ciftiTools: A package for reading, writing, visualizing and manipulating CIFTI files in R

Surface- and grayordinate-based analysis of MR data has well-recognized advantages, including improved whole-cortex visualization, the ability to perform surface smoothing to avoid issues associated with volumetric smoothing, improved inter-subject alignment, and reduced dimensionality. The CIFTI grayordinate file format introduced by the Human Connectome Project further advances grayordinate-based analysis by combining gray matter data from the left and right cortical hemispheres with gray matter data from the subcortex and cerebellum into a single file. Analyses performed in grayordinate space are well-suited to leverage information shared across the brain and across subjects through both traditional analysis techniques and more advanced statistical methods, including Bayesian methods. The R statistical environment facilitates use of advanced statistical techniques, yet little support for grayordinates analysis has been previously available in R. Indeed, few comprehensive programmatic tools for working with CIFTI files have been available in any language. Here, we present the ciftiTools R package, which provides a unified environment for reading, writing, visualizing, and manipulating CIFTI files and related data formats. We illustrate ciftiTools' convenient and user-friendly suite of tools for working with grayordinates and surface geometry data in R, and we describe how ciftiTools is being utilized to advance the statistical analysis of grayordinate-based functional MRI data.Comment: 41 pages, 6 figure

A robust multivariate, non-parametric outlier identification method for scrubbing in fMRI

Functional magnetic resonance imaging (fMRI) data contain high levels of noise and artifacts. To avoid contamination of downstream analyses, fMRI-based studies must identify and remove these noise sources prior to statistical analysis. One common approach is the "scrubbing" of fMRI volumes that are thought to contain high levels of noise. However, existing scrubbing techniques are based on ad hoc measures of signal change. We consider scrubbing via outlier detection, where volumes containing artifacts are considered multidimensional outliers. Robust multivariate outlier detection methods are proposed using robust distances (RDs), which are related to the Mahalanobis distance. These RDs have a known distribution when the data are i.i.d. normal, and that distribution can be used to determine a threshold for outliers where fMRI data violate these assumptions. Here, we develop a robust multivariate outlier detection method that is applicable to non-normal data. The objective is to obtain threshold values to flag outlying volumes based on their RDs. We propose two threshold candidates that embark on the same two steps, but the choice of which depends on a researcher's purpose. Our main steps are dimension reduction and selection, robust univariate outlier imputation to get rid of the effect of outliers on the distribution, and estimating an outlier threshold based on the upper quantile of the RD distribution without outliers. The first threshold candidate is an upper quantile of the empirical distribution of RDs obtained from the imputed data. The second threshold candidate calculates the upper quantile of the RD distribution that a nonparametric bootstrap uses to account for uncertainty in the empirical quantile. We compare our proposed fMRI scrubbing method to motion scrubbing, data-driven scrubbing, and restrictive parametric multivariate outlier detection methods

Sources of residual autocorrelation in multiband task fMRI and strategies for effective mitigation

In task fMRI analysis, OLS is typically used to estimate task-induced activation in the brain. Since task fMRI residuals often exhibit temporal autocorrelation, it is common practice to perform prewhitening prior to OLS to satisfy the assumption of residual independence, equivalent to GLS. While theoretically straightforward, a major challenge in prewhitening in fMRI is accurately estimating the residual autocorrelation at each location of the brain. Assuming a global autocorrelation model, as in several fMRI software programs, may under- or over-whiten particular regions and fail to achieve nominal false positive control across the brain. Faster multiband acquisitions require more sophisticated models to capture autocorrelation, making prewhitening more difficult. These issues are becoming more critical now because of a trend towards subject-level analysis, where prewhitening has a greater impact than in group-average analyses. In this article, we first thoroughly examine the sources of residual autocorrelation in multiband task fMRI. We find that residual autocorrelation varies spatially throughout the cortex and is affected by the task, the acquisition method, modeling choices, and individual differences. Second, we evaluate the ability of different AR-based prewhitening strategies to effectively mitigate autocorrelation and control false positives. We find that allowing the prewhitening filter to vary spatially is the most important factor for successful prewhitening, even more so than increasing AR model order. To overcome the computational challenge associated with spatially variable prewhitening, we developed a computationally efficient R implementation based on parallelization and fast C++ backend code. This implementation is included in the open source R package BayesfMRI.Comment: 26 pages with 1 page of appendix, 11 figures with 1 figure of supplementary figur

Make Reading Fun: Implications of Virtual Reality on Standing Balance and Control

The recent rapid expansion of virtual reality (VR) technology is driving a widespread number of new applications, including providing immersive environments for users to learn and read through commercially-available applications. However, recent research has shown that VR causes symptoms of dizziness and motion sickness, which could disrupt users gait and balance. Thus, it is important to understand how to best mitigate these effects before VR use becomes more widespread across the lay public. PURPOSE: The purpose of this study was to determine the acute effect of VR use on gait and balance control following use, and whether aspects of virtual environment design can mitigate negative effects.. METHODS: 60 young, healthy participants read a short story for 45 minutes while immersed in VR.They were randomly assigned to read in one of three environments: 1) a cluttered library, 2) a bright snowy landscape and 3) a dark outer space scene. These environments were selected due to their differences in visual clutter and lighting–VR design considerations which have been shown in previous work to influence visual fatigue and motion sickness. Prior to and following VR use, participants completed three standing balance tasks(standing balance, eyes open; standing balance, eyes closed and single leg stance) and two gait tasks (tandem walking and regular gait). While completing these tasks, kinematic and ground reaction force data were collected from an 8-camera 3D motion capture system and two force plates in order to assess changes in gait and balance kinematics and kinetics. RESULTS: Preliminary results (n = 12) indicate that those who read in the dark outer space environment demonstrated diminished balance control, as evidenced in an increase in center of pressure velocity during single leg balance. CONCLUSION: This finding indicates that the type of virtual environment a person is immersed in can affect their sense of balance following use. Specific to the dark outer space environment, it is possible the lack of visual anchors (i.e., nothing for them to focus on) lead to visual fatigue and downstream balance effects. Additional data analysis will help to elucidate these findings, which could lend insight to the role of virtual environment design on the user experience

PeerWise: students creating questions for their peers

PeerWise (https://peerwise.cs.auckland.ac.nz/) is a system which allows students to create multiple-choice questions for other students, answer questions posed by their peers and then provide feedback (Denny et al, 2008). There is evidence in the literature to show this method of assessment has a positive impact (e.g., Guilding et al. 2021; Fergus et al. 2021; Feeley and Parris 2012), particularly on students’ attainment and engagement. In a funded project, we introduced PeerWise into the assessment for a module at Sheffield Hallam University (U.K.) and another at La Trobe University (Australia). In this case study, we give an overview of PeerWise and the activities within the platform, results from our evaluation of the activity, and advice for implementation collected within the project from other practitioners around the world who have experience using PeerWise. Cohesive themes arising from our evaluation and the advice collected are summarised to form recommendations for improved student experience and outcomes, for future implementation of the PeerWise platform by practitioners.</jats:p

An insight into the sialotranscriptome of the West Nile mosquito vector, <it>Culex tarsalis</it>

<p>Abstract</p> <p>Background</p> <p>Saliva of adult female mosquitoes help sugar and blood feeding by providing enzymes and polypeptides that help sugar digestion, control microbial growth and counteract their vertebrate host hemostasis and inflammation. Mosquito saliva also potentiates the transmission of vector borne pathogens, including arboviruses. <it>Culex tarsalis </it>is a bird feeding mosquito vector of West Nile Virus closely related to <it>C. quinquefasciatus</it>, a mosquito relatively recently adapted to feed on humans, and the only mosquito of the genus <it>Culex </it>to have its sialotranscriptome so far described.</p> <p>Results</p> <p>A total of 1,753 clones randomly selected from an adult female <it>C. tarsalis </it>salivary glands (SG) cDNA library were sequenced and used to assemble a database that yielded 809 clusters of related sequences, 675 of which were singletons. Primer extension experiments were performed in selected clones to further extend sequence coverage, allowing for the identification of 283 protein sequences, 80 of which code for putative secreted proteins.</p> <p>Conclusion</p> <p>Comparison of the <it>C. tarsalis </it>sialotranscriptome with that of <it>C. quinquefasciatus </it>reveals accelerated evolution of salivary proteins as compared to housekeeping proteins. The average amino acid identity among salivary proteins is 70.1%, while that for housekeeping proteins is 91.2% (P < 0.05), and the codon volatility of secreted proteins is significantly higher than those of housekeeping proteins. Several protein families previously found exclusive of mosquitoes, including only in the <it>Aedes </it>genus have been identified in <it>C. tarsalis</it>. Interestingly, a protein family so far unique to <it>C. quinquefasciatus</it>, with 30 genes, is also found in <it>C. tarsalis</it>, indicating it was not a specific <it>C. quinquefasciatus </it>acquisition in its evolution to optimize mammal blood feeding.</p

Metapopulation dominance and genomic-island acquisition of Bradyrhizobium with superior catabolic capabilities

Root nodule-forming rhizobia exhibit a bipartite lifestyle, replicating in soil and also within plant cells where they fix nitrogen for legume hosts. Host control models posit that legume hosts act as a predominant selective force on rhizobia, but few studies have examined rhizobial fitness in natural populations. Here, we genotyped and phenotyped Bradyrhizobium isolates across more than 800 km of the native Acmispon strigosus host range. We sequenced chromosomal genes expressed under free-living conditions and accessory symbiosis loci expressed in planta and encoded on an integrated ‘symbiosis island’ (SI). We uncovered a massive clonal expansion restricted to the Bradyrhizobium chromosome, with a single chromosomal haplotype dominating populations, ranging more than 700 km, and acquiring 42 divergent SI haplotypes, none of which were spatially widespread. For focal genotypes, we quantified utilization of 190 sole-carbon sources relevant to soil fitness. Chromosomal haplotypes that were both widespread and dominant exhibited superior growth on diverse carbon sources, whereas these patterns were not mirrored among SI haplotypes. Abundance, spatial range and catabolic superiority of chromosomal, but not symbiosis genotypes suggests that fitness in the soil environment, rather than symbiosis with hosts, might be the key driver of Bradyrhizobium dominance

Metapopulation dominance and genomic-island acquisition of Bradyrhizobium with superior catabolic capabilities

Root nodule-forming rhizobia exhibit a bipartite lifestyle, replicating in soil and also within plant cells where they fix nitrogen for legume hosts. Host control models posit that legume hosts act as a predominant selective force on rhizobia, but few studies have examined rhizobial fitness in natural populations. Here, we genotyped and phenotyped Bradyrhizobium isolates across more than 800 km of the native Acmispon strigosus host range. We sequenced chromosomal genes expressed under free-living conditions and accessory symbiosis loci expressed in planta and encoded on an integrated ‘symbiosis island’ (SI). We uncovered a massive clonal expansion restricted to the Bradyrhizobium chromosome, with a single chromosomal haplotype dominating populations, ranging more than 700 km, and acquiring 42 divergent SI haplotypes, none of which were spatially widespread. For focal genotypes, we quantified utilization of 190 sole-carbon sources relevant to soil fitness. Chromosomal haplotypes that were both widespread and dominant exhibited superior growth on diverse carbon sources, whereas these patterns were not mirrored among SI haplotypes. Abundance, spatial range and catabolic superiority of chromosomal, but not symbiosis genotypes suggests that fitness in the soil environment, rather than symbiosis with hosts, might be the key driver of Bradyrhizobium dominance

Rotation Curve Fitting Model

One key piece of evidence for dark matter is the flat rotation curve problem: the disagreement between measured galactic rotation curves and their luminous mass. A novel solution to this problem is presented here. A model of relativistic frame effects on Doppler shifts due to the slightly curved frames of an emitting galaxy and the Milky Way is derived. This model predicts observed Doppler shifted spectra (in excess of the luminous mass) based only on the observed luminous matter profile and one free model parameter. Fits to the 175 galaxies reported in the SPARC database of galactic rotation profiles and accurate photometry measurements are compared between this novel model and dark matter and MOND (RAR) models. We find on the SPARC sample of 175 galaxies; that MOND-RAR has an average reduced chisquare of $\chi^2_r = 4.22$ for 175 galaxies fitted, the isothermal dark matter model has $\chi^2_r = 1.90$ for 165 galaxies fitted, and the new model we present has $\chi^2_r = 2.39$ for 172 galaxies fitted. Implications of this model are discussed.Comment: 27 pages, 9 figure

Priorities for primary health care policy implementation:Recommendations from the combined experience of six countries in the Asia-Pacific

Primary health care is essential for equitable, cost-effective and sustainable health care. It is the cornerstone to achieving universal health coverage against a backdrop of rising health expenditure and aging populations. Implementing strong primary health care requires grassroots understanding of health system performance. Comparing successes and barriers between countries may help identify mutual challenges and possible solutions. This paper compares and analyses primary health care policy in Australia, Malaysia, Mongolia, Myanmar, Thailand and Vietnam. Data were collected at the World Organization of National Colleges, Academies and Academic Associations of General Practitioners/Family Physicians (WONCA) Asia-Pacific regional conference in November 2017 using a predetermined framework. The six countries varied in maturity of their primary health care systems, including the extent to which family doctors contribute to care delivery. Challenges included an insufficient trained and competent workforce, particularly in rural and remote communities, and deficits in coordination within primary health care, as well as between primary and secondary care. Asia-Pacific regional policy needs to: (1) focus on better collaboration between public and private sectors; (2) take a structured approach to information sharing by bridging gaps in technology, health literacy and interprofessional working; (3) build systems that can evaluate and improve quality of care; and (4) promote community-based, high-quality training programs