cypress: an R/Bioconductor package for cell-type-specific differential expression analysis power assessment.

SUMMARY: Recent methodology advances in computational signal deconvolution have enabled bulk transcriptome data analysis at a finer cell-type level. Through deconvolution, identifying cell-type-specific differentially expressed (csDE) genes is drawing increasing attention in clinical applications. However, researchers still face a number of difficulties in adopting csDE detection methods in practice, especially in their experimental design. Here we present cypress, the first experimental design and statistical power analysis tool in csDE identification. This tool can reliably model purified cell-type-specific (CTS) profiles, cell-type compositions, biological and technical variations, offering a high-fidelity simulator for bulk RNA-seq convolution and deconvolution. cypress conducts simulation and evaluates the impact of multiple influencing factors, by various biostatistical metrics, to help researchers optimize experimental design and conduct power analysis. AVAILABILITY AND IMPLEMENTATION: cypress is an open-source R/Bioconductor package at https://bioconductor.org/packages/cypress/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Subarachnoid Hemorrhage Trials: Cutting, Sliding, or Keeping mRS Scores and WFNS Grades.

Rigorous evidence generation with randomized controlled trials has lagged for aneurysmal subarachnoid hemorrhage (SAH) compared with other forms of acute stroke. Besides its lower incidence compared with other stroke subtypes, the presentation and outcome of patients with SAH also differ. This must be considered and adjusted for in designing pivotal randomized controlled trials of patients with SAH. Here, we show the effect of the unique expected distribution of the SAH severity at presentation (World Federation of Neurological Surgeons grade) on the outcome most used in pivotal stroke randomized controlled trials (modified Rankin Scale) and, consequently, on the sample size. Furthermore, we discuss the advantages and disadvantages of different options to analyze the outcome and control the expected distribution of the World Federation of Neurological Surgeons grades in addition to showing their effects on the sample size. Finally, we offer methods that investigators can adapt to more precisely understand the effect of common modified Rankin Scale analysis methods and trial eligibility pertaining to the World Federation of Neurological Surgeons grade in designing their large-scale SAH randomized controlled trials.

Integrating Fréchet distance and AI reveals the evolutionary trajectory and origin of SARS-CoV-2.

A genome, composed of a precisely ordered sequence of four nucleotides (ATCG), encompasses a multitude of specific genome features like AAA motif. Mutations occurring within a genome disrupt the sequential order and composition of these features, thereby influencing the evolutionary trajectories and yielding variants. The evolutionary relatedness between a variant and its ancestor can be estimated by assessing evolutionary distances across a spectrum of genome features. This study develops a novel, alignment-free algorithm that considers both the sequential order and composition of genome features, enabling computation of the Fréchet distance (Fr) across multiple genome features to quantify the evolutionary status of a variant. Integrating this algorithm with an artificial recurrent neural network (RNN) reveals the quantitative evolutionary trajectory and origin of SARS-CoV-2, a puzzle unsolved by alignment-based phylogenetics. The RNN generates the evolutionary trajectory from Fr data at two levels: genome sequence mutations and organism variants. At the genome sequence level, SARS-CoV-2 evolutionarily shortens its genome to enhance its infectious capacity. Mutating signature features, such as TTA and GCT, increases its infectious potential and drives its evolution. At the organism level, variants mutating a single biomarker possess low infectious potential. However, mutating multiple markers dramatically increases their infectious capacity, propelling the COVID-19 pandemic. SARS-CoV-2 likely originates from mink coronavirus variants, with its origin trajectory traced as follows: mink, cat, tiger, mouse, hamster, dog, lion, gorilla, leopard, bat, and pangolin. Together, mutating multiple signature features and biomarkers delineates the evolutionary trajectory of mink-origin SARS-CoV-2, leading to the COVID-19 pandemic.

Species-level characterization of the cervicovaginal microbiota and its role in human papillomavirus-associated cervical carcinogenesis.

The cervicovaginal microbiome may contribute to human papillomavirus (HPV)-associated cervical carcinogenesis, but studies have been limited by low-resolution analysis methods. Using a high-resolution bioinformatics pipeline, we evaluated the relationship of the cervicovaginal microbiome with HPV and cervical intraepithelial neoplasia (CIN). The cervicovaginal microbiome of 186 women was characterized by sequencing 16S rRNA regions (V3-V4 and V5-V6) and annotated with the high-resolution ANCHOR pipeline. Samples were genotyped for HPV using the Roche-Cobas 4800 assay. We fitted logistic regression models using stepwise forward selection to select species (presence/absence) as correlates of CIN1+ and constructed a linear microbiome-based score using the regression coefficients. An HPV-based score was calculated from a separate logistic regression model to detect CIN1+ . Receiver operating characteristic curve analyses were performed; the area under the curve (AUC) and 95% confidence intervals (CI) were compared between scores. Overall, 66.7% of participants were HPV-positive. 77 unique species were identified: 8 using V3-V4, 48 using V5-V6, and 21 shared. Twelve species were retained via stepwise selection. The AUCs for the microbiome-, and HPV-based scores were 0.7656 (95% CI 0.6885-0.8426), and 0.7529 (95% CI 0.6855-0.8204), respectively. Bacterial species may be involved in cervical carcinogenesis as the microbiome- and HPV-based scores performed similarly for CIN1+ detection.

Detection of SARS-CoV-2 virus in middle ear effusions and its association with otitis media with effusion.

A large-scale outbreak of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) occurred in Shanghai, China, in early December 2022. To study the incidence and characteristics of otitis media with effusion (OME) complicating SARS-CoV-2, we collected 267 middle ear effusion (MEE) samples and 172 nasopharyngeal (NP) swabs from patients. The SARS-CoV-2 virus was detected by RT-PCR targeting. The SARS-CoV-2 virus, angiotensin-converting enzyme 2 (ACE2), and transmembrane serine protease 2 (TMPRSS2) expression in human samples was examined via immunofluorescence. During the COVID-19 epidemic in 2022, the incidence of OME (3%) significantly increased compared to the same period from 2020 to 2022. Ear symptoms in patients with SARS-CoV-2 complicated by OME generally appeared late, even after a negative NP swab, an average of 9.33 ± 6.272 days after COVID-19 infection. The SARS-CoV-2 virus was detected in MEE, which had a higher viral load than NP swabs. The insertion rate of tympanostomy tubes was not significantly higher than in OME patients in 2019-2022. Virus migration led to high viral loads in MEE despite negative NP swabs, indicating that OME lagged behind respiratory infections but had a favorable prognosis. Furthermore, middle ear tissue from adult humans coexpressed the ACE2 receptor for the SARS-CoV-2 virus and the TMPRSS2 cofactors required for virus entry.

Looking beyond the mean: quantile regression for comparative physiologists.

Statistical analyses that physiologists use to test hypotheses predominantly centre on means, but the tail ends of the response distribution can behave quite differently and underpin important scientific phenomena. We demonstrate that quantile regression (QR) offers a way to bypass some limitations of least squares regression (LSR) by building a picture of independent variable effects across the whole distribution of a dependent variable. We used LSR and QR with simulated and real datasets. With simulated data, LSR showed no change in the mean response but missed significant effects in the tails of the distribution found using QR. With real data, LSR showed a significant change in the mean response but missed a lack of response in the upper quantiles which was biologically revealing. Together, this highlights that QR can help to ask and answer more questions about variation in nature.

Decline in Explanatory Power of Trauma Mortality Models With Age: Varying Contribution of Glasgow Coma Scale, Injury Severity Score, Comorbidities, and Frailty.

INTRODUCTION: Adjusting for confounding variables is critical for objective comparison of outcomes. The explanatory power of variables used in adjusted models for injury and their relative utility across age groups has not been well-defined. This study aimed to assess the explanatory power of covariates commonly adjusted in injury research and their relative performance across age groups. METHODS: Inpatients 18-100 y (2017-2022) were selected from 90 hospital trauma registries. Patients were grouped into sequential 5-y age blocks. Mortality was defined as the proportion of patients "expired + hospice". Dominance analysis was used to determine the average contribution (McFadden's R2) for covariates commonly included in multivariable logistic regressions. RESULTS: Three hundred seventeen-thousand one hundred thirty-six patients were included (51.1% male, mean age: 63, mean injury severity score [ISS]: 9.8, mean Glasgow Coma Scale: 14.3, 93.5% blunt). Total explanatory power (McFadden's R2) for mortality was highest in youngest age group (52.7% in 18-24 group) and decreased with age, with the lowest R2 (19.6%) in 95-100 group. Regardless of age, the Glasgow Coma Scale was the most important covariate (R2 ranging from 9.0% to 20.4%). At age 18-24 y, ISS was a more dominant contributor than Elixhauser Score, but beyond 55 y, Elixhauser Score became more dominant than ISS. CONCLUSIONS: The explanatory power of adjustment models including common covariates is limited and varies significantly across age groups, decreasing linearly with age. Adjusting for outcomes using these covariates may limit objective comparisons especially for older adults. Additional research is needed to identify covariates that enhance the explanatory power of adjustment models to allow for more objective comparisons across all ages.

Optimizing the doses of cancer drugs after usual dose finding.

Since the middle of the 20th century, oncology's dose-finding paradigm has been oriented toward identifying a drug's maximum tolerated dose, which is then carried forward into phase 2 and 3 trials and clinical practice. For most modern precision medicines, however, maximum tolerated dose is far greater than the minimum dose needed to achieve maximal benefit, leading to unnecessary side effects. Regulatory change may decrease maximum tolerated dose's predominance by enforcing dose optimization of new drugs. Dozens of already approved cancer drugs require re-evaluation, however, introducing a new methodologic and ethical challenge in cancer clinical trials. In this article, we assess the history and current landscape of cancer drug dose finding. We provide a set of strategic priorities for postapproval dose optimization trials of the future. We discuss ethical considerations for postapproval dose optimization trial design and review three major design strategies for these unique trials that would both adhere to ethical standards and benefit patients and funders. We close with a discussion of financial and reporting considerations in the realm of dose optimization. Taken together, we provide a comprehensive, bird's eye view of the postapproval dose optimization trial landscape and offer our thoughts on the next steps required of methodologies and regulatory and funding regimes.

Designing AI for mental health diagnosis: challenges from sub-Saharan African value-laden judgements on mental health disorders.

Recently clinicians have become more reliant on technologies such as artificial intelligence (AI) and machine learning (ML) for effective and accurate diagnosis and prognosis of diseases, especially mental health disorders. These remarks, however, apply primarily to Europe, the USA, China and other technologically developed nations. Africa is yet to leverage the potential applications of AI and ML within the medical space. Sub-Saharan African countries are currently disadvantaged economically and infrastructure-wise. Yet precisely, these circumstances create significant opportunities for the deployment of medical AI, which has already been deployed in some places in the continent. However, while AI and ML have come with enormous promises in Africa, there are still challenges when it comes to successfully applying AI and ML designed elsewhere within the African context, especially in diagnosing mental health disorders. We argue, in this paper, that there ought not to be a homogeneous/generic design of AI and ML used in diagnosing mental health disorders. Our claim is grounded on the premise that mental health disorders cannot be diagnosed solely on 'factual evidence' but on both factual evidence and value-laden judgements of what constitutes mental health disorders in sub-Saharan Africa. For ML to play a successful role in diagnosing mental health disorders in sub-Saharan African medical spaces, with a precise focus on South Africa, we allude that it ought to understand what sub-Saharan Africans consider as mental health disorders, that is, the value-laden judgements of some conditions.

The eye of the beholder: how do public health researchers interpret regression coefficients? A qualitative study.

BACKGROUND: Calls for improved statistical literacy and transparency in population health research are widespread, but empirical accounts describing how researchers understand statistical methods are lacking. To address this gap, this study aimed to explore variation in researchers' interpretations and understanding of regression coefficients, and the extent to which these statistics are viewed as straightforward statements about health. METHODS: Thematic analysis of qualitative data from 45 one-to-one interviews with academics from eight countries, representing 12 disciplines. Three concepts from the sociology of scientific knowledge and science studies aided analysis: Duhem's Paradox, the Agonistic Field, and Mechanical Objectivity. RESULTS: Some interviewees viewed regression as a process of discovering 'real' relationships, while others indicated that regression models are not direct representations, and others blended these perspectives. Regression coefficients were generally not viewed as being mechanically objective, instead interpretation was described as iterative, nuanced, and sometimes depending on prior understandings. Researchers reported considering numerous factors when interpreting and evaluating regression results, including: knowledge from outside the model, whether results are expected or unexpected, 'common-sense', technical limitations, study design, the influence of the researcher, the research question, data quality and data availability. Interviewees repeatedly highlighted the role of the analyst, reinforcing that it is researchers who answer questions and assign meaning, not models. CONCLUSIONS: Regression coefficients were generally not viewed as complete or authoritative statements about health. This contrasts with teaching materials wherein statistical results are presented as straightforward representations, subject to rule-based interpretations. In practice, it appears that regression coefficients are not understood as mechanically objective. Attempts to influence conduct and presentation of regression models in the population health sciences should be attuned to the myriad factors which inform their interpretation.

Data Distribution: Normal or Abnormal?

Determining if the frequency distribution of a given data set follows a normal distribution or not is among the first steps of data analysis. Visual examination of the data, commonly by Q-Q plot, although is acceptable by many scientists, is considered subjective and not acceptable by other researchers. One-sample Kolmogorov-Smirnov test with Lilliefors correction (for a sample size ≥ 50) and Shapiro-Wilk test (for a sample size < 50) are common statistical tests for checking the normality of a data set quantitatively. As parametric tests, which assume that the data distribution is normal (Gaussian, bell-shaped), are more robust compared to their non-parametric counterparts, we commonly use transformations (e.g., log-transformation, Box-Cox transformation, etc.) to make the frequency distribution of non-normally distributed data close to a normal distribution. Herein, I wish to reflect on presenting how to practically work with these statistical methods through examining of real data sets.

Enhancing biostatistics education for medical students in Poland: factors influencing perception and educational recommendations.

BACKGROUND: A number of recommendations for the teaching of biostatistics have been published to date, however, student opinion on them has not yet been studied. For this reason, the aim of the manuscript was to find out the opinions of medical students at universities in Poland on two forms of teaching biostatistics, namely traditional and practical, as well as to indicate, on the basis of the results obtained, the related educational recommendations. METHODS: The study involved a group of 527 students studying at seven medical faculties in Poland, who were asked to imagine two different courses. The traditional form of teaching biostatistics was based on the standard teaching scheme of running a test from memory in a statistical package, while the practical one involved reading an article in which a particular test was applied and then applying it based on the instruction provided. Other aspects related to the teaching of the subject were assessed. RESULTS: According to the students of each course, the practical form of teaching biostatistics reduces the stress level associated with teaching and the student exam (p < 0.001), as well as contributing to an increased level of elevated knowledge (p < 0.001), while the degree of satisfaction after passing the exam is higher (p < 0.001). A greater proportion of students (p < 0.001) believe that credit for the course could be given by doing a statistical review of an article or conducting a survey, followed by the tests learned in class. More than 95% also said that the delivery of the courses should be based on the field of study they were taking, during which time they would also like to have the opportunity to take part in optional activities and hear lectures from experts. CONCLUSION: It is recommended that more emphasis be placed on practical teaching the subject of biostatistics.

Assessing attitudes towards biostatistics education among medical students: adaptation and preliminary evaluation of the Chinese version survey of attitudes towards statistics (SATS-36).

BACKGROUND: Despite the numerous advantages of mastering biostatistics, medical students generally perceive biostatistics as a difficult and challenging subject and even experience anxiety during the courses. Evidence for the correlation between students' academic achievements and their attitudes, indicating that attitudes at the beginning of the biostatistics course may affect cognitive competence at the end of the course and subsequently influence student academic performance. However, there are current disagreements regarding the measurement and evaluation of attitudes related to statistics. Thus, there is a need for standard instruments to assess them. This study was conducted to develop a Chinese version of the Survey of Attitudes Toward Statistics (SATS-36) in order to acquire a valid instrument to measure medical students' attitudes toward biostatistics under Chinese medical educational background. METHODS: The Chinese version SATS-36 was developed through translation and back-translation of the original scale, with subsequent revisions based on expert advice to ensure the most appropriate item content. The local adaption was performed with a cohort of 1709 Chinese-speaking medical undergraduate and graduate students enrolled in biostatistics courses. And then, the reliability, validity and discrimination of the questionnaires were evaluated through correlation coefficient calculation, factor analysis, parallel analysis and other methods. RESULTS: The Chinese version SATS-36 consisted of 36 items and loaded a five-factor structure by factor analysis, which offered an alternative similar but not equal to that original six-factor structure. The cumulative variance contribution rate was 62.20%, the Cronbach's α coefficient was 0.908, the Guttman split-half reliability coefficient was 0.905 and the test-retest reliability coefficient was 0.752. Discriminant analysis revealed small to large significant differences in the five attitude subscales. CONCLUSIONS: The Chinese version SATS-36 with good validity and reliability in this study can be used to evaluate the learning framework of Chinese medical students.

Bayesian estimation in veterinary pharmacology: A conceptual and practical introduction.

Sophisticated mathematical and computational tools have become widespread and important in veterinary pharmacology. Although the theoretical basis and practical applications of these have been widely explored in the literature, statistical inference in the context of these models has received less attention. Optimization methods, often with frequentist statistical inference, have been predominant. In contrast, Bayesian statistics have not been widely applied, but offer both practical utility and arguably greater interpretability. Veterinary pharmacology applications are generally well supported by relevant prior information, from either existing substantive knowledge, or an understanding of study and model design. This facilitates practical implementation of Bayesian analyses that can take advantage of this knowledge. This essay will explore the specification of Bayesian models relevant to veterinary pharmacology, including demonstration of prior selection, and illustrate the capability of these models to generate practically useful statistics, including uncertainty statements, that are difficult or impossible to obtain otherwise. Case studies using simulated data will describe applications in clinical trials, pharmacodynamics, and pharmacokinetics, all including multilevel modeling. This content may serve as a suitable starting point for researchers in veterinary pharmacology and related disciplines considering Bayesian estimation for their applied work.

Use of Pearson and Spearman correlation testing in Indian anesthesia journals: An audit.

Background and Aims: Correct usage and interpretation of biostatistical tests is imperative. Aim of the present article was to evaluate the use of "correlation test" for biostatistical analysis in two leading Indian journals of anesthesia and sensitize the readers regarding its correct usage. Material and Methods: A prospective analysis was done for all original articles using the correlation test (Pearson or Spearman) that were published in "Indian Journal of Anaesthesia" (IJA) or "Journal of Anaesthesiology and Clinical Pharmacology" (JOACP) in the years 2019 and 2020. Results: Amongst all included original studies, correlation test were used in 6% (JOACP) and 6.5% (IJA) respectively (averaged for the years 2019 and 2020). Correlation test was usedinappropriately) for evaluating an aim of prediction/agreement/comparison, rather than association, in 25% and 10% instances each (JOACP and IJA). In both JOACP and IJA, there were high rates of using and interpreting results without citing 95% confidence intervals (CIs) of correlation coefficient (88% and 90%, respectively), P value for significance of the association (50% and 90%, respectively), or coefficient of discrimination (88% and 70%, respectively). In majority of the instances, test to ascertain presence of mandatory prerequisites such as normal distribution of data could not be found (62% and 90%, respectively). Conclusion: The complete potential of correlation test in exploring research questions is probably underappreciated. Further, even when used, its application and interpretation are prone to errors. We hope that the present analysis and narrative is a well-timed appropriate step in bridging the gaps in existing knowledge regarding use of correlation test in national anesthesia literature.

Just how transformative will AI/ML be for immuno-oncology?

Immuno-oncology involves the study of approaches which harness the patient's immune system to fight malignancies. Immuno-oncology, as with every other biomedical and clinical research field as well as clinical operations, is in the midst of technological revolutions, which vastly increase the amount of available data. Recent advances in artificial intelligence and machine learning (AI/ML) have received much attention in terms of their potential to harness available data to improve insights and outcomes in many areas including immuno-oncology. In this review, we discuss important aspects to consider when evaluating the potential impact of AI/ML applications in the clinic. We highlight four clinical/biomedical challenges relevant to immuno-oncology and how they may be able to be addressed by the latest advancements in AI/ML. These challenges include (1) efficiency in clinical workflows, (2) curation of high-quality image data, (3) finding, extracting and synthesizing text knowledge as well as addressing, and (4) small cohort size in immunotherapeutic evaluation cohorts. Finally, we outline how advancements in reinforcement and federated learning, as well as the development of best practices for ethical and unbiased data generation, are likely to drive future innovations.

A retrospective and prospective study of biostatistics in Canada.

Biostatistics is foundational to public health research and Canada has a history of high impact contributions both in seminal methodological advances and in the rigorous application of methods for the design or analysis of public health studies. In this article, we provide a brief and personal review of selected contributions from Canadian biostatisticians to fields such as survival and life history analysis, sampling, clinical trial methodology, environmental risk assessment, infectious disease epidemiology, and early work on prediction. We also provide a brief look forward at the upcoming needs and future directions of biostatistical research.

RéSUMé: La biostatistique est fondamentale pour la recherche en santé publique et le Canada a un historique de contributions à fort impact, tant dans les avancées méthodologiques majeures que dans l'application rigoureuse de méthodes pour la conception ou l'analyse d'études de santé publique. Dans cet article, nous présentons un examen bref et personnel des contributions des biostatisticiens canadiens dans des domaines tels que l'analyse de la survie et de l'histoire de vie, l'échantillonnage, la méthodologie des essais cliniques, le risque environnemental, l'épidémiologie des maladies infectieuses et les premiers travaux sur la prédiction et la classification. Nous fournissons également un bref aperçu des besoins à venir et des orientations futures de la recherche biostatistique.