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  • 1
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    Early Pain Catastrophizing Exacerbates Impaired Limb Loading and 6-Minute Walk Test Distance 12 Months After Lower Extremity Fracture
    Oxford University Press (OUP) ; 2021
    In:  Physical Therapy Vol. 101, No. 11 ( 2021-11-01)
    Details
    In: Physical Therapy, Oxford University Press (OUP), Vol. 101, No. 11 ( 2021-11-01)
    Abstract: Disability is common after lower extremity fracture (LEF). Although psychosocial factors have been associated with patient-reported outcomes after LEF, they have not been associated with objective measures of function. Aberrant gait patterns are important markers of function, but are poorly defined after LEF. The primary purpose of this study was to explore whether pain catastrophizing and fear of movement 6 weeks after surgery were associated with injured limb loading outcomes and 6-minute walk test (6MWT) distance 12 months after femur or tibia fracture. The secondary purpose was to determine if limb loading characteristics differed between injured and uninjured limbs. Methods At 6 weeks after LEF, patients completed validated measures of pain catastrophizing, fear of movement, and depression. At 12 months, patients completed a 6MWT while wearing instrumented insoles that recorded the limb loading outcomes of stance time, impulse, and loading rate. Bivariate correlations assessed how patient and psychosocial characteristics at 6 weeks were associated with injured limb loading outcomes and 6MWT distance. Multivariable regression analyses were performed to determine if psychosocial variables were associated with each outcome after controlling for depression and patient demographic and clinical characteristics. Finally, paired t tests compared limb loading outcomes between limbs. Results Forty-seven participants completed the 6MWT at 12 months (65%), and 38 completed the 6MWT with the instrumented insoles. Fear of movement carried a poor relationship (r = 0.11–0.32) and pain catastrophizing a moderate relationship (r = 0.46–0.54) with 12-month outcomes. The regression results indicated that pain catastrophizing continued to be associated with all outcomes. Finally, the injured limb had significantly lower limb loading outcomes than the uninjured limb at 12 months (Cohen d = 0.54–0.69). Conclusion Pain catastrophizing early after LEF was associated with impaired limb loading and 6MWT distance at 12 months. Impact Impaired limb loading persists 12 months after LEF. Further research is needed to determine whether rehabilitative efforts focused on pain catastrophizing can restore limb loading after LEF.
    Type of Medium: Online Resource
    ISSN: 0031-9023 , 1538-6724
    URL: Article
    DOI: 10.1093/ptj/pzab194
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
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  • 2
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    Comparison of Bone Turnover Biomarkers in Serum and Urine Measured on an Automated Analytical Platform
    Oxford University Press (OUP) ; 2021
    In:  The Journal of Applied Laboratory Medicine Vol. 6, No. 3 ( 2021-04-29), p. 750-755
    Details
    In: The Journal of Applied Laboratory Medicine, Oxford University Press (OUP), Vol. 6, No. 3 ( 2021-04-29), p. 750-755
    Abstract: Matched serum and urine samples from patients who had total hip replacement were used to assess serum-validated immunoassay reagents for use in urine. Methods Samples were evaluated by an automated electrochemiluminescent immunoassay (cobas e411; Roche Diagnostics) for C-terminal telopeptide of type I collagen isoform β (β-Crosslaps), osteocalcin N-terminal midfragment (N-MID OC), N-terminal propeptide of type I collagen (PINP), and interleukin 6 (IL-6). Spike and recovery experiments were utilized to assess urinary matrix effects. Correlations between serum and both raw and creatinine-corrected urinary measures were assessed. Short-term precision was assessed. Results Spike and recovery experiments indicated minimal matrix effects of urine for the β-Crosslaps assay. Potential matrix effects were observed for the other analytes because N-MID OC and IL-6 tended to be slightly overrecovered, whereas PINP was underrecovered. There were strong correlations between serum β-Crosslaps and raw (Spearman ρ [rs] = 0.725, P & lt; 0.0001) and creatinine-corrected (rs = 0.793, P & lt; 0.0001) urinary measures and moderate correlations between serum N-MID OC and raw (rs = 0.582, P & lt; 0.0001) and creatinine-corrected (rs = 0.482, P & lt; 0.0001) urinary measures. PINP was not detected in urine, and no significant serum–urine correlations were found for IL-6. Short-term precision for urinary levels of β-Crosslaps, N-MID OC, and IL-6 were 1.6%, 6.3% and 14.4%, respectively. Conclusions Urinary measurements of β-Crosslaps and N-MID OC assays were correlated with serum measurements and had good short-term precision. Urinary PINP was not detectable. IL-6 can be measured in urine using this technology, but the levels did not correlate with serum levels, and the short-term precision was variable.
    Type of Medium: Online Resource
    ISSN: 2576-9456 , 2475-7241
    URL: Article
    DOI: 10.1093/jalm/jfaa172
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
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  • 3
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    Factors Associated with Long-Term Quadriceps Muscle Function after Surgical Fixation of Lower Extremity Fractures
    Oxford University Press (OUP) ; 2023
    In:  Physical Therapy
    Details
    In: Physical Therapy, Oxford University Press (OUP)
    Abstract: Long-term quadriceps femoris muscle performance and physical function after surgical repair of a lower extremity fracture remains largely undefined. The purpose of this study was to investigate between-limb differences in quadriceps performance 12 months after surgical fixation of a lower extremity fracture. It was hypothesized that the injured limb would be significantly weaker, have a lower rate of torque development, and that there would be a reduced step-down performance compared to the uninjured limb 12 months after surgery. Additionally, this study sought to identify demographic, surgical, and psychological factors associated with poor quadriceps function 12 months after surgery. Methods Quadriceps performance was measured bilaterally in 95 participants (49 female), aged 42 (SD = 14.5) years, 12 months after surgical fixation of a lower extremity fracture. Isometric quadriceps strength and rate of torque development were quantified using isometric dynamometry, and a timed step-down test was used to evaluate quadriceps performance. Independent predictor variables from the time of surgery were extracted from participants’ medical records. Kinesiophobia was screened at the time of testing. Wilcoxon signed-rank tests and linear regression analyses were used to assess between-limb differences in quadriceps performance and to determine factors associated with quadriceps performance 12 months after surgery. Results Significant between-limb differences in each measure of quadriceps performance were identified (peak torque involved: 1.37 [0.71] Nm*kg−1; uninvolved: 1.87 [0.74] Nm*kg−1; rate of torque development involved: 4.16 [2.75] Nm*kg−1*s−1; uninvolved: 6.10 [3.02] Nm*kg−1*s−1; and single-leg step-downs involved: 12.6 [5.0]; uninvolved: 21.7 [14.8] ). Female sex, external fixation, and kinesiophobia at 12 months were associated with reduced after-surgery quadriceps performance outcomes. Conclusion Quadriceps performance is impaired 12 months after surgical repair of a lower extremity fracture, particularly in females, in cases requiring external fixation, and in those with higher kinesiophobia 12 months after surgery. Impact Because long-term quadriceps weakness negatively impacts functional mobility, targeted strengthening should be emphasized after surgical repair of lower extremity fracture.
    Type of Medium: Online Resource
    ISSN: 0031-9023 , 1538-6724
    URL: Article
    DOI: 10.1093/ptj/pzad108
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
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  • 4
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    Drosophila Muller F Elements Maintain a Distinct Set of Genomic Properties Over 40 Million Years of Evolution
    Oxford University Press (OUP) ; 2015
    In:  G3 Genes|Genomes|Genetics Vol. 5, No. 5 ( 2015-05-01), p. 719-740
    Details
    In: G3 Genes|Genomes|Genetics, Oxford University Press (OUP), Vol. 5, No. 5 ( 2015-05-01), p. 719-740
    Abstract: The Muller F element (4.2 Mb, ~80 protein-coding genes) is an unusual autosome of Drosophila melanogaster; it is mostly heterochromatic with a low recombination rate. To investigate how these properties impact the evolution of repeats and genes, we manually improved the sequence and annotated the genes on the D. erecta, D. mojavensis, and D. grimshawi F elements and euchromatic domains from the Muller D element. We find that F elements have greater transposon density (25–50%) than euchromatic reference regions (3–11%). Among the F elements, D. grimshawi has the lowest transposon density (particularly DINE-1: 2% vs. 11–27%). F element genes have larger coding spans, more coding exons, larger introns, and lower codon bias. Comparison of the Effective Number of Codons with the Codon Adaptation Index shows that, in contrast to the other species, codon bias in D. grimshawi F element genes can be attributed primarily to selection instead of mutational biases, suggesting that density and types of transposons affect the degree of local heterochromatin formation. F element genes have lower estimated DNA melting temperatures than D element genes, potentially facilitating transcription through heterochromatin. Most F element genes (~90%) have remained on that element, but the F element has smaller syntenic blocks than genome averages (3.4–3.6 vs. 8.4–8.8 genes per block), indicating greater rates of inversion despite lower rates of recombination. Overall, the F element has maintained characteristics that are distinct from other autosomes in the Drosophila lineage, illuminating the constraints imposed by a heterochromatic milieu.
    Type of Medium: Online Resource
    ISSN: 2160-1836
    URL: Article
    DOI: 10.1534/g3.114.015966
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2015
    detail.hit.zdb_id: 2629978-1
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  • 5
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    Bayesian jackknife tests with a small number of subsets: application to HERA 21 cm power spectrum upper limits
    Oxford University Press (OUP) ; 2022
    In:  Monthly Notices of the Royal Astronomical Society Vol. 518, No. 4 ( 2022-12-08), p. 6041-6058
    Details
    In: Monthly Notices of the Royal Astronomical Society, Oxford University Press (OUP), Vol. 518, No. 4 ( 2022-12-08), p. 6041-6058
    Abstract: We present a Bayesian jackknife test for assessing the probability that a data set contains biased subsets, and, if so, which of the subsets are likely to be biased. The test can be used to assess the presence and likely source of statistical tension between different measurements of the same quantities in an automated manner. Under certain broadly applicable assumptions, the test is analytically tractable. We also provide an open-source code, chiborg, that performs both analytic and numerical computations of the test on general Gaussian-distributed data. After exploring the information theoretical aspects of the test and its performance with an array of simulations, we apply it to data from the Hydrogen Epoch of Reionization Array (HERA) to assess whether different sub-seasons of observing can justifiably be combined to produce a deeper 21 cm power spectrum upper limit. We find that, with a handful of exceptions, the HERA data in question are statistically consistent and this decision is justified. We conclude by pointing out the wide applicability of this test, including to CMB experiments and the H0 tension.
    Type of Medium: Online Resource
    ISSN: 0035-8711 , 1365-2966
    URL: Article
    DOI: 10.1093/mnras/stac3484
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 2016084-7
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  • 6
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    Polygenic risk score prediction of multiple sclerosis in individuals of South Asian ancestry
    Oxford University Press (OUP) ; 2023
    In:  Brain Communications Vol. 5, No. 2 ( 2023-03-02)
    Details
    In: Brain Communications, Oxford University Press (OUP), Vol. 5, No. 2 ( 2023-03-02)
    Abstract: Polygenic risk scores aggregate an individual’s burden of risk alleles to estimate the overall genetic risk for a specific trait or disease. Polygenic risk scores derived from genome-wide association studies of European populations perform poorly for other ancestral groups. Given the potential for future clinical utility, underperformance of polygenic risk scores in South Asian populations has the potential to reinforce health inequalities. To determine whether European-derived polygenic risk scores underperform at multiple sclerosis prediction in a South Asian-ancestry population compared with a European-ancestry cohort, we used data from two longitudinal genetic cohort studies: Genes & Health (2015–present), a study of ∼50 000 British–Bangladeshi and British–Pakistani individuals, and UK Biobank (2006–present), which is comprised of ∼500 000 predominantly White British individuals. We compared individuals with and without multiple sclerosis in both studies (Genes & Health: NCases = 42, NControl = 40 490; UK Biobank: NCases = 2091, NControl = 374 866). Polygenic risk scores were calculated using clumping and thresholding with risk allele effect sizes obtained from the largest multiple sclerosis genome-wide association study to date. Scores were calculated with and without the major histocompatibility complex region, the most influential locus in determining multiple sclerosis risk. Polygenic risk score prediction was evaluated using Nagelkerke’s pseudo-R2 metric adjusted for case ascertainment, age, sex and the first four genetic principal components. We found that, as expected, European-derived polygenic risk scores perform poorly in the Genes & Health cohort, explaining 1.1% (including the major histocompatibility complex) and 1.5% (excluding the major histocompatibility complex) of disease risk. In contrast, multiple sclerosis polygenic risk scores explained 4.8% (including the major histocompatibility complex) and 2.8% (excluding the major histocompatibility complex) of disease risk in European-ancestry UK Biobank participants. These findings suggest that polygenic risk score prediction of multiple sclerosis based on European genome-wide association study results is less accurate in a South Asian population. Genetic studies of ancestrally diverse populations are required to ensure that polygenic risk scores can be useful across ancestries.
    Type of Medium: Online Resource
    ISSN: 2632-1297
    URL: Article
    DOI: 10.1093/braincomms/fcad041
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
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  • 7
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    Optimizing sparse RFI prediction using deep learning
    Oxford University Press (OUP) ; 2019
    In:  Monthly Notices of the Royal Astronomical Society Vol. 488, No. 2 ( 2019-09-11), p. 2605-2615
    Details
    In: Monthly Notices of the Royal Astronomical Society, Oxford University Press (OUP), Vol. 488, No. 2 ( 2019-09-11), p. 2605-2615
    Abstract: Radio frequency interference (RFI) is an ever-present limiting factor among radio telescopes even in the most remote observing locations. When looking to retain the maximum amount of sensitivity and reduce contamination for Epoch of Reionization studies, the identification and removal of RFI is especially important. In addition to improved RFI identification, we must also take into account computational efficiency of the RFI-Identification algorithm as radio interferometer arrays such as the Hydrogen Epoch of Reionization Array (HERA) grow larger in number of receivers. To address this, we present a deep fully convolutional neural network (DFCN) that is comprehensive in its use of interferometric data, where both amplitude and phase information are used jointly for identifying RFI. We train the network using simulated HERA visibilities containing mock RFI, yielding a known ‘ground truth’ data set for evaluating the accuracy of various RFI algorithms. Evaluation of the DFCN model is performed on observations from the 67 dish build-out, HERA-67, and achieves a data throughput of 1.6 × 105 HERA time-ordered 1024 channelled visibilities per hour per GPU. We determine that relative to an amplitude only network including visibility phase adds important adjacent time–frequency context which increases discrimination between RFI and non-RFI. The inclusion of phase when predicting achieves a recall of 0.81, precision of 0.58, and F2 score of 0.75 as applied to our HERA-67 observations.
    Type of Medium: Online Resource
    ISSN: 0035-8711 , 1365-2966
    URL: Article
    DOI: 10.1093/mnras/stz1865
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2019
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  • 8
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    Search for the Epoch of Reionization with HERA: upper limits on the closure phase delay power spectrum
    Oxford University Press (OUP) ; 2023
    In:  Monthly Notices of the Royal Astronomical Society Vol. 524, No. 1 ( 2023-07-04), p. 583-598
    Details
    In: Monthly Notices of the Royal Astronomical Society, Oxford University Press (OUP), Vol. 524, No. 1 ( 2023-07-04), p. 583-598
    Abstract: Radio interferometers aiming to measure the power spectrum of the redshifted 21 cm line during the Epoch of Reionization (EoR) need to achieve an unprecedented dynamic range to separate the weak signal from overwhelming foreground emissions. Calibration inaccuracies can compromise the sensitivity of these measurements to the effect that a detection of the EoR is precluded. An alternative to standard analysis techniques makes use of the closure phase, which allows one to bypass antenna-based direction-independent calibration. Similarly to standard approaches, we use a delay spectrum technique to search for the EoR signal. Using 94 nights of data observed with Phase I of the Hydrogen Epoch of Reionization Array (HERA), we place approximate constraints on the 21 cm power spectrum at z = 7.7. We find at 95 per cent confidence that the 21 cm EoR brightness temperature is ≤(372)2 ‘pseudo’ mK2 at 1.14 ‘pseudo’ h Mpc−1, where the ‘pseudo’ emphasizes that these limits are to be interpreted as approximations to the actual distance scales and brightness temperatures. Using a fiducial EoR model, we demonstrate the feasibility of detecting the EoR with the full array. Compared to standard methods, the closure phase processing is relatively simple, thereby providing an important independent check on results derived using visibility intensities, or related.
    Type of Medium: Online Resource
    ISSN: 0035-8711 , 1365-2966
    URL: Article
    DOI: 10.1093/mnras/stad371
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
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  • 9
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    Characterization of inpaint residuals in interferometric measurements of the epoch of reionization
    Oxford University Press (OUP) ; 2023
    In:  Monthly Notices of the Royal Astronomical Society Vol. 520, No. 4 ( 2023-02-22), p. 5552-5572
    Details
    In: Monthly Notices of the Royal Astronomical Society, Oxford University Press (OUP), Vol. 520, No. 4 ( 2023-02-22), p. 5552-5572
    Abstract: To mitigate the effects of Radio Frequency Interference (RFI) on the data analysis pipelines of 21 cm interferometric instruments, numerous inpaint techniques have been developed. In this paper, we examine the qualitative and quantitative errors introduced into the visibilities and power spectrum due to inpainting. We perform our analysis on simulated data as well as real data from the Hydrogen Epoch of Reionization Array (HERA) Phase 1 upper limits. We also introduce a convolutional neural network that is capable of inpainting RFI corrupted data. We train our network on simulated data and show that our network is capable of inpainting real data without requiring to be retrained. We find that techniques that incorporate high wavenumbers in delay space in their modelling are best suited for inpainting over narrowband RFI. We show that with our fiducial parameters discrete prolate spheroidal sequences (dpss) and clean provide the best performance for intermittent RFI while Gaussian progress regression (gpr) and least squares spectral analysis (lssa) provide the best performance for larger RFI gaps. However, we caution that these qualitative conclusions are sensitive to the chosen hyperparameters of each inpainting technique. We show that all inpainting techniques reliably reproduce foreground dominated modes in the power spectrum. Since the inpainting techniques should not be capable of reproducing noise realizations, we find that the largest errors occur in the noise dominated delay modes. We show that as the noise level of the data comes down, clean and dpss are most capable of reproducing the fine frequency structure in the visibilities.
    Type of Medium: Online Resource
    ISSN: 0035-8711 , 1365-2966
    URL: Article
    DOI: 10.1093/mnras/stad441
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 2016084-7
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  • 10
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    Effects of model incompleteness on the drift-scan calibration of radio telescopes
    Oxford University Press (OUP) ; 2021
    In:  Monthly Notices of the Royal Astronomical Society Vol. 506, No. 3 ( 2021-08-04), p. 4578-4592
    Details
    In: Monthly Notices of the Royal Astronomical Society, Oxford University Press (OUP), Vol. 506, No. 3 ( 2021-08-04), p. 4578-4592
    Abstract: Precision calibration poses challenges to experiments probing the redshifted 21-cm signal of neutral hydrogen from the Cosmic Dawn and Epoch of Reionization (z ∼ 30–6). In both interferometric and global signal experiments, systematic calibration is the leading source of error. Though many aspects of calibration have been studied, the overlap between the two types of instruments has received less attention. We investigate the sky based calibration of total power measurements with a HERA dish and an EDGES-style antenna to understand the role of autocorrelations in the calibration of an interferometer and the role of sky in calibrating a total power instrument. Using simulations we study various scenarios such as time variable gain, incomplete sky calibration model, and primary beam model. We find that temporal gain drifts, sky model incompleteness, and beam inaccuracies cause biases in the receiver gain amplitude and the receiver temperature estimates. In some cases, these biases mix spectral structure between beam and sky resulting in spectrally variable gain errors. Applying the calibration method to the HERA and EDGES data, we find good agreement with calibration via the more standard methods. Although instrumental gains are consistent with beam and sky errors similar in scale to those simulated, the receiver temperatures show significant deviations from expected values. While we show that it is possible to partially mitigate biases due to model inaccuracies by incorporating a time-dependent gain model in calibration, the resulting errors on calibration products are larger and more correlated. Completely addressing these biases will require more accurate sky and primary beam models.
    Type of Medium: Online Resource
    ISSN: 0035-8711 , 1365-2966
    URL: Article
    DOI: 10.1093/mnras/stab2072
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
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