Integration of Multiple Metabolic Signals Determines Cell Fate Prior to Commitment.

Cell-fate decisions are central to the survival and development of both uni- and multicellular organisms. It remains unclear when and to what degree cells can decide on future fates prior to commitment. This uncertainty stems from experimental and theoretical limitations in measuring and integrating multiple signals at the single-cell level during a decision process. Here, we combine six-color live-cell imaging with the Bayesian method of statistical evidence to study the meiosis/quiescence decision in budding yeast. Integration of multiple upstream metabolic signals predicts individual cell fates with high probability well before commitment. Cells "decide" their fates before birth, well before the activation of pathways characteristic of downstream cell fates. This decision, which remains stable through several cell cycles, occurs when multiple metabolic parameters simultaneously cross cell-fate-specific thresholds. Taken together, our results show that cells can decide their future fates long before commitment mechanisms are activated.

A Bayesian approach to estimating COVID-19 incidence and infection fatality rates.

Naive estimates of incidence and infection fatality rates (IFR) of coronavirus disease 2019 suffer from a variety of biases, many of which relate to preferential testing. This has motivated epidemiologists from around the globe to conduct serosurveys that measure the immunity of individuals by testing for the presence of SARS-CoV-2 antibodies in the blood. These quantitative measures (titer values) are then used as a proxy for previous or current infection. However, statistical methods that use this data to its full potential have yet to be developed. Previous researchers have discretized these continuous values, discarding potentially useful information. In this article, we demonstrate how multivariate mixture models can be used in combination with post-stratification to estimate cumulative incidence and IFR in an approximate Bayesian framework without discretization. In doing so, we account for uncertainty from both the estimated number of infections and incomplete deaths data to provide estimates of IFR. This method is demonstrated using data from the Action to Beat Coronavirus erosurvey in Canada.

A Novel Mathematical Approach for Analysis of Integrated Cell-Patient Data Uncovers a 6-Gene Signature Linked to Endocrine Therapy Resistance.

A significant number of breast cancers develop resistance to hormone therapy. This progression, while posing a major clinical challenge, is difficult to predict. Despite important contributions made by cell models and clinical studies to tackle this problem, both present limitations when taken individually. Experiments with cell models are highly reproducible but do not reflect the indubitable heterogenous landscape of breast cancer. On the other hand, clinical studies account for this complexity but introduce uncontrolled noise due to external factors. Here, we propose a new approach for biomarker discovery that is based on a combined analysis of sequencing data from controlled MCF7 cell experiments and heterogenous clinical samples that include clinical and sequencing information from The Cancer Genome Atlas. Using data from differential gene expression analysis and a Bayesian logistic regression model coupled with an original simulated annealing-type algorithm, we discovered a novel 6-gene signature for stratifying patient response to hormone therapy. The experimental observations and computational analysis built on independent cohorts indicated the superior predictive performance of this gene set over previously known signatures of similar scope. Together, these findings revealed a new gene signature to identify patients with breast cancer with an increased risk of developing resistance to endocrine therapy.

Inferring Human Immunodeficiency Virus 1 Proviral Integration Dates With Bayesian Inference.

Human immunodeficiency virus 1 (HIV) proviruses archived in the persistent reservoir currently pose the greatest obstacle to HIV cure due to their evasion of combined antiretroviral therapy and ability to reseed HIV infection. Understanding the dynamics of the HIV persistent reservoir is imperative for discovering a durable HIV cure. Here, we explore Bayesian methods using the software BEAST2 to estimate HIV proviral integration dates. We started with within-host longitudinal HIV sequences collected prior to therapy, along with sequences collected from the persistent reservoir during suppressive therapy. We built a BEAST2 model to estimate integration dates of proviral sequences collected during suppressive therapy, implementing a tip date random walker to adjust the sequence tip dates and a latency-specific prior to inform the dates. To validate our method, we implemented it on both simulated and empirical data sets. Consistent with previous studies, we found that proviral integration dates were spread throughout active infection. Path sampling to select an alternative prior for date estimation in place of the latency-specific prior produced unrealistic results in one empirical data set, whereas on another data set, the latency-specific prior was selected as best fitting. Our Bayesian method outperforms current date estimation techniques with a root mean squared error of 0.89 years on simulated data relative to 1.23-1.89 years with previously developed methods. Bayesian methods offer an adaptable framework for inferring proviral integration dates.

Depression at the intersection of race/ethnicity, sex/gender, and sexual orientation in a nationally representative sample of US adults: A design-weighted intersectional MAIHDA.

This study examined how race/ethnicity, sex/gender, and sexual orientation intersect under interlocking systems of oppression to socially pattern depression among US adults. With cross-sectional data from the 2015-2020 National Survey on Drug Use and Health (NSDUH; n=234,722), we conducted design-weighted multilevel analysis of individual heterogeneity and discriminatory accuracy (MAIHDA) under an intersectional framework to predict past-year and lifetime major depressive episode (MDE). With 42 intersectional groups constructed from seven race/ethnicity, two sex/gender, and three sexual orientation categories, we estimated age-standardized prevalence and excess/reduced prevalence attributable to two-way or higher interaction effects. Models revealed heterogeneity across groups, with prevalence ranging from 1.9-19.7% (past-year) and 4.5-36.5% (lifetime). Approximately 12.7% (past-year) and 12.5% (lifetime) of total individual variance were attributable to between-group differences, indicating key relevance of intersectional groups in describing the population distribution of depression. Main effects indicated, on average, people who were White, women, gay/lesbian, or bisexual had greater odds of MDE. Main effects explained most between-group variance. Interaction effects (past-year: 10.1%; lifetime: 16.5%) indicated a further source of heterogeneity around averages with groups experiencing excess/reduced prevalence compared to main effects expectations. We extend the MAIHDA framework to calculate nationally representative estimates from complex sample survey data using design-weighted, Bayesian methods.

Reassessing pharmacogenomic cell sensitivity with multilevel statistical models.

Pharmacogenomic experiments allow for the systematic testing of drugs, at varying dosage concentrations, to study how genomic markers correlate with cell sensitivity to treatment. The first step in the analysis is to quantify the response of cell lines to variable dosage concentrations of the drugs being tested. The signal to noise in these measurements can be low due to biological and experimental variability. However, the increasing availability of pharmacogenomic studies provides replicated data sets that can be leveraged to gain power. To do this, we formulate a hierarchical mixture model to estimate the drug-specific mixture distributions for estimating cell sensitivity and for assessing drug effect type as either broad or targeted effect. We use this formulation to propose a unified approach that can yield posterior probability of a cell being susceptible to a drug conditional on being a targeted effect or relative effect sizes conditioned on the cell being broad. We demonstrate the usefulness of our approach via case studies. First, we assess pairwise agreements for cell lines/drugs within the intersection of two data sets and confirm the moderate pairwise agreement between many publicly available pharmacogenomic data sets. We then present an analysis that identifies sensitivity to the drug crizotinib for cells harboring EML4-ALK or NPM1-ALK gene fusions, as well as significantly down-regulated cell-matrix pathways associated with crizotinib sensitivity.

A Bayesian MultiLayer Record Linkage Procedure to Analyze Post-Acute Care Recovery of Patients with Traumatic Brain Injury.

Understanding associations between injury severity and postacute care recovery for patients with traumatic brain injury (TBI) is crucial to improving care. Estimating these associations requires information on patients' injury, demographics, and healthcare utilization, which are dispersed across multiple data sets. Because of privacy regulations, unique identifiers are not available to link records across these data sets. Record linkage methods identify records that represent the same patient across data sets in the absence of unique identifiers. With a large number of records, these methods may result in many false links. Health providers are a natural grouping scheme for patients, because only records that receive care from the same provider can represent the same patient. In some cases, providers are defined within each data set, but they are not uniquely identified across data sets. We propose a Bayesian record linkage procedure that simultaneously links providers and patients. The procedure improves the accuracy of the estimated links compared to current methods. We use this procedure to merge a trauma registry with Medicare claims to estimate the association between TBI patients' injury severity and postacute care recovery.

Test-retest reliability of the play-or-pass version of the Iowa Gambling Task.

The Iowa Gambling Task (IGT) is used to assess decision-making in clinical populations. The original IGT does not disambiguate reward and punishment learning; however, an adaptation of the task, the "play-or-pass" IGT, was developed to better distinguish between reward and punishment learning. We evaluated the test-retest reliability of measures of reward and punishment learning from the play-or-pass IGT and examined associations with self-reported measures of reward/punishment sensitivity and internalizing symptoms. Participants completed the task across two sessions, and we calculated mean-level differences and rank-order stability of behavioral measures across the two sessions using traditional scoring, involving session-wide choice proportions, and computational modeling, involving estimates of different aspects of trial-level learning. Measures using both approaches were reliable; however, computational modeling provided more insights regarding between-session changes in performance, and how performance related to self-reported measures of reward/punishment sensitivity and internalizing symptoms. Our results show promise in using the play-or-pass IGT to assess decision-making; however, further work is still necessary to validate the play-or-pass IGT.

A regional genomic surveillance program is implemented to monitor the occurrence and emergence of SARS-CoV-2 variants in Yubei District, China.

BACKGROUND: In December 2022, Chongqing experienced a significant surge in coronavirus disease 2019 (COVID-19) epidemic after adjusting control measures in China. Given the widespread immunization of the population with the BA.5 variant, it is crucial to actively monitor severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant evolution in Chongqing's Yubei district. METHODS: In this retrospective study based on whole genome sequencing, we collected oropharyngeal and nasal swab of native COVID-19 cases from Yubei district between January to May 2023, along with imported cases from January 2022 to January 2023. Through second-generation sequencing, we generated a total of 578 genomes. RESULTS: Phylogenetic analyses revealed these genomes belong to 47 SARS-CoV-2 Pango lineages. BA.5.2.48 was dominant from January to April 2023, rapidly replaced by XBB* variants from April to May 2023. Bayesian Skyline Plot reconstructions indicated a higher evolutionary rate (6.973 × 10-4 subs/site/year) for the XBB.1.5* lineage compared to others. The mean time to the most recent common ancestor (tMRCA) of BA.5.2.48* closely matched BA.2.75* (May 27, 2022). Using multinomial logistic regression, we estimated growth advantages, with XBB.1.9.1 showing the highest growth advantage (1.2, 95% HPI:1.1-1.2), followed by lineage FR.1 (1.1, 95% HPI:1.1-1.2). CONCLUSIONS: Our monitoring reveals the rapid replacement of the previously prevalent BA.5.2.48 variant by XBB and its sub-variants, underscoring the ineffectiveness of herd immunity and breakthrough BA.5 infections against XBB variants. Given the ongoing evolutionary pressure, sustaining a SARS-CoV-2 genomic surveillance program is imperative.

Association between the body mass index of women undergoing IVF and the gender of the offspring.

RESEARCH QUESTION: Is there an association between women's body mass index (BMI) and the gender of offspring generated from fresh or frozen-thawed embryo transfer (FET) cycles? DESIGN: Between 2018 and 2021, 2670 cycles were performed, comprising 786 fresh embryo transfers and 1884 FET cycles. The study analysed the relationship between the BMI of women undergoing IVF and the sex of the newborn and the male-to-female live birth ratio (secondary sex ratio [SSR]). RESULTS: After 2670 single-embryo transfers, 483 (50.31%) male and 477 (49.69%) female infants were born, with an SSR of 101.3. In the fresh embryo transfer group, the SSR ranged from 350 (95% CI 82.67-1481.65) in underweight women (although this was based on very small numbers) to 109.7 (95% CI 67.73-176.61) in overweight women, while in the FET group, SSR values varied correspondingly from 130.8 (95% CI 64.47-265.26) to 63.0 (95% CI 46.02-86.24). Results from Bayesian multinomial logistic regression showed that for each unit increase in BMI within the fresh embryo transfer group, the odds of a boy's birth decreased by 6% (odds ratio [OR] 0.94, 95% CI 0.90-0.99) and the odds of a girl's birth by 5% (OR 0.95, 95% CI 0.90-0.99). Within the FET cohort, the odds of a boy's birth decreased by 4% (OR 0.96, 95% CI 0.92-0.99), while the odds of a girl's birth increased by 3% (OR 1.03, 95% CI 1.00-1.06). CONCLUSIONS: An increase in BMI is associated with the birth of fewer boys in fresh or frozen embryo transfer cycles, and a significant increase in the birth of girls in FET cycles.

Aspirin 162 mg vs 81 mg for preeclampsia prophylaxis in high-risk obese individuals: a comparative effectiveness open-label randomized trial (ASPREO).

BACKGROUND: In the United States, leading medical societies recommend 81 mg of aspirin daily for the prevention of preeclampsia in women at risk, whereas the NICE guidelines in the United Kingdom recommend a dose as high as 150 mg of aspirin. Recent data also suggest that in the obese population, inadequate dosing or aspirin resistance may impact the efficacy of aspirin at the currently recommended doses. OBJECTIVE: We evaluated whether daily administration of 162 mg aspirin would be more effective compared with 81 mg in decreasing the rate of preeclampsia with severe features in high-risk obese pregnant individuals. STUDY DESIGN: We performed a randomized trial between May 2019 and November 2022. Individuals at 12-20 weeks of gestational age with a body mass index ≥30 kg/m2 at the time of enrollment and at least 1 of 3 high-risk factors: history of preeclampsia in a prior pregnancy, at least stage I hypertension documented in the index pregnancy, pregestational diabetes or gestational diabetes diagnosed before 20 weeks of gestational age were randomized to either 162 mg or 81 mg of aspirin daily till delivery, participants were not blinded to treatment allocation. Exclusion criteria were multifetal gestation, known major fetal anomalies, seizure disorder, baseline proteinuria, on aspirin because of other indications, or contraindication to aspirin. The primary outcome was preeclampsia with severe features (preeclampsia or superimposed preeclampsia with severe features; eclampsia; or hemolysis, elevated liver enzymes, low platelet count syndrome). Secondary outcomes included rates of preterm birth because of preeclampsia, small for gestational age, postpartum hemorrhage, abruption, and medication side effects. A sample size of 220 was needed using a preplanned Bayesian analysis of the primary outcome to estimate the posterior probability of benefit or harm with a neutral informative prior. RESULTS: Approximately 220/343 (64.1%) individuals were randomized. The primary outcome was available for 209/220 (95%) individuals. Baseline characteristics were similar between groups, with the median gestational age at enrollment being 15.9 weeks in the 162 mg aspirin group and 15.6 weeks in the 81 mg aspirin group. Enrollment before 16 weeks occurred in 55 of 110 of those assigned to 162 mg and 58 of 110 of those assigned to 81 mg of aspirin. The primary outcome occurred in n of d individuals (35%) in the 162 mg aspirin group and n of d individuals (40%) in the 81 mg aspirin group (posterior relative risk, 0.88; 95% credible interval, 0.64-1.22). Bayesian analysis indicated a 78% probability of a reduction in the primary outcome with 162 mg aspirin compared with 81 mg aspirin dose. Rates of indicated preterm birth because of preeclampsia (21% vs 21%), small for gestational age (6.5% vs 2.9%), abruption (2.8% vs 3.0%), and postpartum hemorrhage (10.0% vs 8.8%) were similar between groups. Medication adverse effects were also similar. CONCLUSION: Among high-risk obese individuals, there was a 78% probability of benefit that 162 mg aspirin compared with 81 mg will decrease the rate of preeclampsia with severe features. With the best estimate of a 12% reduction when using 162 mg of aspirin compared with 81 mg of aspirin in this population. This trial supports doing a larger multicenter trial.

Implementing a Bundle for Evidence-based Cesarean Delivery May Not Be As Beneficial as Expected: A Multi-center, Pre- and Post- Study.

BACKGROUND: Standardization of procedures improves outcomes. Though systematic reviews have summarized the evidence-based steps (EBS) of cesarean delivery (CD), their bundled implementation has not been investigated. OBJECTIVE: In this pre- and post-implementation trial, we sought to ascertain if bundled EBS of CD, compared to surgeon's preference, improves outcomes. STUDY DESIGN: A StaRI (Standards for Reporting Implementation Studies) compliant, multi-center pre- and post-implementation trial at 4 teaching hospitals was conducted. The pre-implementation period consisted of CD done based on the physicians' preferences for 3 months; educational intervention (e.g., didactics, badge cards, posters, video) occurred at the 4th month. CDs in post-implementation period employed the bundled EBS. A pre-planned 10% randomized audit of both groups assessed adherence and uptake of EBS. The primary outcome was a composite maternal morbidity (CMM), which included estimated blood loss > 1,000 mL, blood transfusion, endometritis, post-partum fever, wound complications, sepsis, thrombosis, ICU admission, hysterectomy, or death. The secondary outcome was a composite neonatal morbidity (CNM) and some of its components were 5-min Apgar score < 7, positive pressure oxygen use, hypoglycemia, or sepsis. A priori Bayesian sample size calculation indicated 700 CD in each group was needed to demonstrate 20% relative reduction (from 15% to 12%) of CMM with 75% certainty. Bayesian logistic regression with neutral priors was used to calculate likelihood of net-improvement in adjusted relative risk (aRR) with 95% credible intervals (CrI). RESULTS: A total of 1,425 consecutive CD (721 in pre- and 704 in post-implementation group) were examined. Audited data indicated that the baseline EBS utilization rate during the pre-implementation period was 79%; after the implementation bundled EBS of CD the audited adherence was 89%-an uptake of 10.0% of the EBS. In four aspects, the maternal characteristics differed significantly in the pre- and post-implementation periods: race/ethnicity, hypertensive disorder, and the relative contribution of the 4 centers to the cohorts and the gestational age at delivery, but the indications for CD and whether its duration was < versus > 60 min did not. The rates of CMM in the pre- and post-implementation groups were 26% and 22%, respectively (aRR, 0.88; 95% CrI, 0.73-1.04), with a 94 % Bayesian probability of a reduction in CMM. The CNM occurred in 37% of the pre- and in 41% of the post-implementation group (aRR, 1.12; 95% CrI 0.98-1.39), with a 95% Bayesian probability of worsening in CNM. When CMM were segregated by preterm (<37 wks) and term (> 37 weeks) CD, the improvement in maternal outcomes persisted; when CNM were segregated by gestational age subgroupsthe potential for worsening neonatal outcomes persisted as well. CONCLUSIONS: Standardization of the evidence-based bundled steps of cesarean delivery resulted in a modest reduction of the composite maternal outcome; however, a paradoxical increase in neonatal composite morbidity was noted. Although individual evidence-based steps may be of value, while awaiting additional intervention trials a formal bundling of such steps is currently not recommended.

Bayesian spatio-temporal analysis of malaria prevalence in children between 2 and 10 years of age in Gabon.

BACKGROUND: Gabon still bears significant malaria burden despite numerous efforts. To reduce this burden, policy-makers need strategies to design effective interventions. Besides, malaria distribution is well known to be related to the meteorological conditions. In Gabon, there is limited knowledge of the spatio-temporal effect or the environmental factors on this distribution. This study aimed to investigate on the spatio-temporal effects and environmental factors on the distribution of malaria prevalence among children 2-10 years of age in Gabon. METHODS: The study used cross-sectional data from the Demographic Health Survey (DHS) carried out in 2000, 2005, 2010, and 2015. The malaria prevalence was obtained by considering the weighting scheme and using the space-time smoothing model. Spatial autocorrelation was inferred using the Moran's I index, and hotspots were identified with the local statistic Getis-Ord General Gi. For the effect of covariates on the prevalence, several spatial methods implemented in the Integrated Nested Laplace Approximation (INLA) approach using Stochastic Partial Differential Equations (SPDE) were compared. RESULTS: The study considered 336 clusters, with 153 (46%) in rural and 183 (54%) in urban areas. The prevalence was highest in the Estuaire province in 2000, reaching 46%. It decreased until 2010, exhibiting strong spatial correlation (P < 0.001), decreasing slowly with distance. Hotspots were identified in north-western and western Gabon. Using the Spatial Durbin Error Model (SDEM), the relationship between the prevalence and insecticide-treated bed nets (ITNs) coverage was decreasing after 20% of coverage. The prevalence in a cluster decreased significantly with the increase per percentage of ITNs coverage in the nearby clusters, and per degree Celsius of day land surface temperature in the same cluster. It slightly increased with the number of wet days and mean temperature per month in neighbouring clusters. CONCLUSIONS: In summary, this study showed evidence of strong spatial effect influencing malaria prevalence in household clusters. Increasing ITN coverage by 20% and prioritizing hotspots are essential policy recommendations. The effects of environmental factors should be considered, and collaboration with the national meteorological department (DGM) for early warning systems is needed.

An integrated Bayesian framework for multi-omics prediction and classification.

With the growing commonality of multi-omics datasets, there is now increasing evidence that integrated omics profiles lead to more efficient discovery of clinically actionable biomarkers that enable better disease outcome prediction and patient stratification. Several methods exist to perform host phenotype prediction from cross-sectional, single-omics data modalities but decentralized frameworks that jointly analyze multiple time-dependent omics data to highlight the integrative and dynamic impact of repeatedly measured biomarkers are currently limited. In this article, we propose a novel Bayesian ensemble method to consolidate prediction by combining information across several longitudinal and cross-sectional omics data layers. Unlike existing frequentist paradigms, our approach enables uncertainty quantification in prediction as well as interval estimation for a variety of quantities of interest based on posterior summaries. We apply our method to four published multi-omics datasets and demonstrate that it recapitulates known biology in addition to providing novel insights while also outperforming existing methods in estimation, prediction, and uncertainty quantification. Our open-source software is publicly available at https://github.com/himelmallick/IntegratedLearner.

Gaussian process emulation to improve efficiency of computationally intensive multidisease models: a practical tutorial with adaptable R code.

BACKGROUND: The rapidly growing burden of non-communicable diseases (NCDs) among people living with HIV in sub-Saharan Africa (SSA) has expanded the number of multidisease models predicting future care needs and health system priorities. Usefulness of these models depends on their ability to replicate real-life data and be readily understood and applied by public health decision-makers; yet existing simulation models of HIV comorbidities are computationally expensive and require large numbers of parameters and long run times, which hinders their utility in resource-constrained settings. METHODS: We present a novel, user-friendly emulator that can efficiently approximate complex simulators of long-term HIV and NCD outcomes in Africa. We describe how to implement the emulator via a tutorial based on publicly available data from Kenya. Emulator parameters relating to incidence and prevalence of HIV, hypertension and depression were derived from our own agent-based simulation model and other published literature. Gaussian processes were used to fit the emulator to simulator estimates, assuming presence of noise for design points. Bayesian posterior predictive checks and leave-one-out cross validation confirmed the emulator's descriptive accuracy. RESULTS: In this example, our emulator resulted in a 13-fold (95% Confidence Interval (CI): 8-22) improvement in computing time compared to that of more complex chronic disease simulation models. One emulator run took 3.00 seconds (95% CI: 1.65-5.28) on a 64-bit operating system laptop with 8.00 gigabytes (GB) of Random Access Memory (RAM), compared to > 11 hours for 1000 simulator runs on a high-performance computing cluster with 1500 GBs of RAM. Pareto k estimates were < 0.70 for all emulations, which demonstrates sufficient predictive accuracy of the emulator. CONCLUSIONS: The emulator presented in this tutorial offers a practical and flexible modelling tool that can help inform health policy-making in countries with a generalized HIV epidemic and growing NCD burden. Future emulator applications could be used to forecast the changing burden of HIV, hypertension and depression over an extended (> 10 year) period, estimate longer-term prevalence of other co-occurring conditions (e.g., postpartum depression among women living with HIV), and project the impact of nationally-prioritized interventions such as national health insurance schemes and differentiated care models.

Spatial-temporal distribution of preterm birth in China, 1990-2020: A systematic review and modelling analysis.

BACKGROUND: Little is known about the long-term trends of preterm birth rates in China and their geographic variation by province. OBJECTIVES: To estimate the annual spatial-temporal distribution of preterm birth rates in China by province from 1990 to 2020. DATA SOURCES: We searched PubMed, EMBASE, Web of Science, CNKI, WANFANG and VIP from January 1990 to September 2023. STUDY SELECTION AND DATA EXTRACTION: Studies that provided data on preterm births in China after 1990 were included. Data were extracted following the Guidelines for Accurate and Transparent Health Estimates Reporting. SYNTHESIS: We assessed the quality of each survey using a 9-point checklist. We estimated the annual preterm birth risk by province using Bayesian multilevel logistic regression models considering potential socioeconomic, environmental, and sanitary predictors. RESULTS: Based on 634 survey data from 343 included studies, we found a gradual increase in the preterm birth risk in most provinces in China since 1990, with an average annual increase of 0.7% nationally. However, the preterm birth rates in Inner Mongolia, Hubei, and Fujian Province showed a decline, while those in Sichuan were quite stable since 1990. In 2020, the estimates of preterm birth rates ranged from 2.9% (95% Bayesian credible interval [BCI] 2.1, 3.8) in Inner Mongolia to 8.5% (95% BCI 6.6, 10.9) in Jiangxi, with the national estimate of 5.9% (95% BCI 4.3, 8.1). Specifically, some provinces were identified as high-risk provinces for either consistently high preterm birth rates (e.g. Jiangxi) or relatively large increases (e.g. Shanxi) since 1990. CONCLUSIONS: This study provides annual information on the preterm birth risk in China since 1990 and identifies high-risk provinces to assist in targeted control and intervention for this health issue.

The effect of high protein dosing in critically ill patients: an exploratory, secondary Bayesian analyses of the EFFORT Protein trial.

BACKGROUND: The EFFORT Protein trial assessed the effect of high vs usual dosing of protein in adult ICU patients with organ failure. This study provides a probabilistic interpretation and evaluates heterogeneity in treatment effects (HTE). METHODS: We analysed 60-day all-cause mortality and time to discharge alive from hospital using Bayesian models with weakly informative priors. HTE on mortality was assessed according to disease severity (Sequential Organ Failure Assessment [SOFA] score), acute kidney injury, and serum creatinine values at baseline. RESULTS: The absolute difference in mortality was 2.5% points (95% credible interval -6.9 to 12.4), with a 72% posterior probability of harm associated with high protein treatment. For time to discharge alive from hospital, the hazard ratio was 0.91 (95% credible interval 0.80 to 1.04) with a 92% probability of harm for the high-dose protein group compared with the usual-dose protein group. There were 97% and 95% probabilities of positive interactions between the high protein intervention and serum creatinine and SOFA score at randomisation, respectively. Specifically, there was a potentially relatively higher mortality of high protein doses with higher baseline serum creatinine or SOFA scores. CONCLUSIONS: We found moderate to high probabilities of harm with high protein doses compared with usual protein in ICU patients for the primary and secondary outcomes. We found suggestions of heterogeneity in treatment effects with worse outcomes in participants randomised to high protein doses with renal dysfunction or acute kidney injury and greater illness severity at baseline.

Gender Dysphoria and Sexual Euphoria: A Bayesian Perspective on the Influence of Gender-Affirming Hormone Therapy on Sexual Arousal.

Self-reported sexual orientation of transgender individuals occasionally changes over transition. Using functional magnetic resonance imaging, we tested the hypothesis that neural and behavioral patterns of sexual arousal in transgender individuals would shift from the assigned to the experienced gender (e.g., trans women's responses becoming more dissimilar to those of cis men and more similar to those of cis women). To this aim, trans women (N = 12) and trans men (N = 20) as well as cisgender women (N = 24) and cisgender men (N = 14) rated visual stimuli showing male-female, female-female or male-male intercourse for sexual arousal before and after four months of gender-affirming hormone therapy. A Bayesian framework allowed us to incorporate previous behavioral findings. The hypothesized changes could indeed be observed in the behavioral responses with the strongest results for trans men and female-female scenes. Activation of the ventral striatum supported our hypothesis only for female-female scenes in trans women. The respective application or depletion of androgens in trans men and trans women might partly explain this observation. The prominent role of female-female stimuli might be based on the differential responses they elicit in cis women and men or, in theory, the controversial concept of autogynephilia. We show that correlates of sexual arousal in transgender individuals might change in the direction of the experienced gender. Future investigations should elucidate the mechanistic role of sex hormones and the cause of the differential neural and behavioral findings.The study was registered at ClinicalTrials.gov (NCT02715232), March 22, 2016.

Restrictive versus standard IV fluid therapy in adult ICU patients with septic shock-Bayesian analyses of the CLASSIC trial.

BACKGROUND: The CLASSIC trial assessed the effects of restrictive versus standard intravenous (IV) fluid therapy in adult intensive care unit (ICU) patients with septic shock. This pre-planned study provides a probabilistic interpretation and evaluates heterogeneity in treatment effects (HTE). METHODS: We analysed mortality, serious adverse events (SAEs), serious adverse reactions (SARs) and days alive without life-support within 90 days using Bayesian models with weakly informative priors. HTE on mortality was assessed according to five baseline variables: disease severity, vasopressor dose, lactate levels, creatinine values and IV fluid volumes given before randomisation. RESULTS: The absolute difference in mortality was 0.2%-points (95% credible interval: -5.0 to 5.4; 47% posterior probability of benefit [risk difference <0.0%-points]) with restrictive IV fluid. The posterior probabilities of benefits with restrictive IV fluid were 72% for SAEs, 52% for SARs and 61% for days alive without life-support. The posterior probabilities of no clinically important differences (absolute risk difference ≤2%-points) between the groups were 56% for mortality, 49% for SAEs, 90% for SARs and 38% for days alive without life-support. There was 97% probability of HTE for previous IV fluid volumes analysed continuously, that is, potentially relatively lower mortality of restrictive IV fluids with higher previous IV fluids. No substantial evidence of HTE was found in the other analyses. CONCLUSION: We could not rule out clinically important effects of restrictive IV fluid therapy on mortality, SAEs or days alive without life-support, but substantial effects on SARs were unlikely. IV fluids given before randomisation might interact with IV fluid strategy.

Assessing the use of GEE methods for analyzing binary outcomes in family studies: the Strong Heart Family Study.

The generalized estimating equations method (GEE) is commonly applied to analyze data obtained from family studies. GEE is well known for its robustness on misspecification of correlation structure. However, the unbalanced distribution of family sizes and complicated genetic relatedness structure within each family may challenge GEE performance. We focused our research on binary outcomes. To evaluate the performance of GEE, we conducted a series of simulations, on data generated adopting the kinship matrix (correlation structure within each family) from the Strong Heart Family Study (SHFS). We performed a fivefold cross-validation to further evaluate the GEE predictive power on data from the SHFS. A Bayesian modeling approach, with direct integration of the kinship matrix, was also included to contrast with GEE. Our simulation studies revealed that GEE performs well on a binary outcome from families having a relatively simple kinship structure. However, data with a binary outcome generated from families with complex kinship structures, especially with a large genetic variance, can challenge the performance of GEE.