pinecone/core-2020-05-10-deduplication huggingface dataset:
Controlling the object phase for g factor reduction in phase-constrained parallel MRI using spatially selective RF pulses

Parallel imaging generally entails a reduction in the signal-to-noise ratio (SNR) of the final image. Phase-constrained methods aim to improve reconstruction quality by employing symmetry properties of k space. Noise amplification in phase-constrained reconstruction heavily depends on the object background phase. The purpose of this work is to present a new approach of using tailored RF pulses to optimize the object phase distribution in order to maximize the benefit of phase-constrained reconstruction, and minimize the noise amplification. \ud
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Intrinsic object phase and coil sensitivity profiles are measured in a prescan. Optimal phase distribution is computed to maximize SNR in the given setup. Tailored RF pulses are designed to introduce the optimal phase map in the following accelerated acquisitions, subsequently reconstructed by phase-constrained methods. The potential of the method is demonstrated in vivo with in-plane accelerated (8x) and simultaneous multi-slice (3x) acquisitions.\ud
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Mean g-factors are reduced by up to a factor of 2 compared to conventional techniques when an appropriate phase-constrained reconstruction is applied to phase-optimized acquisitions, enhancing the  SNR of the final images and the visibility of small details.\ud
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Combining phase-constrained reconstruction and phase optimization by tailored RF pulses can provide notable improvement in the SNR and reconstruction quality of accelerated MRI
Reconstruction by Calibration over Tensors for Multi-Coil
  Multi-Acquisition Balanced SSFP Imaging

Purpose: To develop a rapid imaging framework for balanced steady-state free
precession (bSSFP) that jointly reconstructs undersampled data (by a factor of
R) across multiple coils (D) and multiple acquisitions (N). To devise a
multi-acquisition coil compression technique for improved computational
efficiency.
  Methods: The bSSFP image for a given coil and acquisition is modeled to be
modulated by a coil sensitivity and a bSSFP profile. The proposed
reconstruction by calibration over tensors (ReCat) recovers missing data by
tensor interpolation over the coil and acquisition dimensions. Coil compression
is achieved using a new method based on multilinear singular value
decomposition (MLCC). ReCat is compared with iterative self-consistent parallel
imaging (SPIRiT) and profile encoding (PE-SSFP) reconstructions.
  Results: Compared to parallel imaging or profile-encoding methods, ReCat
attains sensitive depiction of high-spatial-frequency information even at
higher R. In the brain, ReCat improves peak SNR (PSNR) by 1.1$\pm$1.0 dB over
SPIRiT and by 0.9$\pm$0.3 dB over PE-SSFP (mean$\pm$std across subjects;
average for N=2-8, R=8-16). Furthermore, reconstructions based on MLCC achieve
0.8$\pm$0.6 dB higher PSNR compared to those based on geometric coil
compression (GCC) (average for N=2-8, R=4-16).
  Conclusion: ReCat is a promising acceleration framework for
banding-artifact-free bSSFP imaging with high image quality; and MLCC offers
improved computational efficiency for tensor-based reconstructions.Comment: To be published in Magnetic Resonance in Medicine.
  http://onlinelibrary.wiley.com/doi/10.1002/mrm.26902/abstrac
An optimized framework for quantitative magnetization transfer imaging of the cervical spinal cord in vivo

Purpose\ud
\ud
To develop a framework to fully characterize quantitative magnetization transfer indices in the human cervical cord in vivo within a clinically feasible time.\ud
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Methods\ud
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A dedicated spinal cord imaging protocol for quantitative magnetization transfer was developed using a reduced field-of-view approach with echo planar imaging (EPI) readout. Sequence parameters were optimized based in the Cramer-Rao-lower bound. Quantitative model parameters (i.e., bound pool fraction, free and bound pool transverse relaxation times [ math formula, math formula], and forward exchange rate [kFB]) were estimated implementing a numerical model capable of dealing with the novelties of the sequence adopted. The framework was tested on five healthy subjects.\ud
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Results\ud
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Cramer-Rao-lower bound minimization produces optimal sampling schemes without requiring the establishment of a steady-state MT effect. The proposed framework allows quantitative voxel-wise estimation of model parameters at the resolution typically used for spinal cord imaging (i.e. 0.75 × 0.75 × 5 mm3), with a protocol duration of ∼35 min. Quantitative magnetization transfer parametric maps agree with literature values. Whole-cord mean values are: bound pool fraction = 0.11(±0.01), math formula = 46.5(±1.6) ms, math formula = 11.0(±0.2) µs, and kFB = 1.95(±0.06) Hz. Protocol optimization has a beneficial effect on reproducibility, especially for math formula and kFB.\ud
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Conclusion\ud
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The framework developed enables robust characterization of spinal cord microstructure in vivo using qMT. Magn Reson Med, 2017. © 2017 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited
Hemodynamic response function (HRF) variability confounds resting-state fMRI functional connectivity

fMRI is the convolution of the hemodynamic response function (HRF) and unmeasured neural activity. HRF variability (HRFv) across the brain could, in principle, alter functional connectivity (FC) estimates from resting‐state fMRI (rs‐fMRI). Given that HRFv is driven by both neural and non‐neural factors, it is problematic when it confounds FC. However, this aspect has remained largely unexplored even though FC studies have grown exponentially. We hypothesized that HRFv confounds FC estimates in the brain's default‐mode‐network
Accelerating CS in Parallel Imaging Reconstructions Using an Efficient
  and Effective Circulant Preconditioner

Purpose: Design of a preconditioner for fast and efficient parallel imaging
and compressed sensing reconstructions. Theory: Parallel imaging and compressed
sensing reconstructions become time consuming when the problem size or the
number of coils is large, due to the large linear system of equations that has
to be solved in l_1 and l_2-norm based reconstruction algorithms. Such linear
systems can be solved efficiently using effective preconditioning techniques.
Methods: In this paper we construct such a preconditioner by approximating the
system matrix of the linear system, which comprises the data fidelity and
includes total variation and wavelet regularization, by a matrix with the
assumption that is a block circulant matrix with circulant blocks. Due to its
circulant structure, the preconditioner can be constructed quickly and its
inverse can be evaluated fast using only two fast Fourier transformations. We
test the performance of the preconditioner for the conjugate gradient method as
the linear solver, integrated into the Split Bregman algorithm. Results: The
designed circulant preconditioner reduces the number of iterations required in
the conjugate gradient method by almost a factor of~5. The speed up results in
a total acceleration factor of approximately 2.5 for the entire reconstruction
algorithm when implemented in MATLAB, while the initialization time of the
preconditioner is negligible. Conclusion: The proposed preconditioner reduces
the reconstruction time for parallel imaging and compressed sensing in a Split
Bregman implementation and can easily handle large systems since it is
Fourier-based, allowing for efficient computations.
  Key words: preconditioning; compressed sensing; Split Bregman; parallel
imagingComment: 27 pages, 8 figures, 2 table
Non-enzymatic glycolysis and pentose phosphate pathway-like reactions in the plausible Archean ocean

The reaction sequences of central metabolism, glycolysis and the pentose phosphate pathway provide essential precursors for nucleic acids, amino acids and lipids. However, their evolutionary origins are not yet understood. Here, we provide evidence that their structure could have been fundamentally shaped by the general chemical environments in earth's earliest oceans. We reconstructed potential scenarios for oceans of the prebiotic Archean based on the composition of early sediments. We report that the resultant reaction milieu catalyses the interconversion of metabolites that in modern organisms constitute glycolysis and the pentose phosphate pathway. The 29 observed reactions include the formation and/or interconversion of glucose, pyruvate, the nucleic acid precursor ribose‐5‐phosphate and the amino acid precursor erythrose‐4‐phosphate, antedating reactions sequences similar to that used by the metabolic pathways. Moreover, the Archean ocean mimetic increased the stability of the phosphorylated intermediates and accelerated the rate of intermediate reactions and pyruvate production. The catalytic capacity of the reconstructed ocean milieu was attributable to its metal content. The reactions were particularly sensitive to ferrous iron Fe(II), which is understood to have had high concentrations in the Archean oceans. These observations reveal that reaction sequences that constitute central carbon metabolism could have been constrained by the iron‐rich oceanic environment of the early Archean. The origin of metabolism could thus date back to the prebiotic world
The Impact of Appearance Concerns on Depression and Anxiety in Rheumatoid Arthritis

Objectives\ud
Increased levels of anxiety and depression are commonly reported by patients with rheumatoid arthritis (RA) in comparison to the general population. Rather than the clinical features of the disease, this difference has been attributed to psychosocial factors. Patients with RA can develop joint swelling and disfigurement as a direct result of the disease, and experience concerns about their altered appearance. This study aimed to identify if appearance-specific issues contribute to our understanding of mood in RA, over and above demographic, functional and generalized psychosocial measures.\ud
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Methods\ud
A total of 89 patients with RA completed a series of psychosocial questionnaires measuring demographics, physical function, general cognitive processes and a number of appearance-specific concepts, to determine the contribution of appearance concerns to mood.\ud
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Results\ud
Hierarchical linear regression suggested that living status, optimism, social support and appearance-related social anxiety and avoidance are associated with levels of depression. The relationship between social support and depression was found to be mediated by appearance-related social anxiety and avoidance. Optimism remained the only variable significantly associated with anxiety.\ud
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Conclusion\ud
These findings confirm the role of optimistic cognitions and a supportive environment in determining the mood of patients with RA and also establishes a possible link between depression and appearance concerns in this population. Interventions targeting social support, optimism and social anxiety and avoidance in relation to appearance are key in the improvement of depression in this patient group
Osteoarthritis: Patient Expectations about Future Pain, Stiffness and Function

Objectives\ud
The aim of the present study was to examine the difference between osteoarthritis patients’ self-reported assessments of current pain, stiffness and physical function and their expectations of these symptoms in one and five years’ time, and to determine the significant predictors of positive expectations.\ud
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Methods\ud
Eighty patients completed ratings of baseline assessments and one- and five-year expectations of pain, stiffness and physical function using the Western Ontario and McMaster Osteoarthritis Index (WOMAC). Measures of illness perceptions, coping styles, health values, satisfaction, quality of life, optimism, self-esteem and moods were also collected at baseline. Agreement between patients’ current assessment and expectations were calculated using intra-class correlations (ICCs). Paired-sample t-tests were conducted to look at differences between assessments. Univariate logistic regressions were then performed to identify the variables significantly associated with positive expectations of pain, stiffness and function. Significant variables (p < 0.05) were entered into a forward stepwise multivariate logistic regression to identify unique independent predictors of positive expectations for each of the WOMAC subscales.\ud
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Results\ud
Differences were found between current assessments and expectations, with the majority of patients being positive about future symptoms. There were some differences between the predictors for one- and five-year expectations, with current assessments of health status only affecting five-year expectations.\ud
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Conclusions\ud
It is necessary to investigate further the variables that may contribute to positive expectations in osteoarthritis patients in order to manage the condition more effectively
A Practice-Focused Overview of Methods to Assess Obesity Before Arthroplasty

Author version made available in accordance with the publisher's policy, under embargo for a period of 12 months from the date of publication.  This is the peer reviewed version of the following article: [Sahafi L, Bramwell D, Harris M, Krishnan J and Battersby M (2015) A practice-focused overview of methods to assess obesity before arthroplasty. Short Report. Musculoskeletal Care [online 15 June 2015].], which has been published in final form at DOI:10.1002/msc.1109. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.Obesity is associated with poorer outcomes after hip and knee arthroplasty. Body mass index is the most commonly used measure of obesity, but it does not reliably assess body composition. This paper reviewed the literature to provide a practice focused overview of existing approaches to measure obesity and discussed their suitability in informing decisions for hip and knee arthroplasty. We found that measures of obesity that are practical in clinical settings and high utility when making decisions on arthroplasty could be clustered into three groups: reliable but costly; inexpensive and assessing body composition; and inexpensive without body composition assessment. Measures of obesity of value to surgeons’ decision making could be drawn from a combination of the first or second group measures with the third group
What impact does written information about fatigue have on patients with autoimmune rheumatic diseases? : Findings from a qualitative study

Objectives Although fatigue is a common symptom for people with rheumatic diseases, limited support is available. This study explored the impact of written information about fatigue, focusing on a booklet, Fatigue and arthritis. Methods Thirteen patients with rheumatic disease and fatigue were recruited purposively from a rheumatology outpatient service. They were interviewed before and after receiving the fatigue booklet. Two patients, plus six professionals with relevant interests, participated in a focus group. Transcripts were analysed thematically and a descriptive summary was produced. Results Interviewees consistently reported that fatigue made life more challenging, and none had previously received any support to manage it. Reflecting on the booklet, most said that it had made a difference to how they thought about fatigue, and that this had been valuable. Around half also said that it had affected, or would affect, how they managed fatigue. No one reported any impact on fatigue itself. Comments from interviewees and focus group members alike suggested that the research process may have contributed to the changes in thought and behaviour reported. Its key contributions appear to have been: clarifying the booklet's relevance; prompting reflection on current management; and introducing accountability. Conclusions This study indicated that written information can make a difference to how people think about fatigue and may also prompt behaviour change. However, context appeared to be important: it seems likely that the research process played a part and that the impact of the booklet may have been less if read in isolation. Aspects of the research appearing to facilitate impact could be integrated into routine care, providing a pragmatic (relatively low-cost) response to an unmet need
Psychosocial variables and presence, severity and prognosis of plantar heel pain: A systematic review of cross-sectional and prognostic associations

Objective Plantar heel pain (PHP) is often disabling, and persistent symptoms are common. Psychosocial variables are known to affect pain and disability but the association of these factors with PHP has yet to be established. The purpose of the present systematic review was to determine if psychosocial variables are associated with the presence, severity and prognosis of PHP. Methods A systematic review of the literature and qualitative synthesis was carried out. Electronic searches of MEDLINE, CINAHL, SPORTDiscus, PsycINFO and EMBASE were undertaken from the inception of the respective databases up to November 2017. Any study design incorporating measurements of psychosocial variables with participants with plantar heel pain were included. The quality of included articles was appraised using the Newcastle Ottawa Scale. Results Five articles from four studies were included in the review, with a total of 422 participants. Moderate‐level evidence suggested a clinically unimportant association with the incidence of PHP and depression, anxiety and stress, and limited evidence suggested a clinically unimportant association with job dissatisfaction. Moderate‐level evidence suggested that there may also be an association between depression, anxiety, stress and catastrophization and PHP pain, and between depression, anxiety, stress, catastrophization and kinesiophobia and PHP function. We also found moderate‐level evidence that a psychological disorder may be associated with a poorer outcome to shockwave therapy. Conclusion In light of this review, the association of psychosocial variables and plantar heel pain cannot be ruled out. Given recommendations to adopt an individualized and stratified approach to other musculoskeletal conditions, clinicians should remain vigilant to their presence
Systems pharmacology modeling: an approach to improving drug safety

Advances in systems biology in conjunction with the expansion in knowledge of drug effects and diseases present an unprecedented opportunity to extend traditional pharmacokinetic and pharmacodynamic modeling/analysis to conduct systems pharmacology modeling. Many drugs that cause liver injury and myopathies have been studied extensively. Mitochondrion‐centric systems pharmacology modeling is important since drug toxicity across a large number of pharmacological classes converges to mitochondrial injury and death. Approaches to systems pharmacology modeling of drug effects need to consider drug exposure, organelle and cellular phenotypes across all key cell types of human organs, organ‐specific clinical biomarkers/phenotypes, gene–drug interaction and immune responses. Systems modeling approaches, that leverage the knowledge base constructed from curating a selected list of drugs across a wide range of pharmacological classes, will provide a critically needed blueprint for making informed decisions to reduce the rate of attrition for drugs in development and increase the number of drugs with an acceptable benefit/risk ratio. Copyright © 2013 John Wiley & Sons, Ltd
Long-term administration of pirfenidone improves cardiac function in mdx mice

Duchenne muscular dystrophy, an X-linked recessive neuromuscular disorder due to lack of the protein dystrophin, manifests as progressive muscle degeneration and cardiomyopathy with increased fibrosis. The exact mechanisms involved in fibrosis are unknown, but the cytokine, TGF-β, is a likely mediator.  This study tested whether the TGF-β antagonist, pirfenidone, could reduce cardiac fibrosis.  Eight-month-old mdx mice were treated for 7 months with 0.4%, 0.8%, and 1.2% of pirfenidone in drinking water:  untreated water was given to control mdx and C57 mice. Mice treated with 0.8% and 1.2% pirfendone had lowered cardiac TGF-β mRNA and improved in vitro cardiac contractility (P<0.05) to levels consistent with C57 mice, yet without a change in cardiac stiffness or fibrosis.  These results show that the TGF-β antagonist, pirfenidone can improve cardiac function in mdx mice, potentially providing a new avenue for developing cardiac therapies for patients with Duchenne muscular dystrophy
Adult polyglucosan body disease: Proton magnetic resonance spectroscopy of the brain and novel mutation in the GBE1 gene

Adult polyglucosan body disease (APBD) is characterized by the accumulation of insoluble glucose polymers within the central and peripheral nervous systems. A common missense mutation in the glycogen branching enzyme (GBE1) gene has been identified in Ashkenazi patients with APBD. We report on a non-Jewish patient with APBD on whom we performed proton magnetic resonance spectroscopic imaging of the brain. GBE activity in fibroblasts was markedly reduced, and a novel heterozygous mutation was identified in the GBE1 gene. Our findings widen the spectrum of APBD genotypes, underline the importance of performing GIBE analysis in all APBD patients, and suggest that brain white matter degeneration in APBD may result from tissue damage involving axons and myelin
Drug-screening platform based on the contractility of tissue-engineered muscle

A tissue-based approach to in vitro drug screening allows for determination of the cumulative positive and negative effects of a drug at the tissue rather than the cellular or subcellular level. Skeletal muscle myoblasts were tissue-engineered into three-dimensional muscle with parallel myofibers generating directed forces. When grown attached to two flexible micro-posts (mu posts) acting as artificial tendons in a 96-well plate format, the miniature bioartificial muscles (mBAMs) generated tetanic (active) forces upon electrical stimulation measured with a novel image-based motion detection system. mBAM myofiber hypertrophy and active force increased in response to insulin-like growth factor 1. In contrast, mBAM deterioration and weakness was observed with a cholesterol-lowering statin. The results described in this study demonstrate the integration of tissue engineering and biomechanical testing into a single platform for the screening of compounds affecting muscle strength.status: publishe
Time-frequency analysis of rhythmic masticatory muscle activity

The aim of this study was to develop and validate under laboratory conditions an algorithm for a time-frequency analysis of rhythmic masticatory muscle activity (RMMA). The algorithm baseband demodulated the electromyographic (EMG) signal to provide a frequency versus time representation. Using appropriate thresholds for frequency and power parameters, it was possible to automatically assess the features of RMMA without examiner interaction. The algorithm was first tested using synthetic EMG signals and then using real EMG signals obtained from the masticatory muscles of 11 human subjects who underwent well-defined rhythmic, static, and possible confounding oral tasks. The accuracy of detection was quantified by receiver operating characteristics (ROC) curves. Sensitivity and specificity values were >/=90% and >/=96%, respectively. The areas under the ROC curves were >/=95% (standard error +/-0.1%). The proposed approach represents a promising tool to effectively investigate rhythmical contractions of the masticatory muscles. Muscle Nerve, 2009