ResearchPad - science-policy https://www.researchpad.co Default RSS Feed en-us © 2020 Newgen KnowledgeWorks <![CDATA[Meta-analysis of the correlation between dietary copper supply and broiler performance]]> https://www.researchpad.co/article/elastic_article_15740 To conduct a meta-analysis assessing the correlation between dietary copper supply and broiler performanceMethodsStudies that were published prior to January 2019 and reported the dietary copper supply and broiler growth performance were identified using search functions in the Web of Science, Springer, Elsevier, Science Direct, and Taylor & Francis Online databases; the Journal of Dairy Research; and China National Knowledge Infrastructure (CNKI). We performed stratified analyses on the possible sources of bias, including differences in the study locations and years of publication. The publication bias was assessed with Egger’s test method.ResultsA total of 12 randomized controlled trial (RCT) studies were eligible for inclusion. The pooled WMDs of the ADG, ADFI and FCR were -0.166 (95% CI: -1.587 to 1.254), -0.844 (95% CI: -1.536 to -0.152) and -0.029 (95% CI: -0.057 to 0.000), respectively. In the Israeli and Indian studies, the ADG and ADFI data in the experimental group were higher than those in the control group; however, in America, a relatively high FCR value was found in the experimental group compared to that in the control group. The analysis of the study period showed that for the 1980s and 2010s, the ADG and ADFI of the experimental group were lower than those of the control group, while, in the 1990s and 2010s, the FCR of the experimental group were lower than those of the control group. The observed values were adjusted for study effects, and a model was used to obtain the copper supplementation under the optimal production performance. The results showed that the adjusted average daily gain (ADG), average daily feed intake (ADFI), and feed to gain ratio (FCR) presented a quadratic relationship with Cu supplementation (P<0.05). The maximum value of ADG (31.84 g/d) is reached when Cu is added at amount of 158 mg/kg, and the minimum value of FCR (1.53) is reached when Cu is added at amount of 217 mg/kg. No significant publication bias existed in the studies (Egger's test: P value were 0.81, 0.71 and 0.14).ConclusionFrom this study, it can be concluded that the traditional copper addition is no longer suitable for modern broiler breeding; the higher copper content may be beneficial for the production performance of broilers. ]]> <![CDATA[Surviving COVID-19: A disease tolerance perspective]]> https://www.researchpad.co/article/elastic_article_15423 <![CDATA[The prevalence of hepatitis C virus in hemodialysis patients in Pakistan: A systematic review and meta-analysis]]> https://www.researchpad.co/article/elastic_article_14616 Hepatitis C virus (HCV) infection is one of the most common bloodborne viral infections reported in Pakistan. Frequent dialysis treatment of hemodialysis patients exposes them to a high risk of HCV infection. The main purpose of this paper is to quantify the prevalence of HCV in hemodialysis patients through a systematic review and meta-analysis.MethodsWe systematically searched PubMed, Medline, EMBASE, Pakistani Journals Online and Web of Science to identify studies published between 1 January 1995 and 30 October 2019, reporting on the prevalence of HCV infection in hemodialysis patients. Meta-analysis was performed using a random-effects model to obtain pooled estimates. A funnel plot was used in conjunction with Egger’s regression test for asymmetry and to assess publication bias. Meta-regression and subgroup analyses were used to identify potential sources of heterogeneity among the included studies. This review was registered on PROSPERO (registration number CRD42019159345).ResultsOut of 248 potential studies, 19 studies involving 3446 hemodialysis patients were included in the meta-analysis. The pooled prevalence of HCV in hemodialysis patients in Pakistan was 32.33% (95% CI: 25.73–39.30; I2 = 94.3%, p < 0.01). The subgroup analysis showed that the prevalence of HCV among hemodialysis patients in Punjab was significantly higher (37.52%; 95% CI: 26.66–49.03; I2 = 94.5, p < 0.01) than 34.42% (95% CI: 14.95–57.05; I2 = 91.3%, p < 0.01) in Baluchistan, 27.11% (95% CI: 15.81–40.12; I2 = 94.5, p < 0.01) in Sindh and 22.61% (95% CI: 17.45–28.2; I2 = 78.6, p < 0.0117) in Khyber Pukhtoonkhuwa.ConclusionsIn this study, we found a high prevalence (32.33%) of HCV infection in hemodialysis patients in Pakistan. Clinically, hemodialysis patients require more attention and resources than the general population. Preventive interventions are urgently needed to decrease the high risk of HCV infection in hemodialysis patients in Pakistan. ]]> <![CDATA[Predicting the impact of patient and private provider behavior on diagnostic delay for pulmonary tuberculosis patients in India: A simulation modeling study]]> https://www.researchpad.co/article/elastic_article_14543 India contributes more than a quarter of the 10 million global tuberculosis (TB) cases every year.Several studies capture long, circuitous care pathways followed by TB patients until their diagnosis. However, these studies do not quantify the link between diagnostic delay and underlying patient and provider behavior characteristics.What did the researchers do and find?We developed a quantitative simulation model to estimate the impact of behavioral characteristics of patients and providers on diagnostic delay and estimated the parameters of this model using data from detailed interviews of 76 patients from Mumbai and 64 patients from Patna.We found that earlier test ordering by providers would yield a much larger reduction in diagnostic delay than increasing their diagnostic accuracy.What do these findings mean?Policy-makers and implementing agencies should encourage early test ordering behavior by providers to reduce diagnostic delay, and, consequently, to reduce disease transmission. ]]> <![CDATA[Natural history museum collection and citizen science data show advancing phenology of Danish hoverflies (Insecta: Diptera, Syrphidae) with increasing annual temperature]]> https://www.researchpad.co/article/elastic_article_14485 We explore the phenological response by Danish hoverflies (Syrphidae) to continually rising annual temperatures by analysing >50.000 natural history collection and citizen science records for 37 species collected between 1900 and 2018, a period during which the annual average temperature in Denmark rose significantly (p << 0.01). We perform a simple linear regression analysis of the 10th percentile observation date for each species against year of observation. Fourteen of the species showed a statistically significant (p < 0.05) negative correlation between 10th percentile date and year of observation, indicating earlier emergence as a likely response to climatic warming. Eighteen species showed a non-significant (p ≥ 0.05) negative correlation between 10th percentile date and year of observation, while four species showed a non-significant (p ≥ 0.05) positive correlation, and one showed neither a positive nor a negative correlation. We explore the possible impact of the length of the data series on the regression analysis by dividing the species into four groups depending on how far back in time we have data: ultra-short series (with data from 2003–2018); short series (data from 1998–2018); medium series (data from 1980–2018); long series (data from 2018 to before 1980). The length of the series seems to have an effect on the results as 60% of the long series species (nine out of 15) showed a statistically significant negative correlation, while for the shorter series species less than 35% showed a statistically significant negative correlation. When we reduced the long series in length to short series, the proportion of statistically significant negative correlations fell to 33%, confirming this assumption. We conclude that northern temperate hoverflies generally react to the ongoing climatic warming by emerging earlier.

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<![CDATA[What makes an effective grants peer reviewer? An exploratory study of the necessary skills]]> https://www.researchpad.co/article/elastic_article_13869 This exploratory mixed methods study describes skills required to be an effective peer reviewer as a member of review panels conducted for federal agencies that fund research, and examines how reviewer experience and the use of technology within such panels impacts reviewer skill development. Two specific review panel formats are considered: in-person face-to-face and virtual video conference. Data were collected through interviews with seven program officers and five expert peer review panelists, and surveys from 51 respondents. Results include the skills reviewers’ consider necessary for effective review panel participation, their assessment of the relative importance of these skills, how they are learned, and how review format affects skill development and improvement. Results are discussed relative to the peer review literature and with consideration of the importance of professional skills needed by successful scientists and peer reviewers.

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<![CDATA[Potential of the economic valuation of soil-based ecosystem services to inform sustainable soil management and policy]]> https://www.researchpad.co/article/N930fd381-1759-4342-9b07-449675973e96

The concept of ecosystem services, especially in combination with economic valuation, can illuminate trade-offs involved in soil management, policy and governance, and thus support decision making. In this paper, we investigate and highlight the potential and limitations of the economic valuation of soil-based ecosystem services to inform sustainable soil management and policy. We formulate a definition of soil-based ecosystem services as basis for conducting a review of existing soil valuation studies with a focus on the inclusion of ecosystem services and the choice of valuation methods. We find that, so far, the economic valuation of soil-based ecosystem services has covered only a small number of such services and most studies have employed cost-based methods rather than state-of-the-art preference-based valuation methods, even though the latter would better acknowledge the public good character of soil related services. Therefore, the relevance of existing valuation studies for political processes is low. Broadening the spectrum of analyzed ecosystem services as well as using preference-based methods would likely increase the informational quality and policy relevance of valuation results. We point out options for improvement based on recent advances in economic valuation theory and practice. We conclude by investigating the specific roles economic valuation results can play in different phases of the policy-making process, and the specific requirements for its usefulness in this context.

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<![CDATA[Association between cigarette smoking and the risk of dysmenorrhea: A meta-analysis of observational studies]]> https://www.researchpad.co/article/N299c77b6-7bcf-4190-8f14-766ff39e61a2

Background

Emerging studies have found inconsistent results on the potential relationship between cigarette smoking and dysmenorrhea. Therefore, the aim of this study was to quantitatively synthesize the previous findings on the preceding relationship using meta-analysis.

Methods

Previous studies on the association between cigarette smoking and dysmenorrhea, published not later than November 2019, were systematically searched, using MeSH heading and/or relevant terms, in the electronic databases of PubMed, Medline, Web of Science and EMBASE. The I2 statistic was used to assess heterogeneity, whose source was explored using subgroup analysis. A pooled effect size was obtained using random effects model, and sensitivity analysis was performed to assess the consistency of the pooled effect size.

Results

After a rigorous screening process, 24 studies involving 27,091 participants were included in this meta-analysis. The results indicated that smokers were 1.45 times more likely to develop dysmenorrhea than non-smokers (odds ratio (OR) = 1.45, 95% confidence interval (CI): 1.30–1.61). In addition, individuals classified as currently smoking were 1.50 times more likely to develop dysmenorrhea than those who were classified as never smoking (OR = 1.50, 95% CI: 1.33–1.70), whereas being a former smoker was 1.31 times more likely to develop dysmenorrhea than being a never smoker (OR = 1.31, 95% CI: 1.18–1.46). Sensitivity analysis showed that exclusion of any single study did not materially alter the overall combined effect.

Conclusion

The evidence from this meta-analysis indicated a significant association between cigarette smoking (both current and former smoking) and dysmenorrhea. The adverse effects of smoking provide further support for prevention of dysmenorrhea and emphasize the need to target women.

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<![CDATA[Beware of vested interests: Epistemic vigilance improves reasoning about scientific evidence (for some people)]]> https://www.researchpad.co/article/Na4c1a7a8-d330-434e-b120-e60e98785391

In public disputes, stakeholders sometimes misrepresent statistics or other types of scientific evidence to support their claims. One of the reasons this is problematic is that citizens often do not have the motivation nor the cognitive skills to accurately judge the meaning of statistics and thus run the risk of being misinformed. This study reports an experiment investigating the conditions under which people become vigilant towards a source’s claim and thus reason more carefully about the supporting evidence. For this, participants were presented with a claim by a vested-interest or a neutral source and with statistical evidence which was cited by the source as being in support of the claim. However, this statistical evidence actually contradicted the source’s claim but was presented as a contingency table, which are typically difficult for people to interpret correctly. When the source was a lobbyist arguing for his company’s product people were better at interpreting the evidence compared to when the same source argued against the product. This was not the case for a different vested-interests source nor for the neutral source. Further, while all sources were rated as less trustworthy when participants realized that the source had misrepresented the evidence, only for the lobbyist source was this seen as a deliberate attempt at deception. Implications for research on epistemic trust, source credibility effects and science communication are discussed.

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<![CDATA[Will COVID-19 become the next neglected tropical disease?]]> https://www.researchpad.co/article/N3ea3a36c-f707-4121-8cab-1c306bbb1993 ]]> <![CDATA[No relationship between researcher impact and replication effect: an analysis of five studies with 100 replications]]> https://www.researchpad.co/article/N9497adc2-63df-4d42-8afd-a78238abd3e3

What explanation is there when teams of researchers are unable to successfully replicate already established ‘canonical’ findings? One suggestion that has been put forward, but left largely untested, is that those researchers who fail to replicate prior studies are of low ‘expertise and diligence’ and lack the skill necessary to successfully replicate the conditions of the original experiment. Here we examine the replication success of 100 scientists of differing ‘expertise and diligence’ who attempted to replicate five different studies. Using a bibliometric tool (h-index) as our indicator of researcher ‘expertise and diligence’, we examine whether this was predictive of replication success. Although there was substantial variability in replication success and in the h-factor of the investigators, we find no relationship between these variables. The present results provide no evidence for the hypothesis that systematic replications fail because of low ‘expertise and diligence’ among replicators.

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<![CDATA[The Global Museum: natural history collections and the future of evolutionary science and public education]]> https://www.researchpad.co/article/N1927fd64-d758-45ec-938c-2f53cec70b33

Natural history museums are unique spaces for interdisciplinary research and educational innovation. Through extensive exhibits and public programming and by hosting rich communities of amateurs, students, and researchers at all stages of their careers, they can provide a place-based window to focus on integration of science and discovery, as well as a locus for community engagement. At the same time, like a synthesis radio telescope, when joined together through emerging digital resources, the global community of museums (the ‘Global Museum’) is more than the sum of its parts, allowing insights and answers to diverse biological, environmental, and societal questions at the global scale, across eons of time, and spanning vast diversity across the Tree of Life. We argue that, whereas natural history collections and museums began with a focus on describing the diversity and peculiarities of species on Earth, they are now increasingly leveraged in new ways that significantly expand their impact and relevance. These new directions include the possibility to ask new, often interdisciplinary questions in basic and applied science, such as in biomimetic design, and by contributing to solutions to climate change, global health and food security challenges. As institutions, they have long been incubators for cutting-edge research in biology while simultaneously providing core infrastructure for research on present and future societal needs. Here we explore how the intersection between pressing issues in environmental and human health and rapid technological innovation have reinforced the relevance of museum collections. We do this by providing examples as food for thought for both the broader academic community and museum scientists on the evolving role of museums. We also identify challenges to the realization of the full potential of natural history collections and the Global Museum to science and society and discuss the critical need to grow these collections. We then focus on mapping and modelling of museum data (including place-based approaches and discovery), and explore the main projects, platforms and databases enabling this growth. Finally, we aim to improve relevant protocols for the long-term storage of specimens and tissues, ensuring proper connection with tomorrow’s technologies and hence further increasing the relevance of natural history museums.

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<![CDATA[Height of overburden fracture based on key strata theory in longwall face]]> https://www.researchpad.co/article/Nb6c965ed-0040-4b7a-b381-dffd2122531d

Among the three overburden zones (the caving zone, the fracture zone, and the continuous deformation zone) in longwall coal mining, the continuous deformation zone is often considered to be continuous without cracks, so continuum mechanics can be used to calculate the subsidence of overburden strata. Longwall coal mining, however, will induce the generation of wide cracks in the surface and thus may cause the continuous deformation zone to fracture. In this paper, whether there are cracks in the continuous deformation zone as well as the height of overburden fracture in longwall face and the subsidence and deformation of strata of different fracture penetration ratios were studied by means of physical simulation, theoretical analysis and numerical simulation. The results show that: (1) Rock stratum starts to fracture as long as it has slightly subsided for only tens of millimeters, and the height of fracture development is the height of working face overburden. (2) With the increase of fracture penetration ratio, the subsidence of key strata remains basically unchanged; the surface deformation range and the maximum compression deformation decrease, while the maximum horizontal movement and maximum horizontal tensile deformation increase. Therefore, the subsidence of overburden strata which have fractured but have not broken can be calculated through the continuum mechanics method.

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<![CDATA[Parametric CAD modeling for open source scientific hardware: Comparing OpenSCAD and FreeCAD Python scripts]]> https://www.researchpad.co/article/N836ce8d9-e17d-43c0-9509-c554011a4818

Open source hardware for scientific equipment needs to provide source files and enough documentation to allow the study, replication and modification of the design. In addition, parametric modeling is encouraged in order to facilitate customization for other experiments. Parametric design using a solid modeling programming language allows customization and provides a source file for the design. OpenSCAD is the most widely used scripting tool for parametric modeling of open source labware. However, OpenSCAD lacks the ability to export to standard parametric formats; thus, the parametric dimensional information of the model is lost. This is an important deficiency because it is key to share the design in the most accessible formats with no information loss. In this work we analyze OpenSCAD and compare it with FreeCAD Python scripts. We have created a parametric open source hardware design to compare these tools. Our findings show that although Python for FreeCAD is more arduous to learn, its advantages counterbalance the initial difficulties. The main benefits are being able to export to standard parametric models; using Python language with its libraries; and the ability to use and integrate the models in its graphical interface. Thus, making it more appropriate to design open source hardware for scientific equipment.

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<![CDATA[On the value of preprints: An early career researcher perspective]]> https://www.researchpad.co/article/5c784facd5eed0c4840072e6

Peer-reviewed journal publication is the main means for academic researchers in the life sciences to create a permanent public record of their work. These publications are also the de facto currency for career progress, with a strong link between journal brand recognition and perceived value. The current peer-review process can lead to long delays between submission and publication, with cycles of rejection, revision, and resubmission causing redundant peer review. This situation creates unique challenges for early career researchers (ECRs), who rely heavily on timely publication of their work to gain recognition for their efforts. Today, ECRs face a changing academic landscape, including the increased interdisciplinarity of life sciences research, expansion of the researcher population, and consequent shifts in employer and funding demands. The publication of preprints, publicly available scientific manuscripts posted on dedicated preprint servers prior to journal-managed peer review, can play a key role in addressing these ECR challenges. Preprinting benefits include rapid dissemination of academic work, open access, establishing priority or concurrence, receiving feedback, and facilitating collaborations. Although there is a growing appreciation for and adoption of preprints, a minority of all articles in life sciences and medicine are preprinted. The current low rate of preprint submissions in life sciences and ECR concerns regarding preprinting need to be addressed. We provide a perspective from an interdisciplinary group of ECRs on the value of preprints and advocate their wide adoption to advance knowledge and facilitate career development.

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<![CDATA[Scrutinizing assortative mating in birds]]> https://www.researchpad.co/article/5c784fead5eed0c4840078f1

It is often claimed that pair bonds preferentially form between individuals that resemble one another. Such assortative mating appears to be widespread throughout the animal kingdom. Yet it is unclear whether the apparent ubiquity of assortative mating arises primarily from mate choice (“like attracts like”), which can be constrained by same-sex competition for mates; from spatial or temporal separation; or from observer, reporting, publication, or search bias. Here, based on a conventional literature search, we find compelling meta-analytical evidence for size-assortative mating in birds (r = 0.178, 95% CI 0.142–0.215, 83 species, 35,591 pairs). However, our analyses reveal that this effect vanishes gradually with increased control of confounding factors. Specifically, the effect size decreased by 42% when we used previously unpublished data from nine long-term field studies, i.e., data free of reporting and publication bias (r = 0.103, 95% CI 0.074–0.132, eight species, 16,611 pairs). Moreover, in those data, assortative mating effectively disappeared when both partners were measured by independent observers or separately in space and time (mean r = 0.018, 95% CI −0.016–0.057). Likewise, we also found no evidence for assortative mating in a direct experimental test for mutual mate choice in captive populations of Zebra finches (r = −0.020, 95% CI −0.148–0.107, 1,414 pairs). These results highlight the importance of unpublished data in generating unbiased meta-analytical conclusions and suggest that the apparent ubiquity of assortative mating reported in the literature is overestimated and may not be driven by mate choice or mating competition for preferred mates.

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<![CDATA[Base-rate expectations modulate the causal illusion]]> https://www.researchpad.co/article/5c8823c7d5eed0c484638fca

Previous research revealed that people’s judgments of causality between a target cause and an outcome in null contingency settings can be biased by various factors, leading to causal illusions (i.e., incorrectly reporting a causal relationship where there is none). In two experiments, we examined whether this causal illusion is sensitive to prior expectations about base-rates. Thus, we pretrained participants to expect either a high outcome base-rate (Experiment 1) or a low outcome base-rate (Experiment 2). This pretraining was followed by a standard contingency task in which the target cause and the outcome were not contingent with each other (i.e., there was no causal relation between them). Subsequent causal judgments were affected by the pretraining: When the outcome base-rate was expected to be high, the causal illusion was reduced, and the opposite was observed when the outcome base-rate was expected to be low. The results are discussed in the light of several explanatory accounts (associative and computational). A rational account of contingency learning based on the evidential value of information can predict our findings.

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<![CDATA[DeephESC 2.0: Deep Generative Multi Adversarial Networks for improving the classification of hESC]]> https://www.researchpad.co/article/5c89774dd5eed0c4847d2963

Human embryonic stem cells (hESC), derived from the blastocysts, provide unique cellular models for numerous potential applications. They have great promise in the treatment of diseases such as Parkinson’s, Huntington’s, diabetes mellitus, etc. hESC are a reliable developmental model for early embryonic growth because of their ability to divide indefinitely (pluripotency), and differentiate, or functionally change, into any adult cell type. Their adaptation to toxicological studies is particularly attractive as pluripotent stem cells can be used to model various stages of prenatal development. Automated detection and classification of human embryonic stem cell in videos is of great interest among biologists for quantified analysis of various states of hESC in experimental work. Currently video annotation is done by hand, a process which is very time consuming and exhaustive. To solve this problem, this paper introduces DeephESC 2.0 an automated machine learning approach consisting of two parts: (a) Generative Multi Adversarial Networks (GMAN) for generating synthetic images of hESC, (b) a hierarchical classification system consisting of Convolution Neural Networks (CNN) and Triplet CNNs to classify phase contrast hESC images into six different classes namely: Cell clusters, Debris, Unattached cells, Attached cells, Dynamically Blebbing cells and Apoptically Blebbing cells. The approach is totally non-invasive and does not require any chemical or staining of hESC. DeephESC 2.0 is able to classify hESC images with an accuracy of 93.23% out performing state-of-the-art approaches by at least 20%. Furthermore, DeephESC 2.0 is able to generate large number of synthetic images which can be used for augmenting the dataset. Experimental results show that training DeephESC 2.0 exclusively on a large amount of synthetic images helps to improve the performance of the classifier on original images from 93.23% to 94.46%. This paper also evaluates the quality of the generated synthetic images using the Structural SIMilarity (SSIM) index, Peak Signal to Noise ratio (PSNR) and statistical p-value metrics and compares them with state-of-the-art approaches for generating synthetic images. DeephESC 2.0 saves hundreds of hours of manual labor which would otherwise be spent on manually/semi-manually annotating more and more videos.

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<![CDATA[Late-life mortality is underestimated because of data errors]]> https://www.researchpad.co/article/5c65dcdbd5eed0c484dec3bf

Knowledge of true mortality trajectory at extreme old ages is important for biologists who test their theories of aging with demographic data. Studies using both simulation and direct age validation found that longevity records for ages 105 years and older are often incorrect and may lead to spurious mortality deceleration and mortality plateau. After age 105 years, longevity claims should be considered as extraordinary claims that require extraordinary evidence. Traditional methods of data cleaning and data quality control are just not sufficient. New, more strict methodologies of data quality control need to be developed and tested. Before this happens, all mortality estimates for ages above 105 years should be treated with caution.

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<![CDATA[Association between commercial funding of Canadian patient groups and their views about funding of medicines: An observational study]]> https://www.researchpad.co/article/5c706777d5eed0c4847c7095

Background

Patient groups represent the interest of their members when it comes to drug funding. Many patient groups receive grants from pharmaceutical companies that make products being considered for funding. This research examines whether there is an association between the positions that Canadian groups take about the products and conflicts of interest with the companies.

Methods

The Common Drug Review (CDR) and panCanadian Oncology Drug Review (pCODR) make recommendations to Canadian provincial and federal drug plans about funding particular drug-indications. Both utilize input from patient groups in making their recommendations. Patient group submissions are available from both organizations and these submissions contain statements about conflicts of interest. Views of the patient groups, with and without a conflict with the company making the drug under consideration and without any conflicts at all, were assessed and then compared with the recommendations from CDR and pCODR.

Results

There was a total of 222 reports for drug-indications. There were 372 submissions from 93 different patient groups. Groups declared a total of 1896 conflicts with drug companies in 324 (87.1%) individual submissions. There were 268 submissions where groups declared a conflict with the company making the product or said they had no conflict. Irrespective of whether there was a conflict, the views of patient groups about the drug-indications under consideration were the same. There was no statistically significant difference between views of patient groups and the recommendations from CDR and/or pCODR.

Conclusions

The large majority of patient groups making submissions about funding of particular drug-indications had conflicts with the companies making the products and their views about the products were almost always positive. This association between funding and views needs to be further investigated to determine if a true cause and effect exists.

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