Are the tests overpowered or underpowered? A unified solution to correctly specify type I errors in design of clinical trials for two sample proportions

As one of the most commonly used data types, methods in testing or designing a trial for binary endpoints from two independent populations are still being developed until recently. However, the power and the minimum required sample size comparisons between different tests may not be valid if their type I errors are not controlled at the same level. In this article, we unify all related testing procedures into a decision framework, including both frequentist and Bayesian methods. Sufficient conditions of the type I error attained at the boundary of hypotheses are derived, which help reduce the magnitude of the exact calculations and lay out a foundation for developing computational algorithms to correctly specify the actual type I error. The efficient algorithms are thus proposed to calculate the cutoff value in a deterministic decision rule and the probability value in a randomized decision rule, such that the actual type I error is under but closest to, or equal to, the intended level, respectively. The algorithm may also be used to calculate the sample size to achieve the prespecified type I error and power. The usefulness of the proposed methodology is further demonstrated in the power calculation for designing superiority and noninferiority trials.

A Bayesian model-based reduced major axis regression

Reduced major axis (RMA) regression, widely used in the fields of zoology, botany, ecology, biology, spectroscopy, and among others, outweighs the ordinary least square regression by relaxing the assumption that the covariates are without measurement errors. A Bayesian implementation of the RMA regression is presented in this paper, and the equivalence of the estimates of the parameters under the Bayesian and the frequentist frameworks is proved. This model-based Bayesian RMA method is advantageous since the posterior estimates, the standard deviations, as well as the credible intervals of the estimates can be obtained through Markov chain Monte Carlo methods directly. In addition, it is straightforward to extend to the multivariate RMA case. The performance of the Bayesian RMA approach is evaluated in the simulation study, and, finally, the proposed method is applied to analyze a dataset in the plantation.

Clinical effectiveness of oral antiviral agents for treating non-hospitalized COVID-19 patients with chronic kidney disease

OBJECTIVES

This study examined the effectiveness of nirmatrelvir plus ritonavir (NMV-r) and molnupiravir (MOV) in treating COVID-19 among chronic kidney disease (CKD) patients.

METHODS

This retrospective cohort study, using the TriNetX research network, identified stage 3-5 CKD and end-stage kidney disease (ESKD) patients with non-hospitalized COVID-19 between 1 January 2022, and 31 May 2023. Propensity score matching (PSM) was used to compare patients on NMV-r or MOV (antiviral group) against those not receiving these treatments (control group). The primary composite outcome was the cumulative hazard ratio (HR) for all-cause hospitalization or death within the 30-day follow-up.

RESULTS

After PSM, two balanced cohorts of 6,275 patients each were established. The antiviral group exhibited a lower incidence of all-cause hospitalization or mortality (5.93% vs. 9.53%; HR: 0.626; 95% CI: 0.550-0.713) than controls. Additionally, antiviral recipients were associated with a lower risk of all-cause hospitalization (HR: 0.679; 95% CI: 0.594-0.777) and mortality (HR: 0.338; 95% CI: 0.227-0.504). The beneficial effects of antiviral agents were consistent across sex, age, vaccination status, antiviral type, and CKD stage.

CONCLUSION

Oral antiviral agents could be associated with lower rates of all-cause hospitalization or death among non-hospitalized COVID-19 patients with CKD.

Autocrine phosphatase PDP2 inhibits ferroptosis by dephosphorylating ACSL4 in the Luminal A Breast Cancer

Phosphatases can dephosphorylate phosphorylated kinases, leading to their inactivation, and ferroptosis is a type of cell death. Therefore, our aim is to identify phosphatases associated with ferroptosis by analyzing the differentially expressed genes (DEGs) of the Luminal A Breast Cancer (LumABC) cohort from the Cancer Genome Atlas (TCGA). An analysis of 260 phosphatase genes from the GeneCard database revealed that out of the 28 DEGs with high expression, only the expression of pyruvate dehydrogenase phosphatase 2 (PDP2) had a significant correlation with patient survival. In addition, an analysis of DEGs using gene ontology, Kyoto Encyclopedia of Genes and Genomes and gene set enrichment analysis revealed a significant variation in the expression of ferroptosis-related genes. To further investigate this, we analyzed 34 ferroptosis-related genes from the TCGA-LumABC cohort. The expression of long-chain acyl-CoA synthetase 4 (ACSL4) was found to have the highest correlation with the expression of PDP2, and its expression was also inversely proportional to the survival rate of patients. Western blot experiments using the MCF-7 cell line showed that the phosphorylation level of ACSL4 was significantly lower in cells transfected with the HA-PDP2 plasmid, and ferroptosis was correspondingly reduced (p < 0.001), as indicated by data from flow cytometry detection of membrane-permeability cell death stained with 7-aminoactinomycin, lipid peroxidation, and Fe2+. Immunoprecipitation experiments further revealed that the phosphorylation level of ACSL4 was only significantly reduced in cells where PDP2 and ACSL4 co-precipitated. These findings suggest that PDP2 may act as a phosphatase to dephosphorylate and inhibit the activity of ACSL4, which had been phosphorylated and activated in LumABC cells. Further experiments are needed to confirm the molecular mechanism of PDP2 inhibiting ferroptosis.

Secondary analysis of late major gastrointestinal and genitourinary toxicities in unfavorable-risk prostate cancer patients receiving docetaxel: Insights from a randomized trial

BACKGROUND

This study sought to evaluate the late toxicity associated with neoadjuvant and concurrent docetaxel and radiation therapy in patients with prostate cancer.

METHODS

A secondary analysis was performed of the phase 3 multicenter randomized trial (Dana-Farber Cancer Institute 05-043) including 350 patients with nonmetastatic unfavorable-risk prostate cancer. Patients were randomized 1:1 to receive androgen deprivation therapy, radiation therapy, and docetaxel versus androgen deprivation therapy and radiation therapy. The study assessed the cumulative incidence rates of grade 2 and grade 3 or higher gastrointestinal, genitourinary, and sexual toxicity. A multivariable Fine and Gray's competing risks regression model adjusted for age at randomization and pelvic lymph node radiation therapy was used to evaluate the treatment effect of docetaxel on time to late genitourinary and gastrointestinal toxicities.

RESULTS

The study included 338 patients who primarily had minimal or no comorbidity (74.9%) and median age 66 years (interquartile range: 61,71). At a median follow-up of 10.2 years, docetaxel was not associated with increased risk of any grade 3 or higher (adjusted hazard ratio [AHR], 0.98; 95% confidence interval [CI], 0.36-2.67; p = .96) or grade 2 gastrointestinal (p = .75), genitourinary (p = .44), and sexual (p = .29) toxicity. Age was associated with increased grade 3 or higher (AHR, 1.08; 95% CI, 1.01-1.16; p = .03) and grade 2 gastrointestinal toxicity (AHR, 1.11; 95% CI, 1.03-1.20; p = .005). A nonsignificant trend (p = .09) toward increased late grade 3 or higher toxicity was observed for pelvic radiation therapy use.

CONCLUSIONS

Docetaxel combined with radiotherapy has an acceptable long-term toxicity profile.

Differences of bioelectrical impedance in the development and healing phase of pressure ulcers and erythema in mouse model

Pressure ulcers (PUs) are economically burdensome medical conditions. Early changes in pressure ulcers are associated with erythema. In this study, bioelectrical impedance was used to measure the differences between PUs and blanchable erythema. We divided 21 ICR mice into three groups: control, 1000 mmHg-1h, and 1000 mmHg-6h. Healthy skin, blanchable erythema, and PUs were induced on the dorsal skin. The results indicated an immediate increase in impedance, resistance, and reactance values in the pressure group after release, followed by a subsequent decrease until two days after release. Compared with the control group, impedance and reactance significantly increased by 30.9% (p < 0.05) and 30.1% (p < 0.01), respectively, in the 6 h-loading group immediately after release. One and two days after release, the 1 h-loading and 6 h-loading groups exhibited significantly different degrees of decline. One day after release, impedance and resistance decreased by 30.2% (p < 0.05) and 19.8% (p < 0.05), respectively, in the 1 h-loading group; while impedance, resistance, and reactance decreased by 39.2% (p < 0.01), 26.8% (p < 0.01), and 45.7% (p < 0.05), respectively, in the 6 h-loading group. Two days after release, in the 1 h-loading group, impedance and resistance decreased by 28.3% (p < 0.05) and 21.7% (p < 0.05), respectively; while in the 6 h-loading group, impedance, resistance, and reactance decreased by 49.8% (p < 0.001), 34.2% (p < 0.001), and 59.8% (p < 0.01), respectively. One and two days after release the pressure group reductions were significantly greater than those in the control group. Additionally, we monitored changes during wound healing. Distinguishing early PUs from blanchable erythema by noninvasive bioelectrical impedance technology may have applications value in early assessment of PUs.

Work-health balance of cancer survivors returning to work: A meta-ethnography

PURPOSE

This meta-ethnography investigates the multifaceted health-related experiences of cancer survivors returning to work (RTW), recognizing the pivotal role of employment in overall well-being, particularly in the context of increasing cancer cases among working-age adults.

METHOD

Following the methodology of Noblit and Hare, a comprehensive literature search was conducted from 2013 to 2023 in databases including PubMed, Scopus, CINAHL, PsycINFO, and Embase. Qualitative studies assessing cancer survivors' experiences, motivation, concern, resilience, and need in the process of RTW were identified. Eligible studies were assessed for quality using the Critical Appraisal Skills Program Checklist, and their findings were subsequently synthesized.

RESULTS

Seventeen studies were included for analysis. The finding revealed five key themes: motivations (voluntary and involuntary), cancer-related concerns, resilience, needs for cancer healthcare support, and workplace accommodation. Voluntarily RTW was primarily linked to desires of normalcy, while involuntary RTW was often financially driven. Cancer survivors often face physical, psychological, and social challenges in the RTW process. Resilience played a crucial role in their readaptation to the workplace. Participants expressed the need for additional guidance from healthcare providers and tailored support from the workplace to facilitate a smoother RTW experience.

CONCLUSION

Cancer survivors aspire to be actively engaged, have their specific needs addressed, and achieve success in their return-to-work endeavors. Occupational guidance and accommodation from healthcare providers and employers play a pivotal role in empowering survivors to balance cancer and work, facilitating the return-to-work process, and enhancing the quality of survivorship.

Pain/Stress, Mitochondrial Dysfunction and Neurodevelopment in Preterm Infants

Introduction Preterm infants experience tremendous early life pain/stress during their neonatal intensive care unit (NICU) hospitalization, which impacts their neurodevelopmental outcomes. Mitochondrial function/dysfunction may interface between perinatal stress events and neurodevelopment. Nevertheless, the specific proteins or pathways linking mitochondrial functions to pain-induced neurodevelopmental outcomes in infants are remain unidentified. Our study aims to investigate the associations among pain/stress, proteins associated with mitochondrial function/dysfunction, and neurobehavioral responses in preterm infants. Methods We conducted a prospective cohort study, enrolling 33 preterm infants between September 2017 and July 2022 at two affiliated NICUs located in Hartford and Farmington, CT. NICU Network Neurobehavioral Scale (NNNS) datasets were evaluated to explore potential association with neurobehavioral outcomes. The daily pain/stress experienced by infant's during their NICU stay was documented. At 36-38 weeks post-menstrual age (PMA), neurobehavioral outcomes were evaluated using the NNNS and buccal swabs were collected for further analysis. Mass spectrometry-based proteomics was conducted on epithelial cells obtained from buccal swabs to evaluate protein expression level. Lasso statistical methods were conducted to study the association between protein abundance and infants' NNNS summary scores. Multiple linear regression and Gene Ontology (GO) enrichment analyses were performed to examine how clinical characteristics and neurodevelopmental outcomes may be associated with protein levels and underlying molecular pathways. Results During NICU hospitalization, preterm premature rupture of membrane (PPROM) were negatively associated with neurobehavioral outcomes. The protein functions including leptin receptor binding activity, glutathione disulfide oxidoreductase activity and response to oxidative stress, lipid metabolism, phosphate and proton transmembrane transporter activity were negatively associated with neurobehavioral outcomes, in the contrast, cytoskeletal regulation, epithelial barrier and protection function were found to be associated with the optimal neurodevelopmental outcomes. In addition, mitochondrial function associated proteins including SPRR2A, PAIP1, S100A3, MT-CO2, PiC, GLRX, PHB2, and BNIPL-2 demonstrated positive association with favorable neurodevelopmental outcomes, while proteins of ABLIM1, UNC45A, Keratins, MUC1, and CYB5B showed positive association with adverse neurodevelopmental outcomes. Conclusion Mitochondrial function-related proteins were observed to be associated with early life pain/stress and neurodevelopmental outcomes in infants. Large-scale studies with longitudinal datasets are warranted. Buccal proteins could be used to predict potential neurobehavioral outcomes.

Reliability and Time Course of Postexercise Hypotension during Exercise Training among Adults with Hypertension

Postexercise hypotension (PEH), or the immediate decrease in blood pressure (BP) lasting for 24 h following an exercise bout, is well-established; however, the influence of exercise training on PEH dynamics is unknown. This study investigated the reliability and time course of change of PEH during exercise training among adults with hypertension. PEH responders (n = 10) underwent 12 weeks of aerobic exercise training, 40 min/session at moderate-to-vigorous intensity for 3 d/weeks. Self-measured BP was used to calculate PEH before and for 10 min after each session. The intraclass correlation coefficient (ICC) and Akaike Information Criterion (AIC) determined PEH reliability and goodness-of-fit for each week, respectively. Participants were obese (30.6 ± 4.3 kg∙m-2), middle-aged (57.2 ± 10.5 years), and mostly men (60%) with stage I hypertension (136.5 ± 12.1/83.4 ± 6.7 mmHg). Exercise training adherence was 90.6 ± 11.8% with 32.6 ± 4.2 sessions completed. PEH occurred in 89.7 ± 8.3% of these sessions with BP reductions of 9.3 ± 13.1/3.2 ± 6.8 mmHg. PEH reliability was moderate (ICC ~0.6). AIC analysis revealed a stabilization of maximal systolic and diastolic BP reductions at 3 weeks and 10 weeks, respectively. PEH persisted throughout exercise training at clinically meaningful levels, suggesting that the antihypertensive effects of exercise training may be largely due to PEH. Further studies in larger samples and under ambulatory conditions are needed to confirm these novel findings.

Morphological and phylogenetic analyses reveal a new species of Anthracophyllum (Omphalotaceae, Agaricales) in Zhejiang Province, China

During the investigations of macrofungi resources in Zhejiang Province, China, an interesting wood rot fungus was collected. Based on morphological and molecular phylogenetic studies, it is described as a new species, Anthracophyllum sinense. A. sinense is characterized by its sessile, charcoal black and pleurotoid pileus, sparse lamellae occasionally branching, clavate basidia with long sterigmata [(3-)6-7(-8) μm], and non-heteromorphous cystidia. A. sinense establishes a separate lineage close to A. archeri and A. lateritium in the phylogenetic tree.

Health disparities in preterm births

Introduction

Black African American (B/AA) women have a 2-fold to 3-fold elevated risk compared with non-Hispanic White (W) women for preterm birth. Further, preterm birth is the leading cause of mortality among B/AA infants, and among survivors, preterm infant adverse health outcomes occur disproportionately in B/AA infants. Racial inequities in maternal and infant health continue to pose a public health crisis despite the discovery >100 years ago. The purpose of this study was to expand on reported preterm infant outcome disparities. A life-course approach, accumulation of lifelong stress, including discrimination, may explain social factors causing preterm birth rate and outcome inequities in B/AA mothers.

Methods

Anthropometric measures and clinical treatment information for 197 consented participants were milled from electronic health records across 4 years. The Neonatal Infant Stressor Scale was used to tally acute and chronic painful/stressful procedures. Neurobehavioral differences were investigated using the Neonatal Intensive Care Unit (NICU) Network Neurobehavioral Scale.

Results

B/AA mothers gave birth to preterm infants earlier than W mothers. NICU hospitalization stays were extended more than 2 weeks for the significantly smaller B/AA preterm infants in comparison to the age-matched W preterm infants. A higher number of chronic lifesaving procedures with demonstrated altered stress response patterns were recorded for B/AA preterm infants.

Discussion

This cross-sectional analysis of preterm birth rates and preterm infant developmental and neurodevelopmental outcomes are presented in the context of NICU stress and pain, with attendant implications for infant mortality and future health disparities. Preterm birth rate and outcome inequities further support the need to develop interventions and policies that will reduce the impact of discrimination and improve social determinants of health for Black, Indigenous, and other People of Color.

Gankyrin inhibits ferroptosis through the p53/SLC7A11/GPX4 axis in triple-negative breast cancer cells

Gankyrin is found in high levels in triple-negative breast cancer (TNBC) and has been established to form a complex with the E3 ubiquitin ligase MDM2 and p53, resulting in the degradation of p53 in hepatocarcinoma cells. Therefore, this study sought to determine whether gankyrin could inhibit ferroptosis through this mechanism in TNBC cells. The expression of gankyrin was investigated in relation to the prognosis of TNBC using bioinformatics. Co-immunoprecipitation and GST pull-down assays were then conducted to determine the presence of a gankyrin and MDM2 complex. RT-qPCR and immunoblotting were used to examine molecules related to ferroptosis, such as gankyrin, p53, MDM2, SLC7A11, and GPX4. Additionally, cell death was evaluated using flow cytometry detection of 7-AAD and a lactate dehydrogenase release assay, as well as lipid peroxide C11-BODIPY. Results showed that the expression of gankyrin is significantly higher in TNBC tissues and cell lines, and is associated with a poor prognosis for patients. Subsequent studies revealed that inhibiting gankyrin activity triggered ferroptosis in TNBC cells. Additionally, silencing gankyrin caused an increase in the expression of the p53 protein, without altering its mRNA expression. Co-immunoprecipitation and GST pull-down experiments indicated that gankyrin and MDM2 form a complex. In mouse embryonic fibroblasts lacking both MDM2 and p53, this gankyrin/MDM2 complex was observed to ubiquitinate p53, thus raising the expression of molecules inhibited by ferroptosis, such as SLC7A11 and GPX4. Furthermore, silencing gankyrin in TNBC cells disrupted the formation of the gankyrin/MDM2 complex, hindered the degradation of p53, increased SLC7A11 expression, impeded cysteine uptake, and decreased GPX4 production. Our findings suggest that TNBC cells are able to prevent cell ferroptosis through the gankyrin/p53/SLC7A11/GPX4 signaling pathway, indicating that gankyrin may be a useful biomarker for predicting TNBC prognosis or a potential therapeutic target.

Hyperoside attenuates carbon tetrachloride-induced hepatic fibrosis via the poly(ADP-ribose)polymerase-1-high mobility group protein 1 pathway

Oxidative stress and inflammation have been implicated in hepatic fibrosis. Antioxidant and anti-inflammatory activities are among the pharmacological effects of hyperoside. This study aimed to evaluate the impact of hyperoside on hepatic fibrosis and elucidate the underlying processes that perpetuate this relationship. The findings indicated that hyperoside significantly protects mouse livers against damage, inflammation, and fibrosis. Specifically, attenuation of hepatic fibrosis is associated with lower expression of HMGB1 protein and reduced expression of Toll-like receptor 4, PARP-1, and nuclear factor-kB (NF-κB) p65 mRNA and protein. Furthermore, hyperoside inhibited the cytoplasmic translocation of HMGB1 and nuclear localization of NF-κB p65 in the hepatic tissues of mice. The results of this study indicate that hyperoside may impose a blocking or reversing effect on hepatic fibrosis; additionally, the corresponding hyperoside-dependent mechanism may be linked to PARP-1-HMGB1 pathway regulation.

Risk of Short-Term Prostate-Specific Antigen Recurrence and Failure in Patients With Prostate Cancer: A Secondary Analysis of a Randomized Clinical Trial

Importance

A shorter time interval to prostate-specific antigen (PSA) failure is associated with worse clinical outcomes; however, specific factors defining this state remain unknown.

Objective

To evaluate the factors of a short time interval to PSA failure in order to identify patients for treatment escalation randomized clinical trials.

Design, Setting, and Participants

This secondary analysis of a randomized clinical trial was a secondary analysis of the Dana-Farber Cancer Institute 05-043 trial and included 350 patients with nonmetastatic unfavorable risk prostate cancer (PC).

Interventions

Patients were randomized 1:1 to receive androgen deprivation therapy (ADT) and radiation therapy (RT) plus docetaxel vs ADT and RT.

Main Outcomes and Measures

Cumulative incidence rates curves of PSA failure, defined as PSA nadir plus 2 ng/mL or initiation of salvage therapies, and the Fine and Gray competing risks regression was used to assess the prognostic association between these factors and time to PSA failure.

Results

The study included 350 males who primarily had a good performance status (330 [94.3%] with Eastern Cooperative Oncology Group score of 0), median (range) age of 66 (43-86) years, with 167 (46.6%) having Gleason scores of 8 to 10, and 195 (55.2%) presenting with a baseline PSA of more than 10 ng/mL. After a median (IQR) follow-up of 10.2 (8.0-11.4) years, having a PSA level of 10 ng/mL to 20 ng/mL (subdistribution hazard ratio [sHR], 1.98; 95% CI, 1.28-3.07; P = .002) and a Gleason score of 8 to 10 (sHR, 2.55; 95% CI, 1.63-3.99; P < .001) were associated with a shorter time to PSA failure, and older age (sHR, 0.82; 95% CI, 0.72-0.93; P = .002) was associated with reduced risk for PSA failure after adjusting for other baseline clinical factors. The high-risk category, defined by these 3 factors, was associated with a shorter time to PSA failure (sHR, 2.69; 95% CI, 1.84-3.93; P < .001).

Conclusions and Relevance

In this secondary analysis of a randomized clinical trial of males with unfavorable risk PC, young age, PSA of 10 ng/mL or more, and a Gleason score of 8 to 10 estimated a shorter time to PSA failure. A subgroup of males at very high-risk for early PSA failure, as defined by our study, may benefit from treatment escalation with androgen receptor signaling inhibitors or cytotoxic chemotherapy and should be the subject of a prospective randomized clinical trial.

Trial Registration

NCT00116142.

Machine Learning for the Prediction of Biochemical Recurrence in Patients Treated with Radical Prostatectomy

PURPOSE/OBJECTIVE(S)

Biochemical recurrence (BCR) occurs in about 40% of patients with prostate cancer following radical prostatectomy (RP). Our goal was to develop a machine learning model for the prediction of BCR five-years after RP, to improve patient prognostication.

MATERIALS/METHODS

Patients treated with RP at a tertiary care medical center between 1990 and 2017 were included. A gradient boosted decision trees-based machine learning model modified to handle survival data was trained on 80% of the dataset. The model's performance was evaluated on the remaining 20%. Input variables were age at surgery, prostate specific antigen (PSA) at diagnosis (in ng/mL), pathologic Gleason grade group (GG), pathologic T stage (organ confined disease vs. extracapsular extension (ECE) vs. seminal vesicle invasion (SVI)), lymph node involvement, and surgical margin status. Model performance was assessed using time-dependent area under curve of the receiver operator curve (AUC).

RESULTS

The full dataset included 11,139 patients, of whom 1,153 (10%) developed BCR. Median age at surgery was 59 and PSA at diagnosis was 5.4 ng/mL. Only 1,080 (9.7%) patients had GG 3, and 707 (6.3%) GG 4 and 5. 1,366 (12%) patients had positive surgical margins and 134 (1.2%) had lymph node involvement. Most patients had organ confined disease with EPE and SVI diagnosed in 2,759 (25%) and 392 (3.5%) patients, respectively. Median follow-up was 5 years and median time to BCR was 4 years. When validated on the hold-out set of 2,228 patients, the model shows a time-dependent AUC of 0.82 (95% CI 0.78 - 0.86) for BCR at t = 5 years.

CONCLUSION

Our machine learning model can be used to estimate risk of BCR following RP and shows exceptional performance, with implications on patient prognostication and follow-up. We are currently working on validating its performance on an external dataset.

Development and External Validation of a Machine Learning Model for Prediction of Lymph Node Metastasis in Patients with Prostate Cancer

BACKGROUND

Pelvic lymph node dissection (PLND) is the gold standard for diagnosis of lymph node involvement (LNI) in patients with prostate cancer. The Roach formula, Memorial Sloan Kettering Cancer Center (MSKCC) calculator, and Briganti 2012 nomogram are elegant and simple traditional tools used to estimate the risk of LNI and select patients for PLND.

OBJECTIVE

To determine whether machine learning (ML) can improve patient selection and outperform currently available tools for predicting LNI using similar readily available clinicopathologic variables.

DESIGN, SETTING, AND PARTICIPANTS

Retrospective data for patients treated with surgery and PLND between 1990 and 2020 in two academic institutions were used.

OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS

We trained three models (two logistic regression models and one gradient-boosted trees-based model [XGBoost]) on data provided from one institution (n = 20267) with age, prostate-specific antigen (PSA) levels, clinical T stage, percentage positive cores, and Gleason scores as inputs. We externally validated these models using data from another institution (n = 1322) and compared their performance to that of the traditional models using the area under the receiver operating characteristic curve (AUC), calibration, and decision curve analysis (DCA).

RESULTS AND LIMITATIONS

LNI was present in 2563 patients (11.9%) overall, and in 119 patients (9%) in the validation data set. XGBoost had the best performance among all the models. On external validation, its AUC outperformed that of the Roach formula by 0.08 (95% confidence interval [CI] 0.042-0.12), the MSKCC nomogram by 0.05 (95% CI 0.016-0.070), and the Briganti nomogram by 0.03 (95% CI 0.0092-0.051; all p < 0.05). It also had better calibration and clinical utility in terms of net benefit on DCA across relevant clinical thresholds. The main limitation of the study is its retrospective design.

CONCLUSIONS

Taking all measures of performance together, ML using standard clinicopathologic variables outperforms traditional tools in predicting LNI.

PATIENT SUMMARY

Determining the risk of cancer spread to the lymph nodes in patients with prostate cancer allows surgeons to perform lymph node dissection only in patients who need it and avoid the side effects of the procedure in those who do not. In this study, we used machine learning to develop a new calculator to predict the risk of lymph node involvement that outperformed traditional tools currently used by oncologists.

Machine Learning for the Prediction of Adverse Pathological Outcomes in Patients Treated with Radical Prostatectomy

PURPOSE/OBJECTIVE(S)

Extracapsular extension (ECE) and seminal vesicle invasion (SVI) are associated with negative oncologic outcomes in patients with prostate cancer. We have developed and validated a machine learning model to more accurately identify patients at risk of these adverse surgical outcomes prior to radical prostatectomy (RP).

MATERIALS/METHODS

This study included a cohort of patients diagnosed with prostate cancer and treated with RP and lymph node dissection at a tertiary care medical center from 2010 to 2020. An ensemble model using a base gradient-boosted trees-based machine learning model and isotonic calibrators was trained on 80% of the cohort, with 20% held out for validation. The model uses age at surgery, prostate specific antigen level (PSA) at diagnosis, biopsy Gleason grade group, numbers of positive and negative cores on biopsy, and clinical T-stage (cT) as input variables. Model performance was assessed on the hold-out set using the area under the receiver operating curve (AUC).

RESULTS

The full dataset included 18,729 eligible patients. Median PSA at diagnosis was 7.3 ng/mL. Most patients had clinically organ confined disease (cT1 - cT2) with only 136 (0.7%) having cT3. The most common biopsy Gleason grade group was 2 (7,118 or 38% of patients), with Gleason grade 4 in 1,796 (9.6%), and 5 in 1,064 (5.7%) patients. After RP, 11,931 (64%) of patients had organ confined disease, 4,298 (23%) had ECE, and 2,500 (13%) had SVI. When validated on the hold-out set (n = 3,746), the model had AUCs of 0.79 (95%-CI 0.77 - 0.80), 0.67 (0.65 - 0.69), and 0.83 (0.81 - 0.85) for the prediction of organ confined disease, ECE, and SVI, respectively.

CONCLUSION

In conclusion, we have developed a machine learning model that predicts individual patient risk of pathologic T-stage. The model can be used to provide more accurate risk assessments and improve surgical treatment planning. We are currently working on externally validating our results on patients from different institutions.

[Anatomical classification of and laparoscopic surgery for left-sided colorectal cancer with persistent descending mesocolon]

Objective: To investigate anatomical morphology and classification of persistent descending mesocolon (PDM) in patients with left-sided colorectal cancer, as well as the safety of laparoscopic radical surgery for these patients. Methods: This is a descriptive study of case series. Relevant clinical data of 995 patients with left colon and rectal cancer who had undergone radical surgery in Fujian Medical University Union Hospital from July 2021 to September 2022 were extracted from the colorectal surgery database of our institution and retrospectively analyzed. Twenty-four (2.4%) were identified as PDM and their imaging data and intra-operative videos were reviewed. We determined the distribution and morphology of the descending colon and mesocolon, and evaluated the feasibility and complications of laparoscopic surgery. We classified PDM according to its anatomical characteristics as follows: Type 0: PDM combined with malrotation of the midgut or persistent ascending mesocolon; Type 1: unfixed mesocolon at the junction between transverse and descending colon; Type 2: PDM with descending colon shifted medially (Type 2A) or to the right side (Type 2B) of the abdominal aorta at the level of the origin of the inferior mesentery artery (IMA); and Type 3: the mesocolon of the descending-sigmoid junction unfixed and the descending colon shifted medially and caudally to the origin of IMA. Results: The diagnosis of PDM was determined based on preoperative imaging findings in 9 of the 24 patients (37.5%) with left-sided colorectal cancer, while the remaining diagnoses were made during intraoperative assessment. Among 24 patients, 22 were male and 2 were female. The mean age was (63±9) years. We classified PDM as follows: Type 0 accounted for 4.2% (1/24); Type 1 for 8.3% (2/24); Types 2A and 2B for 37.5% (9/24) and 25.0% (6/24), respectively; and Type 3 accounted for 25.0% (6/24). All patients with PDM had adhesions of the mesocolon that required adhesiolysis. Additionally, 20 (83.3%) of them had adhesions between the mesentery of the ileum and colon. Twelve patients (50.0%) required mobilization of the splenic flexure. The inferior mesenteric artery branches had a common trunk in 14 patients (58.3%). Twenty-four patients underwent D3 surgery without conversion to laparotomy; the origin of the IMA being preserved in 22 (91.7%) of them. Proximal colon ischemia occurred intraoperatively in two patients (8.3%) who had undergone high ligation at the origin of the IMA. One of these patients had a juxta-anal low rectal cancer and underwent intersphincteric abdominoperineal resection because of poor preoperative anal function. Laparoscopic subtotal colectomy was considered necessary for the other patient. The duration of surgery was (260±100) minutes and the median estimated blood loss was 50 (20-200) mL. The median number of No. 253 lymph nodes harvested was 3 (0-20), and one patient (4.2%) had No.253 nodal metastases. The median postoperative hospital stay was 8 (4-23) days, and the incidence of complications 16.7% (4/24). There were no instances of postoperative colon ischemia or necrosis observed. One patient (4.2%) with stage IIA rectal cancer developed Grade B (Clavien-Dindo III) anastomotic leak and underwent elective ileostomy. The other complications were Grade I-II. Conclusions: PDM is frequently associated with mesenteric adhesions. Our proposed classification can assist surgeons in identifying the descending colon and mesocolon during adhesion lysis in laparoscopic surgery. It is crucial to protect the colorectal blood supply at the resection margin to minimize the need for unplanned extended colectomy, the Hartmann procedure, or permanent stomas.

LoRaD: Marginal likelihood estimation with haste (but no waste)

The Lowest Radial Distance (LoRaD) method is a modification of the recently introduced Partition-Weighted Kernel method for estimating the marginal likelihood of a model, a quantity important for Bayesian model selection. For analyses involving a fixed tree topology, LoRaD improves upon the Steppingstone or Thermodynamic Integration (Path Sampling) approaches now in common use in phylogenetics because it requires sampling only from the posterior distribution, avoiding the need to sample from a series of ad hoc power posterior distributions, and yet is more accurate than other fast methods such as the Generalized Harmonic Mean (GHM) method. We show that the method performs well in comparison to the Generalized Steppingstone method on an empirical fixed-topology example from molecular phylogenetics involving 180 parameters. The LoRaD method can also be used to obtain the marginal likelihood in the variable-topology case if at least one tree topology occurs with sufficient frequency in the posterior sample to allow accurate estimation of the marginal likelihood conditional on that topology. [Bayesian; marginal likelihood; phylogenetics.].

On efficient posterior inference in normalized power prior Bayesian analysis

The power prior has been widely used to discount the amount of information borrowed from historical data in the design and analysis of clinical trials. It is realized by raising the likelihood function of the historical data to a power parameterδ ∈ [ 0 , 1 ] $\delta \in [0, 1]$ , which quantifies the heterogeneity between the historical and the new study. In a fully Bayesian approach, a natural extension is to assign a hyperprior to δ such that the posterior of δ can reflect the degree of similarity between the historical and current data. To comply with the likelihood principle, an extra normalizing factor needs to be calculated and such prior is known as the normalized power prior. However, the normalizing factor involves an integral of a prior multiplied by a fractional likelihood and needs to be computed repeatedly over different δ during the posterior sampling. This makes its use prohibitive in practice for most elaborate models. This work provides an efficient framework to implement the normalized power prior in clinical studies. It bypasses the aforementioned efforts by sampling from the power prior withδ = 0 $\delta = 0$ andδ = 1 $\delta = 1$ only. Such a posterior sampling procedure can facilitate the use of a random δ with adaptive borrowing capability in general models. The numerical efficiency of the proposed method is illustrated via extensive simulation studies, a toxicological study, and an oncology study.

Pain sensation and gut microbiota profiles in older adults with heart failure

Objectives

Patients with heart failure (HF) experience severe pain and may have altered pain sensation; however, the underlying mechanisms of these symptoms are not yet fully understood. Identifying pain sensation and genomic biomarkers of pain in older adults with HF is a critical step toward developing personalized interventions to improve pain management and outcomes. This study aimed to investigate the differences in pain sensation, gut microbiota, self-reported pain, and symptoms in older adults with and without HF.

Methods

Twenty older adults with HF and age-matched healthy controls (HCs) were recruited in the Northeastern United States. Quantitative sensory testing and conditioned pain modulation were performed on the nondominant upper arm to detect the mechanical, thermal, and pressure pain thresholds and pain modulations. Stool samples were collected, and the 16S rRNA V4 gene region of stool samples was sequenced and processed using the Mothur 1.42.3 pipeline. Self-reported pain and symptoms were measured by the Brief Pain Inventory and the NIH Patient-reported Outcomes Measurement Information System. The associations between pain sensation, gut microbiota α-diversity indices, and pain and symptoms were explored using the Spearman correlations.

Results

The HF and HC subjects' mean ages were 73.50 (SD = 8.33) and 67.10 (SD = 7.64), respectively. The HF subjects reported significantly higher pain intensity and interference, sleep disturbance, fatigue, anxiety, and depression than the HCs. The HF subjects also had a significantly lower level of physical function and participation in social roles and activities. Compared with the HCs, the HF subjects had significantly altered conditioned pain modulation heat effect and gut microbiota compositions and predicted metabolic functions. The Statistical Analysis Of Metagenomic Profiles indicated that the HF subjects had a significantly decreased cardiac muscle contraction pathway compared with the HCs. The correlation analysis showed that the quantitative sensory testing profiles and gut microbiota diversity index were significantly associated with pain and symptoms in older adults with HF.

Conclusions

Older adults with HF had more severe self-reported pain and symptoms, altered pain sensation, and different gut microbiota composition and function compared with age-matched HCs. Pain sensation and gut microbiota may contribute to pain and symptoms in older adults with HF and could serve as biomarkers of pain and symptoms of HF. Further research with a larger sample size is warranted to confirm these findings.

Prostate-Specific Antigen Level at the Time of Salvage Therapy After Radical Prostatectomy for Prostate Cancer and the Risk of Death

PURPOSE

Both the performance characteristics of prostate-specific membrane antigen positron emission tomography and insurance approval improves with increasing prostate-specific antigen (PSA) level causing some physicians to delay post-radical prostatectomy salvage radiation therapy (sRT) after PSA failure. Yet, it is unknown for men with at most one high-risk factor (ie, pT3/4 or prostatectomy [p] Gleason score 8-10) whether a PSA level exists above which initiating sRT is associated with increased all-cause mortality (ACM)-risk and was investigated.

METHODS

Using a multinational database of 25,551 patients with pT2-4N0 or NXM0 prostate cancer, multivariable Cox regression analysis evaluated whether an association with a significant increase in ACM-risk existed when sRT was delivered above a prespecified PSA level beginning at 0.10 ng/mL and in 0.05 increments up to 0.50 ng/mL versus at or below that level. The model was adjusted for age at and year of radical prostatectomy, established prostate cancer prognostic factors, institution, and the time-dependent use of androgen deprivation therapy.

RESULTS

After a median follow-up of 6.00 years, patients who received sRT at a PSA level >0.25 ng/mL had a significantly higher ACM-risk (AHR, 1.49; 95% CI, 1.11 to 2.00; P = .008) compared with men who received sRT when the PSA was ≤0.25 mg/mL. This elevated ACM-risk remained significant for all PSA cutpoints up to 0.50 ng/mL but was not significant at PSA cutpoint values below 0.25 ng/mL.

CONCLUSION

Among patients with at most one high-risk factor, initiating sRT above a PSA level of 0.25 ng/mL was associated with increased ACM-risk.

Modeling and maximum likelihood based inference of interval-censored data with unknown upper limits and time-dependent covariates

Due to the nature of study design or other reasons, the upper limits of the interval-censored data with multiple visits are unknown. A naïve approach is to treat the last observed time as the exact event time, which may induce biased estimators of the model parameters. In this paper, we first develop a Cox model with time-dependent covariates for the event time and a proportional hazards model with frailty for the gap time. We then construct the upper limits using the latent gap times to resolve the issue of interval-censored event time data with unknown upper limits. A data-augmentation technique and a Monte Carlo EM (MCEM) algorithm are developed to facilitate computation. Theoretical properties of the computational algorithm are also investigated. Additionally, new model comparison criteria are developed to assess the fit of the gap time data as well as the fit of the event time data conditional on the gap time data. Our proposed method compares favorably with competing methods in both simulation study and real data analysis.

[Analysis of the clinical features and the risk factors of severe human metapneu movirus-associated community acquired pneumonia in children]

Objective: To investigate the clinical characteristics and the risk factors of severe human metapneumovirus (hMPV)-associated community acquired pneumonia (CAP) in children. Methods: A retrospective case summary was conducted. From December 2020 to March 2022, 721 children who were diagnosed with CAP and tested positive for hMPV nucleic acid by PCR-capillary electrophoresis fragment analysis of nasopharyngeal secretions at the Yuying Children's Hospital, the Second Affiliated Hospital of Wenzhou Medical University were selected as the research objects. The clinical characteristics, epidemiological characteristics and mixed pathogens of the two groups were analyzed. According to CAP diagnostic criteria, the children were divided into the severe group and the mild group. Chi-square test or Mann-Whitney rank and contrast analysis was used for comparison between groups, while multivariate Logistic regression was applied to analyze the risk factors of the severe hMPV-associated CAP. Results: A total of 721 children who were diagnosed with hMPV-associated CAP were included in this study, with 397 males and 324 females. There were 154 cases in the severe group. The age of onset was 1.0 (0.9, 3.0) years, <3 years old 104 cases (67.5%), and the length of hospital stay was 7 (6, 9) days. In the severe group, 67 children (43.5%) were complicated with underlying diseases. In the severe group, 154 cases (100.0%) had cough, 148 cases (96.1%) had shortness of breath and pulmonary moist rales, and 132 cases (85.7%) had fever, 23 cases (14.9%) were complicated with respiratory failure. C-reactive protein (CRP) was elevated in 86 children (55.8%), including CRP≥50 mg/L in 33 children (21.4%). Co-infection was detected in 77 cases (50.0%) and 102 strains of pathogen were detected, 25 strains of rhinovirus, 17 strains of Mycoplasma pneumoniae, 15 strains of Streptococcus pneumoniae, 12 strains of Haemophilus influenzae and 10 strains of respiratory syncytial virus were detected. Six cases (3.9%) received heated and humidified high flow nasal cannula oxygen therapy, 15 cases (9.7%) were admitted to intensive care unit, and 2 cases (1.3%) received mechanical ventilation. In the severe group, 108 children were cured, 42 children were improved, 4 chlidren were discharged automatically without recovery and no death occurred. There were 567 cases in the mild group. The age of onset was 2.7 (1.0, 4.0) years, and the length of hospital stay was 4 (4, 6) days.Compared with the mild group, the proportion of children who age of disease onset <6 months, CRP≥50 mg/L, the proportions of preterm birth, congenital heart disease, malnutrition, congenital airway malformation, neuromuscular disease, mixed respiratory syncytial viruses infection were higher (20 cases (13.0%) vs. 31 cases (5.5%), 32 cases (20.8%) vs. 64 cases (11.3%), 23 cases (14.9%) vs. 44 cases (7.8%), 11 cases (7.1%) vs. 18 cases (3.2%), 9 cases (5.8%) vs. 6 cases (1.1%), 11 cases (7.1%) vs. 12 cases (2.1%), 8 cases (5.2%) vs. 4 cases (0.7%), 10 cases (6.5%) vs. 13 cases (2.3%), χ²=0.42, 9.45, 7.40, 4.94, 11.40, 8.35, 3.52, 6.92, all P<0.05). Multivariate Logistic regression analysis showed that age<6 months (OR=2.51, 95%CI 1.29-4.89), CRP≥50 mg/L (OR=2.20, 95%CI 1.36-3.57), prematurity (OR=2.19, 95%CI 1.26-3.81), malnutrition (OR=6.05, 95%CI 1.89-19.39) were the independent risk factors for severe hMPV-associated CAP. Conclusions: Severe hMPV-associated CAP is most likely to occur in infants under 3 years old and has a higher proportion of underlying diseases and co-infection. The main clinical manifestations are cough, shortness of breath and pulmonary moist rales, fever. The overall prognosis is good. Age<6 months, CRP≥50 mg/L, preterm birth, malnutrition are the independent risk factors for severe hMPV-associated CAP.

The Impact of Early Life Experiences and Gut Microbiota on Neurobehavioral Development in Preterm Infants: A Longitudinal Cohort Study

OBJECTIVES

The objective of this study is to investigate the impact of early life experiences and gut microbiota on neurobehavioral development in preterm infants during neonatal intensive care unit (NICU) hospitalization.

METHODS

Preterm infants were followed from NICU admission until their 28th postnatal day or until discharge. Daily stool samples, painful/stressful experiences, feeding patterns, and other clinical and demographic data were collected. Gut microbiota was profiled using 16S rRNA sequencing, and operational taxonomic units (OTUs) were selected to predict the neurobehaviors. The neurobehavioral development was assessed by the Neonatal Neurobehavioral Scale (NNNS) at 36 to 38 weeks of post-menstrual age (PMA). Fifty-five infants who had NNNS measurements were included in the sparse log-contrast regression analysis.

RESULTS

Preterm infants who experienced a high level of pain/stress during the NICU hospitalization had higher NNNS stress/abstinence scores. Eight operational taxonomic units (OTUs) were identified to be associated with NNNS subscales after controlling demographic and clinical features, feeding patterns, and painful/stressful experiences. These OTUs and taxa belonging to seven genera, i.e., Enterobacteriaceae_unclassified, Escherichia-Shigella, Incertae_Sedis, Veillonella, Enterococcus, Clostridium_sensu_stricto_1, and Streptococcus with five belonging to Firmicutes and two belonging to Proteobacteria phylum. The enriched abundance of Enterobacteriaceae_unclassified (OTU17) and Streptococcus (OTU28) were consistently associated with less optimal neurobehavioral outcomes. The other six OTUs were also associated with infant neurobehavioral responses depending on days at NICU stay.

CONCLUSIONS

This study explored the dynamic impact of specific OTUs on neurobehavioral development in preterm infants after controlling for early life experiences, i.e., acute and chronic pain/stress and feeding in the NICU. The gut microbiota and acute pain/stressful experiences dynamically impact the neurobehavioral development in preterm infants during their NICU hospitalization.

A genome-wide association study (GWAS) of the personality constructs in CPAI-2 in Taiwanese Hakka populations

Here in this study we adopted genome-wide association studies (GWAS) to investigate the genetic components of the personality constructs in the Chinese Personality Assessment Inventory 2 (CPAI-2) in Taiwanese Hakka populations, who are likely the descendants of a recent admixture between a group of Chinese immigrants with high emigration intention and a group of the Taiwanese aboriginal population generally without it. A total of 279 qualified participants were examined and genotyped by an Illumina array with 547,644 SNPs to perform the GWAS. Although our sample size is small and that unavoidably limits our statistical power (Type 2 error but not Type 1 error), we still found three genomic regions showing strong association with Enterprise, Diversity, and Logical vs. Affective Orientation, respectively. Multiple genes around the identified regions were reported to be nervous system related, which suggests that genetic variants underlying the certain personalities should indeed exist in the nearby areas. It is likely that the recent immigration and admixture history of the Taiwanese Hakka people created strong linkage disequilibrium between the emigration intention-related genetic variants and their neighboring genetic markers, so that we could identify them despite with only limited statistical power.

New C-indices for assessing importance of longitudinal biomarkers in fitting competing risks survival data in the presence of partially masked causes

Competing risks survival data in the presence of partially masked causes are frequently encountered in medical research or clinical trials. When longitudinal biomarkers are also available, it is of great clinical importance to examine associations between the longitudinal biomarkers and the cause-specific survival outcomes. In this article, we propose a cause-specific C-index for joint models of longitudinal and competing risks survival data accounting for masked causes. We also develop a posterior predictive algorithm for computing the out-of-sample cause-specific C-index using Markov chain Monte Carlo samples from the joint posterior of the in-sample longitudinal and competing risks survival data. We further construct the Δ $$ \Delta $$ C-index to quantify the strength of association between the longitudinal and cause-specific survival data, or between the out-of-sample longitudinal and survival data. Empirical performance of the proposed assessment criteria is examined through an extensive simulation study. An in-depth analysis of the real data from large cancer prevention trials is carried out to demonstrate the usefulness of the proposed methodology.

The impact of early life experiences and gut microbiota on neurobehavioral development among preterm infants: A longitudinal cohort study

Objectives

To investigate the impact of early life experiences and gut microbiota on neurobehavioral development among preterm infants during neonatal intensive care unit (NICU) hospitalization.

Methods

Preterm infants were followed from the NICU admission until their 28 ^th postnatal day or until discharge. Daily stool samples, painful/stressful experiences, feeding patterns, and other clinical and demographic data were collected. Gut microbiota was profiled using 16S rRNA sequencing, and operational taxonomic units (OTUs) were selected to predict the neurobehaviors. The neurobehavioral development was assessed by the Neonatal Neurobehavioral Scale (NNNS) at 36 to 38 weeks of post-menstrual age (PMA). Fifty-five infants who had NNNS measurements were included in the sparse log-contrast regression analysis.

Results

Preterm infants who experienced high level of pain/stress during the NICU hospitalization that were associated with higher NNNS stress/abstinence scores. Eight operational taxonomic units (OTUs) were identified to be associated with of NNNS subscales after controlling demographic and clinical features, feeding patterns, and painful/stressful experiences. These OTUs, taxa belong to seven genera including Enterobacteriaceae_unclassified, Escherichia-Shigella, Incertae_Sedis, Veillonella, Enterococcus, Clostridium_sensu_stricto_1 , and Streptococcus with five belonging to Firmicutes and two belonging to Proteobacteria phylum. The enriched abundance of Enterobacteriaceae_unclassified (OTU17) and Streptococcus (OTU28) were consistently associated with less optimal neurobehavioral outcomes. The other six OTUs were also associated with infant neurobehavioral responses depending on days at NICU stay.

Conclusions

This study explored the dynamic impact of specific OTUs on neurobehavioral development among preterm infants after controlling for early life experiences, i.e., acute and chronic pain/stress, and feeding in the NICU.

[Research progress of CRISPR/Cas biosensors based on different signal amplification strategies]

CRISPR/Cas(the clustered regularly interspaced short palindromic repeats-CRISPR associated)system exists in most bacteria and all archaea. It is an important strategy for bacteria and archaea to resist foreign nucleic acid invasion and use for self-defense. The CRISPR/Cas system is a simple, fast, and specific diagnostic tool, which is widely used in agriculture, industry, animal husbandry, and medicine. This article mainly introduces and discusses recently advantages and limitations of biosensors combining CRISPR/Cas system with fluorescence, visualization and surface enhanced raman related technologies, as well as future research directions.

metapack: An R Package for Bayesian Meta-Analysis and Network Meta-Analysis with a Unified Formula Interface

Meta-analysis, a statistical procedure that compares, combines, and synthesizes research findings from multiple studies in a principled manner, has become popular in a variety of fields. Meta-analyses using study-level (or equivalently aggregate) data are of particular interest due to data availability and modeling flexibility. In this paper, we describe an R package metapack that introduces a unified formula interface for both meta-analysis and network meta-analysis. The user interface-and therefore the package-allows flexible variance-covariance modeling for multivariate meta-analysis models and univariate network meta-analysis models. Complicated computing for these models has prevented their widespread adoption. The package also provides functions to generate relevant plots and perform statistical inferences like model assessments. Use cases are demonstrated using two real data sets contained in metapack.

Bayesian Model Assessment for Jointly Modeling Multidimensional Response Data with Application to Computerized Testing

Computerized assessment provides rich multidimensional data including trial-by-trial accuracy and response time (RT) measures. A key question in modeling this type of data is how to incorporate RT data, for example, in aid of ability estimation in item response theory (IRT) models. To address this, we propose a joint model consisting of a two-parameter IRT model for the dichotomous item response data, a log-normal model for the continuous RT data, and a normal model for corresponding paper-and-pencil scores. Then, we reformulate and reparameterize the model to capture the relationship between the model parameters, to facilitate the prior specification, and to make the Bayesian computation more efficient. Further, we propose several new model assessment criteria based on the decomposition of deviance information criterion (DIC) the logarithm of the pseudo-marginal likelihood (LPML). The proposed criteria can quantify the improvement in the fit of one part of the multidimensional data given the other parts. Finally, we have conducted several simulation studies to examine the empirical performance of the proposed model assessment criteria and have illustrated the application of these criteria using a real dataset from a computerized educational assessment program.

Childhood beverage intake and risk of hypertension and hyperlipidaemia in young adults

An epidemiological analysis assessing beverage consumption and risk factors for cardiovascular disease was conducted. Participants were 9-16 years old at enrolment, completed food frequency questionnaires in 1996-2001 and self-reported outcomes in 2010-2014. Exclusion criteria included missing data on relevant variables and covariates, prevalent disease before 2005, and implausible/extreme weight or energy intake. Intakes of orange juice, apple/other fruit juice, sugar-sweetened beverages and diet soda were related to the risk of incident hypertension or hyperlipidaemia using Cox proportional hazards regression, adjusting for diet, energy intake, age, smoking, physical activity and body mass index. There were 9,043 participants with 618 cases of hypertension and 850 of hyperlipidaemia in 17 years of mean follow-up. Sugar-sweetened beverage intake but not fruit juice nor diet soda was associated with hypertension (hazard ratio (95% confidence interval): 1.16 (1.03, 1.31)) in males. This study can guide beverage consumption as it relates to early predictors of cardiovascular disease.

Memory and Executive Functions Subserving Judgments of Learning: Cognitive Reorganization After Traumatic Brain Injury

We investigated relationships between psychometric measures of memory, executive functions (EFs), and task-based measures of Judgments of Learning (JOLs) in individuals with and without Traumatic Brain Injury (TBI), to study functional reorganization after TBI. We hypothesized that, in controls, accuracy of immediate JOLs would be associated with short-term memory and EFs (but not long-term memory, LTM), while accuracy of delayed JOLs would be associated primarily with LTM. We hypothesized that those with good recovery from TBI would demonstrate functional reorganization of the relationships between memory, EFs, and JOLs. Eighteen individuals with TBI and 18 matched controls completed eight neuropsychological tests of memory and EFs. They studied word-pairs, made immediate and delayed JOLs, and took a cued-recall test for the studied word-pairs. Stepwise regression and Lasso analyses generated a predictive model of JOL accuracy for each group. Accuracy of immediate JOLs in controls was predicted by short-term memory, inhibition, switching, and cognitive fluency, while accuracy of delayed JOLs was predicted by verbal recall. In individuals with TBI, inhibition predicted immediate JOL accuracy and switching predicted delayed JOL accuracy. Cognitive reorganization in those with good long-term recovery from TBI may account for the ability to make JOLs with accuracy similar to controls.

Analysis of genetic diversity among Chinese Cyclocybe chaxingu strains using ISSR and SRAP markers

Background

Cyclocybe chaxingu is an edible and medicinal fungal species commonly cultivated in China. The major problems currently facing by growers of C. chaxingu is the random labeling of strains and strains aging and degeneration. Therefore, an evaluation of genetic diversity is essential for the conservation and reproducing programs of this species.

Methods

In the present study, 24 widely cultivated strains were collected from the main producing areas of China, and the genetic diversity analysis was performed. DNA polymorphism among these Chinese C. chaxingu strains was analyzed using inter-simple sequence repeat (ISSR) and sequence-related amplified polymorphism (SRAP) markers.

Results

Eight ISSR primers amplified a total of 75 DNA fragments of which 61 (81.33%) were polymorphic. Fifteen SRAP primer combinations amplified 166 fragments of which 132 (79.52%) were polymorphic. Cluster analysis showed that the C. chaxnigu strains fall into five groups with a genetic distance values ranging from 0.06 to 0.60 by ISSR analysis, while the SRAP analysis divided the test strains into four groups within the range of genetic distance from 0.03 to 0.57. The results of the present study reveal a high level of genetic diversity among the widely cultivated C. chaxingu strains.

Plasma biomarkers and their correlation in adult children of parents with Alzheimer’s disease

Family history (FH) of late-onset Alzheimer’s disease (AD) is associated with changes in several cerebrospinal fluid (CSF) biomarkers in cognitively normal individuals. However, potential changes in plasma biomarkers remain unknown. This study aimed to evaluate potential plasma biomarkers and their correlation in cognitively normal adult children (AC) and to compare this data with their AD parents and unrelated non-demented controls (NC). Participants with dementia due to AD, their AC and NC were recruited. Plasma samples were assessed for amyloid beta (Aβ)_1–42, Aβ_1–40, total tau (T-tau) and phosphorylated tau (P-tau). Kruskal–Wallis test was used for the comparison of this data between the three groups. Spearman rank correlation was used for evaluation of the correlations between Aβ_1–40 and Aβ_1–42, and T-tau and P-tau in the AD and AC groups. A total of 99 subjects completed the assessment (30 had AD; 38 were AC group; and 31 were NC). Compared with the NC group, there were significantly higher levels of Aβ_1–40, P-tau, and P-tau/T-tau ratio, and lower levels of Aβ_1–42 and Aβ_1–42/Aβ_1–40 ratio in the AD and AC groups. The correlation between the level of Aβ_1–42 and Aβ_1–40 and level of T-tau and P-tau was only observed in the AC but not in the AD group. AC of AD parents demonstrate some indicators of AD like their parents. Disruption to the correlation between Aβ and tau in AD may be a biomarker for the development of AD in AC, which should be examined in a longitudinal cohort.

Application of Micro-Western Array for Identifying Different Serum Protein Expression Profile among Healthy Control, Alzheimer’s Disease Patients and Patients’ Adult Children

(1) Background: Alzheimer’s disease (AD) is the most common form of dementia. Increased levels of inflammatory proteins have been observed in brain and plasma samples of AD patients; however, it is not clear if other serum proteins correlate to the development or disease progression of AD. (2) Methods: Micro-Western Array (MWA) is a high-throughput antibody-based proteomics system which allows detection of the expression levels of 24–96 different proteins within 6–30 samples simultaneously. We applied MWA to explore potential serum protein biomarkers correlated to the development and progression of AD by examining the difference in serum protein profile of 31 healthy control (HC), 30 patients with AD and 30 patients’ adult children (ACS). (3) Results: Compared to HC, AD and ACS express similar pattern of serum proteins, including higher protein levels of ABCA1, ABCG1, SREBP1 and LXRβ but lower protein levels of ApoD, ApoE, ApoH, c_Myc, COX2 and Hippo-YAP signaling proteins. AD patients had higher serum levels of ABCG1, ApoD, ApoH, COX2, LXRα and YAP, but lower levels of ABCA1, ApoE, c_Myc, LATS1, MST1, MST2, Nanog, NFκB_p50, PPARγ and SREBP2, as compared to ACS. Pearson’s correlation analysis revealed that the protein expression level of ApoE, c_Myc, LATS1, MST2, NFκB p50, PPARγ and SREBP1 was negatively correlated to age, while that of ApoE, c_Myc, LATS1, MST1, MST2, Nanog, NFκB p50 and PPARγ was positively correlated to age. (4) Conclusions: We identified a group of serum proteins which may correlate to disease progression of AD and can be potential diagnostic serum protein biomarkers.

Associations of Mitochondrial Function, Stress, and Neurodevelopmental Outcomes in Early Life: A Systematic Review

Early life stress is commonly experienced by infants, especially preterm infants, and may impact their neurodevelopmental outcomes in their early and later lives. Mitochondrial function/dysfunction may play an important role underlying the linkage of prenatal and postnatal stress and neurodevelopmental outcomes in infants. This review aimed to provide insights on the relationship between early life stress and neurodevelopment and the mechanisms of mitochondrial function/dysfunction that contribute to the neuropathology of stress. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement was used to develop this systematic review. PubMed, Scopus, PsycINFO, and Biosis databases were searched for primary research articles published between 2010 and 2021 that examined the relationships among mitochondrial function/dysfunction, infant stress, and neurodevelopment. Thirty studies were identified. There is evidence to support that mitochondrial function/dysfunction mediates the relationship between prenatal and postnatal stress and neurodevelopmental outcomes in infants. Maternal transgenerational transmission of mitochondrial bioenergetic patterns influenced prenatal stress induced neurodevelopmental outcomes and behavioral changes in infants. Multiple functionally relevant mitochondrial proteins, genes, and polymorphisms were associated with stress exposure. This is the first review of the role that mitochondrial function/dysfunction plays in the association between stress and neurodevelopmental outcomes in full-term and preterm infants. Although multiple limitations were found based on the lack of data on the influence of biological sex, and due to invasive sampling, and lack of longitudinal data, many genes and proteins associated with mitochondrial function/dysfunction were found to influence neurodevelopmental outcomes in the early life of infants.

[Spectral characteristics of sesquiterpene pyridine alkaloids from Tripterygium plants]

Sesquiterpene pyridine alkaloids are important components in Tripterygium plants, possessing a wide range of pharmacological activities, such as anti-inflammation immunosuppression, anti-tumor, anti-virus, and deinsectization, and are of great research value. They are composed of highly oxidized dihydro-β-furansquiterpene and pyridine dicarboxylic acid through ester bonds. According to the structural characteristics of pyridine dicarboxylic acid fragments, they can be divided into various structural subtypes. Up to now, more than 110 sesquiterpene pyridine alkaloids have been isolated and identified from Tripterygium plants. This study reviewed the structural features and spectral(i.e., UV, IR, MS, and NMR) characteristics of sesquiterpene pyridine alkaloids and summarized the structural elucidation process in detail to provide references for their further research and development.

The effect of self-management online modules plus nurse-led support on pain and quality of life among young adults with irritable bowel syndrome: A randomized controlled trial

BACKGROUND

Irritable bowel syndrome is a chronic pain condition that needs life-long self-management. However, the effect of self-management among young adults with irritable bowel syndrome is limited.

OBJECTIVES

This study aimed to examine the effect of a nurse-led self-management program on pain, symptoms, and quality of life among young adults with irritable bowel syndrome.

DESIGN

A randomized controlled trial.

SETTINGS AND PARTICIPANTS

Eighty young adults with irritable bowel syndrome recruited from two campuses of a public university and two gastrointestinal clinics were randomly assigned into a self-management online education and learning modules alone group (Online Modules, n = 41) or a nurse-led one-to-one consultation plus self-management online education and learning modules group (Nurse-Led Online Modules, n = 39). Twenty-one healthy controls were also recruited from these two campuses.

METHODS

Both the intervention groups received ten online modules after baseline data collection. Participants in the Nurse-Led Online Modules group received additional three nurse-led one-to-one consultations at baseline, 6- and 12-week follow-ups. Self-reported pain, symptoms, quality of life, self-efficacy for managing chronic disease, and coping were measured at baseline, and 6- and 12-week follow-ups among the participants with irritable bowel syndrome. The healthy controls completed data collection of pain and symptoms at baseline and the 12-week follow-up. The intervention effects across study time points and the comparisons between the two interventional groups were analyzed using linear mixed models. A longitudinal mediation analysis was also conducted to explore the mediation effects of self-management mechanisms of the interventions.

RESULTS

Both the intervention groups showed significant interventional effects on decreasing pain intensity and pain interference and increasing quality of life at the 12-week follow-up (all p < 0.05). At the 12-week follow-up, the Nurse-Led Online Modules significantly reduced anxiety (p = 0.016) and had a significant greater improvement in quality of life than the Online Modules (p = 0.040). Increased self-efficacy mediated the intervention effect of the Nurse-Led Online Modules group on reducing pain interference and improving quality of life, while the effect of the Online Modules was mediated through decreasing inefficient coping strategy-catastrophizing.

CONCLUSIONS

This study showed that both the pain self-management online education and nurse-led intervention were effective for alleviating pain and improving quality of life among young adults with irritable bowel syndrome by targeting the self-management process. The nurse-led intervention had a better outcome than the online education alone in improving quality of life.

REGISTRATION NUMBER

NCT03332537.

Adjuvant Versus Early Salvage Radiation Therapy After Radical Prostatectomy for pN1 Prostate Cancer and the Risk of Death

PURPOSE

An association with a reduction in the risk of all-cause mortality (ACM) and the use of adjuvant as compared with early postradical prostatectomy salvage radiation therapy (sRT) in men with pN1 prostate cancer (PC) has been observed. Yet, whether this finding applies irrespective of the number of positive lymph nodes (LNs) after adjusting for the time-dependent use and duration of androgen deprivation therapy is unknown and is addressed in the current study.

METHODS

Univariable and multivariable Cox regression was used to evaluate whether the ACM risk ratio for time-dependent use of adjuvant versus early sRT per unit increase in positive pelvic LNs was significantly reduced. Adjusted ACM estimates were calculated among men who received adjuvant, early salvage, or no RT stratified by one to three or four or more positive pelvic LNs.

RESULTS

After a median follow-up of 7.02 years, 986 (5.50%) men died, with 223 (22.62%) of PC. Adjuvant compared with early sRT was associated with a significantly lower ACM risk per unit increase in positive pelvic LNs (adjusted hazard ratio: 0.92; 95% CI, 0.85 to 0.99; P = .03). A significant difference in the 7-year adjusted ACM estimates favoring aRT versus early sRT was observed in men with four or more positive LNs (7.74% v 23.36%) in that the 95% CI for the 15.62% difference (5.90 to 25.35) excluded 0.00, but this was not true for men with 1-3 positive LNs (14.27% v 13.89%; 95% CI for the 0.38% difference [-7.02 to 7.79]).

CONCLUSION

Adjuvant compared with early sRT in men with pN1 PC was associated with a decreased ACM risk, and this reduction increased with each additional positive pelvic LN.

Bayesian Item Response Theory Models With Flexible Generalized Logit Links

In educational and psychological research, the logit and probit links are often used to fit the binary item response data. The appropriateness and importance of the choice of links within the item response theory (IRT) framework has not been investigated yet. In this paper, we present a family of IRT models with generalized logit links, which include the traditional logistic and normal ogive models as special cases. This family of models are flexible enough not only to adjust the item characteristic curve tail probability by two shape parameters but also to allow us to fit the same link or different links to different items within the IRT model framework. In addition, the proposed models are implemented in the Stan software to sample from the posterior distributions. Using readily available Stan outputs, the four Bayesian model selection criteria are computed for guiding the choice of the links within the IRT model framework. Extensive simulation studies are conducted to examine the empirical performance of the proposed models and the model fittings in terms of "in-sample" and "out-of-sample" predictions based on the deviance. Finally, a detailed analysis of the real reading assessment data is carried out to illustrate the proposed methodology.

Bayesian Design of Superiority Trials: Methods and Applications

In this paper, we lay out the basic elements of Bayesian sample size determination (SSD) for the Bayesian design of a two-arm superiority clinical trial. We develop a flowchart of the Bayesian SSD that highlights the critical components of a Bayesian design and provides a practically useful roadmap for designing a Bayesian clinical trial in real world applications. We empirically examine the amount of borrowing, the choice of noninformative priors, and the impact of model misspecification on the Bayesian type I error and power. A formal and statistically rigorous formulation of conditional borrowing within the decision rule framework is developed. Moreover, by extending the partial borrowing power priors, a new borrowing-by-parts power prior for incorporating historical data is proposed. Computational algorithms are also developed to calculate the Bayesian type I error and power. Extensive simulation studies are carried out to explore the operating characteristics of the proposed Bayesian design of a superiority trial.

Enzymatic hydrolysis lignin functionalized Ti3C2Tx nanosheets for effective removal of MB and Cu2+ ions

Functionalized two-dimensional Ti₃C₂T_x (TN-EHL) was prepared as an effective adsorbent for removal of methylene blue dye (MB) and copper ions (Cu²⁺). Enzymatic hydrolysis lignin (EHL), a reproducible natural resource, was used to functionalize the Ti₃C₂T_x nanosheets. EHL can not only introduce active functional groups into TN-EHL but also prevent the oxidation of Ti₃C₂T_x, thus promoting the adsorption performance of TN-EHL. The maximum adsorption capacities of TN-EHL50 (in which the EHL content is 50 wt%) for MB and Cu²⁺ were 293.7 mg g^-1 and 49.96 mg g^-1, respectively. The higher correlation coefficients (R²) of MB (0.9996) and Cu²⁺ (0.9995) indicating that their adsorption processes can be described by the pseudo-second-order kinetic model. The MB adsorption data fit the Freundlich isotherm with R² of 0.9953, whereas the Cu²⁺ ions adsorption data fit the Langmuir isotherm with R² of 0.9998. The thermodynamic analysis indicates that the adsorption process of MB and Cu²⁺ on TN-EHL50 is spontaneous and endothermic. Significantly, the Cu²⁺ ions were reduced to Cu₂O and CuO particles during the adsorption process. Therefore, TN-EHL has a great potential as an environmentally friendly adsorbent for MB removal and recovery of Cu²⁺ ions from wastewater.

Prediction of future risk of any and higher-grade prostate cancer based on the PLCO and SELECT trials

Background

A model was built that characterized effects of individual factors on five-year prostate cancer (PCa) risk in the Prostate, Lung, Colon, and Ovarian Cancer Screening Trial (PLCO) and the Selenium and Vitamin E Cancer Prevention Trial (SELECT). This model was validated in a third San Antonio Biomarkers of Risk (SABOR) screening cohort.

Methods

A prediction model for 1- to 5-year risk of developing PCa and Gleason > 7 PCa (HG PCa) was built on PLCO and SELECT using the Cox proportional hazards model adjusting for patient baseline characteristics. Random forests and neural networks were compared to Cox proportional hazard survival models, using the trial datasets for model building and the SABOR cohort for model evaluation. The most accurate prediction model is included in an online calculator.

Results

The respective rates of PCa were 8.9%, 7.2%, and 11.1% in PLCO (n = 31,495), SELECT (n = 35,507), and SABOR (n = 1790) over median follow-up of 11.7, 8.1 and 9.0 years. The Cox model showed higher prostate-specific antigen (PSA), BMI and age, and African American race to be associated with PCa and HGPCa. Five-year risk predictions from the combined SELECT and PLCO model effectively discriminated risk in the SABOR cohort with C-index 0.76 (95% CI [0.72, 0.79]) for PCa, and 0.74 (95% CI [0.65,0.83]) for HGPCa.

Conclusions

A 1- to 5-year PCa risk prediction model developed from PLCO and SELECT was validated with SABOR and implemented online. This model can individualize and inform shared screening decisions.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12894-022-00986-w.

Fruit juice and childhood obesity: a review of epidemiologic studies

Childhood obesity is a national epidemic, and many efforts have been made to understand its risk factors. The purpose of this review was to provide an updated account of the observational studies evaluating the relationship between 100% fruit juice intake and obesity in children and adolescents, and to highlight the major risk factors that may impact this relationship. PubMed and Scopus were searched for terms related to fruit juice and childhood obesity, and studies assessing 100% fruit juice intake in participants ≤ 19 years old, with obesity-related outcomes (BMI or adiposity), and published before March 9, 2021 were included. There were 17 prospective cohort and 14 cross-sectional studies included in the analysis. Overall, the evidence does not support a relationship between 100% fruit juice intake and measures of obesity in most children. There is some evidence to suggest a minor positive association in some overweight or very young children, but due to fundamental differences and limitations in methodology, further investigation is required. Significant gaps in literature on this topic exist particularly in regards to randomized clinical trials in children, and in studies in racially diverse populations.