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result(s) for
"Vagenas, Dimitrios"
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Common misconceptions held by health researchers when interpreting linear regression assumptions, a cross-sectional study
by
Barnett, Adrian
,
Vagenas, Dimitrios
,
Jones, Lee
in
Biomedical Research
,
Computer and Information Sciences
,
Confidence intervals
2025
Statistical models are valuable tools for interpreting complex relationships within health systems. These models rely on a framework of statistical assumptions that, when correctly addressed, enable valid inferences and conclusions. However, failure to appropriately address these assumptions can lead to flawed analyses, resulting in misleading conclusions and contributing to the adoption of ineffective or harmful treatments and poorer health outcomes. This study examines researchers' understanding of the widely used linear regression model, focusing on assumptions, common misconceptions, and recommendations for improving research practices.
One hundred papers were randomly sampled from the journal PLOS ONE, which used linear regression in the materials and methods section and were from the health and biomedical field in 2019. Two independent volunteer statisticians rated each paper for the reporting of linear regression assumptions. The prevalence of assumptions reported by authors was described using frequencies, percentages, and 95% confidence intervals. The agreement of statistical raters was assessed using Gwet's statistic.
Of the 95 papers that met the inclusion and exclusion criteria, only 37% reported checking any linear regression assumptions, 22% reported checking one assumption, and no authors checked all assumptions. The biggest misconception was that the Y variable should be checked for normality, with only 5 of the 28 papers correctly checking the residuals for normality.
The reporting of linear regression assumptions is alarmingly low. When assumptions are checked, the reporting is often inadequate or incorrectly checked. Addressing these issues requires a cultural shift in research practices, including improved statistical training, more rigorous journal review processes, and a broader understanding of regression as a unifying framework. Greater emphasis must be placed on evaluating model assumptions and their implications rather than the rote application of statistical methods. Careful consideration of assumptions helps improve the reliability of statistical conclusions, reducing the risk of misleading findings influencing clinical practice and potentially affecting patient outcomes.
Journal Article
Linear regression reporting practices for health researchers, a cross-sectional meta-research study
by
Barnett, Adrian
,
Vagenas, Dimitrios
,
Jones, Lee
in
Biomedical Research
,
Check lists
,
Confidence intervals
2025
Decisions about health care, such as the effectiveness of new treatments for disease, are regularly made based on evidence from published work. However, poor reporting of statistical methods and results is endemic across health research and risks ineffective or harmful treatments being used in clinical practice. Statistical modelling choices often greatly influence the results. Authors do not always provide enough information to evaluate and repeat their methods, making interpreting results difficult. Our research is designed to understand current reporting practices and inform efforts to educate researchers.
Reporting practices for linear regression were assessed in 95 randomly sampled published papers in the health field from PLOS ONE in 2019, which were randomly allocated to statisticians for post-publication review. The prevalence of reporting practices is described using frequencies, percentages, and Wilson 95% confidence intervals.
While 92% of authors reported p-values and 81% reported regression coefficients, only 58% of papers reported a measure of uncertainty, such as confidence intervals or standard errors. Sixty-nine percent of authors did not discuss the scientific importance of estimates, and only 23% directly interpreted the size of coefficients.
Our results indicate that statistical methods and results were often poorly reported without sufficient detail to reproduce them. To improve statistical quality and direct health funding to effective treatments, we recommend that statisticians be involved in the research cycle, from study design to post-peer review. The research environment is an ecosystem, and future interventions addressing poor statistical quality should consider the interactions between the individuals, organisations and policy environments. Practical recommendations include journals producing templates with standardised reporting and using interactive checklists to improve reporting practices. Investments in research maintenance and quality control are required to assess and implement these recommendations to improve the quality of health research.
Journal Article
Intestinal Colonization Traits of Pandemic Multidrug-Resistant Escherichia coli ST131
2018
Epidemiological studies point to the gut as a key reservoir of multidrug resistant Escherichia coli multilocus sequence type 131 (ST131), a globally dominant pathogenic clone causing urinary tract and bloodstream infections. Here we report a detailed investigation of its intestinal lifestyle.
Clinical ST131 isolates and type 1 fimbriae null mutants were assessed for colonization of human intestinal epithelia and in mouse intestinal colonization models. Mouse gut tissue underwent histologic analysis for pathology and ST131 localization. Key findings were corroborated in mucus-producing human cell lines and intestinal biopsy specimens.
ST131 strains adhered to and invaded human intestinal epithelial cells more than probiotic and commensal strains. The reference ST131 strain EC958 established persistent intestinal colonization in mice, and expression of type 1 fimbriae mediated higher colonization levels. Bacterial loads were highest in the distal parts of the mouse intestine and did not cause any obvious pathology. Further analysis revealed that EC958 could bind to both mucus and underlying human intestinal epithelia.
ST131 strains can efficiently colonize the mammalian gut and persist long term. Type 1 fimbriae enhance ST131 intestinal colonization, suggesting that mannosides, currently developed as therapeutics for bladder infections and Crohn's disease, could also be used to limit intestinal ST131 reservoirs.
Journal Article
Implementation of negative pressure for acute pediatric burns (INPREP): A stepped-wedge cluster randomized controlled trial protocol
by
Dimanopoulos, Tanesha A.
,
Griffin, Bronwyn R.
,
Storey, Kristen
in
Adolescent
,
Australia
,
Biology and Life Sciences
2024
Acute application of adjunctive negative pressure wound therapy (NPWT) significantly improves time to re-epithelialization in pediatric burn patients. This adjunctive treatment has not yet been broadly or routinely adopted as a standard primary burns dressing strategy. The Implementation of Negative PRessurE for acute Pediatric burns (INPREP) trial will implement and evaluate the impact of adjunctive NPWT in parallel with co-designed implementation strategies and resources across four major pediatric hospitals.
We will conduct a multi-center, prospective, stepped-wedge cluster randomized controlled trial to implement adjunctive NPWT for acute pediatric burns. Participants will include pediatric burn patients presenting to one of four Australian tertiary pediatric hospitals for burn treatment. The intervention is adjunctive NPWT in parallel with co-designed and tailored implementation strategies and a suite of NPWT implementation resources, which form the INPREP toolkit. Using a hybrid type III design, this trial aims to evaluate the effectiveness of NPWT implementation in parallel with the INPREP toolkit using (i) implementation outcomes (e.g., adoption, appropriateness, acceptability, feasibility, and sustainability) and (ii) clinical outcomes (e.g., days to re-epithelialization, scar management requirements, skin grafting requirements). The primary outcome of this trial is treatment adoption-the proportion of eligible patients who receive NPWT.
This manuscript outlines a protocol for a hybrid type III stepped-wedge cluster randomized controlled trial of adjunctive NPWT implementation in acute pediatric burn care. We anticipate that NPWT implementation in parallel with the INPREP toolkit will be generalizable to emergency departments and burn services across Australia, and evidence generated will inform pediatric burn care internationally.
Australian and New Zealand Clinical Trials Registry: ACTRN12622000166774. Registered 1 February 2022.
Journal Article
Co-Assembled Nanosystems Exhibiting Intrinsic Fluorescence by Complexation of Amino Terpolymer and Its Quaternized Analog with Aggregation-Induced Emission (AIE) Dye
by
Rotas, Georgios
,
Pantelaiou, Michaila Akathi
,
Vagenas, Dimitrios
in
aggregation-induced emission
,
Amino compounds
,
Amino groups
2024
Aggregation-induced emission dyes (AIEs) have gained significant interest due to their unique optical properties. Upon aggregation, AIEs can exhibit remarkable fluorescence enhancement. These systems are ideal candidates for applications in bioimaging, such as image-guided drug delivery or surgery. Encapsulation of AIEs in polymeric nanocarriers can result in biocompatible and efficient nanosystems. Herein, we report the fabrication of novel nanoaggregates formulated by amino terpolymer and tetraphenylethylene (TPE) AIE in aqueous media. Poly(di(ethylene glycol) methyl ether methacrylate-co-2-(dimethylamino)ethylmethacrylate-co-oligoethylene glycol methyl ether methacrylate), P(DEGMA-co-DMAEMA-co-OEGMA) hydrophilic terpolymer was utilized for the complexation of the sodium tetraphenylethylene 4,4′,4″,4‴-tetrasulfonate AIE dye. Fluorescence spectroscopy, physicochemical studies, and self-assembly in aqueous and fetal bovine serum media were carried out. The finely dispersed nanoparticles exhibited enhanced fluorescence compared to the pure dye. To investigate the role of tertiary amino groups in the aggregation phenomenon, the polymer was quaternized, and quaternized polymer nanocarriers were fabricated. The increase in fluorescence intensity indicated stronger interaction between the cationic polymer analog and the dye. A stronger interaction between the nanoparticles and fetal bovine serum was observed in the case of the quaternized polymer. Thus, P(DEGMA-co-DMAEMA-co-OEGMA) formulations are better candidates for bioimaging applications than the quaternized ones, presenting both aggregation-induced emission and less interaction with fetal bovine serum.
Journal Article
Salivary DNA methylation panel to diagnose HPV-positive and HPV-negative head and neck cancers
by
Lim, Yenkai
,
Vagenas, Dimitrios
,
Punyadeera, Chamindie
in
Biomedical and Life Sciences
,
Biomedicine
,
Biopsy
2016
Background
Head and neck squamous cell carcinoma (HNSCC) is a heterogeneous group of tumours with a typical 5 year survival rate of <40 %. DNA methylation in tumour-suppressor genes often occurs at an early stage of tumorigenesis, hence DNA methylation can be used as an early tumour biomarker. Saliva is an ideal diagnostic medium to detect early HNSCC tumour activities due to its proximity to tumour site, non-invasiveness and ease of sampling. We test the hypothesis that the surveillance of DNA methylation in five tumour-suppressor genes (
RASSF1α
,
p16
INK4a
,
TIMP3
,
PCQAP
/
MED15
) will allow us to diagnose HNSCC patients from a normal healthy control group as well as to discriminate between Human Papillomavirus (HPV)-positive and HPV-negative patients.
Methods
Methylation-specific PCR (MSP) was used to determine the methylation levels of
RASSF1α
,
p16
INK4a
,
TIMP3
and
PCQAP
/
MED15
in DNA isolated from saliva. Statistical analysis was carried out using non-parametric Mann-Whitney’s
U
-test for individually methylated genes. A logistic regression analysis was carried out to determine the assay sensitivity when combing the five genes. Further, a five-fold cross-validation with a bootstrap procedure was carried out to determine how well the panel will perform in a real clinical scenario.
Results
Salivary DNA methylation levels were not affected by age. Salivary DNA methylation levels for
RASSF1α
,
p16
INK4a
,
TIMP3
and
PCQAP
/
MED15
were higher in HPV-negative HNSCC patients (
n
= 88) compared with a normal healthy control group (
n
= 122) (sensitivity of 71 % and specificity of 80 %). Conversely, DNA methylation levels for these genes were lower in HPV-positive HNSCC patients (
n
= 45) compared with a normal healthy control group (sensitivity of 80 % and specificity of 74 %), consistent with the proposed aetiology of HPV-positive HNSCCs.
Conclusions
Salivary DNA tumour-suppressor methylation gene panel has the potential to detect early-stage tumours in HPV-negative HNSCC patients. HPV infection was found to deregulate the methylation levels in HPV-positive HNSCC patients. Large-scale double-blinded clinical trials are crucial before this panel can potentially be integrated into a clinical setting.
Journal Article
Effectiveness of a Regenerative Epithelial Suspension (RES), on the pigmentation of split-thickness skin graft donor sites in children: the dRESsing pilot randomised controlled trial protocol
by
Tyack, Zephanie
,
McPhail, Steven M
,
Dettrick, Zoe
in
Clinical trials
,
Data collection
,
General anesthesia
2024
BackgroundPaediatric donor site wounds are often complicated by dyspigmentation following a split-thickness skin graft. These easily identifiable scars can potentially never return to normal pigmentation. A Regenerative Epidermal Suspension (RES) has been shown to improve pigmentation in patients with vitiligo, and in adult patients following a burn injury. Very little is known regarding the efficacy of RES for the management of donor site scars in children.Methods and analysisA pilot randomised controlled trial of 40 children allocated to two groups (RES or no RES) standard dressing applied to donor site wounds will be conducted. All children aged 16 years or younger requiring a split thickness skin graft will be screened for eligibility. The primary outcome is donor site scar pigmentation 12 months after skin grafting. Secondary outcomes include re-epithelialisation time, pain, itch, dressing application ease, treatment satisfaction, scar thickness and health-related quality of life. Commencing 7 days after the skin graft, the dressing will be changed every 3–5 days until the donor site is ≥ 95% re-epithelialised. Data will be collected at each dressing change and 3, 6 and 12 months post skin graft.Ethics and disseminationEthics approval was confirmed on 11 February 2019 by the study site Human Research Ethics Committee (HREC) (HREC/18/QCHQ/45807). Study findings will be published in peer-reviewed journals and presented at national and international conferences. This study was prospectively registered on the Australian New Zealand Clinical Trials Registry (available at https://anzctr.org.au/ACTRN12620000227998.aspx).Trial registration numberAustralian New Zealand Clinical Trials Registry [Available at https://anzctr.org.au/ACTRN12620000227998.aspx]
Journal Article
Pre-post feasibility trial of a telephone-delivered exercise intervention for patients during chemotherapy for recurrent ovarian cancer: the ECHO-R trial protocol
by
Rye, Sheree
,
Gordon, Louisa G
,
Hayes, Sandra C
in
Cancer therapies
,
Chemotherapy
,
Chronic illnesses
2024
IntroductionThe benefits of exercise in reducing treatment-related morbidity and improving quality of life following a primary diagnosis of cancer have been well documented and have led to exercise being recommended by oncology societies for all people with a cancer diagnosis. However, these recommendations are derived from research typically involving cohorts with more common cancers and relatively good prognosis, such as breast and prostate. Evidence from these cancers may not apply to women with recurrent ovarian cancer. Therefore, the primary objective of this trial is to evaluate the feasibility and safety of a home-based, telephone-delivered exercise intervention for women undergoing chemotherapy for recurrent ovarian cancer.Methods and analysisThe Exercise During Chemotherapy for Recurrent Ovarian Cancer (ECHO-R) trial is a single-arm, phase II, pre/postintervention trial of a 6-month, telephone-delivered exercise intervention (consistent with recommended exercise oncology prescription). The target sample size is 80 women who are currently undergoing (or are scheduled to receive) chemotherapy for recurrent ovarian cancer. Recruitment is through participating hospital sites in Queensland, Australia, or via self-referral. The exercise intervention comprises 12 telephone sessions over a 6-month period delivered by trial-trained exercise professionals and supplemented (where feasible) by five sessions face to face. Exercise prescription is individualised and works towards an overall goal of achieving a weekly target of 150 min of moderate-intensity, mixed-mode exercise. Assessments via self-administered survey and physical fitness and function tests occur at baseline and then at 6 and 9 months postbaseline. Data to inform feasibility and safety are recorded as case notes by the exercise professional during each session.Ethics and disseminationEthics approval for the ECHO-R trial was granted by the Metro North Human Research Ethics Committee (HREC/2020/QRBW/67223) on 6 November 2020. Findings from the trial are planned to be disseminated via peer-reviewed publications and both national and international exercise and oncology conferences.Trial registration numberACTRN12621000042842.
Journal Article
Four-Component Statistical Copolymers by RAFT Polymerization
2024
This manuscript serves as the starting point for in-depth research of multicomponent, statistical, methacrylate-based copolymers that potentially mimic the behavior of proteins in aqueous solutions. These synthetic macromolecules are composed of specially chosen comonomers: methacrylic acid (MAA), oligoethylene glycol methyl ether methacrylate (OEGMA475), 2-(dimethylamino)ethyl methacrylate (DMAEMA) and benzyl methacrylate (BzMA). Monomer choice was based on factors such as the chemical nature of pendant functional groups, the polyelectrolyte/polyampholyte and amphiphilic character and the overall hydrophobic–hydrophilic balance (HLB) of the obtained quaterpolymers. Their synthesis was achieved via a one-pot reversible addition fragmentation chain transfer (RAFT) polymerization in two distinct compositions and molecular architectures, linear and hyperbranched, respectively, in order to explore the effects of macromolecular topology. The resulting statistical quaterpolymers were characterized via 1H-NMR and ATR-FTIR spectroscopies. Their behavior in aqueous solutions was studied by dynamic (DLS) and electrophoretic light scattering (ELS) and fluorescence spectroscopy (FS), producing vital information concerning their self-assembly and the structure of the formed aggregates. The physicochemical studies were extended by tuning parameters such as the solution pH and ionic strength. Finally, the quaterpolymer behavior in FBS/PBS solutions was investigated to test their colloid stability and biocompatibility in an in vivo-mimicking, biological fluid environment.
Journal Article