Genomic Patterns of De Novo Mutation in Simplex Autism.

To further our understanding of the genetic etiology of autism, we generated and analyzed genome sequence data from 516 idiopathic autism families (2,064 individuals). This resource includes >59 million single-nucleotide variants (SNVs) and 9,212 private copy number variants (CNVs), of which 133,992 and 88 are de novo mutations (DNMs), respectively. We estimate a mutation rate of ∼1.5 × 10-8 SNVs per site per generation with a significantly higher mutation rate in repetitive DNA. Comparing probands and unaffected siblings, we observe several DNM trends. Probands carry more gene-disruptive CNVs and SNVs, resulting in severe missense mutations and mapping to predicted fetal brain promoters and embryonic stem cell enhancers. These differences become more pronounced for autism genes (p = 1.8 × 10-3, OR = 2.2). Patients are more likely to carry multiple coding and noncoding DNMs in different genes, which are enriched for expression in striatal neurons (p = 3 × 10-3), suggesting a path forward for genetically characterizing more complex cases of autism.

Disruptive CHD8 mutations define a subtype of autism early in development.

Autism spectrum disorder (ASD) is a heterogeneous disease in which efforts to define subtypes behaviorally have met with limited success. Hypothesizing that genetically based subtype identification may prove more productive, we resequenced the ASD-associated gene CHD8 in 3,730 children with developmental delay or ASD. We identified a total of 15 independent mutations; no truncating events were identified in 8,792 controls, including 2,289 unaffected siblings. In addition to a high likelihood of an ASD diagnosis among patients bearing CHD8 mutations, characteristics enriched in this group included macrocephaly, distinct faces, and gastrointestinal complaints. chd8 disruption in zebrafish recapitulates features of the human phenotype, including increased head size as a result of expansion of the forebrain/midbrain and impairment of gastrointestinal motility due to a reduction in postmitotic enteric neurons. Our findings indicate that CHD8 disruptions define a distinct ASD subtype and reveal unexpected comorbidities between brain development and enteric innervation.

Intrathecal Gene Therapy for Giant Axonal Neuropathy.

BACKGROUND: Giant axonal neuropathy is a rare, autosomal recessive, pediatric, polysymptomatic, neurodegenerative disorder caused by biallelic loss-of-function variants in GAN, the gene encoding gigaxonin. METHODS: We conducted an intrathecal dose-escalation study of scAAV9/JeT-GAN (a self-complementary adeno-associated virus-based gene therapy containing the GAN transgene) in children with giant axonal neuropathy. Safety was the primary end point. The key secondary clinical end point was at least a 95% posterior probability of slowing the rate of change (i.e., slope) in the 32-item Motor Function Measure total percent score at 1 year after treatment, as compared with the pretreatment slope. RESULTS: One of four intrathecal doses of scAAV9/JeT-GAN was administered to 14 participants - 3.5×1013 total vector genomes (vg) (in 2 participants), 1.2×1014 vg (in 4), 1.8×1014 vg (in 5), and 3.5×1014 vg (in 3). During a median observation period of 68.7 months (range, 8.6 to 90.5), of 48 serious adverse events that had occurred, 1 (fever) was possibly related to treatment; 129 of 682 adverse events were possibly related to treatment. The mean pretreatment slope in the total cohort was -7.17 percentage points per year (95% credible interval, -8.36 to -5.97). At 1 year after treatment, posterior mean changes in slope were -0.54 percentage points (95% credible interval, -7.48 to 6.28) with the 3.5×1013-vg dose, 3.23 percentage points (95% credible interval, -1.27 to 7.65) with the 1.2×1014-vg dose, 5.32 percentage points (95% credible interval, 1.07 to 9.57) with the 1.8×1014-vg dose, and 3.43 percentage points (95% credible interval, -1.89 to 8.82) with the 3.5×1014-vg dose. The corresponding posterior probabilities for slowing the slope were 44% (95% credible interval, 43 to 44); 92% (95% credible interval, 92 to 93); 99% (95% credible interval, 99 to 99), which was above the efficacy threshold; and 90% (95% credible interval, 89 to 90). Between 6 and 24 months after gene transfer, sensory-nerve action potential amplitudes increased, stopped declining, or became recordable after being absent in 6 participants but remained absent in 8. CONCLUSIONS: Intrathecal gene transfer with scAAV9/JeT-GAN for giant axonal neuropathy was associated with adverse events and resulted in a possible benefit in motor function scores and other measures at some vector doses over a year. Further studies are warranted to determine the safety and efficacy of intrathecal AAV-mediated gene therapy in this disorder. (Funded by the National Institute of Neurological Disorders and Stroke and others; ClinicalTrials.gov number, NCT02362438.).

MLKL Requires the Inositol Phosphate Code to Execute Necroptosis.

Necroptosis is an important form of lytic cell death triggered by injury and infection, but whether mixed lineage kinase domain-like (MLKL) is sufficient to execute this pathway is unknown. In a genetic selection for human cell mutants defective for MLKL-dependent necroptosis, we identified mutations in IPMK and ITPK1, which encode inositol phosphate (IP) kinases that regulate the IP code of soluble molecules. We show that IP kinases are essential for necroptosis triggered by death receptor activation, herpesvirus infection, or a pro-necrotic MLKL mutant. In IP kinase mutant cells, MLKL failed to oligomerize and localize to membranes despite proper receptor-interacting protein kinase-3 (RIPK3)-dependent phosphorylation. We demonstrate that necroptosis requires IP-specific kinase activity and that a highly phosphorylated product, but not a lowly phosphorylated precursor, potently displaces the MLKL auto-inhibitory brace region. These observations reveal control of MLKL-mediated necroptosis by a metabolite and identify a key molecular mechanism underlying regulated cell death.

Neuron-specific transcriptomic signatures indicate neuroinflammation and altered neuronal activity in ASD temporal cortex.

Autism spectrum disorder (ASD) is a highly heterogeneous disorder, yet transcriptomic profiling of bulk brain tissue has identified substantial convergence among dysregulated genes and pathways in ASD. However, this approach lacks cell-specific resolution. We performed comprehensive transcriptomic analyses on bulk tissue and laser-capture microdissected (LCM) neurons from 59 postmortem human brains (27 ASD and 32 controls) in the superior temporal gyrus (STG) of individuals ranging from 2 to 73 years of age. In bulk tissue, synaptic signaling, heat shock protein-related pathways, and RNA splicing were significantly altered in ASD. There was age-dependent dysregulation of genes involved in gamma aminobutyric acid (GABA) (GAD1 and GAD2) and glutamate (SLC38A1) signaling pathways. In LCM neurons, AP-1-mediated neuroinflammation and insulin/IGF-1 signaling pathways were upregulated in ASD, while mitochondrial function, ribosome, and spliceosome components were downregulated. GABA synthesizing enzymes GAD1 and GAD2 were both downregulated in ASD neurons. Mechanistic modeling suggested a direct link between inflammation and ASD in neurons, and prioritized inflammation-associated genes for future study. Alterations in small nucleolar RNAs (snoRNAs) associated with splicing events suggested interplay between snoRNA dysregulation and splicing disruption in neurons of individuals with ASD. Our findings supported the fundamental hypothesis of altered neuronal communication in ASD, demonstrated that inflammation was elevated at least in part in ASD neurons, and may reveal windows of opportunity for biotherapeutics to target the trajectory of gene expression and clinical manifestation of ASD throughout the human lifespan.

Efficacy and Safety of an Extravascular Implantable Cardioverter-Defibrillator.

BACKGROUND: The extravascular implantable cardioverter-defibrillator (ICD) has a single lead implanted substernally to enable pause-prevention pacing, antitachycardia pacing, and defibrillation energy similar to that of transvenous ICDs. The safety and efficacy of extravascular ICDs are not yet known. METHODS: We conducted a prospective, single-group, nonrandomized, premarket global clinical study involving patients with a class I or IIa indication for an ICD, all of whom received an extravascular ICD system. The primary efficacy end point was successful defibrillation at implantation. The efficacy objective would be met if the lower boundary of the one-sided 97.5% confidence interval for the percentage of patients with successful defibrillation was greater than 88%. The primary safety end point was freedom from major system- or procedure-related complications at 6 months. The safety objective would be met if the lower boundary of the one-sided 97.5% confidence interval for the percentage of patients free from such complications was greater than 79%. RESULTS: A total of 356 patients were enrolled, 316 of whom had an implantation attempt. Among the 302 patients in whom ventricular arrhythmia could be induced and who completed the defibrillation testing protocol, the percentage of patients with successful defibrillation was 98.7% (lower boundary of the one-sided 97.5% confidence interval [CI], 96.6%; P<0.001 for the comparison with the performance goal of 88%); 299 of 316 patients (94.6%) were discharged with a working ICD system. The Kaplan-Meier estimate of the percentage of patients free from major system- or procedure-related complications at 6 months was 92.6% (lower boundary of the one-sided 97.5% CI, 89.0%; P<0.001 for the comparison with the performance goal of 79%). No major intraprocedural complications were reported. At 6 months, 25 major complications were observed, in 23 of 316 patients (7.3%). The success rate of antitachycardia pacing, as assessed with generalized estimating equations, was 50.8% (95% CI, 23.3 to 77.8). A total of 29 patients received 118 inappropriate shocks for 81 arrhythmic episodes. Eight systems were explanted without extravascular ICD replacement over the 10.6-month mean follow-up period. CONCLUSIONS: In this prospective global study, we found that extravascular ICDs were implanted safely and were able to detect and terminate induced ventricular arrhythmias at the time of implantation. (Funded by Medtronic; ClinicalTrials.gov number, NCT04060680.).

Ischemic Stroke with Comorbid Cancer Has Specific miRNA-mRNA Networks in Blood That Vary by Ischemic Stroke Mechanism.

OBJECTIVE: Approximately half of ischemic strokes (IS) in cancer patients are cryptogenic, with many presumed cardioembolic. We evaluated whether there were specific miRNA and mRNA transcriptome architectures in peripheral blood of IS patients with and without comorbid cancer, and between cardioembolic versus noncardioembolic IS etiologies in comorbid cancer. METHODS: We studied patients with cancer and IS (CS; n = 42), stroke only (SO; n = 41), and cancer only (n = 28), and vascular risk factor-matched controls (n = 30). mRNA-Seq and miRNA-Seq data, analyzed with linear regression models, identified differentially expressed genes in CS versus SO and in cardioembolic versus noncardioembolic CS, and miRNA-mRNA regulatory pairs. Network-level analyses identified stroke etiology-specific responses in CS. RESULTS: A total of 2,085 mRNAs and 31 miRNAs were differentially expressed between CS and SO. In CS, 122 and 35 miRNA-mRNA regulatory pairs, and 5 and 3 coexpressed gene modules, were associated with cardioembolic and noncardioembolic CS, respectively. Complement, growth factor, and immune/inflammatory pathways showed differences between IS etiologies in CS. A 15-gene biomarker panel assembled from a derivation cohort (n = 50) correctly classified 81% of CS and 71% of SO participants in a validation cohort (n = 33). Another 15-gene panel correctly identified etiologies for 13 of 13 CS-cardioembolic and 11 of 11 CS-noncardioembolic participants upon cross-validation; 11 of 16 CS-cryptogenic participants were predicted cardioembolic. INTERPRETATION: We discovered unique mRNA and miRNA transcriptome architecture in CS and SO, and in CS with different IS etiologies. Cardioembolic and noncardioembolic etiologies in CS showed unique coexpression networks and potential master regulators. These may help distinguish CS from SO and identify IS etiology in cryptogenic CS patients. ANN NEUROL 2024.

Mechanism by which T7 bacteriophage protein Gp1.2 inhibits Escherichia coli dGTPase.

Levels of the cellular dNTPs, the direct precursors for DNA synthesis, are important for DNA replication fidelity, cell cycle control, and resistance against viruses. Escherichia coli encodes a dGTPase (2'-deoxyguanosine-5'-triphosphate [dGTP] triphosphohydrolase [dGTPase]; dgt gene, Dgt) that establishes the normal dGTP level required for accurate DNA replication but also plays a role in protecting E. coli against bacteriophage T7 infection by limiting the dGTP required for viral DNA replication. T7 counteracts Dgt using an inhibitor, the gene 1.2 product (Gp1.2). This interaction is a useful model system for studying the ongoing evolutionary virus/host "arms race." We determined the structure of Gp1.2 by NMR spectroscopy and solved high-resolution cryo-electron microscopy structures of the Dgt-Gp1.2 complex also including either dGTP substrate or GTP coinhibitor bound in the active site. These structures reveal the mechanism by which Gp1.2 inhibits Dgt and indicate that Gp1.2 preferentially binds the GTP-bound form of Dgt. Biochemical assays reveal that the two inhibitors use different modes of inhibition and bind to Dgt in combination to yield enhanced inhibition. We thus propose an in vivo inhibition model wherein the Dgt-Gp1.2 complex equilibrates with GTP to fully inactivate Dgt, limiting dGTP hydrolysis and preserving the dGTP pool for viral DNA replication.

Optimization of 3D dynamic speech MRI: Poisson-disc undersampling and locally higher-rank reconstruction through partial separability model with regional optimized temporal basis.

PURPOSE: To improve the spatiotemporal qualities of images and dynamics of speech MRI through an improved data sampling and image reconstruction approach. METHODS: For data acquisition, we used a Poisson-disc random under sampling scheme that reduced the undersampling coherence. For image reconstruction, we proposed a novel locally higher-rank partial separability model. This reconstruction model represented the oral and static regions using separate low-rank subspaces, therefore, preserving their distinct temporal signal characteristics. Regional optimized temporal basis was determined from the regional-optimized virtual coil approach. Overall, we achieved a better spatiotemporal image reconstruction quality with the potential of reducing total acquisition time by 50%. RESULTS: The proposed method was demonstrated through several 2-mm isotropic, 64 mm total thickness, dynamic acquisitions with 40 frames per second and compared to the previous approach using a global subspace model along with other k-space sampling patterns. Individual timeframe images and temporal profiles of speech samples were shown to illustrate the ability of the Poisson-disc under sampling pattern in reducing total acquisition time. Temporal information of sagittal and coronal directions was also shown to illustrate the effectiveness of the locally higher-rank operator and regional optimized temporal basis. To compare the reconstruction qualities of different regions, voxel-wise temporal SNR analysis were performed. CONCLUSION: Poisson-disc sampling combined with a locally higher-rank model and a regional-optimized temporal basis can drastically improve the spatiotemporal image quality and provide a 50% reduction in overall acquisition time.

Measuring CSF shunt flow with MRI using flow enhancement of signal intensity (FENSI).

PURPOSE: To develop and validate a noninvasive imaging technique for accurately assessing very slow CSF flow within shunt tubes in pediatric patients with hydrocephalus, aiming to identify obstructions that might impede CSF drainage. THEORY AND METHODS: A simulation of shunt flow enhancement of signal intensity (shunt-FENSI) signal is used to establish the relationship between signal change and flow rate. The quantification of flow enhancement of signal intensity data involves normalization, curve fitting, and calibration to match simulated data. Additionally, a phase sweep method is introduced to accommodate the impact of magnetic field inhomogeneity on the flow measurement. The method is tested in flow phantoms, healthy adults, intensive care unit patients with external ventricular drains (EVD), and shunt patients. EVDs enable shunt-flow measurements to be acquired with a ground truth measure of CSF drainage. RESULTS: The flow-rate-to-signal simulation establishes signal-flow relationships and takes into account the T1 of draining fluid. The phase sweep method accurately accounts for phase accumulation due to frequency offsets at the shunt. Results in phantom and healthy human participants reveal reliable quantification of flow rates using controlled flows and agreement with the flow simulation. EVD patients display reliable measures of flow rates. Shunt patient results demonstrate feasibility of the method and consistent flow rates for functional shunts. CONCLUSION: The results demonstrate the technique's applicability, accuracy, and potential for diagnosing and noninvasively monitoring hydrocephalus. Limitations of the current approach include a high sensitivity to motion and strict requirement of imaging slice prescription.

Recommendations for risk allele evidence curation, classification, and reporting from the ClinGen Low Penetrance/Risk Allele Working Group.

PURPOSE: Genetic variants at the low end of the penetrance spectrum have historically been challenging to interpret because their high population frequencies exceed the disease prevalence of the associated condition, leading to a lack of clear segregation between the variant and disease. There is currently substantial variation in the classification of these variants, and no formal classification framework has been widely adopted. The Clinical Genome Resource Low Penetrance/Risk Allele Working Group was formed to address these challenges and promote harmonization within the clinical community. METHODS: The work presented here is the product of internal and community Likert-scaled surveys in combination with expert consensus within the Working Group. RESULTS: We formally recognize risk alleles and low-penetrance variants as distinct variant classes from those causing highly penetrant disease that require special considerations regarding their clinical classification and reporting. First, we provide a preferred terminology for these variants. Second, we focus on risk alleles and detail considerations for reviewing relevant studies and present a framework for the classification these variants. Finally, we discuss considerations for clinical reporting of risk alleles. CONCLUSION: These recommendations support harmonized interpretation, classification, and reporting of variants at the low end of the penetrance spectrum.

Comparison of transseptal puncture using a dedicated RF wire versus a mechanical needle with and without electrification in an animal model.

INTRODUCTION: Mechanical force to achieve transseptal puncture (TSP) using a standard needle may lead to overshooting and injury, and can potentially be avoided using a radiofrequency (RF)-powered needle or wire. Applying electrocautery to needles and guidewires as an alternative to purpose-built RF systems has been associated with safety risks, such as tissue coring and thermal damage. The commercially available AcQCross needle-dilator system (Medtronic) features a sharp open-ended needle for mechanical puncture, as well as a built-in connector to enable energy delivery for RF puncture. This investigation compares the safety and efficacy of the AcQCross needle to the dedicated VersaCross RF wire system and generator (Baylis Medical/Boston Scientific). METHODS: In an ex vivo porcine model, VersaCross wire punctures were performed using 1 s, constant mode (approx. 10 W) with maximum two attempts. AcQCross punctures were performed by applying energy for 2 s using a standard electrosurgical generator at 10 W (max. five attempts), 20 W (max. two attempts), and 30 W (max. two attempts). Efficacy was assessed in terms of puncture success and a number of energy applications required for TSP. Safety was assessed quantitatively as force required for TSP, energy required to puncture, and incidence of tissue coring, as well as by qualitative assessment of puncture sites. Additional qualitative observation of tissue cores and debris were obtained from TSP performed in live swine. RESULTS: RF TSP was 100% successful using the VersaCross wire with 1.0 ± 0.0 attempts. When power was used with the AcQCross needle, it failed to puncture at low (10 and 20 W) power settings; TSP was achieved with 30 W of energy with 91% success using 1.53 ± 0.51 attempts (p < .05 vs. VC) with greater variability (F1,33 = 9223.5, p < .0001). Compared to RF puncture using the VersaCross system, mechanical puncture, alone, using the AcQcross needle required six times more force (8 mm additional forward device displacement) to perforate the septum. Qualitative assessment of puncture sites revealed larger defects and more tissue charring with the AcQCross needle at 30 W compared to punctures with VersaCross wire. Tissue coring with the open-ended AcQCross needle was observed in vivo and measured to occur in 57% of punctures using the ex vivo model; no coring was observed with the closed-tip VersaCross wire. CONCLUSIONS: The AcQCross needle frequently required higher energy of 30 W to achieve RF TSP and was associated with tissue coring and charring, which have been, previously, reported when electrifying a standard open-ended mechanical needle or guidewire. These findings may limit safety and effectiveness compared to the VersaCross system.

The clinical and economic impact of extended battery longevity of a substernal extravascular implantable cardioverter defibrillator.

INTRODUCTION: The extravascular implantable cardioverter defibrillator (EV ICD) has extended projected battery longevity compared to the subcutaneous implantable cardioverter defibrillator (S-ICD). This study used modeling to characterize the need for generator changes, long-term complications, and overall costs for both the EV ICD and S-ICD in healthcare systems of various countries. METHODS: Battery longevity data were modeled using a Markov model from averages reported in device labeling for the S-ICD and with engineering estimates based on real life usage from EV ICD Pivotal Study patient data to introduce variability. Clinical demographic data were derived from published literature. The primary outcomes were defined as the number of generator replacement surgeries, complications, and total healthcare system costs due to battery depletion over the expected lifetime of patients receiving EV ICD or S-ICD therapy. RESULTS: Average modeled battery longevity was determined to be 7.3 years for the S-ICD versus 11.8 years for the EV ICD. The probability of a complication after a replacement procedure was 1.4%, with an operative mortality rate of 0.02%. The use of EV ICD was associated with 1.4-1.6 fewer replacements on average over an expected patient lifetime as compared to S-ICD and a 24.3%-26.0% reduction in cost. A one-way sensitivity analysis of the model for the US healthcare system found that use of an EV ICD resulted in a reduction in replacement surgeries of greater than 1 (1.1-1.6) along with five-figure cost savings in all scenarios ($18 602-$40 948). CONCLUSION: The longer projected battery life of the EV ICD has the potential to meaningfully reduce long-term morbidity and healthcare resources related to generator changes from the perspective of multiple diverse healthcare systems.

Patient-reported quality of life and acceptance of the extravascular implantable cardioverter-defibrillator: Results from pivotal study.

INTRODUCTION: The pivotal study of the extravascular implantable cardioverter-defibrillator (EV ICD) recently demonstrated primary efficacy and safety endpoints comparable to previous ICD systems. Patient experience with this novel device has not been reported. The current study examined the standardized patient-reported outcome (PRO) metrics of quality of life (QOL) and patient acceptance of the device. METHODS: The EV ICD Pivotal Study was a prospective, single-arm, nonrandomized, global, premarket approval trial. Patients completed the 12-Item Short Form Survey (SF-12) QOL surveys at baseline and at 6 months following implant. Additionally, patients completed the Florida Patient Acceptance Survey (FPAS) QOL survey at 6 months. RESULTS: From baseline to 6 months, patients within the EV ICD Pivotal Study (n = 247) reported statistically significant SF-12 improvements in physical QOL (45.4 ± 9.4 vs. 46.8 ± 9.1 respectively, p = .020) and no changes in mental QOL (49.3 ± 10.4 vs. 50.5 ± 9.7, p = .061). No differences were noted by sex, atrial fibrillation, or the experience of ICD shock. EV ICD patients reported better total FPAS patient acceptance of their ICD than TV-ICD or S-ICD patients using historical norms comparisons (80.4 ± 15.7 vs. 70.2 ± 17.8, p < .0001 for S-ICD and 73.0 ± 17.4, p = .004 for TV-ICD). CONCLUSION: The initial PROs for EV ICD patients indicated that patients had improvements in physical QOL from baseline to 6-month follow-up and markedly better overall acceptance of their ICD compared to a previous study with S-ICD and TV-ICD data. These initial results suggest that the EV ICD is evaluated positively by patients.

Association between high-density mapping of atypical atrial flutter, clinical outcomes and healthcare utilization.

BACKGROUND: Success of atypical atrial flutter (AAFL) ablation has historically been limited by difficulty mapping the complex re-entrant circuits involved. While high-density (HD) mapping has become commonplace in clinical practice, there are limited data on outcomes of HD versus non-HD mapping for AAFL ablation. OBJECTIVE: To compare clinical outcomes and healthcare utilization using HD mapping versus non-HD mapping for AAFL ablation. METHODS: Retrospective analysis of all AAFL procedures between 2005 and 2022 at an academic medical center was conducted. Procedures utilizing a 16-electrode HD Grid catheter and Precision mapping system were compared to procedures using prior generation 10-20 electrode spiral catheters and the Velocity system (Abbott, IL). Cox regression models and Poisson regression models were utilized to examine procedural and healthcare utilization outcomes. Models were adjusted for left ventricular ejection fraction, CHA2DS2-VASc, and history of prior ablation. RESULTS: There were 108 patients (62% HD mapping) included in the analysis. Baseline clinical characteristics were similar between groups. Use of HD mapping was associated with a higher rate of AAFL circuit delineation (92.5% vs. 76%; p = .014) and a greater adjusted procedure success rate, defined as non-inducibility at procedure end, (aRR (95% CI) 1.26 (1.02-1.55) p = .035) than non-HD mapping. HD mapping was also associated with a lower rate of ED visits (aIRR (95% CI) 0.32 (0.14-0.71); p = .007) and hospitalizations (aIRR (95% CI) 0.32 (0.14-0.68); p = .004) for AF/AFL/HF through 1 year. While there was a lower rate of recurrent AFL through 1 year among HD mapping cases (aHR (95% CI) 0.60 (0.31-1.16) p = .13), statistical significance was not met likely due to the low sample size and higher rate of ambulatory rhythm monitoring in the HD group (61% vs. 39%, p = .025). CONCLUSION: Compared to non-HD mapping, AAFL ablation with HD mapping is associated with improvements in the ability to define the AAFL circuit, greater procedural success, and a reduction in the number of ED visits and hospitalization for AF/AFL/HF.

Bayesian inference for prediction of survival probability in prime-boost vaccination regimes.

We focus on Bayesian inference for survival probabilities in a prime-boost vaccination regime in the development of an Ebola vaccine. We are interested in the heterologous prime-boost regimen (unmatched vaccine deliverys using the same antigen) due to its demonstrated durable immunity, well-tolerated safety profile, and suitability as a population vaccination strategy. Our research is motivated by the need to estimate the survival probability given the administered dosage. To do so, we establish two key relationships. Firstly, we model the connection between the designed dose concentration and the induced antibody count using a Bayesian response surface model. Secondly, we model the association between the antibody count and the probability of survival when experimental subjects are exposed to the Ebola virus in a controlled setting using a Bayesian probability of survival model. Finally, we employ a combination of the two models with dose concentration as the predictor of the survival probability for a future vaccinated population. We implement our two-level Bayesian model in Stan, and illustrate its use with simulated and real-world data. Performance of this model is evaluated via simulation. Our work offers a new application of drug synergy models to examine prime-boost vaccine efficacy, and does so using a hierarchical Bayesian framework that allows us to use dose concentration to predict survival probability.

Associations between infant amygdala functional connectivity and social engagement following a stressor: A preliminary investigation.

Functional architecture of the infant brain, especially functional connectivity (FC) within the amygdala network and between the amygdala and other networks (i.e., default-mode [DMN] and salience [SAL] networks), provides a neural basis for infant socioemotional functioning. Yet, little is known about the extent to which early within- and between-network amygdala FC are related to infant stress recovery across the first year of life. In this study, we examined associations between amygdala FC (i.e., within-network amygdala connectivity, and between-network amygdala connectivity with the DMN and SAL) at 3 months and infant recovery from a mild social stressor at 3, 6 and 9 months. At 3 months, thirty-five infants (13 girls) underwent resting-state functional magnetic resonance imaging during natural sleep. Infants and their mothers completed the still-face paradigm at 3, 6, and 9 months, and infant stress recovery was assessed at each time point as the proportion of infant social engagement during the reunion episode. Bivariate correlations indicated that greater positive within-network amygdala FC and greater positive amygdala-SAL FC, but not amygdala-DMN FC, at 3 months predicted lower levels of stress recovery at 3 and 6 months, but were nonsignificant at 9 months. These findings provide preliminary evidence that early functional synchronization within the amygdala network, as well as segregation between the amygdala and the SAL, may contribute to infant stress recovery in the context of infant-mother interaction.

Functional neural network connectivity at 3 months predicts infant-mother dyadic flexibility during play at 6 months.

Early functioning of neural networks likely underlies the flexible switching between internal and external orientation and may be key to the infant's ability to effectively engage in social interactions. To test this hypothesis, we examined the association between infants' neural networks at 3 months and infant-mother dyadic flexibility (denoting the structural variability of their interaction dynamics) at 3, 6, and 9 months. Participants included thirty-five infants (37% girls) and their mothers (87% White). At 3 months, infants participated in a resting-state functional magnetic resonance imaging session, and functional connectivity (FC) within the default mode (DMN) and salience (SN) networks, as well as DMN-SN internetwork FC, were derived using a seed-based approach. When infants were 3, 6, and 9 months, infant-mother dyads completed the Still-Face Paradigm where their individual engagement behaviors were observed and used to quantify dyadic flexibility using state space analysis. Results revealed that greater within-DMN FC, within-SN FC, and DMN-SN anticorrelation at 3 months predicted greater dyadic flexibility at 6 months, but not at 3 and 9 months. Findings suggest that early synchronization and interaction between neural networks underlying introspection and salience detection may support infants' flexible social interactions as they become increasingly active and engaged social partners.

Thinking of food: The mental representation of healthy foods as unprepared.

We find that people implicitly and explicitly represent healthy foods they categorize as healthy in their purest, least prepared forms but represent foods they categorize as unhealthy in their most prepared forms (e.g., a veggie patty is represented as frozen while a beef burger is represented in a bun with melted cheese and ready to eat). We find this effect across several studies using both image and word sorting measures in explicit tasks and implicit association tasks. The effect results from the perception of health and taste as two conflicting goals. Preparation (e.g., cooking, adding toppings) makes food more delicious, which creates categorization ambiguity. Hence, healthy food is thought of as unprepared. Indeed, individual differences in perceived health-taste goal conflict moderate the effect. Critically, the representation of healthy foods matters for food decisions. In an experiment that manipulated the descriptive language on a restaurant menu, emphasizing the preparation of foods increased participants' preference for healthy foods (with no improvement for unhealthy foods).

Structure and activation mechanism of the yeast RNA Pol II CTD kinase CTDK-1 complex.

The C-terminal domain (CTD) kinase I (CTDK-1) complex is the primary RNA Polymerase II (Pol II) CTD Ser2 kinase in budding yeast. CTDK-1 consists of a cyclin-dependent kinase (CDK) Ctk1, a cyclin Ctk2, and a unique subunit Ctk3 required for CTDK-1 activity. Here, we present a crystal structure of CTDK-1 at 1.85-Å resolution. The structure reveals that, compared to the canonical two-component CDK-cyclin system, the third component Ctk3 of CTDK-1 plays a critical role in Ctk1 activation by stabilizing a key element of CDK regulation, the T-loop, in an active conformation. In addition, Ctk3 contributes to the assembly of CTDK-1 through extensive interactions with both Ctk1 and Ctk2. We also demonstrate that CTDK-1 physically and genetically interacts with the serine/arginine-like protein Gbp2. Together, the data in our work reveal a regulatory mechanism of CDK complexes.