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1.
Ann Appl Stat ; 18(1): 729-748, 2024 Mar.
Article in English | MEDLINE | ID: mdl-39281709

ABSTRACT

Risk-adjusted quality measures are used to evaluate healthcare providers with respect to national norms while controlling for factors beyond their control. Existing healthcare provider profiling approaches typically assume that the between-provider variation in these measures is entirely due to meaningful differences in quality of care. However, in practice, much of the between-provider variation will be due to trivial fluctuations in healthcare quality, or unobservable confounding risk factors. If these additional sources of variation are not accounted for, conventional methods will disproportionately identify larger providers as outliers, even though their departures from the national norms may not be "extreme" or clinically meaningful. Motivated by efforts to evaluate the quality of care provided by transplant centers, we develop a composite evaluation score based on a novel individualized empirical null method, which robustly accounts for overdispersion due to unobserved risk factors, models the marginal variance of standardized scores as a function of the effective sample size, and only requires the use of publicly-available center-level statistics. The evaluations of United States kidney transplant centers based on the proposed composite score are substantially different from those based on conventional methods. Simulations show that the proposed empirical null approach more accurately classifies centers in terms of quality of care, compared to existing methods.

2.
Cell Rep Med ; 5(9): 101713, 2024 Sep 17.
Article in English | MEDLINE | ID: mdl-39241771

ABSTRACT

Reliably detecting potentially misleading patterns in automated diagnostic assistance systems, such as those powered by artificial intelligence (AI), is crucial for instilling user trust and ensuring reliability. Current techniques fall short in visualizing such confounding factors. We propose DiffChest, a self-conditioned diffusion model trained on 515,704 chest radiographs from 194,956 patients across the US and Europe. DiffChest provides patient-specific explanations and visualizes confounding factors that might mislead the model. The high inter-reader agreement, with Fleiss' kappa values of 0.8 or higher, validates its capability to identify treatment-related confounders. Confounders are accurately detected with 10%-100% prevalence rates. The pretraining process optimizes the model for relevant imaging information, resulting in excellent diagnostic accuracy for 11 chest conditions, including pleural effusion and heart insufficiency. Our findings highlight the potential of diffusion models in medical image classification, providing insights into confounding factors and enhancing model robustness and reliability.


Subject(s)
Artificial Intelligence , Humans , Male , Female , Reproducibility of Results , Radiographic Image Interpretation, Computer-Assisted/methods , Middle Aged , Radiography, Thoracic/methods , Aged , Adult , Algorithms , Image Processing, Computer-Assisted/methods
3.
HGG Adv ; 5(4): 100338, 2024 Aug 02.
Article in English | MEDLINE | ID: mdl-39095990

ABSTRACT

Multivariable Mendelian randomization allows simultaneous estimation of direct causal effects of multiple exposure variables on an outcome. When the exposure variables of interest are quantitative omic features, obtaining complete data can be economically and technically challenging: the measurement cost is high, and the measurement devices may have inherent detection limits. In this paper, we propose a valid and efficient method to handle unmeasured and undetectable values of the exposure variables in a one-sample multivariable Mendelian randomization analysis with individual-level data. We estimate the direct causal effects with maximum likelihood estimation and develop an expectation-maximization algorithm to compute the estimators. We show the advantages of the proposed method through simulation studies and provide an application to the Hispanic Community Health Study/Study of Latinos, which has a large amount of unmeasured exposure data.

4.
Rev Endocr Metab Disord ; 25(3): 457-465, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38609701

ABSTRACT

The diagnostic approach to hypopituitarism involves many disciplines. Clinical symptoms rarely are specific. Imaging techniques are helpful but cannot prove the specific functional defects. Therefore, the definitive diagnosis of pituitary insufficiency is largely based on laboratory tests. However, also laboratory methods come with inherent limitations, and it is essential for the clinician to know and recognize typical pitfalls. Most factors potentially impairing the quality of hormone measurements are introduced in the preanalytical phase, i.e. before the hormones are measured by the laboratory. For example, the timing of blood drawing with respect to circadian rhythm, stress, and medication can have an influence on hormone concentrations. During the actual analysis of the hormones, cross-reactions with molecules present in the sample presenting the same or similar epitopes than the intended analyte may affect immunoassays. Interference can also come from heterophilic or human anti-animal antibodies. Unexpected problems can also be due to popular nutritional supplements which interfere with the measurement procedures. An important example in this respect is the interference from biotin. It became only clinically visible when the use of this vitamin became popular among patients. The extreme serum concentrations reached when patients take it as a supplement can lead to incorrect measurements in immunoassays employing the biotin-streptavidin system. To some extent, hormone analyses using liquid chromatography mass spectrometry (LCMS) can overcome problems, although availability and cost-effectiveness of this method still imposes restrictions. In the post-analytical phase, appropriateness of reference intervals and cut-offs with respect to the specific analytical method used is of outmost importance. Furthermore, for interpretation, additional biological and pharmacological factors like BMI, age and concomitant diseases must be considered to avoid misinterpretation of the measured concentrations. It is important for the clinician and the laboratory to recognize when one or more laboratory values do not match the clinical picture. In an interdisciplinary approach, the search for the underlying cause should be initiated.


Subject(s)
Hypopituitarism , Humans , Hypopituitarism/diagnosis , Hypopituitarism/blood , Immunoassay/methods , Immunoassay/standards
5.
J Evid Based Med ; 17(2): 307-316, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38556728

ABSTRACT

AIM: It is essential for health researchers to have a systematic understanding of third-party variables that influence both the exposure and outcome under investigation, as shown by a directed acyclic graph (DAG). The traditional construction of DAGs through literature review and expert knowledge often needs to be more systematic and consistent, leading to potential biases. We try to introduce an automatic approach to building network linking variables of interest. METHODS: Large-scale text mining from medical literature was utilized to construct a conceptual network based on the Semantic MEDLINE Database (SemMedDB). SemMedDB is a PubMed-scale repository of the "concept-relation-concept" triple format. Relations between concepts are categorized as Excitatory, Inhibitory, or General. RESULTS: To facilitate the use of large-scale triple sets in SemMedDB, we have developed a computable biomedical knowledge (CBK) system (https://cbk.bjmu.edu.cn/), a website that enables direct retrieval of related publications and their corresponding triples without the necessity of writing SQL statements. Three case studies were elaborated to demonstrate the applications of the CBK system. CONCLUSIONS: The CBK system is openly available and user-friendly for rapidly capturing a set of influencing factors for a phenotype and building candidate DAGs between exposure-outcome variables. It could be a valuable tool to reduce the exploration time in considering relationships between variables, and constructing a DAG. A reliable and standardized DAG could significantly improve the design and interpretation of observational health research.


Subject(s)
Data Mining , Data Mining/methods , Humans , Knowledge Bases , MEDLINE
6.
Cureus ; 16(3): e55346, 2024 Mar.
Article in English | MEDLINE | ID: mdl-38559506

ABSTRACT

INTRODUCTION: Although safety climate, teamwork, and other non-technical skills in operating rooms probably influence clinical outcomes, direct associations have not been shown, at least partially due to sample size considerations. We report data from a retrospective cohort of anesthesia evaluations that can simplify the design of prospective observational studies in this area. Associations between non-technical skills in anesthesia, specifically anesthesiologists' quality of clinical supervision and nurse anesthetists' work habits, and patient and operational factors were examined. METHODS: Eight fiscal years of evaluations and surgical cases from one hospital were included. Clinical supervision by anesthesiologists was evaluated daily using a nine-item scale. Work habits of nurse anesthetists were evaluated daily using a six-item scale. The dependent variables for both groups of staff were binary, whether all items were given the maximum score or not. Associations were tested with patient and operational variables for the entire day. RESULTS: There were 40,718 evaluations of faculty anesthesiologists by trainees, 53,772 evaluations of nurse anesthetists by anesthesiologists, and 296,449 cases that raters and ratees started together. Cohen's d values were small (≤0.10) for all independent variables, suggesting a lack of any clinically meaningful association between patient and operational factors and evaluations given the maximum scores. For supervision quality, the day's count of orthopedic cases was a significant predictor of scores (P = 0.0011). However, the resulting absolute marginal change in the percentage of supervision scores equal to the maximum was only 0.8% (99% confidence interval: 0.2% to 1.4%), i.e., too small to be of clinical or managerial importance. Neurosurgical cases may have been a significant predictor of work habits (P = 0.0054). However, the resulting marginal change in the percentage of work habits scores equal to the maximum, an increase of 0.8% (99% confidence interval: 0.1% to 1.6%), which was again too small to be important. CONCLUSIONS: When evaluating the effect of assigning anesthesiologists and nurse anesthetists with different clinical performance quality on clinical outcomes, supervision quality and work habits scores may be included as independent variables without concern that their effects are confounded by association with the patient or case characteristics. Clinical supervision and work habits are measures of non-technical skills. Hence, these findings suggest that non-technical performance can be judged by observing the typical small sample size of cases. Then, associations can be tested with administrative data for a far greater number of patients because there is unlikely to be a confounding association between patient and case characteristics and the clinicians' non-technical performance.

7.
J Proteome Res ; 23(8): 3064-3075, 2024 Aug 02.
Article in English | MEDLINE | ID: mdl-38520676

ABSTRACT

Metabolomics is an emerging and powerful bioanalytical method supporting clinical investigations. Serum and plasma are commonly used without rational prioritization. Serum is collected after blood coagulation, a complex biochemical process involving active platelet metabolism. This may affect the metabolome and increase the variance, as platelet counts and function may vary substantially in individuals. A multiomics approach systematically investigating the suitability of serum and plasma for clinical studies demonstrated that metabolites correlated well (n = 461, R2 = 0.991), whereas lipid mediators (n = 83, R2 = 0.906) and proteins (n = 322, R2 = 0.860) differed substantially between specimen. Independently, analysis of platelet releasates identified most biomolecules significantly enriched in serum compared to plasma. A prospective, randomized, controlled parallel group metabolomics trial with acetylsalicylic acid administered for 7 days demonstrated that the apparent drug effects significantly differ depending on the analyzed specimen. Only serum analyses of healthy individuals suggested a significant downregulation of TXB2 and 12-HETE, which were specifically formed during coagulation in vitro. Plasma analyses reliably identified acetylsalicylic acid effects on metabolites and lipids occurring in vivo such as an increase in serotonin, 15-deoxy-PGJ2 and sphingosine-1-phosphate and a decrease in polyunsaturated fatty acids. The present data suggest that plasma should be preferred above serum for clinical metabolomics studies as the serum metabolome may be substantially confounded by platelets.


Subject(s)
Aspirin , Blood Platelets , Metabolomics , Plasma , Humans , Blood Platelets/metabolism , Blood Platelets/drug effects , Metabolomics/methods , Aspirin/pharmacology , Plasma/metabolism , Plasma/chemistry , Serum/metabolism , Serum/chemistry , Lysophospholipids/blood , Sphingosine/analogs & derivatives , Sphingosine/blood , Metabolome/drug effects , Thromboxane B2/blood , 12-Hydroxy-5,8,10,14-eicosatetraenoic Acid/blood , 12-Hydroxy-5,8,10,14-eicosatetraenoic Acid/metabolism , Male , Female , Prospective Studies , Adult
8.
Microbiome Res Rep ; 3(1): 1, 2024.
Article in English | MEDLINE | ID: mdl-38455088

ABSTRACT

Observational studies have determined numerous correlations between sequence-based gut microbiota data and human mental traits. However, these associations are often inconsistent across studies. This inconsistency is one of the reasons that mechanistic validation studies of the observed correlations are lagging, making it difficult to establish causal associations. The absence of consistent study findings may partially be due to the lack of clear guidelines for identifying confounders of relations between complex microbial communities and mental conditions. Gut microbial complexity also impedes deciphering microbiota-host relations by using a single analytical approach. The aim of the current review is to help solve these problems by providing methodological recommendations for future human microbiota-gut-brain axis research on the selection of confounders, the use of integrative biostatistical methods, and the steps needed to translate correlative findings into causal conclusions.

9.
Biostatistics ; 25(3): 818-832, 2024 Jul 01.
Article in English | MEDLINE | ID: mdl-38330064

ABSTRACT

Traditional linear mediation analysis has inherent limitations when it comes to handling high-dimensional mediators. Particularly, accurately estimating and rigorously inferring mediation effects is challenging, primarily due to the intertwined nature of the mediator selection issue. Despite recent developments, the existing methods are inadequate for addressing the complex relationships introduced by confounders. To tackle these challenges, we propose a novel approach called DP2LM (Deep neural network-based Penalized Partially Linear Mediation). This approach incorporates deep neural network techniques to account for nonlinear effects in confounders and utilizes the penalized partially linear model to accommodate high dimensionality. Unlike most existing works that concentrate on mediator selection, our method prioritizes estimation and inference on mediation effects. Specifically, we develop test procedures for testing the direct and indirect mediation effects. Theoretical analysis shows that the tests maintain the Type-I error rate. In simulation studies, DP2LM demonstrates its superior performance as a modeling tool for complex data, outperforming existing approaches in a wide range of settings and providing reliable estimation and inference in scenarios involving a considerable number of mediators. Further, we apply DP2LM to investigate the mediation effect of DNA methylation on cortisol stress reactivity in individuals who experienced childhood trauma, uncovering new insights through a comprehensive analysis.


Subject(s)
Deep Learning , Mediation Analysis , Humans , Models, Statistical
10.
Chemosphere ; 353: 141495, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38373448

ABSTRACT

The cardiovascular risk associated with short-term ambient air pollution exposure is well-documented. However, recent advancements in geospatial techniques have provided new insights into this risk. This systematic review focuses on short-term exposure studies that applied advanced geospatial pollution modelling to estimate cardiovascular disease (CVD) risk and accounted for additional unconventional neighbourhood-level confounders to analyse their modifier effect on the risk. Four databases were investigated to select publications between 2018 and 2023 that met the inclusion criteria of studying the effect of particulate matter (PM2.5 and PM10), SO2, NOx, CO, and O3 on CVD mortality or morbidity, utilizing pollution modelling techniques, and considering spatial and temporal confounders. Out of 3277 publications, 285 were identified for full-text review, of which 34 satisfied the inclusion criteria for qualitative analysis, and 12 of them were chosen for additional quantitative analysis. Quality assessment revealed that 28 out of 34 included articles scored 4 or above, indicating high quality. In 30 studies, advanced pollution modelling techniques were used, while in 4 only simpler methods were applied. The most pertinent confounders identified were socio-demographic variables (e.g., socio-economic status, population percentage by race or ethnicity) and neighbourhood-level built environment variables (e.g., urban/rural area, percentage of green space, proximity to healthcare), which exhibited varying modifier effects depending on the context. In the quantitative analysis, only PM 2.5 showed a significant positive association to all-cause CVD-related hospitalisation. Other pollutants did not show any significant effect, likely due to the high inter-study heterogeneity and a limited number of cases. The application of advanced geospatial measurement and modelling of air pollution exposure, as well as its risk, is increasing. This review underscores the importance of accounting for unconventional neighbourhood-level confounders to enhance the understanding of the CVD risk associated with short-term pollution exposure.


Subject(s)
Air Pollutants , Air Pollution , Cardiovascular Diseases , Environmental Exposure , Particulate Matter , Cardiovascular Diseases/mortality , Cardiovascular Diseases/epidemiology , Humans , Air Pollution/statistics & numerical data , Air Pollution/adverse effects , Air Pollutants/analysis , Environmental Exposure/statistics & numerical data , Particulate Matter/analysis , Spatial Analysis
12.
Eur Arch Psychiatry Clin Neurosci ; 274(5): 1215-1222, 2024 Aug.
Article in English | MEDLINE | ID: mdl-38243017

ABSTRACT

The role of the complement system in schizophrenia (Sz) is inconclusive due to heterogeneity of the disease and study designs. Here, we assessed the levels of complement activation products and functionality of the classical pathway in acutely ill unmedicated Sz patients at baseline and after 6 weeks of treatment versus matched controls. The study included analyses of the terminal complement complex (sTCC) and C5a in plasma from 96 patients and 96 controls by enzyme-linked immunosorbent assay. Sub-group analysis of serum was conducted for measurement of C4 component and activity of the classical pathway (28 and 24 cases per cohort, respectively). We found no differences in levels of C5a, C4 and classical pathway function in patients versus controls. Plasma sTCC was significantly higher in patients [486 (392-659) ng/mL, n = 96] compared to controls [389 (304-612) ng/mL, n = 96] (p = 0.027, δ = 0.185), but not associated with clinical symptom ratings or treatment. The differences in sTCC between Sz and controls were confirmed using an Aligned Rank Transformation model considering the covariates age and sex (p = 0.040). Additional analysis showed that sTCC was significantly associated with C-reactive protein (CRP; p = 0.006). These findings suggest that sTCC plays a role in Sz as a trait marker of non-specific chronic immune activation, as previously described for CRP. Future longitudinal analyses with more sampling time points from early recognition centres for psychoses may be helpful to better understand the temporal dynamics of innate immune system changes during psychosis development.


Subject(s)
Schizophrenia , Humans , Schizophrenia/blood , Male , Female , Adult , Middle Aged , Complement C4/analysis , Complement C4/metabolism , Complement C5a , Young Adult , C-Reactive Protein/metabolism , C-Reactive Protein/analysis , Complement Membrane Attack Complex/metabolism
13.
Emerg Radiol ; 31(1): 63-71, 2024 Feb.
Article in English | MEDLINE | ID: mdl-38194212

ABSTRACT

PURPOSE: Assessing the diagnostic performance and supplementary value of whole-body computed tomography scout view (SV) images in the detection of thoracolumbar spine injuries in early resuscitation phase and identifying frequent image quality confounders. METHODS: In this retrospective database analysis at a tertiary emergency center, three blinded senior experts independently assessed SV to detect thoracolumbar spine injuries. The findings were categorized according to the AO Spine classification system. Confounders impacting SV image quality were identified. The suspected injury level and severity, along with the confidence level, were indicated. Diagnostic performance was estimated using the caret package in R programming language. RESULTS: We assessed images of 199 patients, encompassing 1592 vertebrae (T10-L5), and identified 56 spinal injuries (3.5%). Among the 199 cases, 39 (19.6%) exhibited at least one injury in the thoracolumbar spine, with 12 (6.0%) of them displaying multiple spinal injuries. The pooled sensitivity, specificity, and accuracy were 47%, 99%, and 97%, respectively. All experts correctly identified the most severe injury of AO type C. The most common image confounders were medical equipment (44.6%), hand position (37.6%), and bowel gas (37.5%). CONCLUSION: SV examination holds potential as a valuable supplementary tool for thoracolumbar spinal injury detection when CT reconstructions are not yet available. Our data show high specificity and accuracy but moderate sensitivity. While not sufficient for standalone screening, reviewing SV images expedites spinal screening in mass casualty incidents. Addressing modifiable factors like medical equipment or hand positioning can enhance SV image quality and assessment.


Subject(s)
Multiple Trauma , Spinal Fractures , Spinal Injuries , Humans , Retrospective Studies , Lumbar Vertebrae/diagnostic imaging , Lumbar Vertebrae/injuries , Thoracic Vertebrae/diagnostic imaging , Thoracic Vertebrae/injuries , Tomography, X-Ray Computed/methods , Spinal Injuries/diagnostic imaging
14.
MethodsX ; 12: 102513, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38192361

ABSTRACT

Multiple mental health disorders affect on decisions of people. The disorders are also outcomes of other factors. Health studies commonly follow an inverse propensity weight (IPW) method to address estimation errors associated with the presence of one confounder or covariate number exceeding the recommended sample size. However, approaches of IPW appropriate to alleviate the estimation error associated with multiple confounders distributed unequally in the study samples were not explained in our search literature. This study used longitudinal cohort data from Christchurch Health and Development Study and demonstrated IPW approach to address two confounders with similar natures in terms of etiological process. In our sample, some individuals had no mental health disorder at all, while others had either one of depression or anxiety or both. The methodological step to evaluate a new IPW approach include * Estimated IPWs from all possible combinations of the major depression and anxiety disorder: (a) IPW based on anxiety factor only assuming both mental health problems resulted from the same etiological processes; (b) IPW based on major depression factor only assuming both mental health problems resulted from the same etiological processes; (c) IPW assuming three (independent) categories of etiological processes: neither; either; both of major depression or anxiety disorder, (d) IPW assuming four (independent) categories of etiological processes: neither; major depression only; any anxiety disorder only; both. (e) No IPW or control model (no confounding problem.•Estimated outcome model with one each IPW at a time and one without IPw (control model).•Compared fit statistics of all estimated models.•The IPW derived assuming four categories of etiological processes produced the robust based fit statistics criteria. The study showed significant effects of both mental health problems on investment but the anxiety revealed a stronger effect than that of major depression.

15.
Cell Rep Med ; 5(1): 101361, 2024 01 16.
Article in English | MEDLINE | ID: mdl-38232695

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with enhanced transmissibility and immune escape have emerged periodically throughout the coronavirus disease 2019 (COVID-19) pandemic, but the impact of these variants on disease severity has remained unclear. In this single-center, retrospective cohort study, we examined the association between SARS-CoV-2 clade and patient outcome over a two-year period in Chicago, Illinois. Between March 2020 and March 2022, 14,252 residual diagnostic specimens were collected from SARS-CoV-2-positive inpatients and outpatients alongside linked clinical and demographic metadata, of which 2,114 were processed for viral whole-genome sequencing. When controlling for patient demographics and vaccination status, several viral clades were associated with risk for hospitalization, but this association was negated by the inclusion of population-level confounders, including case count, sampling bias, and shifting standards of care. These data highlight the importance of integrating non-virological factors into disease severity and outcome models for the accurate assessment of patient risk.


Subject(s)
COVID-19 , Humans , COVID-19/epidemiology , SARS-CoV-2/genetics , Molecular Epidemiology , Retrospective Studies , COVID-19 Testing
16.
Mater Today Bio ; 24: 100879, 2024 Feb.
Article in English | MEDLINE | ID: mdl-38130429

ABSTRACT

Non-destructive assessments are required for the quality control of tissue-engineered constructs and the optimization of the tissue culture process. Near-infrared (NIR) spectroscopy coupled with machine learning (ML) provides a promising approach for such assessment. However, due to its nonspecific nature, each spectrum incorporates information on both neotissue and non-neotissue constituents of the construct; the effect of these constituents on the NIR-based assessments of tissue-engineered constructs has been overlooked in previous studies. This study investigates the effect of scaffolds, growth factors, and buffers on NIR-based assessments of tissue-engineered constructs. To determine if these non-neotissue constituents have a measurable effect on the NIR spectra of the constructs that can introduce bias in their assessment, nine ML algorithms were evaluated in classifying the NIR spectra of engineered cartilage according to the scaffold used to prepare the constructs, the growth factors added to the culture media, and the buffers used for storing the constructs. The effect of controlling for these constituents was also evaluated using controlled and uncontrolled NIR-based ML models for predicting tissue maturity as an example of neotissue-related properties of interest. Samples used in this study were prepared using norbornene-modified hyaluronic acid scaffolds with or without the conjugation of an N-cadherin mimetic peptide. Selected samples were supplemented with transforming growth factor-beta1 or bone morphogenetic protein-9 growth factor. Some samples were frozen in cell lysis buffer, while the remaining samples were frozen in PBS until required for NIR analysis. The ML models for classifying the spectra of the constructs according to the four constituents exhibited high to fair performances, with F1 scores ranging from 0.9 to 0.52. Moreover, controlling for the four constituents significantly improved the performance of the models for predicting tissue maturity, with improvement in F1 scores ranging from 0.09 to 0.77. In conclusion, non-neotissue constituents have measurable effects on the NIR spectra of tissue-engineered constructs that can be detected by ML algorithms and introduce bias in the assessment of the constructs by NIR spectroscopy. Therefore, controlling for these constituents is necessary for reliable NIR-based assessments of tissue-engineered constructs.

17.
Brief Bioinform ; 24(6)2023 09 22.
Article in English | MEDLINE | ID: mdl-37985453

ABSTRACT

Gene regulatory networks (GRNs) and gene co-expression networks (GCNs) allow genome-wide exploration of molecular regulation patterns in health and disease. The standard approach for obtaining GRNs and GCNs is to infer them from gene expression data, using computational network inference methods. However, since network inference methods are usually applied on aggregate data, distortion of the networks by demographic confounders might remain undetected, especially because gene expression patterns are known to vary between different demographic groups. In this paper, we present a computational framework to systematically evaluate the influence of demographic confounders on network inference from gene expression data. Our framework compares similarities between networks inferred for different demographic groups with similarity distributions obtained for random splits of the expression data. Moreover, it allows to quantify to which extent demographic groups are represented by networks inferred from the aggregate data in a confounder-agnostic way. We apply our framework to test four widely used GRN and GCN inference methods as to their robustness w. r. t. confounding by age, ethnicity and sex in cancer. Our findings based on more than $ {44000}$ inferred networks indicate that age and sex confounders play an important role in network inference for certain cancer types, emphasizing the importance of incorporating an assessment of the effect of demographic confounders into network inference workflows. Our framework is available as a Python package on GitHub: https://github.com/bionetslab/grn-confounders.


Subject(s)
Gene Regulatory Networks , Neoplasms , Humans , Neoplasms/genetics , Demography , Algorithms
18.
Neurosurg Rev ; 46(1): 286, 2023 Oct 28.
Article in English | MEDLINE | ID: mdl-37891361

ABSTRACT

Although frozen section pathology (FSP) is commonly performed during surgery for glioma-suspicious lesions, confounders of accuracy are largely unknown. FSP and final diagnosis were compared in 398 surgeries for glioma-suspicious lesions. Diagnostic accuracy, risk factors for diagnostic shift from neoplastic to non-neoplastic tissue and vice versa according to the final diagnosis, and the impact on intraoperative and postoperative decision-making were analyzed. Diagnostic shift occurred in 70 cases (18%), and sensitivity, specificity, and the positive (PPV) and negative (NPV) predictive value of FSP were 82.5%, 77.8%, 99.4%, and 9.3%, respectively. No correlations between shift and patients' age and sex, sample fluorescence or volume, tumor location, correct information on the pathology form, final high- or low-grade histology, or molecular alterations were found (p > .05, each). Shift was more common after irradiation (25% vs 15%; p = .025) or chemotherapy (26% vs 15%; p = .022) than in treatment naïve cases and correlated with the type of surgery (p = .002). FSP altered intraoperative decision-making in 25 cases (6%). Postoperative shift led to repeated surgery in 12 patients (3%). In 45 cases, in which FSP and final diagnosis based on the same tissue, shift occurred in only 5 patients (11%), and sensitivity, specificity, PPV, and NPV for FSP were 77.4%, 78.6%, 88.9%, and 61.1%, respectively. No correlations between diagnostic shift and any of the analyzed variables were found (p > .05, each). Although accuracy of FSP during glioma surgery is sufficient, moderate NPV should be considered during intraoperative decision-making. While confounders are sparse, accuracy might be increased by repeated sampling. Diagnostic shift rarely alters postoperative treatment strategy.


Subject(s)
Frozen Sections , Glioma , Humans , Sensitivity and Specificity , Glioma/surgery , Glioma/diagnosis , Retrospective Studies
19.
Stat Med ; 42(23): 4257-4281, 2023 10 15.
Article in English | MEDLINE | ID: mdl-37497859

ABSTRACT

Instrumental variables regression is a tool that is commonly used in the analysis of observational data. The instrumental variables are used to make causal inference about the effect of a certain exposure in the presence of unmeasured confounders. A valid instrumental variable is a variable that is associated with the exposure, affects the outcome only through the exposure (exclusion), and is not confounded with the outcome (exogeneity). Unlike the first assumption, the other two are generally untestable and rely on subject-matter knowledge. Therefore, a sensitivity analysis is desirable to assess the impact of assumptions' violation on the estimated parameters. In this paper, we propose and demonstrate a new method of sensitivity analysis for G-estimators in causal linear and non-linear models. We introduce two novel aspects of sensitivity analysis in instrumental variables studies. The first is a single sensitivity parameter that captures violations of exclusion and exogeneity assumptions. The second is an application of the method to non-linear models. The introduced framework is theoretically justified and is illustrated via a simulation study. Finally, we illustrate the method by application to real-world data and provide guidelines on conducting sensitivity analysis.


Subject(s)
Bias , Humans , Computer Simulation , Causality
20.
Conserv Biol ; 37(6): e14150, 2023 Dec.
Article in English | MEDLINE | ID: mdl-37461881

ABSTRACT

Programs to protect biodiversity on private land are increasingly being used worldwide. To understand the efficacy of such programs, it is important to determine their impact: the difference between the program's outcome and what would have happened without the program. Typically, these programs are evaluated by estimating the average program-level impact, which readily allows comparisons between programs or regions, but masks important heterogeneity in impact across the individual conservation interventions. We used synthetic control design, statistical matching, and time-series data to estimate the impact of individual protected areas over time and combined individual-level impacts to estimate program-level impact with a meta-analytic approach. We applied the method to private protected areas governed by conservation covenants (legally binding on-title agreements to protect biodiversity) in the Goldfields region of Victoria, Australia using woody vegetation cover as our outcome variable. We compared our results with traditional approaches to estimating program-level impact based on a subset of covenants that were the same age. Our results showed an overall program-level impact of a 0.3-0.8% increase in woody vegetation cover per year. However, there was significant heterogeneity in the temporal pattern of impact for individual covenants, ranging from -4 to +7% change in woody vegetation cover per year. Results of our approach were consistent with results based on traditional approaches to estimating program-level impact. Our study provides a transparent and robust workflow to estimate individual and program-level impacts of private protected areas.


Evaluación del impacto del suelo privado de conservación con diseño de control sintético Resumen Los programas de protección de la biodiversidad en suelo privado se utilizan cada vez más en todo el mundo. Para entender la eficacia de estos programas, es importante determinar la diferencia entre el resultado del programa y lo que habría ocurrido sin él. Normalmente, estos programas se evalúan estimando el impacto medio a nivel de programa, lo que permite fácilmente las comparaciones entre programas o regiones, pero oculta una importante heterogeneidad en el impacto entre las intervenciones individuales de conservación. Utilizamos un diseño de control sintético, un emparejamiento estadístico y datos de series temporales para estimar el impacto de las áreas protegidas individuales a lo largo del tiempo y combinamos los impactos a nivel individual para estimar el impacto a nivel de programa con un enfoque meta-analítico. Aplicamos el método a áreas protegidas privadas regidas por acuerdos de conservación (acuerdos con vínculos jurídicos sobre la titularidad para proteger la biodiversidad) destinados a mejorar la cubierta vegetal leñosa en la región de Goldfields de Victoria, Australia. Comparamos nuestros resultados con los métodos tradicionales de estimación del impacto a nivel de programa basados en un subconjunto de pactos de la misma antigüedad. Nuestros resultados mostraron un impacto global a nivel de programa de un aumento del 0.3-0.8% de la cubierta vegetal leñosa al año. Sin embargo, hubo una heterogeneidad significativa en el patrón temporal del impacto para los pactos individuales, que osciló entre −4 y +7% de cambio en la cubierta vegetal leñosa por año. Los resultados de nuestra estrategia fueron consecuentes con los resultados basados en las estrategias tradicionales usadas para estimar el impacto a nivel de programa. Nuestro estudio proporciona un flujo de trabajo transparente y sólido para estimar el impacto individual a nivel de programa de las áreas protegidas privadas.


Subject(s)
Biodiversity , Conservation of Natural Resources , Conservation of Natural Resources/methods , Victoria , Ecosystem
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