Despite the many advances of the genomic era, there is a persistent problem in assessing the uncertainty of phylogenomic hypotheses. We see this in the recent history of phylogenetics for cockroaches and termites (Blattodea), where huge advances have been made, but there are still major inconsistencies between studies. To address this, we present a phylogenetic analysis of Blattodea that emphasizes identification and quantification of uncertainty. We analyze 1183 gene domains using three methods (multi-species coalescent inference, concatenation, and a supermatrix-supertree hybrid approach) and assess support for controversial relationships while considering data quality. The hybrid approach-here dubbed \"tiered phylogenetic inference\"-incorporates information about data quality into an incremental tree building framework. Leveraging this method, we are able to identify cases of low or misleading support that would not be possible otherwise, and explore them more thoroughly with follow-up tests. In particular, quality annotations pointed towards nodes with high bootstrap support that later turned out to have large ambiguities, sometimes resulting from low-quality data. We also clarify issues related to some recalcitrant nodes: Anaplectidae\'s placement lacks unbiased signal, Ectobiidae s.s. and Anaplectoideini need greater taxon sampling, the deepest relationships among most Blaberidae lack signal. As a result, several previous phylogenetic uncertainties are now closer to being resolved (e.g., African and Malagasy \"Rhabdoblatta\" spp. are the sister to all other Blaberidae, and Oxyhaloinae is sister to the remaining Blaberidae). Overall, we argue for more approaches to quantifying support that take data quality into account to uncover the nature of recalcitrant nodes.

UNASSIGNED: To describe the prevalence of missing sociodemographic data in the IRIS® (Intelligent Research in Sight) Registry and to identify practice-level characteristics associated with missing sociodemographic data.
UNASSIGNED: Cross-sectional study.
UNASSIGNED: All patients with clinical encounters at practices participating in the IRIS Registry prior to December 31, 2020.
UNASSIGNED: We describe geographic and temporal trends in the prevalence of missing data for each sociodemographic variable (age, sex, race, ethnicity, geographic location, insurance type, and smoking status). Each practice contributing data to the registry was categorized based on the number of patients, number of physicians, geographic location, patient visit frequency, and patient population demographics.
UNASSIGNED: Multivariable linear regression was used to describe the association of practice-level characteristics with missing patient-level sociodemographic data.
UNASSIGNED: This study included the electronic health records of 66 477 365 patients receiving care at 3306 practices participating in the IRIS Registry. The median number of patients per practice was 11 415 (interquartile range: 5849-24 148) and the median number of physicians per practice was 3 (interquartile range: 1-7). The prevalence of missing patient sociodemographic data were 0.1% for birth year, 0.4% for sex, 24.8% for race, 30.2% for ethnicity, 2.3% for 3-digit zip code, 14.8% for state, 5.5% for smoking status, and 17.0% for insurance type. The prevalence of missing data increased over time and varied at the state-level. Missing race data were associated with practices that had fewer visits per patient (P < 0.001), cared for a larger nonprivately insured patient population (P = 0.001), and were located in urban areas (P < 0.001). Frequent patient visits were associated with a lower prevalence of missing race (P < 0.001), ethnicity (P < 0.001), and insurance (P < 0.001), but a higher prevalence of missing smoking status (P < 0.001).
UNASSIGNED: There are geographic and temporal trends in missing race, ethnicity, and insurance type data in the IRIS Registry. Several practice-level characteristics, including practice size, geographic location, and patient population, are associated with missing sociodemographic data. While the prevalence and patterns of missing data may change in future versions of the IRIS registry, there will remain a need to develop standardized approaches for minimizing potential sources of bias and ensure reproducibility across research studies.
UNASSIGNED: Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.

OBJECTIVE: Scales often arise from multi-item questionnaires, yet commonly face item non-response. Traditional solutions use weighted mean (WMean) from available responses, but potentially overlook missing data intricacies. Advanced methods like multiple imputation (MI) address broader missing data, but demand increased computational resources. Researchers frequently use survey data in the All of Us Research Program (All of Us), and it is imperative to determine if the increased computational burden of employing MI to handle non-response is justifiable.
OBJECTIVE: Using the 5-item Physical Activity Neighborhood Environment Scale (PANES) in All of Us, this study assessed the tradeoff between efficacy and computational demands of WMean, MI, and inverse probability weighting (IPW) when dealing with item non-response.
METHODS: Synthetic missingness, allowing 1 or more item non-response, was introduced into PANES across 3 missing mechanisms and various missing percentages (10%-50%). Each scenario compared WMean of complete questions, MI, and IPW on bias, variability, coverage probability, and computation time.
RESULTS: All methods showed minimal biases (all <5.5%) for good internal consistency, with WMean suffered most with poor consistency. IPW showed considerable variability with increasing missing percentage. MI required significantly more computational resources, taking >8000 and >100 times longer than WMean and IPW in full data analysis, respectively.
CONCLUSIONS: The marginal performance advantages of MI for item non-response in highly reliable scales do not warrant its escalated cloud computational burden in All of Us, particularly when coupled with computationally demanding post-imputation analyses. Researchers using survey scales with low missingness could utilize WMean to reduce computing burden.

Ranked set sampling (RSS) is known to increase the efficiency of the estimators while comparing it with simple random sampling. The problem of missingness creates a gap in the information that needs to be addressed before proceeding for estimation. Negligible amount of work has been carried out to deal with missingness utilizing RSS. This paper proposes some logarithmic type methods of imputation for the estimation of population mean under RSS using auxiliary information. The properties of the suggested imputation procedures are examined. A simulation study is accomplished to show that the proposed imputation procedures exhibit better results in comparison to some of the existing imputation procedures. Few real applications of the proposed imputation procedures is also provided to generalize the simulation study.

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.

Body Mass Index (BMI) trajectories are important for understanding how BMI develops over time. Missing data is often stated as a limitation in studies that analyse BMI over time and there is limited research exploring how missing data influences BMI trajectories. This study explores the influence missing data has in estimating BMI trajectories and the impact on subsequent analysis. This study uses data from the English Longitudinal Study of Ageing. Distinct BMI trajectories are estimated for adults aged 50 years and over. Next, multiple methods accounting for missing data are implemented and compared. Estimated trajectories are then used to predict the risk of developing type 2 diabetes mellitus (T2DM). Four distinct trajectories are identified using each of the missing data methods: stable overweight, elevated BMI, increasing BMI, and decreasing BMI. However, the likelihoods of individuals following the different trajectories differ between the different methods. The influence of BMI trajectory on T2DM is reduced after accounting for missing data. More work is needed to understand which methods for missing data are most reliable. When estimating BMI trajectories, missing data should be considered. The extent to which accounting for missing data influences cost-effectiveness analyses should be investigated.

BACKGROUND: The impact of missing data on individual continuous glucose monitoring (CGM) data is unknown but can influence clinical decision-making for patients.
OBJECTIVE: We aimed to investigate the consequences of data loss on glucose metrics in individual patient recordings from continuous glucose monitors and assess its implications on clinical decision-making.
METHODS: The CGM data were collected from patients with type 1 and 2 diabetes using the FreeStyle Libre sensor (Abbott Diabetes Care). We selected 7-28 days of 24 hours of continuous data without any missing values from each individual patient. To mimic real-world data loss, missing data ranging from 5% to 50% were introduced into the data set. From this modified data set, clinical metrics including time below range (TBR), TBR level 2 (TBR2), and other common glucose metrics were calculated in the data sets with and that without data loss. Recordings in which glucose metrics deviated relevantly due to data loss, as determined by clinical experts, were defined as expert panel boundary error (εEPB). These errors were expressed as a percentage of the total number of recordings. The errors for the recordings with glucose management indicator <53 mmol/mol were investigated.
RESULTS: A total of 84 patients contributed to 798 recordings over 28 days. With 5%-50% data loss for 7-28 days recordings, the εEPB varied from 0 out of 798 (0.0%) to 147 out of 736 (20.0%) for TBR and 0 out of 612 (0.0%) to 22 out of 408 (5.4%) recordings for TBR2. In the case of 14-day recordings, TBR and TBR2 episodes completely disappeared due to 30% data loss in 2 out of 786 (0.3%) and 32 out of 522 (6.1%) of the cases, respectively. However, the initial values of the disappeared TBR and TBR2 were relatively small (<0.1%). In the recordings with glucose management indicator <53 mmol/mol the εEPB was 9.6% for 14 days with 30% data loss.
CONCLUSIONS: With a maximum of 30% data loss in 14-day CGM recordings, there is minimal impact of missing data on the clinical interpretation of various glucose metrics.
BACKGROUND: ClinicalTrials.gov NCT05584293; https://clinicaltrials.gov/study/NCT05584293.

We consider the problem of optimal model averaging for partially linear models when the responses are missing at random and some covariates are measured with error. A novel weight choice criterion based on the Mallows-type criterion is proposed for the weight vector to be used in the model averaging. The resulting model averaging estimator for the partially linear models is shown to be asymptotically optimal under some regularity conditions in terms of achieving the smallest possible squared loss. In addition, the existence of a local minimizing weight vector and its convergence rate to the risk-based optimal weight vector are established. Simulation studies suggest that the proposed model averaging method generally outperforms existing methods. As an illustration, the proposed method is applied to analyze an HIV-CD4 dataset.

BACKGROUND: Vital signs are important factors in assessing injury severity and guiding trauma resuscitation, especially among severely injured patients. Despite this, physiological data are frequently missing from trauma registries. This study aimed to evaluate the extent of missing prehospital data in a hospital-based trauma registry and to assess the associations between prehospital physiological data completeness and indicators of injury severity.
METHODS: A retrospective review was conducted on all adult trauma patients brought directly to a level 1 trauma center in Toronto, Ontario by paramedics from January 1, 2015, to December 31, 2019. The proportion of missing data was evaluated for each variable and patterns of missingness were assessed. To investigate the associations between prehospital data completeness and injury severity factors, descriptive and unadjusted logistic regression analyses were performed.
RESULTS: A total of 3,528 patients were included. We considered prehospital data missing if any of heart rate, systolic blood pressure, respiratory rate or oxygen saturation were incomplete. Each individual variable was missing from the registry in approximately 20 % of patients, with oxygen saturation missing most frequently (n = 831; 23.6 %). Over 25 % (n = 909) of patients were missing at least one prehospital vital sign, of which 69.1 % (n = 628) were missing all four of these variables. Patients with incomplete data were more severely injured, had higher mortality, and more frequently received lifesaving interventions such as blood transfusion and intubation. Patients were most likely to have missing prehospital physiological data if they died in the trauma bay (unadjusted OR: 9.79; 95 % CI: 6.35-15.10), did not survive to discharge (unadjusted OR: 3.55; 95 % CI: 2.76-4.55), or had a prehospital GCS less than 9 (OR: 3.24; 95 % CI: 2.59-4.06).
CONCLUSIONS: In this single center trauma registry, key prehospital variables were frequently missing, particularly among more severely injured patients. Patients with missing data had higher mortality, more severe injury characteristics and received more life-saving interventions in the trauma bay, suggesting an injury severity bias in prehospital vital sign missingness. To ensure the validity of research based on trauma registry data, patterns of missingness must be carefully considered to ensure missing data is appropriately addressed.

BACKGROUND: Electronic Health Records (EHR) are widely used to develop clinical prediction models (CPMs). However, one of the challenges is that there is often a degree of informative missing data. For example, laboratory measures are typically taken when a clinician is concerned that there is a need. When data are the so-called Not Missing at Random (NMAR), analytic strategies based on other missingness mechanisms are inappropriate. In this work, we seek to compare the impact of different strategies for handling missing data on CPMs performance.
METHODS: We considered a predictive model for rapid inpatient deterioration as an exemplar implementation. This model incorporated twelve laboratory measures with varying levels of missingness. Five labs had missingness rate levels around 50%, and the other seven had missingness levels around 90%. We included them based on the belief that their missingness status can be highly informational for the prediction. In our study, we explicitly compared the various missing data strategies: mean imputation, normal-value imputation, conditional imputation, categorical encoding, and missingness embeddings. Some of these were also combined with the last observation carried forward (LOCF). We implemented logistic LASSO regression, multilayer perceptron (MLP), and long short-term memory (LSTM) models as the downstream classifiers. We compared the AUROC of testing data and used bootstrapping to construct 95% confidence intervals.
RESULTS: We had 105,198 inpatient encounters, with 4.7% having experienced the deterioration outcome of interest. LSTM models generally outperformed other cross-sectional models, where embedding approaches and categorical encoding yielded the best results. For the cross-sectional models, normal-value imputation with LOCF generated the best results.
CONCLUSIONS: Strategies that accounted for the possibility of NMAR missing data yielded better model performance than those did not. The embedding method had an advantage as it did not require prior clinical knowledge. Using LOCF could enhance the performance of cross-sectional models but have countereffects in LSTM models.