Bonferroni-Holm and permutation tests to compare health data: methodological and applicative issues

Metabolomic profiling reveals altered phenylalanine metabolism in Parkinson's disease in an Egyptian cohort

Introduction: Parkinson's disease (PD) is the most common motor neurodegenerative disease worldwide. Given the complexity of PD etiology and the different metabolic derangements correlated to the disease, metabolomics profiling of patients is a helpful tool to identify patho-mechanistic pathways for the disease development. Dopamine metabolism has been the target of several previous studies, of which some have reported lower phenylalanine and tyrosine levels in PD patients compared to controls. Methods: In this study, we have collected plasma from 27 PD patients, 18 reference controls, and 8 high-risk controls to perform a metabolomic study using liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS). Results: Our findings revealed higher intensities of trans-cinnamate, a phenylalanine metabolite, in patients compared to reference controls. Thus, we hypothesize that phenylalanine metabolism has been shifted to produce trans-cinnamate via L-phenylalanine ammonia lyase (PAL), instead of producing tyrosine, a dopamine precursor, via phenylalanine hydroxylase (PAH). Discussion: Given that these metabolites are precursors to several other metabolic pathways, the intensities of many metabolites such as dopamine, norepinephrine, and 3-hydroxyanthranilic acid, which connects phenylalanine metabolism to that of tryptophan, have been altered. Consequently, and in respect to Metabolic Control Analysis (MCA) theory, the levels of tryptophan metabolites have also been altered. Some of these metabolites are tryptamine, melatonin, and nicotinamide. Thus, we assume that these alterations could contribute to the dopaminergic, adrenergic, and serotonergic neurodegeneration that happen in the disease.

Concentrating to avoid falling: interaction between peripheral sensory and central attentional demands during a postural stability limit task in sedentary seniors

Evidence suggests falls and postural instabilities among seniors are attributed to a decline in both the processing of afferent signals (e.g., proprioceptive, vestibular) and attentional resources. We investigated the interaction between the non-visual and attentional demands of postural control in sedentary seniors. Old and young adults performed a postural stability limit task involving a maximal voluntary leaning movement with and without vision as well as a cognitive-attentional subtraction task. These tasks were performed alone (single-task) or simultaneously (dual-task) to vary the sensory-attentional demands. The functional limits of stability were quantified as the maximum center of pressure excursion during voluntary leaning. Seniors showed significantly smaller limits of postural stability compared to young adults in all sensory-attentional conditions. However, surprisingly, both groups of subjects reduced their stability limits by a similar amount when vision was removed. Furthermore, they similarly decreased their anterior-posterior stability limits when concurrently performing the postural and the cognitive-attentional tasks with vision. The overall average cognitive performance of young adults was higher than seniors and was only slightly affected during dual-tasking. In contrast, older adults markedly degraded their cognitive performance from the single- to the dual-task situations, especially when vision was unavailable. Thus, their dual-task costs were higher than those of young adults and increased in the eyes-closed condition, when postural control relied more heavily on non-visual sensory signals. Our findings provide the first evidence that as posture approaches its stability limits, sedentary seniors allot increasingly large cognitive attentional resources to process critical sensory inputs.

Fat Body Mass and Vertebral Fracture Progression in Women With Breast Cancer

Importance

Women with early breast cancer (EBC) exposed to aromatase inhibitors (AIs) may experience fragility fractures despite treatment with bone-active drugs. Risk factors for fractures in patients receiving AIs and denosumab have not been explored to date.

Objectives

To evaluate whether an association exists between dual x-ray absorptiometry (DXA)-measured fat body mass (FBM) and vertebral fracture (VF) progression in postmenopausal women with EBC undergoing adjuvant therapy with AIs in combination with denosumab and to examine whether VF was associated with common risk factors for bone fracture and parameters of body composition other than FBM.

Design, Setting, and Participants

For this prospective, single-center, cohort study, 237 patients with EBC who were undergoing adjuvant treatment with AIs and denosumab (60 mg every 6 months) were enrolled at the Breast Unit of the ASST Spedali Civili of Brescia from September 2014 to June 2018. Data analysis was conducted in June 2022.

Exposure

Body composition parameters, bone mineral density, and morphometric VFs were assessed by DXA at study entry and after 18 months of therapy.

Main Outcomes and Measures

VF progression, defined as either new or worsening of preexisting VFs, between the 2 time points.

Results

Of the 237 patients enrolled (median [range] age, 61 [28-84] years), 17 (4.4%) reported VF progression. Univariable analysis found an association between VF progression and a history of clinical fractures (odds ratio [OR], 3.22; 95% CI, 1.19-8.74; P = .02), Fracture Risk Assessment Tool (FRAX) score for major fractures (OR, 4.42; 95% CI, 1.23-13.79; P = .04), percentage of FBM (OR, 6.04; 95% CI, 1.69-21.63; P = .006), and android fat (OR, 9.58; 95% CI, 1.17-78.21; P = .04) and an inverse association with appendicular lean mass index-FBM ratio (OR, 0.25, 95% CI, 0.08-0.82; P = .02). Multivariable analysis revealed percentage of FBM (OR, 5.41; 95% CI, 1.49-19.59; P = .01) and FRAX score (OR, 3.95; 95% CI, 1.09-14.39; P = .04) as independent variables associated with VF progression.

Conclusions and Relevance

The findings of this study suggest that baseline FBM is an independent factor for VF progression in patients with EBC treated with adjuvant AIs and denosumab. This observation is new and indicates that diet and exercise may synergize with denosumab in the management of bone health in this patient setting.

Incorporating Data from Multiple Endpoints in the Analysis of Clinical Trials: Example from RSV Vaccines

BACKGROUND

To meet regulatory approval, interventions must demonstrate efficacy against a primary outcome in randomized clinical trials. However, when there are multiple clinically relevant outcomes, selecting a single primary outcome is challenging. Incorporating data from multiple outcomes may increase statistical power in clinical trials. We examined methods for analyzing data on multiple endpoints, inspired by real-world trials of interventions against respiratory syncytial virus (RSV).

METHOD

We developed a novel permutation test representing a weighted average of individual outcome test statistics ( wavP ) to evaluate intervention efficacy in a multiple endpoint analysis. We compared the power and type I error rate of this approach to the Bonferroni correction ( bonfT ) and the minP permutation test. We evaluated the different approaches using simulated data from three hypothetical trials varying the intervention efficacy, correlation, and incidence of the outcomes, and data from a real-world RSV clinical trial.

RESULTS

When the vaccine efficacy against different outcomes was similar, wavP yielded higher power than bonfT and minP ; in some scenarios the improvement in power was substantial. In settings where vaccine efficacy was notably larger against one endpoint compared with the others, all three methods had similar power. We developed an R package, PERmutation basEd ANalysis of mulTiple Endpoints (PERMEATE), to guide the selection of the most appropriate method for analyzing multiple endpoints in clinical trials.

CONCLUSIONS

Analyzing multiple endpoints using a weighted permutation method can increase power, whereas controlling the type I error rate compared with established methods under conditions mirroring real-world RSV clinical trials.

Impact of Polytherapy on Memory Functioning in Patients With Drug-Resistant Epilepsy: The Role of Attention and Executive Functions

OBJECTIVE

The aim was to examine the effect of polytherapy (i.e., the number of administered anti-seizure medications (ASMs)) on memory, and whether the interaction between the number of ASMs and attentional/executive functioning affect presurgical memory functioning and postsurgical memory changes in patients with drug-resistant epilepsy.

METHODS

Two studies were carried out. Study 1 consisted of a presurgical assessment of 125 adult patients, in which attention/executive function (EpiTrack screening tool) and memory were assessed (cross-sectional study). Of them, 72 patients underwent a second postsurgical evaluation, in which memory was assessed (Study 2). Patients were distributed into groups based on EpiTrack performance and number of ASMs.

RESULTS

The interaction between the number of ASMs and the attentional/executive functioning significantly affected presurgical memory, with patients with impaired EpiTrack performance taking three-four ASMs having poorer scores than patients with intact EpiTrack performance taking three-four ASMs (for all, p < .0001). This interaction also affected postsurgical memory changes, with patients with impaired Epitrack performance taking three-four ASMs having higher postsurgical decline than those with intact Epitrack performance taking three-four ASMs (for all, p < .005). No differences were found in patients taking two ASMs. Furthermore, the number of ASMs was associated with presurgical memory performance and postsurgical memory changes only in patients with impaired EpiTrack performance (for all, p < .05).

CONCLUSIONS

Our findings underline the utility of EpiTrack, together with the clinical information on the number of prescribed ASMs, to corroborate the impact of polytherapy on memory and to optimize the prediction of postsurgical memory changes.

The Influence of Food Regimes on Oxidative Stress: A Permutation-Based Approach Using the NPC Test

(1) Background: This paper aims to assess the existence of significant differences between two dietary regimes (omnivorous vs. semi-vegetarian) with reference to some oxidative stress markers (SOD, GPx, TRxR, GR, AGEs, and AOPPs) using non-parametric combination methodology based on a permutation test. (2) Methods: At the endocrinology unit of Messina University Hospital, two hundred subjects were asked to fill out a questionnaire about their dietary habits. None were under any pharmacological treatment. Using the NPC test, all comparisons were performed stratifying patients according to gender, age (≤40 or >40 years), BMI (normal weight vs. overweight), physical activity (sedentary vs. active lifestyle), TSH, FT4 levels in quartiles, and diagnosis of Hashimoto's thyroiditis. We evaluated differences in oxidative stress parameters in relation to two examined dietary regimes (omnivorous vs. semi-vegetarian). (3) Results: The antioxidant parameters GPx and TRxR were significantly lower in subjects with an omnivorous diet than in semi-vegetarians, particularly in females, both age groups, subjects with normal weight, those not affected by Hashimoto's thyroiditis, and both the sedentary and active lifestyle groups. Finally, the AGE and AOPP markers were significantly lower in semi-vegetarians. (4) Conclusion: Thanks to the NPC methodology, we can state that dietary patterns exert a significant influence on some oxidative stress parameters.

Delayed cortical thinning in children and adolescents with prenatal alcohol exposure

BACKGROUND

Prenatal alcohol exposure (PAE) is associated with abnormalities in cortical structure and maturation, including cortical thickness (CT), cortical volume, and surface area. This study provides a longitudinal context for the developmental trajectory and timing of abnormal cortical maturation in PAE.

METHODS

We studied 35 children with PAE and 30 nonexposed typically developing children (Comparisons), aged 8-17 at enrollment, who were recruited from the University of Minnesota FASD Program. Participants were matched on age and sex. They underwent a formal evaluation of growth and dysmorphic facial features associated with PAE and completed cognitive testing. MRI data were collected on a Siemens Prisma 3T scanner. Two sessions, each including MRI scans and cognitive testing, were spaced approximately 15 months apart on average. Change in CT and performance on tests of executive function (EF) were examined.

RESULTS

Significant age-by-group (PAE vs. Comparison) linear interaction effects in CT were observed in the parietal, temporal, occipital, and insular cortices suggesting altered developmental trajectories in the PAE vs. Comparison groups. Results suggest a pattern of delayed cortical thinning in PAE, with the Comparison group showing more rapid thinning at younger ages and those with PAE showing accelerated thinning at older ages. Overall, children in the PAE group showed reduced cortical thinning across time relative to the Comparison participants. Symmetrized percent change (SPC) in CT in several regions was significantly correlated with EF performance at 15-month follow-up for the Comparison group but not the group with PAE.

CONCLUSIONS

Regional differences were seen longitudinally in the trajectory and timing of CT change in children with PAE, suggesting delayed cortical maturation and an atypical pattern of development compared with typically developing individuals. In addition, exploratory correlation analyses of SPC and EF performance suggest the presence of atypical brain-behavior relationships in PAE. The findings highlight the potential role of altered developmental timing of cortical maturation in contributing to long-term functional impairment in PAE.

Incorporating data from multiple endpoints in the analysis of clinical trials: example from RSV vaccines

Background

To achieve licensure, interventions typically must demonstrate efficacy against a primary outcome in a randomized clinical trial. However, selecting a single primary outcome a priori is challenging. Incorporating data from multiple and related outcomes might help to increase statistical power in clinical trials. Inspired by real-world clinical trials of interventions against respiratory syncytial virus (RSV), we examined methods for analyzing data on multiple endpoints.

Method

We simulated data from three different populations in which the efficacy of the intervention and the correlation among outcomes varied. We developed a novel permutation-based approach that represents a weighted average of individual outcome test statistics ( varP ) to evaluate intervention efficacy in a multiple endpoint analysis. We compared the power and type I error rate of this approach to two alternative methods: the Bonferroni correction ( bonfT ) and another permutation-based approach that uses the minimum P-value across all test statistics ( minP ).

Results

When the vaccine efficacy against different outcomes was similar, VarP yielded higher power than bonfT and minP; in some scenarios the improvement in power was substantial. In settings where vaccine efficacy was notably larger against one endpoint compared to the others, all three methods had similar power.

Conclusions

Analyzing multiple endpoints using a weighted permutation method can increase power while controlling the type I error rate in settings where outcomes share similar characteristics, like RSV outcomes. We developed an R package, PERMEATE , to guide selection of the most appropriate method for analyzing multiple endpoints in clinical trials.

Long-term follow-up of a randomized controlled trial of choline for neurodevelopment in fetal alcohol spectrum disorder: corpus callosum white matter microstructure and neurocognitive outcomes

BACKGROUND

Fetal alcohol spectrum disorder (FASD) is a lifelong condition. Early interventions targeting core neurocognitive deficits have the potential to confer long-term neurodevelopmental benefits. Time-targeted choline supplementation is one such intervention that has been shown to provide neurodevelopmental benefits that emerge with age during childhood. We present a long-term follow-up study evaluating the neurodevelopmental effects of early choline supplementation in children with FASD approximately 7 years on average after an initial efficacy trial.

METHODS

The initial study was a randomized, double-blind, placebo-controlled trial of choline vs. placebo in 2.5 to 5 year olds with FASD. Participants in this long-term follow-up study include 18 children (9 placebo; 9 choline) seen 7 years on average following initial trial completion. The mean age at follow-up was 11.0 years old. Diagnoses were 28% fetal alcohol syndrome (FAS), 28% partial FAS, and 44% alcohol-related neurodevelopmental disorder. The follow-up included measures of executive functioning and an MRI scan.

RESULTS

Children who received choline had better performance on several tasks of lower-order executive function (e.g., processing speed) and showed higher white matter microstructure organization (i.e., greater axon coherence) in the splenium of the corpus callosum compared to the placebo group.

CONCLUSIONS

These preliminary findings, although exploratory at this stage, highlight potential long-term benefits of choline as a neurodevelopmental intervention for FASD and suggest that choline may affect white matter development, representing a potential target of choline in this population.

TRIAL REGISTRATION

Prior to enrollment, this trial was registered with clinicaltrials.gov ( NCT01149538 ) on June 23, 2010.

Effects of chronic exposure to arsenic on the fecal carriage of antibiotic-resistant Escherichia coli among people in rural Bangladesh

Antibiotic resistance is a leading cause of hospitalization and death worldwide. Heavy metals such as arsenic have been shown to drive co-selection of antibiotic resistance, suggesting arsenic-contaminated drinking water is a risk factor for antibiotic resistance carriage. This study aimed to determine the prevalence and abundance of antibiotic-resistant Escherichia coli (AR-Ec) among people and drinking water in high (Hajiganj, >100 μg/L) and low arsenic-contaminated (Matlab, <20 μg/L) areas in Bangladesh. Drinking water and stool from mothers and their children (<1 year) were collected from 50 households per area. AR-Ec was detected via selective culture plating and isolates were tested for antibiotic resistance, arsenic resistance, and diarrheagenic genes by PCR. Whole-genome sequencing (WGS) analysis was done for 30 E. coli isolates from 10 households. Prevalence of AR-Ec was significantly higher in water in Hajiganj (48%) compared to water in Matlab (22%, p <0.05) and among children in Hajiganj (94%) compared to children in Matlab (76%, p <0.05), but not among mothers. A significantly higher proportion of E. coli isolates from Hajiganj were multidrug-resistant (83%) compared to isolates from Matlab (71%, p <0.05). Co-resistance to arsenic and multiple antibiotics (MAR index >0.2) was observed in a higher proportion of water (78%) and child stool (100%) isolates in Hajiganj than in water (57%) and children (89%) in Matlab (p <0.05). The odds of arsenic-resistant bacteria being resistant to third-generation cephalosporin antibiotics were higher compared to arsenic-sensitive bacteria (odds ratios, OR 1.2-7.0, p <0.01). WGS-based phylogenetic analysis of E. coli isolates did not reveal any clustering based on arsenic exposure and no significant difference in resistome was found among the isolates between the two areas. The positive association detected between arsenic exposure and antibiotic resistance carriage among children in arsenic-affected areas in Bangladesh is an important public health concern that warrants redoubling efforts to reduce arsenic exposure.

Changes in the Behavior and Body Weight of Mature, Adult Male Wistar Han Rats after Reduced Social Grouping and Social Isolation

Changes in housing density, including individual housing, are commonly necessary in animal research. Obtaining reproducibility and translational validity in biomedical research requires an understanding of how animals adapt to changes in housing density. Existing literature mainly addresses acclimatization after transportation. We used a within-subject design to examine changes in behavior and weight gain of 4-mo-old male Wistar Han rats after reduction of their social group (RSG; due to removal of one rat from a cage containing 3 rats) and social isolation (SI; the removed rat) for the subsequent 2 wk. Changes in weight gain and in exploratory and center-avoidance behavior in an inescapable open arena (OA) were measured before (D0) and on days 7 and 14 (D7 and D14, respectively) after social change. The motor response to d-amphetamine (1.5 mg/kg), which stimulates behavioral arousal in response to novelty, was assessed at D14. Within-subject design revealed that RSG rats in OA had less locomotion at D7 but not more center-avoidance behavior and had returned to the D0 activity level at D14; SI rats in OA had consistently less locomotion and more center-avoidance behavior. Rearing behavior during OA exposure did not change in either group. However, SI rats showed more center-avoidance behavior in OA, greater weight gain, and less amphetamine-induced rearing at D14 as compared with RSG rats. These data indicate that after RSG, mature adult male rats require 2 wk to return to their baseline level of OA-related behavior, while after SI they gain weight and acquire maladaptive exploratory and center-avoidance behavior. The finding that SI produces maladaptive behavioral and physiologic alterations in adult male rats deserves attention because these changes could have confounding effects on research findings.

Impact of a package of health, nutrition, psychosocial support, and WaSH interventions delivered during preconception, pregnancy, and early childhood periods on birth outcomes and on linear growth at 24 months of age: factorial, individually randomised controlled trial

OBJECTIVE

To determine the effect of integrated and concurrent delivery of health, nutrition, water, sanitation and hygiene (WaSH), and psychosocial care interventions during the preconception period alone, during pregnancy and early childhood, and throughout preconception, pregnancy, and early childhood on birth outcomes and linear growth at 24 months of age compared with routine care.

DESIGN

Individually randomised factorial trial.

SETTING

Low and middle income neighbourhoods of Delhi, India.

PARTICIPANTS

13 500 women were randomised to receive preconception interventions (n=6722) or routine care (n=6778). 2652 and 2269 pregnant women were randomised again to receive pregnancy and early childhood interventions or routine care. The analysis of birth outcomes included 1290 live births for the preconception, pregnancy, and early childhood interventions (group A), 1276 for the preconception intervention (group B), 1093 for the pregnancy and early childhood interventions (group C), and 1093 for the control (group D). Children aged 24 months by 30 June 2021 were included in the 24 month outcome analysis (453 in group A, 439 in B, 293 in C, and 271 in D).

INTERVENTIONS

Health, nutrition, psychosocial care and support, and WaSH interventions were delivered during preconception, pregnancy, and early childhood periods.

MAIN OUTCOME MEASURES

The primary outcomes were low birth weight, small for gestational age, preterm, and mean birth weight. At 24 months, the outcomes were mean length-for-age z scores and proportion stunted. Three prespecified comparisons were made: preconception intervention groups (A+B) versus no preconception intervention groups (C+D); pregnancy and early childhood intervention groups (A+C) versus routine care during pregnancy and early childhood (B+D) and preconception, pregnancy, and early childhood interventions groups (A) versus control group (D).

RESULTS

The proportion with low birth weight was lower in the preconception intervention groups (506/2235) than in the no preconception intervention groups (502/1889; incidence rate ratio 0.85, 98.3% confidence interval 0.75 to 0.97; absolute risk reduction -3.80%, 98.3% confidence interval -6.99% to -0.60%). The proportion with low birth weight was lower in the pregnancy intervention groups (502/2096) than in the no pregnancy intervention groups (506/2028) but the upper limit of the confidence interval crossed null effect (0.87, 0.76 to 1.01; -1.71%, -4.96% to 1.54%). There was a larger effect on proportion with low birth weight in the group that received interventions in the preconception and pregnancy periods (267/1141) compared with the control group (267/934; 0.76, 0.62 to 0.91; -5.59%, -10.32% to -0.85%). The proportion stunted at 24 months of age was substantially lower in the pregnancy and early childhood intervention groups (79/746) compared with the groups that did not receive these interventions (136/710; 0.51, 0.38 to 0.70; -8.32%, -12.31% to -4.32%), and in the group that received preconception, pregnancy, and early childhood interventions (47/453) compared with the control group (51/271; 0.49, 0.32 to 0.75; -7.98%, -14.24% to -1.71%). No effect on stunting at 24 months was observed in the preconception intervention groups (132/892) compared with the no preconception intervention groups (83/564).

CONCLUSIONS

An intervention package delivered during preconception, pregnancy, and early childhood substantially reduced low birth weight and stunting at 24 months. Pregnancy and early childhood interventions alone had lower but important effects on birth outcomes and 24 month outcomes. Preconception interventions alone had an important effect on birth outcomes but not on 24 month outcomes.

TRIAL REGISTRATION

Clinical Trial Registry-India CTRI/2017/06/008908.

Making shared decisions with older men selecting treatment for lower urinary tract symptoms secondary to benign prostatic hyperplasia (LUTS/BPH): a pilot randomized trial

Background

Making high-quality decisions when selecting treatment for lower urinary tract symptoms due to benign prostatic hyperplasia (LUTS/BPH) requires a shared decision-making approach. However, older people with lower health literacy face barriers. The pilot study aimed to evaluate the feasibility of recruiting participants and evaluate the effectiveness of a multi-level intervention on decision quality for the treatment of LUTS/BPH.

Method

In this 2-arm, randomized controlled trial, multi-ethnic Asian men aged ≥ 50 years with moderate or severe symptoms (IPSS ≥ 8 and/or QOL ≥ 3) and physicians were recruited at a Singapore public primary care clinic. Men were randomized to either physicians trained in shared decision-making and used a pictorial patient-reported symptom score (Visual Analogue Uroflowmetry Score) during the consultation or to physicians untrained in shared decision-making who did not use the score. Decision quality was measured using SDMQ-9 scores from men and their physicians after the consultation.

Results

60 men (intervention [n = 30], control [n = 30]) receiving care from 22 physicians were recruited. Men’s mean age was 70 ± 9 years: 87% were Chinese, 40% had no formal education, and 32% were of lower socioeconomic status. No difference in decision quality from the men’s nor their physicians’ perspectives was noted [for men: mean score = 70.8 (SD 20.3) vs. 59.5 (SD 22.4); adjusted p = 0.352] [for physicians: mean score = 78.1 (SD 14.1) vs. 73.2 (SD 19.8); adjusted p > 0.999].

Conclusion

It was feasible to recruit the intended participants. There was no difference in decision quality between men who used shared decision-making and usual care for the treatment of LUTS/BPH.

Supplementary Information

The online version contains supplementary material available at 10.1186/s41687-022-00519-x.

Non-Motherhood between Obligation and Choice: Statistical Analysis Based on Permutation Tests of Spontaneous and Induced Abortion Rates in the Italian Context

(1) Background: This paper aims to examine two relevant phenomena in the context of public health: spontaneous abortion (SA) and induced abortion (IA). SA is one of the most common complications of pregnancies; IA is a conscious choice that is made by the mother/couple. (2) Methods: Permutation tests were applied to SA and IA standardized rates detected by ISTAT (2016–2020). The NPC test, chosen for its optimal properties, was applied to compare different Italian territorial divisions (stratifying for year and age classes of women) and analyze the trend of years by stochastic ordering. (3) Results: Only for SA, there are significant differences among the three territorial divisions: the South records higher SA standardized rates than the North and the Center; the rates of IA are similar. Relating to distinct women age classes, the SA standardized rates do not show significant differences among the three analyzed geographical areas; different results are highlighted for IA. Stochastic ordering shows that only the IA standardized rates are characterized by a significant monotonous decreasing trend over the years. (4) Conclusion: The SA phenomenon has shown a decreasing trend that could be justified by the progress of science. For IA, we can certainly say that the general decrease in the phenomenon is due to the greater use of contraceptive methods that help to prevent unwanted pregnancies.

Variants of SLC2A10 may be Linked to Poor Response to Metformin

Purpose

A study among Filipinos revealed that only 15% of patients with diabetes achieved glycemic control, and poor response to metformin could be one of the possible reasons. Recent studies demonstrate how genetic variations influence response to metformin. Hence, the present study aimed to determine genetic variants associated with poor response to metformin.

Methods

Using a candidate variant approach, 195 adult Filipino participants with newly diagnosed type 2 diabetes mellitus (T2DM) were enrolled in a case-control study. Genomic DNA from blood samples were collected. Allelic and genotypic associations of variants with poor response to metformin were determined using exact statistical methods.

Results

Several polymorphisms were nominally associated with poor response to metformin (P_uncorr < 0.05). The most notable is the association of multiple variants in the SLC2A10 gene—rs2425911, rs3092412, and rs2425904—with common additive genetic mode of inheritance. Other variants that have possible associations with poor drug response include rs340874 (PROX-AS1), rs815815 (CALM2), rs1333049 (CDKN2B-AS1), rs2010963 (VEGFA), rs1535435 and rs9494266 (AHI1), rs11128347 (PDZRN3), rs1805081 (NPC1), and rs13266634 (SLC30A8).

Conclusion

In Filipinos, a trend for the association for several variants was noted, with further observation that several mechanisms may be involved. The results may serve as pilot data for further validation of candidate variants for T2DM pharmacotherapy.

Loss-of-function, gain-of-function and dominant-negative mutations have profoundly different effects on protein structure

Most known pathogenic mutations occur in protein-coding regions of DNA and change the way proteins are made. Taking protein structure into account has therefore provided great insight into the molecular mechanisms underlying human genetic disease. While there has been much focus on how mutations can disrupt protein structure and thus cause a loss of function (LOF), alternative mechanisms, specifically dominant-negative (DN) and gain-of-function (GOF) effects, are less understood. Here, we investigate the protein-level effects of pathogenic missense mutations associated with different molecular mechanisms. We observe striking differences between recessive vs dominant, and LOF vs non-LOF mutations, with dominant, non-LOF disease mutations having much milder effects on protein structure, and DN mutations being highly enriched at protein interfaces. We also find that nearly all computational variant effect predictors, even those based solely on sequence conservation, underperform on non-LOF mutations. However, we do show that non-LOF mutations could potentially be identified by their tendency to cluster in three-dimensional space. Overall, our work suggests that many pathogenic mutations that act via DN and GOF mechanisms are likely being missed by current variant prioritisation strategies, but that there is considerable scope to improve computational predictions through consideration of molecular disease mechanisms.

Most known pathogenic mutations occur in protein-coding regions of DNA and change the way proteins are made. Here the authors analyse the locations of thousands of human disease mutations and their predicted effects on protein structure and show that,while loss-of-function mutations tend to be highly disruptive, non-loss-of-function mutations are in general much milder at a protein structural level.

What MRI-based tumor size measurement is best for predicting long-term survival in uterine cervical cancer?

Background

Tumor size assessment by MRI is central for staging uterine cervical cancer. However, the optimal role of MRI-derived tumor measurements for prognostication is still unclear.

Material and methods

This retrospective cohort study included 416 women (median age: 43 years) diagnosed with cervical cancer during 2002–2017 who underwent pretreatment pelvic MRI. The MRIs were independently read by three radiologists, measuring maximum tumor diameters in three orthogonal planes and maximum diameter irrespective of plane (MAX_imaging). Inter-reader agreement for tumor size measurements was assessed by intraclass correlation coefficients (ICCs). Size was analyzed in relation to age, International Federation of Gynecology and Obstetrics (FIGO) (2018) stage, histopathological markers, and disease-specific survival using Kaplan–Meier-, Cox regression-, and time-dependent receiver operating characteristics (tdROC) analyses.

Results

All MRI tumor size variables (cm) yielded high areas under the tdROC curves (AUCs) for predicting survival (AUC 0.81–0.84) at 5 years after diagnosis and predicted outcome (hazard ratios [HRs] of 1.42–1.76, p < 0.001 for all). Only MAX_imaging independently predicted survival (HR = 1.51, p = 0.03) in the model including all size variables. The optimal cutoff for maximum tumor diameter (≥ 4.0 cm) yielded sensitivity (specificity) of 83% (73%) for predicting disease-specific death after 5 years. Inter-reader agreement for MRI-based primary tumor size measurements was excellent, with ICCs of 0.83–0.85.

Conclusion

Among all MRI-derived tumor size measurements, MAX_imaging was the only independent predictor of survival. MAX_imaging ≥ 4.0 cm represents the optimal cutoff for predicting long-term disease-specific survival in cervical cancer. Inter-reader agreement for MRI-based tumor size measurements was excellent.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13244-022-01239-y.

Honeysuckle extract (Lonicera pallasii L.) exerts antioxidant properties and extends the lifespan and healthspan of Drosophila melanogaster

Honeysuckle Lonicera pallasii (Lonicera caerulea L.) is an excellent source of anthocyanins which have a number of health-promoting properties mainly associated with antioxidant and anti-inflammatory activities. Cyanidin-3-O-glucoside (C3G) is one of the most common anthocyanins naturally found in honeysuckle. The goal of the present study was to investigate antioxidant and anti-aging properties of Lonicera pallasii (Lonicera caerulea L.) extract (LE) and C3G using red blood cells (RBC) and Drosophila melanogaster models. LE and C3G treatment at a concentration of 100 μM induced enhancement of median and maximum lifespan up to 8%. LE and C3G supplementation at a concentration of 100 μM increased stress resistance up to 10%. The locomotor activity decreased during LE and C3G treatment in 4 and 6 weeks up to 52% in females. The integrity of the intestinal barrier was increased by 4% after LE treatment. These effects were accompanied by increased expression of Hif1 (pro-longevity gene) in response to C3G treatment and decreased expression of Keap1 (anti-longevity gene) after C3G and LE supplementation. RNA interference-mediated knockdown of Sirt6 completely abolished the positive effect obtained of LE and C3G supplementation in males which indicates that lifespan-extending effect is associated with Sirt6 activation. The experiments on the various in-vitro models (including radical scavenging activity and oxidative hemolysis of RBC demonstrated antioxidant and membrane-protective activities of LE and C3G. The present study indicates that Lonicera extract can prolong the lifespan and improve the healthspan of Drosophila model through biological and antioxidant activities.

Patients' perspective on supposedly patient-relevant process and outcome parameters: a cross-sectional survey within the 'PRO patients study'

BACKGROUND

To be able to make informed choices based on their individual preferences, patients need to be adequately informed about treatment options and their potential outcomes. This implies that studies measure the effects of care based on parameters that are relevant to patients. In a previous scoping review, we found a wide variety of supposedly patient-relevant parameters that equally addressed processes and outcomes of care. We were unable to identify a consistent understanding of patient relevance and therefore aimed to develop an empirically based concept including a generic set of patient-relevant parameters. As a first step we evaluated the process and outcome parameters identified in the scoping review from the patients' perspective.

METHODS

We conducted a cross-sectional survey among German general practice patients. Ten research practices of Witten/Herdecke University supported the study. During a two-week period in the fall of 2020, patients willing to participate self-administered a short questionnaire. It evaluated the relevance of the 32 parameters identified in the scoping review on a 5-point Likert scale and offered a free-text field for additional parameters. These free-text answers were inductively categorized by two researchers. Quantitative data were analyzed using descriptive statistics. Bivariate analyses were performed to determine whether there are any correlations between rating a parameter as highly relevant and patients' characteristics.

RESULTS

Data from 299 patients were eligible for analysis. All outcomes except 'sexuality' and 'frequency of healthcare service utilization' were rated important. 'Confidence in therapy' was rated most important, followed by 'prevention of comorbidity' and 'mobility'. Relevance ratings of five parameters were associated with patients' age and gender, but not with their chronic status. The free-text analysis revealed 15 additional parameters, 12 of which addressed processes of care, i.e., 'enough time in physician consultation'.

CONCLUSION

Patients attach great value to parameters addressing processes of care. It appears as though the way in which patients experience the care process is not less relevant than what comes of it. Relevance ratings were not associated with chronic status, but few parameters were gender- and age-related.

TRIAL REGISTRATION

Core Outcome Measures in Effectiveness Trials Initiative, registration number: 1685.

High-Intensity Statin vs. Low-Density Lipoprotein Cholesterol Target for Patients Undergoing Percutaneous Coronary Intervention: Insights From a Territory-Wide Cohort Study in Hong Kong

Background: Different guidelines recommend different approaches to lipid management in patients with atherosclerotic cardiovascular disease. We aim to determine the best strategy for lipid management in Asian patients undergoing percutaneous coronary intervention (PCI).

Method: This was a retrospective cohort study conducted in patients who underwent first-ever PCI from 14 hospitals in Hong Kong. All participants either achieved low-density lipoprotein cholesterol (LDL-C) target of <55 mg/dl with ≥50% reduction from baseline (group 1), or received high-intensity statin (group 2), or both (group 3) within 1 yr after PCI. The primary endpoint was a composite outcome of all-cause mortality, myocardial infarction, stroke, and any unplanned coronary revascularization between 1 and 5 yr after PCI.

Results: A total of 8,650 patients were analyzed with a median follow-up period of 4.2 yr. After the adjustment of baseline characteristics, complexity of PCI and medications prescribed and the risks of the primary outcome were significantly lower in group 2 (hazard ratio [HR], 0.82; 95% confidence interval [CI], 0.74–0.93, P = 0.003) and group 3 (HR, 0.75; 95% CI, 0.62–0.90; P = 0.002). The primary outcome occurred at similar rates between group 2 and group 3.

Conclusions: Use of high intensity statin, with or without the attainment of guidelines recommended LDL-C target, was associated with a lower adjusted risk of MACE at 5 yr, compared with patients who attained LDL-C target without high intensity statin.

The Impact of Roads on the Redistribution of Plants and Associated Arthropods in a Hyper-Arid Ecosystem

The construction of vehicular roads likely affects the distribution of natural resources. Although the effects of roads on different ecosystem aspects have been extensively studied, studies in arid and, particularly, in hyper-arid ecosystems are scarce. In drylands, where water is the main limiting factor, the effect of roads on the redistribution of water may have strong subsequent effects on the ecosystem, especially when roads cross natural water flow paths. To fill this knowledge gap, we studied the effects of a road that runs across a slope on the distribution of plants and animals in a hyper-arid environment. Changes in shrub cover, below and above the road, were quantified by remote sensing and image classification, while plant-associated arthropods were vacuum-sampled from shrub canopies and from open (inter-shrub) areas. We found that the spatial distribution of shrubs, a vital resource facilitating many other organisms, was affected by the road, with an increase in the shrub cover immediately above the road and a decrease below it. Arthropod abundance generally followed shrub cover, but the exact pattern depended on the specific group sampled. While some arthropod groups (e.g., aphids, parasitic wasps and barklice) thrived under the disturbed conditions above the road, other arthropod groups (e.g., mites and true bugs) were less abundant in the disturbed patches. Our results highlight the strong effects of human-made structures on the distribution of flora and fauna in arid ecosystems.

Hidden talents: Poly (I:C)-induced maternal immune activation improves mouse visual discrimination performance and reversal learning in a sex-dependent manner

While there is a strong focus on the negative consequences of maternal immune activation (MIA) on developing brains, very little attention is directed towards potential advantages of early life challenges. In this study, we utilized a polyinosine-polycytidylic acid (poly(I:C)) MIA model to test visual pairwise discrimination (PD) and reversal learning (RL) in mice using touchscreen technology. Significant sex differences emerged in that MIA reduced the latency for males to make a correct choice in the PD task while females reached criterion sooner, made fewer errors, and utilized fewer correction trials in RL compared to saline controls. These surprising improvements were accompanied by the sex-specific upregulation of several genes critical to cognitive functioning, indicative of compensatory plasticity in response to MIA. In contrast, when exposed to a 'two-hit' stress model (MIA + loss of the social component of environmental enrichment [EE]), mice did not display anhedonia but required an increased number of PD and RL correction trials. These animals also had significant reductions of CamK2a mRNA in the prefrontal cortex. Appropriate functioning of synaptic plasticity, via mediators such as this protein kinase and others, are critical for behavioral flexibility. Although EE has been implicated in, delaying the appearance of symptoms associated with certain brain disorders, these findings are in line with evidence that it also makes individuals more vulnerable to its loss. Overall, with the right 'dose', early life stress exposure can confer at least some functional advantages, which are lost when the number or magnitude of these exposures become too great.

Effectiveness of radiologist training in improving reader agreement for Lung-RADS 4X categorization

OBJECTIVES

To identify the agreement on Lung CT Screening Reporting and Data System 4X categorization between radiologists and an expert-adjudicated reference standard and to investigate whether training led to improvement of the agreement measures and diagnostic potential for lung cancer.

METHODS

Category 4 nodules in the Korean Lung Cancer Screening Project were identified retrospectively, and each 4X nodule was matched with one 4A or 4B nodule. An expert panel re-evaluated the categories and determined the reference standard. Nineteen radiologists were asked to determine the presence of CT features of malignancy and 4X categorization for each nodule. A review was performed in two sessions, and training material was given after session 1. Agreement on 4X categorization between radiologists and the expert-adjudicated reference standard and agreement between radiologist-assessed 4X categorization and lung cancer diagnosis were evaluated.

RESULTS

The 48 expert-adjudicated 4X nodules and 64 non-4X nodules were evenly distributed in each session. The proportion of category 4X decreased after training (56.4% ± 16.9% vs. 33.4% ± 8.0%; p < 0.001). Cohen's κ indicated poor agreement (0.39 ± 0.16) in session 1, but agreement improved in session 2 (0.47 ± 0.09; p = 0.03). The increase in agreement in session 2 was observed among inexperienced radiologists (p < 0.05), and experienced and inexperienced reviewers exhibited comparable agreement performance in session 2 (p > 0.05). All agreement measures between radiologist-assessed 4X categorization and lung cancer diagnosis increased in session 2 (p < 0.05).

CONCLUSION

Radiologist training can improve reader agreement on 4X categorization, leading to enhanced diagnostic performance for lung cancer.

KEY POINTS

• Agreement on 4X categorization between radiologists and an expert-adjudicated reference standard was initially poor, but improved significantly after training. • The mean proportion of 4X categorization by 19 radiologists decreased from 56.4% ± 16.9% in session 1 to 33.4% ± 8.0% in session 2. • All agreement measures between the 4X categorization and lung cancer diagnosis increased significantly in session 2, implying that appropriate training and guidance increased the diagnostic potential of category 4X.

Potential of 2D qNMR spectroscopy for distinguishing chicken breeds based on the metabolic differences

Two-dimensional quantitative NMR spectroscopy (2D qNMR) was set up and multivariate analyses were performed on metabolites obtained from breast meat extracts of broilers and four native chicken (KNC) strains. It can accurately identify more metabolites than 1D ¹H NMR via separation of peak overlap by dimensional expansion with good linearity, but has a problem of numerical quantification; Complementation of 1D and 2D qNMR is necessary. Among breeds, KNC-D had higher amounts of free amino acids, sugars, and bioactive compounds than others. Noticeable differences between KNCs and broilers were observed; KNCs contained higher amounts of inosine 5'-monophosphate, α-glucose, anserine, and lactic acid, and lower amounts of free amino acids and their derivatives. The 2D qNMR combined with multivariate analyses distinguished the breast meat of KNCs from broilers but showed similarities among KNCs. Also, 2D qNMR may provide fast metabolomics information compared to conventional analysis.

Sex- and Gender-Stratified Risks of Psychological Factors for Incident Ischemic Heart Disease: Systematic Review and Meta-Analysis

Background

Psychological factors are associated with an increased risk of developing ischemic heart disease (IHD). Women more often report psychological factors, and sex and gender differences are present in IHD. In this meta‐analysis we examine the risks of psychological factors for IHD incidence in women and men. We hypothesize that a broad range of psychological factors are related to a higher risk for incident IHD, with a higher risk for women.

Methods and Results

PubMed, EMBASE, and PsycINFO were searched for studies assessing the risk between psychological factors and incident IHD. Psychological factors included depression, anxiety or panic disorder, social support, hostility, anger, personality (type D), type A behavior pattern, posttraumatic stress disorder, and psychological distress. In the primary analyses, 62 studies (77 separate reports) that included 2 145 679 women and 3 119 879 men and reported confounder‐adjusted hazard ratios or relative risks were included. Pooled effect confounder‐adjusted estimates from random‐effects models showed that psychological factors (all combined) were associated with incident IHD in women (hazard ratio: 1.22; 95% CI, 1.14–1.30) and men (hazard ratio: 1.25; 95% CI, 1.19–1.31). No sex and gender differences were found for these pooled effect estimates (P=0.547).

Conclusions

Psychological factors are associated with incident IHD in both women and men, but no significant differences were observed between women and men. IHD is predominantly being studied as obstructive coronary artery disease, which is more prevalent in men. Data are needed on psychological predictors and other manifestations of IHD such as coronary microvascular disease, which is more common in women.

A Diet High in Processed Foods, Total Carbohydrates and Added Sugars, and Low in Vegetables and Protein Is Characteristic of Youth with Avoidant/Restrictive Food Intake Disorder

Avoidant/restrictive food intake disorder (ARFID) is characterized in part by limited dietary variety, but dietary characteristics of this disorder have not yet been systematically studied. Our objective was to examine dietary intake defined by diet variety, macronutrient intake, and micronutrient intake in children and adolescents with full or subthreshold ARFID in comparison to healthy controls. We collected and analyzed four-day food record data for 52 participants with full or subthreshold ARFID, and 52 healthy controls, aged 9-22 years. We examined frequency of commonly reported foods by logistic regression and intake by food groups, macronutrients, and micronutrients between groups with repeated-measures ANOVA. Participants with full or subthreshold ARFID did not report any fruit or vegetable category in their top five most commonly reported food categories, whereas these food groups occupied three of the top five groups for healthy controls. Vegetable and protein intake were significantly lower in full or subthreshold ARFID compared to healthy controls. Intakes of added sugars and total carbohydrates were significantly higher in full or subthreshold ARFID compared to healthy controls. Individuals with full or subthreshold ARFID had lower intake of vitamins K and B12, consistent with limited vegetable and protein intake compared to healthy controls. Our results support the need for diet diversification as part of therapeutic interventions for ARFID to reduce risk for nutrient insufficiencies and related complications.