING

Enthesitis-related arthritis is a category of juvenile idiopathic arthritis. It is characterized by the presence of enthesitis, peripheral arthritis, as well as axial involvement. The only validated tool for disease activity measurement in juvenile idiopathic arthritis is the Disease Activity Score: It has proven its reliability and sensitivity. Nevertheless, due to an absence of validated evaluation tools, the extent of functional impairment, as well as the children and parents' perception of the disease, could not be objectively perceived. Despite the great progress in the field of imaging modalities, the role they play in the evaluation of disease activity is still controversial. This is partially due to the lack of validated scoring systems.

CONCLUSIONS

Further work is still required to standardize the monitoring strategy and validate the outcome measures in enthesitis-related arthritis.

Prehospital triage tools across the world: a scoping review of the published literature

Background

Accurate triage of the undifferentiated patient is a critical task in prehospital emergency care. However, there is a paucity of literature synthesizing currently available prehospital triage tools. This scoping review aims to identify published tools used for prehospital triage globally and describe their performance characteristics.

Methods

A comprehensive search was performed of primary literature in English-language journals from 2009 to 2019. Papers included focused on emergency medical services (EMS) triage of single patients. Two blinded reviewers and a third adjudicator performed independent title and abstract screening and subsequent full-text reviews.

Results

Of 1521 unique articles, 55 (3.6%) were included in the final synthesis. The majority of prehospital triage tools focused on stroke (n = 19; 35%), trauma (19; 35%), and general undifferentiated patients (15; 27%). All studies were performed in high income countries, with the majority in North America (23, 42%) and Europe (22, 40%). 4 (7%) articles focused on the pediatric population. General triage tools aggregate prehospital vital signs, mental status assessments, history, exam, and anticipated resource need, to categorize patients by level of acuity. Studies assessed the tools’ ability to accurately predict emergency department triage assignment, hospitalization and short-term mortality. Stroke triage tools promote rapid identification of patients with acute large vessel occlusion ischemic stroke to trigger timely transport to diagnostically- and therapeutically-capable hospitals. Studies evaluated tools’ diagnostic performance, impact on tissue plasminogen activator administration rates, and correlation with in-hospital stroke scales. Trauma triage tools identify patients that require immediate transport to trauma centers with emergency surgery capability. Studies evaluated tools’ prediction of trauma center need, under-triage and over-triage rates for major trauma, and survival to discharge.

Conclusions

The published literature on prehospital triage tools predominantly derive from high-income health systems and mostly focus on adult stroke and trauma populations. Most studies sought to further simplify existing triage tools without sacrificing triage accuracy, or assessed the predictive capability of the triage tool. There was no clear ‘gold-standard’ singular prehospital triage tool for acute undifferentiated patients.

Trial registration

Not applicable.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13049-022-01019-z.

Identification of tools used to assess the external validity of randomized controlled trials in reviews: a systematic review of measurement properties

Background

Internal and external validity are the most relevant components when critically appraising randomized controlled trials (RCTs) for systematic reviews. However, there is no gold standard to assess external validity. This might be related to the heterogeneity of the terminology as well as to unclear evidence of the measurement properties of available tools. The aim of this review was to identify tools to assess the external validity of RCTs. It was further, to evaluate the quality of identified tools and to recommend the use of individual tools to assess the external validity of RCTs in future systematic reviews.

Methods

A two-phase systematic literature search was performed in four databases: PubMed, Scopus, PsycINFO via OVID, and CINAHL via EBSCO. First, tools to assess the external validity of RCTs were identified. Second, studies investigating the measurement properties of these tools were selected. The measurement properties of each included tool were appraised using an adapted version of the COnsensus based Standards for the selection of health Measurement INstruments (COSMIN) guidelines.

Results

38 publications reporting on the development or validation of 28 included tools were included. For 61% (17/28) of the included tools, there was no evidence for measurement properties. For the remaining tools, reliability was the most frequently assessed property. Reliability was judged as “sufficient” for three tools (very low certainty of evidence). Content validity was rated as “sufficient” for one tool (moderate certainty of evidence).

Conclusions

Based on these results, no available tool can be fully recommended to assess the external validity of RCTs in systematic reviews. Several steps are required to overcome the identified difficulties to either adapt and validate available tools or to develop a better suitable tool.

Trial registration

Prospective registration at Open Science Framework (OSF): 10.17605/OSF.IO/PTG4D.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12874-022-01561-5.

Workplace physical and psychosocial hazards: A systematic review of evidence informed hazard identification tools

Prevention of musculoskeletal disorders (MSDs) requires the identification of physical and psychosocial hazards. This systematic review aimed to identify accessible and validated tools, for the assessment of workplace physical and psychosocial hazards, and consolidate the results into a matrix for use by work health and safety (WHS) professionals. Web of Science, Medline, ProQuest Central, and PsychInfo electronic databases, along with grey literature, were searched (Jan 1990 to July 2020). Studies that included tools with evidence of validity for the identification of physical hazards, psychosocial hazards, or both were included. A total of 83 tools were identified and then reviewed to ensure the tools were accessible. The final matrix included a total of 26 tools (16 physical, 4 psychosocial, and 6 comprehensive [physical and psychosocial]). Evidence on best practice for MSD mitigation supports the need for a comprehensive approach; however, the current review identified limitations in the availability of such tools to support WHS professionals.

starMC: an automata based CTL* model checker

Model-checking of temporal logic formulae is a widely used technique for the verification of systems. CTL ∗ is a temporal logic that allows to consider an intermix of both branching behaviours (like in CTL) and linear behaviours (LTL), overcoming the limitations of LTL (that cannot express "possibility") and CTL (cannot fully express fairness). Nevertheless CTL ∗ model-checkers are uncommon. This paper presents (1) the algorithms for a fully symbolic automata-based approach for CTL ∗ , and (2) their implementation in the open-source tool starMC, a CTL ∗ model checker for systems specified as Petri nets. Testing has been conducted on thousands of formulas over almost a hundred models. The experiments show that the fully symbolic automata-based approach of starMC can compute the set of states that satisfy a CTL ∗ formula for very large models (non trivial formulas for state spaces larger than 10⁴⁸⁰ states are evaluated in less than a minute).

Polypharmacy in elderly people

Polypharmacy characterizes ongoing prescription of multiple medications in a patient. Following the demographic change and growing number of elderly patients, polypharmacy is of major concern due to the associated risks and even mortality. Many causes made this geriatric syndrome more common in the past decade. First, the management of comorbidities is often lacking in disease-specific guidelines. Second, multimorbidity is rising due to the ageing population. Third, deprescribing methods are sparse, and results are conflicting. This mini review integrates the effects of polypharmacy on mortality and morbidity, the causes and confounders of polypharmacy, and presents a practical stepwise manual of deprescribing. The work is based on a literature search for randomized control trials and reviews in English and German from 2015 onwards in the PubMed database, with integration of relevant citations as a result of this search.

Lean 4.0 tools and technologies to improve companies' maturity level: the COVID-19 context

The global pandemic triggered by the new COVID-19 led to severe limitations in daily life, both private and professional. Almost all companies have been affected in one way or another. The COVID-19 crisis imposed new challenges for enterprises. As a result, many companies have been forced to rethink how to align many of their processes and practices with the new COVID-19 context, and fulfill their mission while maintaining a safe and secure management business operating environment for both employees and customers. This paper aims to bring empirical evidence, through a questionnaire survey, of the positive influence of using Lean Management tools and Industry 4.0 technologies on five organizational dimensions (strategy, leadership, culture, operations and products, and technology). Data from 98 Algerian and French companies of different sizes and representing various activity sectors was collected. Respondents were asked to answer 5 organizational dimensions (strategy, leadership, culture, operations and products, and technology) in the context COVID-19 crisis. Statistical analysis was performed through path coefficient using a Smart PLS. The results show that Industry 4.0 technologies tend to be strongly associated with Lean management tools, and that understanding the relationship between Lean management tools and Industry 4.0 technologies can improve the organizational dimensions: leadership, strategy, operation, and production. This research provides managerial implications that can help managers to understand the synergies and benefits of integrating and implementing Lean 4.0 tools and technologies in organizations in both crises and regular contexts.

MicroRNA Databases and Tools

In this era of big data, sets of methodologies and strategies are designed to extract knowledge from huge volumes of data. However, the cost of where and how to get this information accurately and quickly is extremely important, given the diversity of genomes and the different ways of representing that information. Among the huge set of information and relationships that the genome carries, there are sequences called miRNAs (microRNAs). These sequences were described in the 1990s and are mainly involved in mechanisms of regulation and gene expression. Having this in mind, this chapter focuses on exploring the available literature and providing useful and practical guidance on the miRNA database and tools topic. For that, we organized and present this text in two ways: (a) the update reviews and articles, which best summarize and discuss the theme; and (b) our update investigation on miRNA literature and portals about databases and tools. Finally, we present the main challenge and a possible solution to improve resources and tools.

Assessment tools measuring health-related empowerment in psychosocially vulnerable populations: a systematic review

BACKGROUND

Many programs are undertaken to facilitate the empowerment of vulnerable populations across the world. However, an overview of appropriate empowerment measurements to evaluate such initiatives remains incomplete to date. This systematic review aims to describe and summarise psychometric properties, feasibility and clinical utility of the available tools for measuring empowerment in psychosocially vulnerable populations.

METHODS

A systematic literature review following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines was completed. A descriptive approach was used for data analysis. Papers were eligible if they explored the development, validation, cross-cultural translation or the utility of an empowerment measurement tool in the context of psychosocially vulnerable populations.

RESULTS

Twenty-six included articles described twenty-six separate studies in which 16 empowerment measurement tools were developed, validated/translated, or used. There was heterogeneity in empowerment constructs, samples targeted, and psychometric properties measured. The measurement of reliability of the included instruments was satisfactory in most cases. However, the validity, responsiveness, interpretability, feasibility and clinical utility of the identified measurement tools were often not adequately described or measured.

CONCLUSION

This systematic review provides a useful snapshot of the strengths as well as limitations of existing health related empowerment measurement tools used with psychosocially vulnerable populations in terms of their measurement properties, and constructs captured. It highlights significant gaps in empowerment tool measurement, development and evaluation processes. In particular, the results suggest that in addition to systematic assessments of psychometric properties, the inclusion of feasibility and clinical utility as outcome measures are important to assess relevance to clinical practice.

Tools for studying and modulating (cardiac muscle) cell mechanics and mechanosensing across the scales

Cardiomyocytes generate force for the contraction of the heart to pump blood into the lungs and body. At the same time, they are exquisitely tuned to the mechanical environment and react to e.g. changes in cell and extracellular matrix stiffness or altered stretching due to reduced ejection fraction in heart disease, by adapting their cytoskeleton, force generation and cell mechanics. Both mechanical sensing and cell mechanical adaptations are multiscale processes. Receptor interactions with the extracellular matrix at the nanoscale will lead to clustering of receptors and modification of the cytoskeleton. This in turn alters mechanosensing, force generation, cell and nuclear stiffness and viscoelasticity at the microscale. Further, this affects cell shape, orientation, maturation and tissue integration at the microscale to macroscale. A variety of tools have been developed and adapted to measure cardiomyocyte receptor-ligand interactions and forces or mechanics at the different ranges, resulting in a wealth of new information about cardiomyocyte mechanobiology. Here, we take stock at the different tools for exploring cardiomyocyte mechanosensing and cell mechanics at the different scales from the nanoscale to microscale and macroscale.

Performance of the Simple Clinical Score (SCS) and the Rapid Emergency Medicine Score (REMS) to predict severity level and mortality rate among patients with sepsis in the emergency department

Nurses play a key role as the first line of service for patients with medical conditions and injuries in the emergency department (ED), which includes assessing patients for sepsis. The researchers evaluated tools to examine the performance of the Simple Clinical Score (SCS) and the Rapid Emergency Medicine Score (REMS) to predict sepsis severity and mortality among sepsis patients in the ED. A retrospective survey was performed, selecting participants by using a purposive sampling method, and including the medical records of all patients diagnosed with sepsis admitted to the ED at Singburi Hospital, Thailand. Data were analysed using the ROC curve and the Area Under Curve (AUC) to calculate the accuracy of each patient's mortality prediction. A total of 225 patients diagnosed with sepsis was identified, with a mortality rate of 59.11% after admission to the medical service and intensive care unit. The AUC analysis showed that the accuracy of the model generated from the REMS (88.6%) was higher than that of the SCS (76.7%). The authors also recommend that key variables identified in this research should be used to develop screening and assessment tools for sepsis in the context of the ED.

Developing the first pan-Canadian survey on patient engagement in patient safety

BACKGROUND

Patient safety is a worldwide problem, and the patient contribution to mitigate the risk of patient harm is now recognized as a cornerstone to its solution. In order to understand the nature of integrating patients into patient safety and healthcare organizations and to monitor their integration, a Canadian survey tool has been co-constructed by patients, researchers and the Canadian Patient Safety Institute (CPSI). This questionnaire has been adapted from the French version of the patient engagement (PE) in patient safety (PS) questionnaire created for the province of Quebec, Canada.

METHODOLOGY

The pan-Canadian PE in PS survey tool was developed in a five-step process: (1) a literature review and revision of the initial tool developed in the province of Quebec; (2) translation of the French questionnaire into an English version tool; (3) creation of a Canadian expert advisory group; (4) adaptation of the English version tool based on feedback from the expert advisory group (assessment and development of the construct's dimensions, wording assessment and adaptation for pan-Canadian use, technical testing of the online platform for the survey); and (5) pilot testing and pre-validation of the tool before pan-Canadian use.

RESULTS AND CONCLUSION

Eight pan-Canadian PE in PS surveys were completed from five Canadian provinces by the expert advisory group and six surveys were completed during the pilot project by participants from different provinces in Canada. This survey tool comprises 5 sections: (1) demographic identification of the participants (Q1 to Q5); (2) general questions (Q6 to Q17); (3) the patient engagement process (experience level of participants and organizational incentives for PE in general) (Q18 to Q33); (4) PE in PS processes, such as current activities, strategies, structures, resources and factors (Q34 to Q67); and (5) the context and impact of PE in PS initiatives in Canadian healthcare organizations (CHOs) (Q68 to Q75), including outcome identification, improvement mechanisms and strategies, evaluation mechanisms, and indicators.

The bayberry database: a multiomic database for Myrica rubra, an important fruit tree with medicinal value

BACKGROUND

Chinese bayberry (Myrica rubra Sieb. & Zucc.) is an important fruit tree in China, and has high medicinal value. At present, the genome, transcriptome and germplasm resources of bayberry have been reported. In order to make more convenient use of these data, the Bayberry Database was established.

RESULTS

The Bayberry Database is a comprehensive and intuitive data platform for examining the diverse annotated genome and germplasm resources of this species. This database contains nine central functional domains to interact with multiomic data: home, genome, germplasm, markers, tools, map, expression, reference, and contact. All domains provide pathways to a variety of data types composed of a reference genome sequence, transcriptomic data, gene patterns, phenotypic data, fruit images of Myrica rubra varieties, gSSR data, gene maps with annotation and evolutionary analyses. The tools module includes BLAST search, keyword search, sequence fetch and enrichment analysis functions.

CONCLUSIONS

The web address of the database is as follows http://www.bayberrybase.cn/ . The Myrica rubra database is an intelligent, interactive, and user-friendly system that enables researchers, breeders and horticultural personnel to browse, search and retrieve relevant and useful information and thus facilitate genomic research and breeding efforts concerning Myrica rubra. This database will be of great help to bayberry research and breeding in the future.

[Digital diagnostic support in rheumatology]

Only the correct diagnosis enables an effective treatment of rheumatic diseases. Digitalization has already significantly accelerated and simplified our everyday life. An increasing number of digital options are available to patients and medical personnel in rheumatology to accelerate and improve the diagnosis. This work gives an overview of current developments and tools for patients and rheumatologists, regarding digital diagnostic support in rheumatology.

Translating health information into policy-making: A pragmatic framework

Knowledge translation (KT) is increasingly acknowledged to have the potential to improve policy-making. The value of health information (HI), as part of the KT context, is now also increasingly understood. This paper aims to identify existing tools for the translation of HI into policy-making and to develop a related framework facilitating future application of these identified tools. Updating and building upon a scoping review undertaken for the Health Evidence Network (HEN) Synthesis Report No. 54, commissioned by the World Health Organization (WHO) Regional Office for Europe in 2017, a literature search was conducted using the same databases (PubMed and Scopus) and the same keywords as in the WHO/HEN scoping review. All papers elaborating on tools enhancing the use of HI in policy-making were included. Of the 2549 records screened, 17 publications were included in this study. This review identified four different types of tools: 1) Visualisation and modelling tools, 2) Information packaging and synthesis tools, 3) Communication and dissemination tools and 4) Information linkage and exchange tools. The distinctions between these are fluid as different tools can be combined or incorporated into one another to complement each other. Our framework shows that communication/dissemination or linkage tools are crucial to effectively inform policy decisions through HI. This study helps to understand and guide the processes of KT of HI.