Facilitating the analysis of COVID-19 literature through a knowledge graph

At the end of 2019, Chinese authorities alerted the World Health Organization (WHO) of the outbreak of a new strain of the coronavirus, called SARS-CoV-2, which struck humanity by an unprecedented disaster a few months later. In response to this pandemic, a publicly available dataset was released on Kaggle which contained information of over 63,000 papers. In order to facilitate the analysis of this large mass of literature, we have created a knowledge graph based on this dataset. Within this knowledge graph, all information of the original dataset is linked together, which makes it easier to search for relevant information. The knowledge graph is also enriched with additional links to appropriate, already existing external resources. In this paper, we elaborate on the different steps performed to construct such a knowledge graph from structured documents. Moreover, we discuss, on a conceptual level, several possible applications and analyses that can be built on top of this knowledge graph. As such, we aim to provide a resource that allows people to more easily build applications that give more insights into the COVID-19 pandemic

Socio-demographic and clinical characteristics of re-presentation to an Australian inner-city emergency department: implications for service delivery

BACKGROUND: People who have complex health care needs frequently access emergency departments for treatment of acute illness and injury. In particular, evidence suggests that those who are homeless, or suffer mental illness, or have a history of substance misuse, are often repeat users of emergency departments. The aim of this study was to describe the socio-demographic and clinical characteristics of emergency department re-presentations. Re-presentation was defined as a return visit to the same emergency department within 28 days of discharge from hospital. METHODS: A retrospective cohort study was conducted of emergency department presentations occurring over a 24-month period to an Australian inner-city hospital. Characteristics were examined for their influence on the binary outcome of re-presentation within 28 days of discharge using logistic regression with the variable patient fitted as a random effect. RESULTS: From 64,147 presentations to the emergency department the re-presentation rate was 18.0% (n = 11,559) of visits and 14.4% (5,894/40,942) of all patients. Median time to re-presentation was 6 days, with more than half occurring within one week of discharge (60.8%; n = 6,873), and more than three-quarters within two weeks (80.9%; n = 9,151). The odds of re-presentation increased three-fold for people who were homeless compared to those living in stable accommodation (adjusted OR 3.09; 95% CI, 2.83 to 3.36). Similarly, the odds of re-presentation were significantly higher for patients receiving a government pension compared to those who did not (adjusted OR 1.73; 95% CI, 1.63 to 1.84), patients who left part-way through treatment compared to those who completed treatment and were discharged home (adjusted OR 1.64; 95% CI, 1.36 to 1.99), and those discharged to a residential-care facility compared to those who were discharged home (adjusted OR 1.46: 95% CI, 1.03 to 2.06). CONCLUSION: Emergency department re-presentation rates cluster around one week after discharge and rapidly decrease thereafter. Housing status and being a recipient of a government pension are the most significant risk factors. Early identification and appropriate referrals for those patients who are at risk of emergency department re-presentation will assist in the development of targeted strategies to improve health service delivery to this vulnerable group

Using coherence to enhance function in chemical and biophysical systems

Coherence phenomena arise from interference, or the addition, of wave-like amplitudes with fixed phase differences. Although coherence has been shown to yield transformative ways for improving function, advances have been confined to pristine matter and coherence was considered fragile. However, recent evidence of coherence in chemical and biological systems suggests that the phenomena are robust and can survive in the face of disorder and noise. Here we survey the state of recent discoveries, present viewpoints that suggest that coherence can be used in complex chemical systems, and discuss the role of coherence as a design element in realizing function

Stakeholder involvement in systematic reviews:a scoping review

Abstract Background There is increasing recognition that it is good practice to involve stakeholders (meaning patients, the public, health professionals and others) in systematic reviews, but limited evidence about how best to do this. We aimed to document the evidence-base relating to stakeholder involvement in systematic reviews and to use this evidence to describe how stakeholders have been involved in systematic reviews. Methods We carried out a scoping review, following a published protocol. We searched multiple electronic databases (2010–2016), using a stepwise searching approach, supplemented with hand searching. Two authors independently screened and discussed the first 500 abstracts and, after clarifying selection criteria, screened a further 500. Agreement on screening decisions was 97%, so screening was done by one reviewer only. Pre-planned data extraction was completed, and the comprehensiveness of the description of methods of involvement judged. Additional data extraction was completed for papers judged to have most comprehensive descriptions. Three stakeholder representatives were co-authors for this systematic review. Results We included 291 papers in which stakeholders were involved in a systematic review. Thirty percent involved patients and/or carers. Thirty-two percent were from the USA, 26% from the UK and 10% from Canada. Ten percent (32 reviews) were judged to provide a comprehensive description of methods of involving stakeholders. Sixty-nine percent (22/32) personally invited people to be involved; 22% (7/32) advertised opportunities to the general population. Eighty-one percent (26/32) had between 1 and 20 face-to-face meetings, with 83% of these holding ≤ 4 meetings. Meetings lasted 1 h to ½ day. Nineteen percent (6/32) used a Delphi method, most often involving three electronic rounds. Details of ethical approval were reported by 10/32. Expenses were reported to be paid to people involved in 8/32 systematic reviews. Discussion/conclusion We identified a relatively large number (291) of papers reporting stakeholder involvement in systematic reviews, but the quality of reporting was generally very poor. Information from a subset of papers judged to provide the best descriptions of stakeholder involvement in systematic reviews provide examples of different ways in which stakeholders have been involved in systematic reviews. These examples arguably currently provide the best available information to inform and guide decisions around the planning of stakeholder involvement within future systematic reviews. This evidence has been used to develop online learning resources. Systematic review registration The protocol for this systematic review was published on 21 April 2017. Publication reference: Pollock A, Campbell P, Struthers C, Synnot A, Nunn J, Hill S, Goodare H, Watts C, Morley R: Stakeholder involvement in systematic reviews: a protocol for a systematic review of methods, outcomes and effects. Research Involvement and Engagement 2017, 3:9. https://doi.org/10.1186/s40900-017-0060-4

A longitudinal study of tobacco use among American Indian and Alaska Native tribal college students

<p>Abstract</p> <p>Background</p> <p>American Indians (AI) have the highest smoking rates of any ethnic group in the US (40.8%), followed most closely by African Americans (24.3%) and European Americans (23.6%). AI smokers also have more difficulty quitting smoking compared to other ethnic groups, evidenced by their significantly lower quit ratios, and are among the least successful in maintaining long term abstinence. While health disparities like these have existed for years among AI, the epidemiology of smoking and nicotine dependence has not been optimally described among this underserved population.</p> <p>Our overarching hypothesis is that the susceptibility of AI to cigarette smoking and nicotine dependence and its consequences has both an underlying nicotine metabolism component as well as psychosocial, cultural, and environment causes. We are well-positioned to explore this issue for the first time in this population. Our objective is to establish a cohort of AI tribal college/university students to determine the predictors of smoking initiation (non-use to experimentation), progression (experimentation to established use), and cessation (established use to cessation). Much of what is known about the process of smoking initiation and progression comes from quantitative studies with non-Native populations. Information related to smoking use among AI tribal college/university (TCU) students is entirely unknown and critically needs further investigation. This study will be the first of its kind among AI college students who are at the highest risk among all ethnic groups for tobacco dependence.</p> <p>Methods/design</p> <p>First year students at Haskell Indian Nations University in Kansas will be recruited over four consecutive years and will be surveyed annually and repeatedly through year 5 of the study. We will use both longitudinal quantitative surveys and qualitative focus group methods to examine key measures and determinants of initiation and use among this high risk group.</p

Expression variability of co-regulated genes differentiates Saccharomyces cerevisiae strains

Background: Saccharomyces cerevisiae (Baker’s yeast) is found in diverse ecological niches and is characterized by high adaptive potential under challenging environments. In spite of recent advances on the study of yeast genome diversity, little is known about the underlying gene expression plasticity. In order to shed new light onto this biological question, we have compared transcriptome profiles of five environmental isolates, clinical and laboratorial strains at different time points of fermentation in synthetic must medium, during exponential and stationary growth phases. Results: Our data unveiled diversity in both intensity and timing of gene expression. Genes involved in glucose metabolism and in the stress response elicited during fermentation were among the most variable. This gene expression diversity increased at the onset of stationary phase (diauxic shift). Environmental isolates showed lower average transcript abundance of genes involved in the stress response, assimilation of nitrogen and vitamins, and sulphur metabolism, than other strains. Nitrogen metabolism genes showed significant variation in expression among the environmental isolates. Conclusions: Wild type yeast strains respond differentially to the stress imposed by nutrient depletion, ethanol accumulation and cell density increase, during fermentation of glucose in synthetic must medium. Our results support previous data showing that gene expression variability is a source of phenotypic diversity among closely related organisms.Fundação para a Ciência e TecnologiaThe authors wish to thank Adega Cooperativa da Bairrada, Cantanhede, Portugal, for providing the commercial strains

Developing and testing an instrument for identifying performance incentives in the Greek health care sector

BACKGROUND: In the era of cost containment, managers are constantly pursuing increased organizational performance and productivity by aiming at the obvious target, i.e. the workforce. The health care sector, in which production processes are more complicated compared to other industries, is not an exception. In light of recent legislation in Greece in which efficiency improvement and achievement of specific performance targets are identified as undisputable health system goals, the purpose of this study was to develop a reliable and valid instrument for investigating the attitudes of Greek physicians, nurses and administrative personnel towards job-related aspects, and the extent to which these motivate them to improve performance and increase productivity. METHODS: A methodological exploratory design was employed in three phases: a) content development and assessment, which resulted in a 28-item instrument, b) pilot testing (N = 74) and c) field testing (N = 353). Internal consistency reliability was tested via Cronbach's alpha coefficient and factor analysis was used to identify the underlying constructs. Tests of scaling assumptions, according to the Multitrait-Multimethod Matrix, were used to confirm the hypothesized component structure. RESULTS: Four components, referring to intrinsic individual needs and external job-related aspects, were revealed and explain 59.61% of the variability. They were subsequently labeled: job attributes, remuneration, co-workers and achievement. Nine items not meeting item-scale criteria were removed, resulting in a 19-item instrument. Scale reliability ranged from 0.782 to 0.901 and internal item consistency and discriminant validity criteria were satisfied. CONCLUSION: Overall, the instrument appears to be a promising tool for hospital administrations in their attempt to identify job-related factors, which motivate their employees. The psychometric properties were good and warrant administration to a larger sample of employees in the Greek healthcare system

Positive Darwinian Selection in the Piston That Powers Proton Pumps in Complex I of the Mitochondria of Pacific Salmon

The mechanism of oxidative phosphorylation is well understood, but evolution of the proteins involved is not. We combined phylogenetic, genomic, and structural biology analyses to examine the evolution of twelve mitochondrial encoded proteins of closely related, yet phenotypically diverse, Pacific salmon. Two separate analyses identified the same seven positively selected sites in ND5. A strong signal was also detected at three sites of ND2. An energetic coupling analysis revealed several structures in the ND5 protein that may have co-evolved with the selected sites. These data implicate Complex I, specifically the piston arm of ND5 where it connects the proton pumps, as important in the evolution of Pacific salmon. Lastly, the lineage to Chinook experienced rapid evolution at the piston arm

Variations in Stress Sensitivity and Genomic Expression in Diverse S. cerevisiae Isolates

Interactions between an organism and its environment can significantly influence phenotypic evolution. A first step toward understanding this process is to characterize phenotypic diversity within and between populations. We explored the phenotypic variation in stress sensitivity and genomic expression in a large panel of Saccharomyces strains collected from diverse environments. We measured the sensitivity of 52 strains to 14 environmental conditions, compared genomic expression in 18 strains, and identified gene copy-number variations in six of these isolates. Our results demonstrate a large degree of phenotypic variation in stress sensitivity and gene expression. Analysis of these datasets reveals relationships between strains from similar niches, suggests common and unique features of yeast habitats, and implicates genes whose variable expression is linked to stress resistance. Using a simple metric to suggest cases of selection, we found that strains collected from oak exudates are phenotypically more similar than expected based on their genetic diversity, while sake and vineyard isolates display more diverse phenotypes than expected under a neutral model. We also show that the laboratory strain S288c is phenotypically distinct from all of the other strains studied here, in terms of stress sensitivity, gene expression, Ty copy number, mitochondrial content, and gene-dosage control. These results highlight the value of understanding the genetic basis of phenotypic variation and raise caution about using laboratory strains for comparative genomics