Antisense suppression of donor splice site mutations in the dystrophin gene transcript

We describe two donor splice site mutations, affecting dystrophin exons 16 and 45 that led to Duchenne muscular dystrophy (DMD), through catastrophic inactivation of the mRNA. These gene lesions unexpectedly resulted in the retention of the downstream introns, thereby increasing the length of the dystrophin mRNA by 20.2 and 36 kb, respectively. Splice-switching antisense oligomers targeted to exon 16 excised this in-frame exon and the following intron from the patient dystrophin transcript very efficiently in vitro, thereby restoring the reading frame and allowing synthesis of near-normal levels of a putatively functional dystrophin isoform. In contrast, targeting splice-switching oligomers to exon 45 in patient cells promoted only modest levels of an out-of-frame dystrophin transcript after transfection at high oligomer concentrations, whereas dual targeting of exons 44 and 45 or 45 and 46 resulted in more efficient exon skipping, with concomitant removal of intron 45. The splice site mutations reported here appear highly amenable to antisense oligomer intervention. We suggest that other splice site mutations may need to be evaluated for oligomer interventions on a case-by-case basis

The state of the art in integrating machine learning into visual analytics

Visual analytics systems combine machine learning or other analytic techniques with interactive data visualization to promote sensemaking and analytical reasoning. It is through such techniques that people can make sense of large, complex data. While progress has been made, the tactful combination of machine learning and data visualization is still under-explored. This state-of-the-art report presents a summary of the progress that has been made by highlighting and synthesizing select research advances. Further, it presents opportunities and challenges to enhance the synergy between machine learning and visual analytics for impactful future research directions

Andreev bound states in ferromagnet-superconductor nanostructures

We discuss the properties of a ferromagnet - superconductor heterostructure on the basis of a Hubbard model featuring exchange splitting in the ferromagnet and electron - electron attraction in the superconductor. We have solved the spin - polarized Hartree - Fock - Gorkov equations together with the Maxwell's equation (Ampere's law) fully self-consistently. We have found that a Proximity Effect - Fulde - Ferrell - Larkin - Ovchinnikov state is realized in such a heterostructure. It manifests itself in an oscillatory behavior of the pairing amplitude in the ferromagnet and spontaneously generated spin polarized current in the ground state. We argue that it is built up from the Andreev bound states, whose energy can be tuned by the exchange splitting and hence can coincide with the Fermi energy giving rise to a current carrying $\pi$-state. We also suggest experiments to verify these predictions.Comment: 12 pages, 5 figures included; to be published in Physica

Deletion of dystrophin In-Frame Exon 5 leads to a severe phenotype: Guidance for Exon skipping strategies

Duchenne and Becker muscular dystrophy severity depends upon the nature and location of the DMD gene lesion and generally correlates with the dystrophin open reading frame. However, there are striking exceptions where an in-frame genomic deletion leads to severe pathology or protein-truncating mutations (nonsense or frame-shifting indels) manifest as mild disease. Exceptions to the dystrophin reading frame rule are usually resolved after molecular diagnosis on muscle RNA. We report a moderate/severe Becker muscular dystrophy patient with an in-frame genomic deletion of DMD exon 5. This mutation has been reported by others as resulting in Duchenne or Intermediate muscular dystrophy, and the loss of this in-frame exon in one patient led to multiple splicing events, including omission of exon 6, that disrupts the open reading frame and is consistent with a severe phenotype. The patient described has a deletion of dystrophin exon 5 that does not compromise recognition of exon 6, and although the deletion does not disrupt the reading frame, his clinical presentation is more severe than would be expected for classical Becker muscular dystrophy. We suggest that the dystrophin isoform lacking the actin-binding sequence encoded by exon 5 is compromised, reflected by the phenotype resulting from induction of this dystrophin isoform in mouse muscle in vivo. Hence, exon skipping to address DMD-causing mutations within DMD exon 5 may not yield an isoform that confers marked clinical benefit. Additional studies will be required to determine whether multi-exon skipping strategies could yield more functional dystrophin isoforms, since some BMD patients with larger in-frame deletions in this region have been reported with mild phenotypes

Progress in the determination of the J/ψ−πJ/\psi-\pi cross section

Improving previous calculations, we compute the $J/\psi \pi\to {charmed mesons}$ cross section using QCD sum rules. Our sum rules for the $J/\psi \pi\to \bar{D} D^*$, $D \bar{D}^*$, ${\bar D}^* D^*$ and ${\bar D} D$ hadronic matrix elements are constructed by using vaccum-pion correlation functions, and we work up to twist-4 in the soft-pion limit. Our results suggest that, using meson exchange models is perfectly acceptable, provided that they include form factors and that they respect chiral symmetry. After doing a thermal average we get $\sim 0.3$ mb at T=150\MeV.Comment: 22 pages, RevTeX4 including 7 figures in ps file

Relativistic Calculation of the Meson Spectrum: a Fully Covariant Treatment Versus Standard Treatments

A large number of treatments of the meson spectrum have been tried that consider mesons as quark - anti quark bound states. Recently, we used relativistic quantum "constraint" mechanics to introduce a fully covariant treatment defined by two coupled Dirac equations. For field-theoretic interactions, this procedure functions as a "quantum mechanical transform of Bethe-Salpeter equation". Here, we test its spectral fits against those provided by an assortment of models: Wisconsin model, Iowa State model, Brayshaw model, and the popular semi-relativistic treatment of Godfrey and Isgur. We find that the fit provided by the two-body Dirac model for the entire meson spectrum competes with the best fits to partial spectra provided by the others and does so with the smallest number of interaction functions without additional cutoff parameters necessary to make other approaches numerically tractable. We discuss the distinguishing features of our model that may account for the relative overall success of its fits. Note especially that in our approach for QCD, the resulting pion mass and associated Goldstone behavior depend sensitively on the preservation of relativistic couplings that are crucial for its success when solved nonperturbatively for the analogous two-body bound-states of QED.Comment: 75 pages, 6 figures, revised content

Configurations of mother-child and father-child attachment as predictors of internalizing and externalizing behavioral problems: An individual participant data (IPD) meta-analysis

An unsettled question in attachment theory and research is the extent to which children's attachment patterns with mothers and fathers jointly predict developmental outcomes. In this study, we used individual participant data (IPD) meta-analysis to assess whether early attachment networks with mothers and fathers are associated with children's internalizing and externalizing behavioral problems. Following a pre-registered protocol, data from 9 studies and 1,097 children (mean age: 28.67 months) with attachment classifications to both mothers and fathers were included in analyses. We used a linear mixed effects analysis to assess differences in children's internalizing and externalizing behavioral problems as assessed via the average of both maternal and paternal reports based on whether children had two, one, or no insecure (or disorganized) attachments. Results indicated that children with an insecure attachment relationship with one or both parents were at higher risk for elevated internalizing behavioral problems compared with children who were securely attached to both parents. Children whose attachment relationships with both parents were classified as disorganized had more externalizing behavioral problems compared to children with either one or no disorganized attachment relationship with their parents. Across attachment classification networks and behavioral problems, findings suggest (a) an increased vulnerability to behavioral problems when children have insecure or disorganized attachment to both parents, and (b) that mother-child and father-child attachment relationships may not differ in the roles they play in children's development of internalizing and externalizing behavioral problems

MRI vastus lateralis fat fraction predicts loss of ambulation in Duchenne muscular dystrophy

ObjectiveWe studied the potential of quantitative MRI (qMRI) as a surrogate endpoint in Duchennemuscular dystrophy by assessing the additive predictive value of vastus lateralis (VL) fat fraction(FF) to age on loss of ambulation (LoA).MethodsVL FFs were determined on longitudinal Dixon MRI scans from 2 natural history studies inLeiden University Medical Center (LUMC) and Cincinnati Children’s Hospital MedicalCenter (CCHMC). CCHMC included ambulant patients, while LUMC included a mixedambulant and nonambulant population. We fitted longitudinal VL FF values to a sigmoidalcurve using a mixed model with random slope to predict individual trajectories. The additivevalue of VL FF over age to predict LoA was calculated from a Cox model, yielding a hazard ratio.ResultsEighty-nine MRIs of 19 LUMC and 15 CCHMC patients were included. At similar age,6-minute walking test distances were smaller and VL FFs were correspondingly higher inLUMC compared to CCHMC patients. Hazard ratio of a percent-point increase in VL FF forthe time to LoA was 1.15 for LUMC (95% confidence interval [CI] 1.05–1.26; p = 0.003) and0.96 for CCHMC (95% CI 0.84–1.10; p = 0.569).ConclusionsThe hazard ratio of 1.15 corresponds to a 4.11-fold increase of the instantaneous risk of LoA inpatients with a 10% higher VL FF at any age. Although results should be confirmed in a largercohort with prospective determination of the clinical endpoint, this added predictive value ofVL FF to age on LoA supports the use of qMRI FF as an endpoint or stratification tool inclinical trials.Development and application of statistical models for medical scientific researc