Beyond Bonferroni revisited: concerns over inflated false positive research findings in the fields of conservation genetics, biology, and medicine

Genomics and conservation: Guidance from training to analyses and applications

Environmental change is intensifying the biodiversity crisis and threatening species across the tree of life. Conservation genomics can help inform conservation actions and slow biodiversity loss. However, more training, appropriate use of novel genomic methods and communication with managers are needed. Here, we review practical guidance to improve applied conservation genomics. We share insights aimed at ensuring effectiveness of conservation actions around three themes: (1) improving pedagogy and training in conservation genomics including for online global audiences, (2) conducting rigorous population genomic analyses properly considering theory, marker types and data interpretation and (3) facilitating communication and collaboration between managers and researchers. We aim to update students and professionals and expand their conservation toolkit with genomic principles and recent approaches for conserving and managing biodiversity. The biodiversity crisis is a global problem and, as such, requires international involvement, training, collaboration and frequent reviews of the literature and workshops as we do here.

A new sampling device for metabarcoding surveillance of port communities and detection of non-indigenous species

Metabarcoding techniques are revolutionizing studies of marine biodiversity. They can be used for monitoring non-indigenous species (NIS) in ports and harbors. However, they are often biased by inconsistent sampling methods and incomplete reference databases. Logistic constraints in ports prompt the development of simple, easy-to-deploy samplers. We tested a new device called polyamide mesh for ports organismal monitoring (POMPOM) with a high surface-to-volume ratio. POMPOMS were deployed inside a fishing and recreational port in the Mediterranean alongside conventional settlement plates. We also compiled a curated database with cytochrome oxidase (COI) sequences of Mediterranean NIS. COI metabarcoding of the communities settled in the POMPOMs captured a similar biodiversity than settlement plates, with shared molecular operational units (MOTUs) representing ca. 99% of reads. 38 NIS were detected in the port accounting for ca. 26% of reads. POMPOMs were easy to deploy and handle and provide an efficient method for NIS surveillance.

Expecting the Unexpected: Predicting Panic Attacks From Mood, Twitter, and Apple Watch Data

OBJECTIVE

Panic attacks are an impairing mental health problem that affects 11% of adults every year. Current criteria describe them as occurring without warning, despite evidence suggesting individuals can often identify attack triggers. We aimed to prospectively explore qualitative and quantitative factors associated with the onset of panic attacks.

RESULTS

Of 87 participants, 95% retrospectively identified a trigger for their panic attacks. Worse individually reported mood and state-level mood, as indicated by Twitter ratings, were related to greater likelihood of next-day panic attack. In a subsample of participants who uploaded their wearable sensor data (n = 32), louder ambient noise and higher resting heart rate were related to greater likelihood of next-day panic attack.

CONCLUSIONS

These promising results suggest that individuals who experience panic attacks may be able to anticipate their next attack which could be used to inform future prevention and intervention efforts.

Transcriptomic changes in glomeruli in response to a high salt challenge in the Dahl SS rat

Salt sensitivity impacts a significant portion of the population and is an important contributor to the development of chronic kidney disease. One of the significant early predictors of salt-induced damage is albuminuria, which reflects the deterioration of the renal filtration barrier: the glomerulus. Despite significant research efforts, there is still a gap in knowledge regarding the molecular mechanisms and signaling networks contributing to instigating and/or perpetuating salt-induced glomerular injury. To address this gap, we used 8-wk-old male Dahl salt-sensitive rats fed a normal-salt diet (0.4% NaCl) or challenged with a high-salt diet (4% NaCl) for 3 wk. At the end of the protocol, a pure fraction of renal glomeruli obtained by differential sieving was used for next-generation RNA sequencing and comprehensive semi-automatic transcriptomic data analyses, which revealed 149 differentially expressed genes (107 and 42 genes were downregulated and upregulated, respectively). Furthermore, a combination of predictive gene correlation networks and computational bioinformatic analyses revealed pathways impacted by a high salt dietary challenge, including renal metabolism, mitochondrial function, apoptotic signaling and fibrosis, cell cycle, inflammatory and immune responses, circadian clock, cytoskeletal organization, G protein-coupled receptor signaling, and calcium transport. In conclusion, we report here novel transcriptomic interactions and corresponding predicted pathways affecting glomeruli under salt-induced stress.NEW & NOTEWORTHY Our study demonstrated novel pathways affecting glomeruli under stress induced by dietary salt. Predictive gene correlation networks and bioinformatic semi-automatic analysis revealed changes in the pathways relevant to mitochondrial function, inflammatory, apoptotic/fibrotic processes, and cell calcium transport.

Stability of olfactory behavior syndromes in the Drosophila larva

Individuals of many animal populations exhibit idiosyncratic behaviors. One measure of idiosyncratic behavior is a behavior syndrome, defined as the stability of one or more behavior traits in an individual across different situations. While behavior syndromes have been described in various animal systems, their properties and the circuit mechanisms that generate them are poorly understood. We thus have an incomplete understanding of how circuit properties influence animal behavior. Here, we characterize olfactory behavior syndromes in the Drosophila larva. We show that larvae exhibit idiosyncrasies in their olfactory behavior over short time scales. They are influenced by the larva's satiety state and odor environment. Additionally, we identified a group of antennal lobe local neurons that influence the larva's idiosyncratic behavior. These findings reveal previously unsuspected influences on idiosyncratic behavior. They further affirm the idea that idiosyncrasies are not simply statistical phenomena but manifestations of neural mechanisms. In light of these findings, we discuss more broadly the importance of idiosyncrasies to animal survival and how they might be studied.

Poverty from fetal life onward and child brain morphology

Poverty is a risk factor for impaired child development, an association possibly mediated by brain morphology. Previous studies lacked prospective poverty assessments during pregnancy and did not stratify by majority/minority status. We investigated the association of household poverty from fetal life forward with brain morphological differences at age 10 years, in 2166 mother-child dyads. Overall, the results showed no associations between any poverty exposure early in life and brain volumes. However, there was the evidence of timing effects: children exposed to poverty in utero had smaller amygdala volumes (B =  - 0.18, 95%CI - 0.30; - 0.07, pFDR-adjusted = 0.009). There were also differences in associations by majority/minority status (cerebral white matter: p for interaction = 0.04). Dutch children exposed to childhood poverty showed smaller cerebral white matter volumes than their control (B =  - 0.26, 95%CI - 0.45; - 0.06, pFDR-adjusted = 0.035). This association was not observed in the minority population (B =  - 0.05, 95%CI - 0.23; 0.12, pFDR-adjusted = 0.542). The smaller cerebral white matter volume mediated the association between childhood poverty and poorer school performance in Dutch children. Our findings point to the importance of poverty exposure in the fetal period and suggest different mechanisms and vulnerabilities across majority/minority groups.

Genetics of spot blotch resistance in bread wheat (Triticum aestivum L.) using five models for GWAS

Genetic architecture of resistance to spot blotch in wheat was examined using a Genome-Wide Association Study (GWAS) involving an association panel comprising 303 diverse genotypes. The association panel was evaluated at two different locations in India including Banaras Hindu University (BHU), Varanasi (Uttar Pradesh), and Borlaug Institute for South Asia (BISA), Pusa, Samastipur (Bihar) for two consecutive years (2017-2018 and 2018-2019), thus making four environments (E1, BHU 2017-18; E2, BHU 2018-19; E3, PUSA, 2017-18; E4, PUSA, 2018-19). The panel was genotyped for 12,196 SNPs based on DArT-seq (outsourced to DArT Ltd by CIMMYT); these SNPs included 5,400 SNPs, which could not be assigned to individual chromosomes and were therefore, described as unassigned by the vendor. Phenotypic data was recorded on the following three disease-related traits: (i) Area Under Disease Progress Curve (AUDPC), (ii) Incubation Period (IP), and (iii) Lesion Number (LN). GWAS was conducted using each of five different models, which included two single-locus models (CMLM and SUPER) and three multi-locus models (MLMM, FarmCPU, and BLINK). This exercise gave 306 MTAs, but only 89 MTAs (33 for AUDPC, 30 for IP and 26 for LN) including a solitary MTA detected using all the five models and 88 identified using four of the five models (barring SUPER) were considered to be important. These were used for further analysis, which included identification of candidate genes (CGs) and their annotation. A majority of these MTAs were novel. Only 70 of the 89 MTAs were assigned to individual chromosomes; the remaining 19 MTAs belonged to unassigned SNPs, for which chromosomes were not known. Seven MTAs were selected on the basis of minimum P value, number of models, number of environments and location on chromosomes with respect to QTLs reported earlier. These 7 MTAs, which included five main effect MTAs and two for epistatic interactions, were considered to be important for marker-assisted selection (MAS). The present study thus improved our understanding of the genetics of resistance against spot blotch in wheat and provided seven MTAs, which may be used for MAS after due validation.

Predicting behavioral and brain markers of inhibitory control at preschool age from early measures of executive attention

Background

Inhibitory control (IC) is the ability to prevent prepotent responses when inappropriate. Longitudinal research on IC development has mainly focused on early childhood and adolescence, while research on IC development in the first years of life is still scarce. To address this gap in the literature, we explored the association between executive attention (EA) and elementary forms of IC in infancy and toddlerhood, with individual differences in IC later at 5 years of age.

Method

We conducted a five-wave longitudinal study in which children's EA and IC (n = 96) were tested at the age of 9 and 16 months and 2, 3, and 5 years. Children performed various age-appropriate EA and IC tasks in each wave, measuring inhibition of attention, endogenous control of attention, inhibition of the response, and conflict inhibition. At 5 years of age, IC was measured with a Go/No-go task while recording event-related potentials. After correlation analyses, structural equation model analyses were performed to predict IC at 5 years of age from EA and early IC measures.

Results

The results revealed that EA at 9 months predicted IC measures at 2 years of age. Likewise, measures of IC at 2 years predicted performance on the Go/No-go task at behavioral and neural levels. No direct association was found between EA at 9 months and IC at 5 years of age. We further observed that some EA and IC measures were not associated across time.

Conclusion

As we expected, EA skills in infancy and toddlerhood were related to better performance of children on IC tasks, toghether with a more mature inhibition-related brain functioning. Altogether, the results indicate that IC in early childhood could be predicted from EA and IC at 9 months and 2 years of age and suggest that the early emergence of IC relies on the development of particular EA and basic IC skills. However, some discontinuities in the longitudinal development of IC are observed in the first 5 years of life. These findings provide further support for the hierarchical model of IC development.

Childhood adversity and cardiometabolic biomarkers in mid-adulthood in the 1958 British birth cohort

Studies that have examined associations between adverse childhood experiences (ACEs) and cardiometabolic biomarkers in adulthood are limited as they mainly focus on childhood maltreatment. This study aimed to examine the association between a range of prospectively and retrospectively reported ACEs and cardiometabolic biomarkers in mid-adulthood. Multiply-imputed data on 8511 participants from the National Child Development Study (1958 British birth cohort) were used. ACEs were prospectively reported at ages 7, 11 and 16, and retrospectively reported at age 33/44/45. Cardiometabolic outcomes assessed at age 44/45 included glycated haemoglobin (HbA1c), cholesterol (total, low-density lipoprotein (LDL) and high-density lipoprotein (HDL)), triglycerides, blood pressure (systolic and diastolic), body mass index, waist circumference and metabolic syndrome. Parental separation/divorce, physical neglect, emotional neglect and psychological abuse were associated with lower HDL cholesterol. Parental offending and physical neglect were associated with higher triglyceride concentrations. Parental offending was also associated with increased HbA1c. Exposure to 2+ (vs. 0) prospective ACEs was associated with lower HDL cholesterol. All these associations were after adjustment for sex and multiple early life factors. To conclude, several individual ACEs are associated with poorer cardiometabolic risk factor profiles in mid-adulthood. Furthermore, exposure to two or more prospective ACEs is associated with lower HDL cholesterol concentrations in mid-adulthood.

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Parental separation/divorce in childhood is associated with lower high-density lipoprotein cholesterol in mid-adulthood.

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Physical neglect in childhood is associated with poorer lipid profiles in mid-adulthood.

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Psychological abuse in childhood is associated with lower high-density lipoprotein cholesterol in mid-adulthood.

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Parental offending in childhood is associated with higher triglycerides and glycated haemoglobin in mid-adulthood.

Internal state affects local neuron function in an early sensory processing center to shape olfactory behavior in Drosophila larvae

Crawling insects, when starved, tend to have fewer head wavings and travel in straighter tracks in search of food. We used the Drosophila melanogaster larva to investigate whether this flexibility in the insect's navigation strategy arises during early olfactory processing and, if so, how. We demonstrate a critical role for Keystone-LN, an inhibitory local neuron in the antennal lobe, in implementing head-sweep behavior. Keystone-LN responds to odor stimuli, and its inhibitory output is required for a larva to successfully navigate attractive and aversive odor gradients. We show that insulin signaling in Keystone-LN likely mediates the starvation-dependent changes in head-sweep magnitude, shaping the larva's odor-guided movement. Our findings demonstrate how flexibility in an insect's navigation strategy can arise from context-dependent modulation of inhibitory neurons in an early sensory processing center. They raise new questions about modulating a circuit's inhibitory output to implement changes in a goal-directed movement.

Using the Parent Risk Screening Measure (PRISM) to Assess Pain-Related Risk Factors in Parents of Youth Seeking Treatment for Acute Musculoskeletal Pain

OBJECTIVES

The Parent Risk Screening Measure (PRISM) rapidly assesses parent distress, psychosocial function, and behaviors associated with child pain-related dysfunction in parents of youth with chronic pain. Recognizing the importance of parent pain-related cognitions and responses to pain during the acute pain period, the current study examined the utility of the PRISM in screening parents of youth with acute pain.

METHODS

Participants were 175 parent-youth dyads taking part in a larger study examining risk and resilience in youth with acute musculoskeletal pain. Parents completed the PRISM and a battery of measures reporting on their child's pain-related disability and cognitions and behaviors in response to their child's pain. Youth reported on their pain, pain-related disability, pain-related fear, catastrophizing, and pain self-efficacy.

RESULTS

PRISM total scores ( M =2.55, SD=2.77) were correlated with many parent and child report measures (eg, protectiveness, catastrophizing, and pain-related fear), with higher scores associated with greater symptoms. Using published PRISM cutoffs, 86.9% of parents were classified as low and 13.13% as elevated risk. t tests revealed significant differences between elevated and low-risk groups on several measures. Moreover, youth of parents in the elevated risk group were more likely to meet clinical cutoffs on pain catastrophizing and fear avoidance measures.

DISCUSSION

Findings suggest the PRISM is useful in screening for parent distress and behaviors associated with elevated pain symptomatology in a pediatric acute musculoskeletal pain sample. The important next steps are to identify the ideal time for administering the PRISM and to examine the associations among PRISM scores and pain outcomes over time.

Testing exchangeability of multivariate distributions

Although there have been a number of available tests of bivariate exchangeability, i.e. bivariate symmetry for bivariate distributions, the literature is void of tests whether a multivariate distribution with more than two dimensions is exchangeable or not. In this paper, multivariate permutation tests of exchangeability of multivariate distributions are proposed, which are based on the non-parametric combination methodology, i.e. on combining non-parametric bivariate exchangeability tests. Numerical experiments on real as well as simulated multivariate data with more than two dimensions are presented here. The multivariate permutation test turns out to be typically more powerful than a bivariate exchangeability test performed only over a single pair of variables, and also more suitable compared to tests exploiting the approaches of Benjamini-Yekutieli or Bonferroni.

ADAM10 and ADAM17 promote SARS-CoV-2 cell entry and spike protein-mediated lung cell fusion

The severe‐acute‐respiratory‐syndrome‐coronavirus‐2 (SARS‐CoV‐2) is the causative agent of COVID‐19, but host cell factors contributing to COVID‐19 pathogenesis remain only partly understood. We identify the host metalloprotease ADAM17 as a facilitator of SARS‐CoV‐2 cell entry and the metalloprotease ADAM10 as a host factor required for lung cell syncytia formation, a hallmark of COVID‐19 pathology. ADAM10 and ADAM17, which are broadly expressed in the human lung, cleave the SARS‐CoV‐2 spike protein (S) in vitro, indicating that ADAM10 and ADAM17 contribute to the priming of S, an essential step for viral entry and cell fusion. ADAM protease‐targeted inhibitors severely impair lung cell infection by the SARS‐CoV‐2 variants of concern alpha, beta, delta, and omicron and also reduce SARS‐CoV‐2 infection of primary human lung cells in a TMPRSS2 protease‐independent manner. Our study establishes ADAM10 and ADAM17 as host cell factors for viral entry and syncytia formation and defines both proteases as potential targets for antiviral drug development.

Genetic Variations in Metallothionein Genes and Susceptibility to Hypertensive Disorders of Pregnancy: A Case-Control Study

Background: The involvement of oxidative stress in the pathological process of hypertensive disorders of pregnancy (HDP) gives rise to the interest in exploring the association of genetic variations in antioxidant metallothionein (MT) genes with HDP susceptibility.

Methods: Seventeen single-nucleotide polymorphisms(SNPs) in MT genes were selected to conduct genotyping based on a case-control study consisting of 371 HDP cases (pregnancy with chronic hypertension (66), gestational hypertension (172), and preeclampsia or preeclampsia superimposed on chronic hypertension (133)) and 479 controls. The association between SNPs in MTs and the risk of HDP was estimated with unconditional logistic regression analysis and further tested with the false-positive report probability (FPRP) procedure. The joint effects of SNPs on the HDP risk were assessed by haplotype analysis.

Results: After the adjustment for age and pre-pregnancy body mass index (pre-BMI) in the logistic regress analysis and followed by the FPRP test, the genetic variation rs10636 (OR = 0.46, 95% CI: 0.30–0.71 for GG vs. CC, p = 0.000 and OR = 0.48, 95% CI: 0.32–0.73 for GG vs. CG/CC, p = 0.001) in MT2A was associated with gestational hypertension. Other four SNPs, that is, rs11076161 (OR = 1.89, 95% CI: 1.35–2.63 for GG vs. GA/AA, p = 0.000) in MT1A; rs7191779 (OR = 1.54, 95% CI: 1.11–2.13 for CC vs. CG/GG, p = 0.010) in MT1B; rs8044719 (OR = 0.57, 95% CI: 0.40–0.80 for GT vs. GG, p = 0.001) in MT1DP; and rs8052334 (OR = 1.52, 95% CI: 1.10–2.11 for TT vs. TC/CC, p = 0.012) in MT1B were significantly associated with the susceptibility of HDP. The haplotype analysis among 11, 10, 10, and seven SNPs in MT (MT1A, MT2A, MT1M, MT1B, and MT1DP) genes showed that eight (A-C-G-T-C-G-A-G-C-G-C, OR = 4.559; A-C-T-C-C-C-A-G-C-G-C, OR = 5.777; A-C-T-T-C-G-A-G-C-G-C, OR = 4.590; G-A-T-C-C-G-C-G-G-C-C, OR = 4.065; G-A-T-C-G-C-C-G-G-C-C, OR = 4.652; G-A-T-T-C-C-C-G-G-C-C, OR = 0.404; G-C-T-C-C-C-A-G-G-C-C, OR = 1.901; G-C-T-T-C-C-A-G-G-C-C, and OR = 3.810), five (C-G-A-T-C-A-C-C-G-G, OR = 2.032; C-G-A-T-C-G-C-C-G-G, OR = 2.077; G-A-C-T-C-A-C-C-T-G, OR = 0.564; G-G-A-G-C-A-C-C-G-G, OR = 5.466; G-G-A-T-T-A-G-C-G-G, and OR = 0.284), five (A-C-G-T-C-G-A-G-C-C, OR = 2.399; A-C-T-C-C-C-C-T-G-G, OR = 0.259; G-A-T-C-C-C-C-G-G-C, OR = 1.572; G-A-T-C-G-C-C-G-G-C, OR = 0.001; G-C-T-C-G-C-A-G-G-C, and OR = 2.512), and five (A-C-T-C-C-C-G, OR = 0.634; G-A-G-C-C-C-G, OR = 4.047; G-A-T-T-G-C-G, OR = 0.499; G-C-G-T-C-A-G, and OR = 7.299; G-C-T-C-C-A-G, OR = 1.434) haplotypes were significantly associated with pregnancy with chronic hypertension, gestational hypertension, preeclampsia, or preeclampsia superimposed on chronic hypertension and HDP.

Conclusion: These variant MT alleles and their combination patterns may be used as genetic markers for predicting HDP susceptibility.

Impact of dimensions of early adversity on adult health and functioning: A 2-decade, longitudinal study

Recent neurodevelopmental and evolutionary theories offer strong theoretical rationales and some empirical evidence to support the importance of specific dimensions of early adversity. However, studies have often been limited by omission of other adversity dimensions, singular outcomes, and short follow up durations. 1,420 participants in the community, Great Smoky Mountains Study, were assessed up to eight times between age 9 and 16 for four dimensions of early adversity: Threat, Material Deprivation, Unpredictability, and Loss (as well as a Cumulative Adversity measure). Participants were followed up to four times in adulthood (ages 19, 21, 25, and 30) to measure psychiatric disorders, substance disorder, and "real-world" functioning. Every childhood adversity dimension was associated with multiple adult psychiatric, substance, or functional outcomes when tested simultaneously in a multivariable analysis that accounted for other childhood adversities. There was evidence of differential impact of dimensions of adversity exposure on proximal outcomes (e.g., material deprivation and IQ) and even on distal outcomes (e.g., threat and emotional functioning). There were similar levels of prediction between the best set of individual adversity scales and a single cumulative adversity measure when considering distal outcomes. All dimensions of childhood adversity have lasting, pleiotropic effects, on adult health and functioning, but these dimensions may act via distinct proximal pathways.

Venn Diagrams May Indicate Erroneous Statistical Reasoning in Transcriptomics

A common application of differential expression analysis is finding genes that are differentially expressed upon treatment in only one out of several groups of samples. One of the approaches is to test for significant difference in expression between treatment and control separately in the two groups, and then select genes that show statistical significance in one group only. This approach is then often combined with a gene set enrichment analysis to find pathways and gene sets regulated by treatment in only this group. Here we show that this procedure is statistically incorrect and that the interaction between treatment and group should be tested instead. Moreover, we show that gene set enrichment analysis applied to such incorrectly defined genes group-specific genes may result in misleading artifacts. Due to the presence of false negatives, genes significant in one, but not the other group are enriched in gene sets which correspond to the overall effect of the treatment. Thus, the results appear related to the problem at hand, but do not reflect the group-specific effect of a treatment. A literature search revealed that more than a quarter of papers which used a Venn diagram to illustrate the results of separate differential analysis have also applied this incorrect reasoning.

Intact mitochondrial substrate efflux is essential for prevention of tubular injury in a sex-dependent manner

The importance of healthy mitochondrial function is implicated in the prevention of chronic kidney disease (CKD) and diabetic kidney disease (DKD). Sex differences also play important roles in DKD. Our previous studies revealed that mitochondrial substrate overload (modeled by homozygous deletion of carnitine acetyl-transferase [CrAT]) in proximal tubules causes renal injury. Here, we demonstrate the importance of intact mitochondrial substrate efflux by titrating the amount of overload through the generation of a heterozygous CrAT-KO model (PT-CrATHET mouse). Intriguingly, these animals developed renal injury similarly to their homozygous counterparts. Mitochondria were structurally and functionally impaired in both sexes. Transcriptomic analyses, however, revealed striking sex differences. Male mice shut down fatty acid oxidation and several other metabolism-related pathways. Female mice had a significantly weaker transcriptional response in metabolism, but activation of inflammatory pathways was prominent. Proximal tubular cells from PT-CrATHET mice of both sexes exhibited a shift toward a more glycolytic phenotype, but female mice were still able to oxidize fatty acid-based substrates. Our results demonstrate that maintaining mitochondrial substrate metabolism balance is crucial to satisfying proximal tubular energy demand. Our findings have potentially broad implications, as both the glycolytic shift and the sexual dimorphisms discovered herein offer potentially new modalities for future interventions for treating kidney disease.

The architecture of assisted colonisation in sea turtles: building new populations in a biodiversity crisis

Due to changing environmental conditions, many species will have to migrate or occupy new suitable areas to avoid potential extinction in the current biodiversity crisis. Long-lived animals are especially vulnerable and ex-situ conservation actions can provide solutions through assisted colonisations. However, there is little empirical evidence on the process of founding new populations for such species or the feasibility of assisted colonisations as a viable conservation measure. Here, we combined genetics with reproductive data to study the rise of two wild populations of green turtles (Chelonia mydas) in the Cayman Islands as a possible outcome of a reintroduction program started 50 years ago. We show that both populations are highly related to the captive population but rapidly diverged due to genetic drift. Individuals from the reintroduced populations showed high levels of nest fidelity, within and across nesting seasons, indicating that philopatry may help reinforce the success of new populations. Additionally, we show that reintroduction from captive populations has not undermined the reproductive fitness of first generation individuals. Sea turtle reintroduction programs can, therefore, establish new populations but require scientific evaluation of costs and benefits and should be monitored over time to ensure viability in the long-term.

Empirical evidence on the process of founding new populations for assisted colonisations is limited. This work examined two wild populations of green turtles in the Cayman Islands following a reintroduction program started 50 years ago. They show both populations are highly related to the captive population and that philopatry may reinforce the success of new populations.

A randomized-controlled trial comparing supervised aerobic training to resistance training followed by unsupervised exercise on physical functioning in older breast cancer survivors

INTRODUCTION

This study compared the relative efficacy of aerobic training to resistance training on physical functioning in older breast cancer survivors and determined whether benefits could be maintained by transitioning to unsupervised home-based training.

MATERIALS AND METHODS

Early-stage, post-treatment, older (≥65 years) breast cancer survivors (n = 114; mean age 72 years) were randomized to 12 months of supervised aerobic (n = 37), resistance (n = 39) or stretching (active control; n = 38) training followed by 6 months of unsupervised home-based training. Outcomes included aerobic capacity by 6-min walk distance (6MWD; m), maximal upper and lower body strength (1-repetition maximum; kg); physical function by short physical performance battery (SPPB), SF-36 and Late Life Function and Disability Instruments.

RESULTS

Over 12-months of supervised exercise, all groups improved in muscle strength and SPPB scores, but resistance trained women also improved 6MWD. Improvements in upper and lower body strength in the resistance group were significantly greater than those in the stretching control (+2.5 kg vs. +1.8 kg; p = 0.05) and aerobic groups (+8.3 kg vs +2.7 kg; p = 0.047), respectively, with trends for greater improvements in 6MWD (+57.9 m vs. +22.5 m; p = 0.057) and self-report physical function (+4.8 vs. -4.4; 0.066) in resistance trained women versus controls. Compared to values at 12 months, there were no changes during unsupervised training in any measure within or between groups, except for self-reported advanced lower extremity function which improved in the resistance group and fell in the aerobic group (+1.3 vs. -3.1; p = 0.043).

DISCUSSION

Supervised exercise can improve strength and physical functioning among older breast cancer survivors. Resistance training may lead to better improvements compared to aerobic or flexibility training, whether in a supervised or unsupervised setting. Clinicaltrials.govNCT00662103.

Altered processing of communication signals in the subcortical auditory sensory pathway in autism

Autism spectrum disorder (ASD) is characterised by social communication difficulties. These difficulties have been mainly explained by cognitive, motivational, and emotional alterations in ASD. The communication difficulties could, however, also be associated with altered sensory processing of communication signals. Here, we assessed the functional integrity of auditory sensory pathway nuclei in ASD in three independent functional magnetic resonance imaging experiments. We focused on two aspects of auditory communication that are impaired in ASD: voice identity perception, and recognising speech‐in‐noise. We found reduced processing in adults with ASD as compared to typically developed control groups (pairwise matched on sex, age, and full‐scale IQ) in the central midbrain structure of the auditory pathway (inferior colliculus [IC]). The right IC responded less in the ASD as compared to the control group for voice identity, in contrast to speech recognition. The right IC also responded less in the ASD as compared to the control group when passively listening to vocal in contrast to non‐vocal sounds. Within the control group, the left and right IC responded more when recognising speech‐in‐noise as compared to when recognising speech without additional noise. In the ASD group, this was only the case in the left, but not the right IC. The results show that communication signal processing in ASD is associated with reduced subcortical sensory functioning in the midbrain. The results highlight the importance of considering sensory processing alterations in explaining communication difficulties, which are at the core of ASD.

Relating Global and Local Connectome Changes to Dementia and Targeted Gene Expression in Alzheimer's Disease

Networks are present in many aspects of our lives, and networks in neuroscience have recently gained much attention leading to novel representations of brain connectivity. The integration of neuroimaging characteristics and genetics data allows a better understanding of the effects of the gene expression on brain structural and functional connections. The current work uses whole-brain tractography in a longitudinal setting, and by measuring the brain structural connectivity changes studies the neurodegeneration of Alzheimer's disease. This is accomplished by examining the effect of targeted genetic risk factors on the most common local and global brain connectivity measures. Furthermore, we examined the extent to which Clinical Dementia Rating relates to brain connections longitudinally, as well as to gene expression. For instance, here we show that the expression of PLAU gene increases the change over time in betweenness centrality related to the fusiform gyrus. We also show that the betweenness centrality metric impact dementia-related changes in distinct brain regions. Our findings provide insights into the complex longitudinal interplay between genetics and brain characteristics and highlight the role of Alzheimer's genetic risk factors in the estimation of regional brain connectivity alterations.

A metabolome-wide association study of in utero metal and trace element exposures with cord blood metabolome profile: Findings from the Boston Birth Cohort

BACKGROUND

Exposure to metals lead (Pb), mercury (Hg), and cadmium (Cd) and trace elements selenium (Se) and manganese (Mn) has been linked to the developmental origins of cardiometabolic diseases, but the mechanisms are not well-understood.

OBJECTIVE

Conduct a metabolome-wide association study to understand how in utero exposure to Pb, Hg, Cd, Se, and Mn affects the metabolic programming of fetuses.

METHODS

We used data from the Boston Birth Cohort, which enrolled mother-child pairs from Boston, MA. We measured metals and trace elements in maternal red blood cells (RBCs) collected 24-72 h after delivery, and metabolites in cord blood collected at birth. We used multivariable linear regression to examine associations of metals and trace elements with metabolites and Bonferroni correction to account for multiple comparisons. We assessed non-linear associations of metals and trace elements with metabolites using restricted cubic spline plots.

RESULTS

This analysis included 670 mother-child pairs (57% non-Hispanic Black and 24% Hispanic). After Bonferroni correction, there were 25 cord metabolites associated with at least one of the metals or trace elements. Pb was negatively associated with the xenobiotic piperine, Cd was positively associated with xenobiotics cotinine and hydroxycotinine, and Hg was associated with 8 lipid metabolites (in both directions). Se and Mn shared associations with 6 metabolites (in both directions), which mostly included nucleotides and amino acids; Se was additionally associated with 7 metabolites (mostly amino acids, nucleotides, and carnitines) and Mn was additionally associated with C36:4 hydroxy phosphatidylcholine. Restricted cubic spline plots showed that most associations were linear.

DISCUSSION

Maternal RBC metal and trace element concentrations were associated in a dose-dependent fashion with cord blood metabolites. What remains to be determined is whether these metals- and trace elements-associated changes in cord metabolites can influence a child's risk of cardiometabolic diseases.

Exploring predictors of and barriers to online prostate cancer community use: A cross-sectional survey of users and non-users

OBJECTIVE

Prostate cancer survivors are increasingly turning to online communities for support. This study explored predictors of and barriers to use.

METHODS

A prospective survey of 141 Australian prostate cancer survivors assessed sociodemographic, clinical, psychosocial, and attitudinal characteristics associated with intention to use, and subsequent use of online communities.

RESULTS

The sample was divided into current, past, and non-user groups. Current users reported more intent to use online communities and had higher levels of social support. Current and past users, and their close contacts, held a more positive attitude towards use. Non-users experienced more barriers to use, fewer life impacts due to health changes, and were more likely to live in rural or remote regions. According to current users online prostate cancer communities are too informal, to past users they are too time intensive, and non-users believe they are too shallow. The most critical barriers to use were finding a suitable community, time to use them, and being capable of talking about or articulating their illness on the Internet. While these forums allow men to share experiences, gain recognition and understanding, and receive information, they may lead men to becoming too preoccupied with their illness and feeling more concerned about the consequences of their disease.

CONCLUSION

Improving attitudes towards online communities and reducing barriers to use may help better encourage men with unmet supportive care needs to seek help from these groups. Future research exploring supporter attitudes towards use and explicating how men are supported online is needed.

Are all threats equal? Associations of childhood exposure to physical attack versus threatened violence with preadolescent brain structure

Background

Neurodevelopmental studies of childhood adversity often define threatening experiences as those involving harm or the threat of harm. Whether effects differ between experiences involving harm (“physical attack”) versus the threat of harm alone (“threatened violence”) remains underexplored. We hypothesized that while both types of experiences would be associated with smaller preadolescent global and corticolimbic brain volumes, associations with physical attack would be greater.

Methods

Generation R Study researchers (the Netherlands) acquired T1-weighted scans from 2905 preadolescent children, computed brain volumes using FreeSurfer, and asked mothers whether their children ever experienced physical attack (n = 202) or threatened violence (n = 335). Using standardized global (cortical, subcortical, white matter) and corticolimbic (amygdala, hippocampus, anterior cingulate cortex, orbitofrontal cortex) volumes, we fit confounder-adjusted models.

Results

Physical attack was associated with smaller global volumes (β_cortical=−0.14; 95% CI: −0.26, −0.02); β_{white matter}= −0.16; 95% CI: − 0.28, − 0.03) and possibly some corticolimbic volumes, e.g., β_{amygdala/ICV-adjusted}= −0.10 (95% CI: −0.21, 0.01). We found no evidence of associations between threatened violence and smaller volumes in any outcome; instead, such estimates were small, highly uncertain, and positive in direction.

Conclusions

Experiences of physical attack and threatened violence may have quantitively different neurodevelopmental effects. Thus, differences between types of threatening experiences may be neurodevelopmentally salient.

GWAS for genetics of complex quantitative traits: Genome to pangenome and SNPs to SVs and k-mers

The development of improved methods for genome-wide association studies (GWAS) for genetics of quantitative traits has been an active area of research during the last 25 years. This activity initially started with the use of mixed linear model (MLM), which was variously modified. During the last decade, however, with the availability of high throughput next generation sequencing (NGS) technology, development and use of pangenomes and novel markers including structural variations (SVs) and k-mers for GWAS has taken over as a new thrust area of research. Pangenomes and SVs are now available in humans, livestock, and a number of plant species, so that these resources along with k-mers are being used in GWAS for exploring additional genetic variation that was hitherto not available for analysis. These developments have resulted in significant improvement in GWAS methodology for detection of marker-trait associations (MTAs) that are relevant to human healthcare and crop improvement.

Temporal analysis shows relaxed genetic erosion following improved stocking practices in a subarctic transnational brown trout population

Maintaining standing genetic variation is a challenge in human-dominated landscapes. We used genetic (i.e., 16 short tandem repeats) and morphological (i.e., length and weight) measurements of 593 contemporary and historical brown trout (Salmo trutta) samples to study fine-scale and short-term impacts of different management practices. These had changed from traditional breeding practices, using the same broodstock for several years, to modern breeding practices, including annual broodstock replacement, in the transnational subarctic Pasvik River. Using population genetic structure analyses (i.e., Bayesian assignment tests, DAPCs, and PCAs), four historical genetic clusters (E2001A-D), likely representing family lineages resulting from different crosses, were found in zone E. These groups were characterized by consistently lower genetic diversity, higher within-group relatedness, lower effective population size, and significantly smaller body size than contemporary stocked (E2001E) and wild fish (E2001F). However, even current breeding practices are insufficient to prevent genetic diversity loss and morphological changes as demonstrated by on average smaller body sizes and recent genetic bottleneck signatures in the modern breeding stock compared to wild fish. Conservation management must evaluate breeding protocols for stocking programs and assess if these can preserve remaining natural genetic diversity and morphology in brown trout for long-term preservation of freshwater fauna.

Dealing with false positive risk as an indicator of misperceived effectiveness of conservation interventions

As human pressures on the environment continue to spread and intensify, effective conservation interventions are direly needed to prevent threats, reduce conflicts, and recover populations and landscapes in a liaison between science and conservation. It is practically important to discriminate between true and false (or misperceived) effectiveness of interventions as false perceptions may shape a wrong conservation agenda and lead to inappropriate decisions and management actions. This study used the false positive risk (FPR) to estimate the rates of misperceived effectiveness of electric fences (overstated if reported as effective but actually ineffective based on FPR; understated otherwise), explain their causes and propose recommendations on how to improve the representation of true effectiveness. Electric fences are widely applied to reduce damage to fenced assets, such as livestock and beehives, or increase survival of fenced populations. The analysis of 109 cases from 50 publications has shown that the effectiveness of electric fences was overstated in at least one-third of cases, from 31.8% at FPR = 0.2 (20% risk) to 51.1% at FPR = 0.05 (5% risk, true effectiveness). In contrast, understatement reduced from 23.8% to 9.5% at these thresholds of FPR. This means that truly effective applications of electric fences were only 48.9% of all cases reported as effective, but truly ineffective cases were 90.5%, implying that the effectiveness of electric fences was heavily overstated. The main reasons of this bias were the lack of statistical testing or improper reporting of test results (63.3% of cases) and interpretation of marginally significant results (p < 0.05, p < 0.1 and p around 0.05) as indicators of effectiveness (10.1%). In conclusion, FPR is an important tool for estimating true effectiveness of conservation interventions and its application is highly recommended to disentangle true and false effectiveness for planning appropriate conservation actions. Researchers are encouraged to calculate FPR, publish its constituent statistics (especially treatment and control sample sizes) and explicitly provide test results with p values. It is suggested to call the effectiveness “true” if FPR < 0.05, “suggestive” if 0.05 ≤ FPR < 0.2 and “false” if FPR ≥ 0.2.

Peripubertal serum levels of dioxins, furans and PCBs in a cohort of Russian boys: can empirical grouping methods yield meaningful exposure variables?

BACKGROUND

Dioxins, furans and polychlorinated biphenyls (PCBs) are endocrine disruptors with half-lives of months to years in humans. Peripubertal exposure to these chemicals may disrupt pubertal timing. Biomarker exposure metrics like the sum of non-dioxin-like PCBs in serum (∑NDL-PCBs) involve chemicals with different hypothetical effects. Empirical exposure metrics represent an alternative that requires no knowledge of biological mechanisms.

METHODS

From 2003 to 2005, 516 Russian boys aged 8-9 residing near a plant that historically produced organochlorine pesticides were enrolled in the Russian Children's Study. At enrollment, blood was collected for measurement of organochlorine chemicals by the Centers for Disease Control and Prevention (CDC). Variable cluster analysis was used to empirically group serum levels of 45 dioxins, furans and PCBs into eight cluster scores. These scores were compared to the sum of dioxin-like toxic equivalents (∑TEQs) and ∑NDL-PCBs using Spearman correlation coefficients.

RESULTS

Clustering appeared to reflect number and position of chlorine atoms. Clusters 4, 7 and 1 contained, respectively, tri/tetra-, tetra/penta-, and hexa/hepta-chlorinated PCBs with chlorines at the 4,4' positions. Clusters 2, 8 and 5 contained, respectively, tetra-to hexa-, hexa/hepta-, and hepta/octa-chlorinated PCBs with chlorines at the 2,2' positions. ∑NDL-PCBs were highly correlated with 4,4'-chlorinated clusters 1 and 7 (Spearman's ρ = 0.8) and less so with all other clusters (Spearman's ρ = 0.4-0.5).

CONCLUSIONS

In this cohort of Russian boys, baseline serum dioxins, furans and PCBs seemed to cluster by chlorination pattern, possibly reflecting shared persistence, metabolism or source of exposure. The widely used measure ∑NDL-PCB seemed most representative of 4,4'-chlorinated PCBs.

Single-trait, multi-locus and multi-trait GWAS using four different models for yield traits in bread wheat

A genome-wide association study (GWAS) for 10 yield and yield component traits was conducted using an association panel comprising 225 diverse spring wheat genotypes. The panel was genotyped using 10,904 SNPs and evaluated for three years (2016-2019), which constituted three environments (E1, E2 and E3). Heritability for different traits ranged from 29.21 to 97.69%. Marker-trait associations (MTAs) were identified for each trait using data from each environment separately and also using BLUP values. Four different models were used, which included three single trait models (CMLM, FarmCPU, SUPER) and one multi-trait model (mvLMM). Hundreds of MTAs were obtained using each model, but after Bonferroni correction, only 6 MTAs for 3 traits were available using CMLM, and 21 MTAs for 4 traits were available using FarmCPU; none of the 525 MTAs obtained using SUPER could qualify after Bonferroni correction. Using BLUP, 20 MTAs were available, five of which also figured among MTAs identified for individual environments. Using mvLMM model, after Bonferroni correction, 38 multi-trait MTAs, for 15 different trait combinations were available. Epistatic interactions involving 28 pairs of MTAs were also available for seven of the 10 traits; no epistatic interactions were available for GNPS, PH, and BYPP. As many as 164 putative candidate genes (CGs) were identified using all the 50 MTAs (CMLM, 3; FarmCPU, 9; mvLMM, 6, epistasis, 21 and BLUP, 11 MTAs), which ranged from 20 (CMLM) to 66 (epistasis) CGs. In-silico expression analysis of CGs was also conducted in different tissues at different developmental stages. The information generated through the present study proved useful for developing a better understanding of the genetics of each of the 10 traits; the study also provided novel markers for marker-assisted selection (MAS) to be utilized for the development of wheat cultivars with improved agronomic traits.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-021-01240-1.

Prevalence of Gastrointestinal Symptoms, Severity of Dysphagia, and Their Correlation with Severity of Amyotrophic Lateral Sclerosis in a Mexican Cohort

OBJECTIVES

Our study aimed to identify the prevalence and severity of gastrointestinal (GI) symptoms and dysphagia in patients with amyotrophic lateral sclerosis (ALS) and to assess whether a correlation exists between these symptoms and the severity of ALS progression.

METHODS

The presence and severity of GI symptoms and dysphagia were identified by means of the Gastrointestinal Symptom Rating Scale (GSRS) and the Functional Outcome Swallowing Scale (FOSS). The Revised ALS Functional Rating Scale (ALSFRS-R) was utilized to determine the severity of ALS. Analysis of data was performed with Spearman correlations in semi-qualitative variables of clinical scales. ALSFRS-R scores were divided into 2 categories: those with mild to moderate ALS (≥40-30 points) and patients with moderate to advanced ALS (29-≤20 points).

RESULTS

We studied 43 patients with definite ALS. The most frequent GI symptoms were constipation (60.5%), rectal tenesmus (57.5%), hard stools (55.0%), and borborygmus (42.5%). The moderate to advanced ALS stage was correlated with constipation (r = 0.334; p = 0.028), acid regurgitation (r = 0.384; p = 0.013), eructation (r = 0.334; p = 0.032), rectal tenesmus (r = 0.498; p = 0.001), and functional dysphagia (r = 0.656; p = <0.001).

CONCLUSIONS

Early detection of these GI symptoms can guide timely therapeutic decisions to avoid weight loss, a predictor for worse prognosis. This study highlights the relevance of the detection of these symptoms in ALS patients who score ≤29 points in the ALSFRS-R scale to establish an appropriate treatment, prevent systemic complications, provide more comfort, and improve quality of life.

A Clinical Trial for the Identification of Metabolic Biomarkers in Hashimoto’s Thyroiditis and in Psoriasis: Study Protocol

Hashimoto’s thyroiditis and psoriasis are inflammatory disorders that significantly impact patients’ quality of life, stressing the need for novel biomarkers of early diagnosis. This randomized clinical trial (NCT04693936) aims to identify Hashimoto’s thyroiditis’ and psoriasis’ metabolic biomarkers and to investigate the effect of environmental factors on the disease-related metabolic imprint and quality of life. Patients with Hashimoto’s thyroiditis, patients with psoriasis, and healthy individuals aged 18–60 will be recruited, enrolled according to eligibility criteria (medical history, clinical thyroid markers and the PASI score) and randomized to two groups. The intervention group will receive a combination of nutraceuticals for 6 months as part of a Mediterranean diet, and the control group will follow their usual diet. Data will be collected at baseline and the end of the study, including metabolite levels, lifestyle and anthropometric measurements, adherence to the Mediterranean diet (through the Mediterranean Diet Score) and disease-specific quality of life (through the Thyroid Patient Report Outcome for Hashimoto’s group, and the Dermatology Life Quality Index for the psoriasis group). This study will investigate metabolic biomarkers and related changes in Hashimoto’s thyroiditis and psoriasis and evaluate the association of metabolic changes with dietary factors and quality of life.

Comparing multiple comparisons: practical guidance for choosing the best multiple comparisons test

Multiple comparisons tests (MCTs) include the statistical tests used to compare groups (treatments) often following a significant effect reported in one of many types of linear models. Due to a variety of data and statistical considerations, several dozen MCTs have been developed over the decades, with tests ranging from very similar to each other to very different from each other. Many scientific disciplines use MCTs, including >40,000 reports of their use in ecological journals in the last 60 years. Despite the ubiquity and utility of MCTs, several issues remain in terms of their correct use and reporting. In this study, we evaluated 17 different MCTs. We first reviewed the published literature for recommendations on their correct use. Second, we created a simulation that evaluated the performance of nine common MCTs. The tests examined in the simulation were those that often overlapped in usage, meaning the selection of the test based on fit to the data is not unique and that the simulations could inform the selection of one or more tests when a researcher has choices. Based on the literature review and recommendations: planned comparisons are overwhelmingly recommended over unplanned comparisons, for planned non-parametric comparisons the Mann-Whitney-Wilcoxon U test is recommended, Scheffé’s S test is recommended for any linear combination of (unplanned) means, Tukey’s HSD and the Bonferroni or the Dunn-Sidak tests are recommended for pairwise comparisons of groups, and that many other tests exist for particular types of data. All code and data used to generate this paper are available at: https://github.com/stevemidway/MultipleComparisons.

Environment-Wide Association Study (En WAS) of Prenatal and Perinatal Factors Associated With Autistic Traits: A Population-Based Study

A combination of genetic and environmental factors contributes to the origins of autism spectrum disorder (ASD). While a number of studies have described specific environmental factors associating with emerging ASD, studies that compare and contrast multiple environmental factors in the same study are lacking. Thus, the goal of this study was to perform a prospective, data-driven environmental-wide association study of pre- and perinatal factors associated with the later development of autistic symptoms in childhood. The participants included 3891 6-year-old children from a birth cohort with pre- and perinatal data. Autistic symptoms were measured using the Social Responsiveness Scale in all children. Prior to any analyses, the sample was randomly split into a discovery set (2920) and a test set (921). Multiple linear regression analyses were performed for each of 920 variables, correcting for six of the most common covariates in epidemiological studies. We found 111 different pre- and perinatal factors associated with autistic traits during childhood. In secondary analyses where we controlled for parental psychopathology, 23 variables in the domains of family and interpersonal relationships were associated with the development of autistic symptoms during childhood. In conclusion, a data-driven approach was used to identify a number of pre- and perinatal risk factors associating with higher childhood autistic symptoms. These factors include measures of parental psychopathology and family and interpersonal relationships. These measures could potentially be used for the early identification of those at increased risk to develop ASD. LAY SUMMARY: A combination of genetic and environmental factors contributes to the development of autism spectrum disorder (ASD). Each environmental factor may affect the risk of ASD. In a study on 6-year-old children, a number of pre- and perinatal risk factors were identified that are associated with autistic symptoms in childhood. These factors include measures of parental psychopathology and family and interpersonal relationships. These variables could potentially serve as markers to identify those at increased risk to develop ASD or autistic symptoms. Autism Res 2020, 13: 1582-1600. © 2020 International Society for Autism Research, Wiley Periodicals, Inc.

Springtail phylogeography highlights biosecurity risks of repeated invasions and intraregional transfers among remote islands

Human-mediated transport of species outside their natural range is a rapidly growing threat to biodiversity, particularly for island ecosystems that have evolved in isolation. The genetic structure underpinning island populations will largely determine their response to increased transport and thus help to inform biosecurity management. However, this information is severely lacking for some groups, such as the soil fauna. We therefore analysed the phylogeographic structure of an indigenous and an invasive springtail species (Collembola: Poduromorpha), each distributed across multiple remote sub-Antarctic islands, where human activity is currently intensifying. For both species, we generated a genome-wide SNP data set and additionally analysed all available COI barcodes. Genetic differentiation in the indigenous springtail Tullbergia bisetosa is substantial among (and, to a lesser degree, within) islands, reflecting low dispersal and historic population fragmentation, while COI patterns reveal ancestral signatures of postglacial recolonization. This pronounced geographic structure demonstrates the key role of allopatric divergence in shaping the region's diversity and highlights the vulnerability of indigenous populations to genetic homogenization via human transport. For the invasive species Hypogastrura viatica, nuclear genetic structure is much less apparent, particularly for islands linked by regular shipping, while diverged COI haplotypes indicate multiple independent introductions to each island. Thus, human transport has likely facilitated this species' persistence since its initial colonization, through the ongoing introduction and inter-island spread of genetic variation. These findings highlight the different evolutionary consequences of human transport for indigenous and invasive soil species. Crucially, both outcomes demonstrate the need for improved intraregional biosecurity among remote island systems, where the policy focus to date has been on external introductions.

A comparison of random-field-theory and false-discovery-rate inference results in the analysis of registered one-dimensional biomechanical datasets

Background

The inflation of falsely rejected hypotheses associated with multiple hypothesis testing is seen as a threat to the knowledge base in the scientific literature. One of the most recently developed statistical constructs to deal with this problem is the false discovery rate (FDR), which aims to control the proportion of the falsely rejected null hypotheses among those that are rejected. FDR has been applied to a variety of problems, especially for the analysis of 3-D brain images in the field of Neuroimaging, where the predominant form of statistical inference involves the more conventional control of false positives, through Gaussian random field theory (RFT). In this study we considered FDR and RFT as alternative methods for handling multiple testing in the analysis of 1-D continuum data. The field of biomechanics has recently adopted RFT, but to our knowledge FDR has not previously been used to analyze 1-D biomechanical data, nor has there been a consideration of how FDR vs. RFT can affect biomechanical interpretations.

Methods

We reanalyzed a variety of publicly available experimental datasets to understand the characteristics which contribute to the convergence and divergence of RFT and FDR results. We also ran a variety of numerical simulations involving smooth, random Gaussian 1-D data, with and without true signal, to provide complementary explanations for the experimental results.

Results

Our results suggest that RFT and FDR thresholds (the critical test statistic value used to judge statistical significance) were qualitatively identical for many experimental datasets, but were highly dissimilar for others, involving non-trivial changes in data interpretation. Simulation results clarified that RFT and FDR thresholds converge as the true signal weakens and diverge when the signal is broad in terms of the proportion of the continuum size it occupies. Results also showed that, while sample size affected the relation between RFT and FDR results for small sample sizes (<15), this relation was stable for larger sample sizes, wherein only the nature of the true signal was important.

Discussion

RFT and FDR thresholds are both computationally efficient because both are parametric, but only FDR has the ability to adapt to the signal features of particular datasets, wherein the threshold lowers with signal strength for a gain in sensitivity. Additional advantages and limitations of these two techniques as discussed further. This article is accompanied by freely available software for implementing FDR analyses involving 1-D data and scripts to replicate our results.