Interval-wise testing for functional data

Electrocortical activity associated with movement-related fear: a methodological exploration of a threat-conditioning paradigm involving destabilising perturbations during quiet standing

Musculoskeletal trauma often leads to lasting psychological impacts stemming from concerns of future injuries. Often referred to as kinesiophobia or re-injury anxiety, such concerns have been shown to hinder return to physical activity and are believed to increase the risk for secondary injuries. Screening for re-injury anxiety is currently restricted to subjective questionnaires, which are prone to self-report bias. We introduce a novel approach to objectively identify electrocortical activity associated with the threat of destabilising perturbations. We aimed to explore its feasibility among non-injured persons, with potential future implementation for screening of re-injury anxiety. Twenty-three participants stood blindfolded on a translational balance perturbation platform. Consecutive auditory stimuli were provided as low (neutral stimulus [CS-]) or high (conditioned stimulus [CS+]) tones. For the main experimental protocol (Protocol I), half of the high tones were followed by a perturbation in one of eight unpredictable directions. A separate validation protocol (Protocol II) requiring voluntary squatting without perturbations was performed with 12 participants. Event-related potentials (ERP) were computed from electroencephalography recordings and significant time-domain components were detected using an interval-wise testing procedure. High-amplitude early contingent negative variation (CNV) waves were significantly greater for CS+ compared with CS- trials in all channels for Protocol I (> 521-800ms), most prominently over frontal and central midline locations (P ≤ 0.001). For Protocol II, shorter frontal ERP components were observed (541-609ms). Our test paradigm revealed electrocortical activation possibly associated with movement-related fear. Exploring the discriminative validity of the paradigm among individuals with and without self-reported re-injury anxiety is warranted.

Inverse set estimation and inversion of simultaneous confidence intervals

Motivated by the questions of risk assessment in climatology (temperature change in North America) and medicine (impact of statin usage and coronavirus disease 2019 on hospitalized patients), we address the problem of estimating the set in the domain of a function whose image equals a predefined subset of the real line. Existing methods require strict assumptions. We generalize the estimation of such sets to dense and nondense domains with protection against inflated Type I error in exploratory data analysis. This is achieved by proving that confidence sets of multiple upper, lower, or interval sets can be simultaneously constructed with the desired confidence nonasymptotically through inverting simultaneous confidence intervals. Nonparametric bootstrap algorithm and code are provided.

Whole-body kinematics of squats two decades following anterior cruciate ligament injury

BACKGROUND

Kinematic studies suggest that injury of the anterior cruciate ligament (ACL) leads to long-lasting movement deficits or compensations to unload the injured knee. This study evaluated lower body kinematics during squats in individuals who suffered unilateral ACL-injury more than 20 years ago.

METHOD

Using motion capture, we compared maximum squat depth, time to complete the squat task, detailed kinematics, estimated kinetic-chain joint moments 0- 80° knee flexion, and weight distribution between legs across three groups with (ACLR, n = 27) and without ACL-reconstructive surgery (ACLPT, physiotherapy only, n = 28), and age-matched non-injured asymptomatic Controls (n = 31, average age across groups 47 years).

RESULTS

ACLPT demonstrated significantly reduced squat depth compared to Controls (p = 0.004), whereas ACLR performed similarly to Controls (p = 1.000). Other outcome variables were comparable between groups. All participants nevertheless demonstrated asymmetric weight distribution between legs but without systematic unloading of the injured side in the ACLgroups.

CONCLUSION

Expected compensatory strategies were not found in the ACL-groups, while poorer squat performance in the ACL-deficient group may depend on pure knee-joint mechanics, or lifestyle factors attributed to a less stable knee decades after ACL-injury.

Strategies for knee stabilising and pivot-shift avoidance in a step-down and cross-over task observed sub-acutely after anterior cruciate ligament reconstruction

BACKGROUND

Individuals with a recent anterior cruciate ligament reconstruction may demonstrate an altered movement strategy for protecting the knee and maintaining stability. Altered knee movement might lead to abnormal intra-articular load, potentially contributing to early knee osteoarthritis onset. A protective strategy may be particularly evident during active tasks that induce a pivot-shift manoeuvre, such as a step-down and cross-over task. In this study, we investigated whether knee joint mechanics and muscle activity differed between participants early (∼3 months) following reconstruction (n = 35) to uninjured controls (n = 35) during a step-down and cross-over task with a 45° change-of-direction.

METHODS

We used motion capture, force plates and surface electromyography to compare time-normalised curves of sagittal and transverse-plane knee mechanics and muscle activity during the cross-over phase between groups using functional t-tests. We also compared knee mechanics between sides within the injured group and compared discrete outcomes describing the cross-over phase between groups.

FINDINGS

Compared to controls, the injured participants had greater knee flexion angle and moment, lower internal rotation moment, more preparatory foot rotation of the pivoting leg, a smaller cross-over angle, and a longer cross-over phase for both the injured and uninjured sides. The injured leg also had greater biceps femoris and vastus medialis muscle activity compared to controls and different knee mechanics than the uninjured leg.

INTERPRETATION

Individuals with anterior cruciate ligament reconstruction showed a knee-stabilising and pivot-shift avoidance strategy for both legs early in rehabilitation. These results may reflect an altered motor representation and motivate considerations early in rehabilitation.

Asymmetric loading strategies during squats following anterior cruciate ligament reconstruction: A longitudinal investigation with curve analyses throughout and after rehabilitation

Investigations of kinetic asymmetries during bilateral squats following anterior cruciate ligament reconstruction (ACLR) are limited to mainly cross-sectional studies and discrete value data extracted at specific knee angles. We assessed loading asymmetries during squats longitudinally throughout rehabilitation using curve analysis and compared patient-reported outcome measures (PROMs) between those with and without asymmetry. Bodyweight squats were performed by 24 individuals (13 females) post-ACLR on three occasions: (1) Early 2.9 (1.1) months; (2) Mid 8.8 (3.1) months; (3) at Return to Sport (RTS) 13.1 (3.6) months; and 29 asymptomatic controls (22 females) once. Time-normalized between-leg asymmetry curves of sagittal plane hip, knee, and ankle moments and vertical ground reaction forces were compared using functional data analysis methods. Individual asymmetrical loading for ACLR was classified when exceeding the 95% confidence interval of controls during ≥50% of the squat. At Early, ACLR had greater asymmetry than controls for knee (15%-100% eccentric phase; 0%-100% concentric) and ankle flexion moments (56%-65% concentric). At Mid, ACLR had greater asymmetry for knee (41%-72% eccentric) and ankle flexion moments (56%-69% concentric). No between-group differences were found at RTS. From Early to RTS, ACLR reduced asymmetry for hip (21%-46% eccentric), knee (27%-58% concentric), and ankle flexion moments (21%-57% eccentric). At Early, 11/24 underloaded their ACLR knee and 1 overloaded compared with controls. At RTS, 4 underloaded and 6 overloaded. No differences in PROMs were found based on loading asymmetry. Beyond the early phase of rehabilitation from ACLR, individual-level analyses are required to reveal differing loading strategies during bilateral squats.

Imaging-based representation and stratification of intra-tumor heterogeneity via tree-edit distance

Personalized medicine is the future of medical practice. In oncology, tumor heterogeneity assessment represents a pivotal step for effective treatment planning and prognosis prediction. Despite new procedures for DNA sequencing and analysis, non-invasive methods for tumor characterization are needed to impact on daily routine. On purpose, imaging texture analysis is rapidly scaling, holding the promise to surrogate histopathological assessment of tumor lesions. In this work, we propose a tree-based representation strategy for describing intra-tumor heterogeneity of patients affected by metastatic cancer. We leverage radiomics information extracted from PET/CT imaging and we provide an exhaustive and easily readable summary of the disease spreading. We exploit this novel patient representation to perform cancer subtyping according to hierarchical clustering technique. To this purpose, a new heterogeneity-based distance between trees is defined and applied to a case study of prostate cancer. Clusters interpretation is explored in terms of concordance with severity status, tumor burden and biological characteristics. Results are promising, as the proposed method outperforms current literature approaches. Ultimately, the proposed method draws a general analysis framework that would allow to extract knowledge from daily acquired imaging data of patients and provide insights for effective treatment planning.

The lock-down effects of COVID-19 on the air pollution indices in Iran and its neighbors

Introduction

The COVID-19 restrictions have a lot of various peripheral negative and positive effects, like economic shocks and decreasing air pollution, respectively. Many studies showed NO2 reduction in most parts of the world.

Methods

Iran and its land and maritime neighbors have about 7.4% of the world population and 6.3% and 5.8% of World COVID-19 cases and deaths, respectively. The air pollution indices of them such as CH4 (Methane), CO_1 (CO), H2O (Water), HCHO (Tropospheric Atmospheric Formaldehyde), NO2 (Nitrogen oxides), O3 (ozone), SO2 (Sulfur Dioxide), UVAI_AAI [UV Aerosol Index (UVAI)/Absorbing Aerosol Index (AAI)] are studied from the First quarter of 2019 to the fourth quarter of 2021 with Copernicus Sentinel 5 Precursor (S5P) satellite data set from Google Earth Engine. The outliers are detected based on the depth functions. We use a two-sample t test, Wilcoxon test, and interval-wise testing for functional data to control the familywise error rate.

Result

The adjusted p value comparison between Q2 of 2019 and Q2 of 2020 in NO2 for almost all countries is statistically significant except Iraq, UAE, Bahrain, Qatar, and Kuwait. But, the CO and HCHO are not statistically significant in any country. Although CH4, O3, and UVAI_AAI are statistically significant for some countries. In the Q2 comparison for NO2 between 2020 and 2021, only Iran, Armenia, Turkey, UAE, and Saudi Arabia are statistically significant. However, Ch4 is statistically significant for all countries except Azerbaijan.

Conclusions

The comparison with and without adjusted p values declares the decreases in some air pollution in these countries.

Supplementary Information

The online version contains supplementary material available at 10.1007/s40808-022-01528-x.

Atypical Lower Limb Mechanics During Weight Acceptance of Stair Descent at Different Time Frames After Anterior Cruciate Ligament Reconstruction

BACKGROUND

An anterior cruciate ligament (ACL) rupture may result in poor sensorimotor knee control and, consequentially, adapted movement strategies to help maintain knee stability. Whether patients display atypical lower limb mechanics during weight acceptance of stair descent at different time frames after ACL reconstruction (ACLR) is unknown.

PURPOSE

To compare the presence of atypical lower limb mechanics during the weight acceptance phase of stair descent among athletes at early, middle, and late time frames after unilateral ACLR.

STUDY DESIGN

Controlled laboratory study.

METHODS

A total of 49 athletes with ACLR were classified into 3 groups according to time after ACLR-early (<6 months; n = 17), middle (6-18 months; n = 16), and late (>18 months; n = 16)-and compared with asymptomatic athletes (control; n = 18). Sagittal plane hip, knee, and ankle angles; angular velocities; moments; and powers were compared between the ACLR groups' injured and noninjured legs and the control group as well as between legs within groups using functional data analysis methods.

RESULTS

All 3 ACLR groups showed greater knee flexion angles and moments than the control group for injured and noninjured legs. For the other outcomes, the early group had, compared with the control group, less hip power absorption, more knee power absorption, lower ankle plantarflexion angle, lower ankle dorsiflexion moment, and less ankle power absorption for the injured leg and more knee power absorption and higher vertical ground reaction force for the noninjured leg. In addition, the late group showed differences from the control group for the injured leg revealing more knee power absorption and lower ankle plantarflexion angle. Only the early group took a longer time than the control group to complete weight acceptance and demonstrated asymmetry for multiple outcomes.

CONCLUSION

Athletes with different time frames after ACLR revealed atypically large knee angles and moments during weight acceptance of stair descent for both the injured and the noninjured legs. These findings may express a chronically adapted strategy to increase knee control. In contrast, atypical hip and ankle mechanics seem restricted to an early time frame after ACLR.

CLINICAL RELEVANCE

Rehabilitation after ACLR should include early training in controlling weight acceptance. Including a control group is essential when evaluating movement patterns after ACLR because both legs may be affected.

Angle-specific torque profiles of concentric and eccentric thigh muscle strength 20 years after anterior cruciate ligament injury

Thigh muscle weakness prevails following anterior cruciate ligament (ACL) injury, as usually evaluated by peak concentric quadriceps strength. Assessment throughout the range of motion (ROM), and for antagonists may provide more comprehensive information. We evaluated angle-specific torque profiles and ratios of isokinetic thigh muscle strength in 70 individuals 23 ± 2 years post-ACL injury (44males, 46.9 ± 5.4 years); 33 treated with ACL-reconstruction (ACL-R), and 37 treated only with physiotherapy (ACL-PT), and 33 controls. Quadriceps and hamstrings torques for concentric/eccentric contractions (90°/s) and ratios between hamstrings/quadriceps strength (HQ) were compared between and within groups using inferential functional data methods. The injured ACL-R leg had lower concentric and eccentric quadriceps strength compared to non-injured leg throughout the ROM, and lower concentric (interval 70-79°) and eccentric (64-67°) quadriceps strength compared to controls. The injured ACL-PT leg showed lower eccentric quadriceps strength (53-77°) than non-injured leg and lower concentric (41-79°) and eccentric (52-81°) quadriceps and eccentric hamstrings (30-77°) strength than controls. There were no group differences for HQ-ratios. The injured ACL-R leg had higher HQ-ratio (34-37°) than non-injured leg. Angle-specific torque profiles revealed strength deficits, masked if using only peak values, and seem valuable for ACL-injury rehabilitation.

Domain selection and family-wise error rate for functional data: a unified framework

Functional data are smooth, often continuous, random curves, which can be seen as an extreme case of multivariate data with infinite dimensionality. Just as component-wise inference for multivariate data naturally performs feature selection, subset-wise inference for functional data performs domain selection. In this paper, we present a unified testing framework for domain selection on populations of functional data. In detail, p-values of hypothesis tests performed on point-wise evaluations of functional data are suitably adjusted for providing a control of the family-wise error rate (FWER) over a family of subsets of the domain. We show that several state-of-the-art domain selection methods fit within this framework and differ from each other by the choice of the family over which the control of the FWER is provided. In the existing literature, these families are always defined a priori. In this work, we also propose a novel approach, coined threshold-wise testing, in which the family of subsets is instead built in a data-driven fashion. The method seamlessly generalizes to multidimensional domains in contrast to methods based on a-priori defined families. We provide theoretical results with respect to consistency and control of the FWER for the methods within the unified framework. We illustrate the performance of the methods within the unified framework on simulated and real data examples, and compare their performance with other existing methods. This article is protected by copyright. All rights reserved.

Regional differences in initial labour market conditions and dynamics in lifetime income trajectories

We use longitudinal register data from Sweden to study patterns and dynamics in lifetime income trajectories. We examine divergences in these income trajectories by local economic conditions at labour market entry, in combination with other factors such as gender, education level and socio-economic background. We cannot assume that these relationships are constant over the course of individuals' working lives. Therefore, we use methods from functional data analysis, allowing for a time-varying relationship between income and the explanatory variables. Our results show a large degree of heterogeneity in how lifetime income trajectories develop for different subgroups. We find that, for men, entering the labour market in an urban area is associated with higher cumulative lifetime income, especially later in life. The exception is men with only primary education, for whom those starting their working lives in a large city have lower incomes on average. This divergence increases in size over time. Women who enter into a large urban labour market receive higher lifetime income at all education levels. This relationship is strongest for women with primary education but decreases in strength over time for these women.

Analysis Choices Impact Movement Evaluation: A Multi-Aspect Inferential Method Applied to Kinematic Curves of Vertical Hops in Knee-Injured and Asymptomatic Persons

Three-dimensional human motion analysis provides in-depth understanding in order to optimize sports performance or rehabilitation following disease or injury. Recent developments of statistical methods for functional data allow for novel ways to analyze often complex biomechanical data. Even so, for such methods as well as for traditional well-established statistical methods, the interpretations of the results may be influenced by analysis choices made prior to the analysis. We evaluated the consequences of three such choices when comparing one-leg vertical hop (OLVH) performance in individuals who had ruptured their anterior cruciate ligament (ACL), to that of asymptomatic controls, and also athletes. Kinematic data were analyzed using a statistical approach for functional data, targeting entire curve data. This was done not only for one joint at a time but also for multiple lower limb joints and movement planes simultaneously using a multi-aspect methodology, testing for group differences while also accounting for covariates. We present the results of when an individual representative curve out of three available was either: (1) a mean curve (Mean), (2) a curve from the highest hop (Max), or (3) a curve describing the variability (Var), as a representation of performance stability. We also evaluated choice of sample leg comparison; e.g., ACL-injured leg compared to either the dominant or non-dominant leg of asymptomatic groups. Finally, we explored potential outcome effects of different combinations of included joints. There were slightly more pronounced group differences when using Mean compared to Max, while the specifics of the observed differences depended on the outcome variable. For Var there were less significant group differences. Generally, there were more disparities throughout the hop movement when comparing the injured leg to the dominant leg of controls, resulting in e.g., group differences for trunk and ankle kinematics, for both Mean and Max. When the injured leg was instead compared to the non-dominant leg of controls, there were trunk, hip and knee joint differences. For a more stringent comparison, we suggest considering to compare the injured leg to the non-dominant leg. Finally, the multiple-joint analyses were coherent with the single-joint analyses. The direct effects of analysis choices can be explored interactively by the reader in the Supplementary Material. To summarize, the choices definitively have an impact on the interpretation of a hop test results commonly used in rehabilitation following knee injuries. We therefore strongly recommend well-documented methodological analysis choices with regards to comparisons and representative values of the measures of interests.

Inclination angles of the ankle and head relative to the centre of mass identify gait deviations post-stroke

BACKGROUND

Whole-body movement adjustments during gait are common post-stroke, but comprehensive ways of quantifying and evaluating gait from a whole-body perspective are lacking.

RESEARCH QUESTION

Can novel kinematic variables related to Center of Mass (CoM) position discriminate side asymmetries as well as coordination between the upper and lower body during gait within persons post-stroke and compared to non-disabled controls?

METHODS

Thirty-one persons post-stroke and 41 age-matched non-disabled controls walking at their self-selected speed were recorded by 3D motion capture. The Ankle-CoM Inclination Angle (A-CoMIA) and the Head-CoM Inclination Angle (H-CoMIA) defined the angle between the CoM and the ankle and the head, respectively, in the frontal plane. These angles and their angular velocities were compared between groups, and with regard to motor impairment severity during all phases of the gait cycle (GC) using a functional interval-wise testing analysis suitable for curve data. Upper and lower body coordination was assessed using cross- correlation.

RESULTS

The A-CoMIA was symmetrical between body sides in persons post-stroke but larger compared to controls. The angular velocity of A-CoMIA also differed when compared to controls. The H-CoMIA was consistently asymmetrical in persons post-stroke and larger than in controls throughout the stance phase. There were only minor group differences in the angular velocity of H-CoMIA, with some side asymmetry in persons post-stroke. The A-CoMIA of the non-affected side, and the H- CoMIA, discriminated between persons with more severe impairments compared to those with milder impairments post-stroke. The variables showed strong cross- correlations in both groups.

SIGNIFICANCE

The A-CoMIA and Head-CoMIA discriminated post-stroke gait from non-disabled, as well as motor impairment severity. These variables with the advantageous curve analysis during the entire GC add valuable whole-body information to existing parameters of post-stroke gait analysis through assessment of symmetry and upper and lower body coordination.

Halogen-Mediated Partial Oxidation of Polyvinyl Alcohol for Tissue Engineering Purposes

Partial oxidation of polyvinyl alcohol (PVA) with potassium permanganate turned out to be an efficient method to fabricate smart scaffolds for tissue engineering, endowed with biodegradation and protein delivery capacity. This work considered for the first time the use of halogens (bromine, chlorine and iodine) as less aggressive agents than potassium permanganate to perform controlled PVA oxidation, in order to prevent degradation of polymer molecular size upon chemical modification. Oxidized PVA solutions were chemically characterized (i.e., dinitrophenylhydrazine assay, viscosity measurements, molecular size distribution) before preparing physically cross-linked hydrogels. Scaffolds were assessed for their mechanical properties and cell/tissue biocompatibiliy through cytotoxic extract test on IMR-90 fibroblasts and subcutaneous implantation into BALB/c mice. According to chemical investigations, bromine and iodine allowed for minor alteration of polymer molecular weight. Uniaxial tensile tests demonstrated that oxidized scaffolds had decreased mechanical resistance to deformation, suggesting tunable hydrogel stiffness. Finally, oxidized hydrogels exhibited high biocompatibility both in vitro and in vivo, resulting neither to be cytotoxic nor to elicit severe immunitary host reaction in comparison with atoxic PVA. In conclusion, PVA hydrogels oxidized by halogens were successfully fabricated in the effort of adapting polymer characteristics to specific tissue engineering applications.

IWTomics: testing high-resolution sequence-based 'Omics' data at multiple locations and scales

Summary

With increased generation of high-resolution sequence-based 'Omics' data, detecting statistically significant effects at different genomic locations and scales has become key to addressing several scientific questions. IWTomics is an R/Bioconductor package (integrated in Galaxy) that, exploiting sophisticated Functional Data Analysis techniques (i.e. statistical techniques that deal with the analysis of curves), allows users to pre-process, visualize and test these data at multiple locations and scales. The package provides a friendly, flexible and complete workflow that can be employed in many genomic and epigenomic applications.

Availability and implementation

IWTomics is freely available at the Bioconductor website (http://bioconductor.org/packages/IWTomics) and on the main Galaxy instance (https://usegalaxy.org/).

Supplementary information

Supplementary data are available at Bioinformatics online.

Functional Data Analysis of high-frequency load curves reveals drivers of residential electricity consumption

Smart energy meters generate real time, high frequency data which can foster demand management and response of consumers and firms, with potential private and social benefits. However, proper statistical techniques are needed to make sense of this large amount of data and translate them into usable recommendations. Here, we apply Functional Data Analysis (FDA), a novel branch of Statistics that analyses functions-to identify drivers of residential electricity load curves. We evaluate a real time feedback intervention which involved about 1000 Italian households for a period of three years. Results of the FDA modelling reveal, for the first time, daytime-indexed patterns of residential electricity consumption which depend on the ownership of specific clusters of electrical appliances and an overall reduction of consumption after the introduction of real time feedback, unrelated to appliance ownership characteristics.

Dynamic knee control and movement strategies in athletes and non-athletes in side hops: Implications for knee injury

Athletes exposed to rapid maneuvers need a high level of dynamic knee stability and robustness, while also controlling whole body movement, to decrease the risk of non-contact knee injury. The effects of high-level athletic training on such measures of movement control have not, however, been thoroughly evaluated. This study investigated whether elite athletes (who regularly perform knee-specific neuromuscular training) show greater dynamic knee robustness and/or different movement strategies than non-athletic controls, in relation to overall knee function. Thirty-nine women (19 athletes, 20 controls) performed standardized rebound side hops (SRSH) while a motion capture system synchronized with two force plates registered three-dimensional trunk, hip, and knee joint angles and moments. Dynamic knee robustness was evaluated using finite helical axis (FHA) inclination angles extracted from knee rotation intervals of 10°, analyzed with independent t tests. Angle and moment curves were analyzed with inferential methods for functional data. Athletes had superior knee function (less laxity, greater hop performances, and strength) but presented similar FHA inclination angles to controls. Movement strategies during the landing phase differed; athletes presented larger (a) hip flexion angles (during 9%-29% of the phase), (b) hip adduction moments (59%-99%), (c) hip internal rotation moments (83%-89%), and (d) knee flexion moments (79%-93%). Thus, elite athletes may have a greater ability than non-athletes to keep the knee robust while performing SRSH more efficiently through increased engagement of the hip. However, dynamic knee robustness associated with lower FHA inclination angles still show room for improvement, thus possibly decreasing knee injury risk.

Long-read sequencing technology indicates genome-wide effects of non-B DNA on polymerization speed and error rate

DNA conformation may deviate from the classical B-form in ∼13% of the human genome. Non-B DNA regulates many cellular processes; however, its effects on DNA polymerization speed and accuracy have not been investigated genome-wide. Such an inquiry is critical for understanding neurological diseases and cancer genome instability. Here, we present the first simultaneous examination of DNA polymerization kinetics and errors in the human genome sequenced with Single-Molecule Real-Time (SMRT) technology. We show that polymerization speed differs between non-B and B-DNA: It decelerates at G-quadruplexes and fluctuates periodically at disease-causing tandem repeats. Analyzing polymerization kinetics profiles, we predict and validate experimentally non-B DNA formation for a novel motif. We demonstrate that several non-B motifs affect sequencing errors (e.g., G-quadruplexes increase error rates), and that sequencing errors are positively associated with polymerase slowdown. Finally, we show that highly divergent G4 motifs have pronounced polymerization slowdown and high sequencing error rates, suggesting similar mechanisms for sequencing errors and germline mutations.