Documenting and modeling the acoustic variability of intervocalic alveolar taps in conversational Peninsular Spanish.

This study constitutes an investigation into the acoustic variability of intervocalic alveolar taps in a corpus of spontaneous speech from Madrid, Spain. Substantial variability was documented in this segment, with highly reduced variants constituting roughly half of all tokens during spectrographic inspection. In addition to qualitative documentation, the intensity difference between the tap and surrounding vowels was measured. Changes in this intensity difference were statistically modeled using Bayesian finite mixture models containing lexical and phonetic predictors. Model comparisons indicate predictive performance is improved when we assume two latent categories, interpreted as two pronunciation variants for the Spanish tap. In interpreting the model, predictors were more often related to categorical changes in which pronunciation variant was produced than to gradient intensity changes within each tap type. Variability in tap production was found according to lexical frequency, speech rate, and phonetic environment. These results underscore the importance of evaluating model fit to the data as well as what researchers modeling phonetic variability can gain in moving past linear models when they do not adequately fit the observed data.

The Mason-Alberta Phonetic Segmenter: a forced alignment system based on deep neural networks and interpolation.

Given an orthographic transcription, forced alignment systems automatically determine boundaries between segments in speech, facilitating the use of large corpora. In the present paper, we introduce a neural network-based forced alignment system, the Mason-Alberta Phonetic Segmenter (MAPS). MAPS serves as a testbed for two possible improvements we pursue for forced alignment systems. The first is treating the acoustic model as a tagger, rather than a classifier, motivated by the common understanding that segments are not truly discrete and often overlap. The second is an interpolation technique to allow more precise boundaries than the typical 10 ms limit in modern systems. During testing, all system configurations we trained significantly outperformed the state-of-the-art Montreal Forced Aligner in the 10 ms boundary placement tolerance threshold. The greatest difference achieved was a 28.13 % relative performance increase. The Montreal Forced Aligner began to slightly outperform our models at around a 30 ms tolerance. We also reflect on the training process for acoustic modeling in forced alignment, highlighting how the output targets for these models do not match phoneticians' conception of similarity between phones and that reconciling this tension may require rethinking the task and output targets or how speech itself should be segmented.

Elemental Composition at Silicone Hydrogel Contact Lens Surfaces.

OBJECTIVES: The outermost surface composition of 11 silicone hydrogel (SiHy) lenses was measured using X-ray photoelectron spectroscopy (XPS) to understand differences in wettability and potential interactions within an ocular environment. The SiHy lenses tested included balafilcon A, lotrafilcon A, lotrafilcon B, senofilcon A, comfilcon A, and somofilcon A reusable 2-week or monthly replacement lenses and delefilcon A, samfilcon A, narafilcon A, stenfilcon A, and somofilcon A daily disposable lenses. METHODS: All lenses were soaked for 24 hr in phosphate-buffered saline to remove all packaging solution and dried under vacuum overnight before analysis. X-ray photoelectron spectroscopy measurements were performed at 2 take-off angles, 55° and 75°, to evaluate changes in elemental composition as a function of depth from the surface. RESULTS: Detailed analysis of the XPS data revealed distinct differences in the chemical makeup of the different lens types. For all lenses, carbon, oxygen, and nitrogen were observed in varying quantities. In addition, fluorine was detected at the outermost surface region of comfilcon A (3.4%) and lotrafilcon A and B (<0.5%). The silicon content of the near-surface region analyzed varied among lens types, ranging from a low of 1.6% (lotrafilcon B) to a high of 16.5% (comfilcon A). In most instances, silicon enrichment at the outermost surface was observed, resulting from differences in lens formulation and design. CONCLUSIONS: Lenses differed most in their surface silicon concentration, with lotrafilcon B and delefilcon A exhibiting the lowest silicon contents and comfilcon A lens exhibiting the highest. Silicon has hydrophobic properties, which, when found at the surface, may influence the wettability of the contact lenses and their interaction with the tear film and ocular tissues. Higher surface silicon contents have been previously correlated with adverse effects, such as enhanced lipid uptake, thus underscoring the importance of monitoring their presence.

Mutations in centrosomal protein CEP152 in primary microcephaly families linked to MCPH4.

Primary microcephaly is a rare condition in which brain size is substantially diminished without other syndromic abnormalities. Seven autosomal loci have been genetically mapped, and the underlying causal genes have been identified for MCPH1, MCPH3, MCPH5, MCPH6, and MCPH7 but not for MCPH2 or MCPH4. The known genes play roles in mitosis and cell division. We ascertained three families from an Eastern Canadian subpopulation, each with one microcephalic child. Homozygosity analysis in two families using genome-wide dense SNP genotyping supported linkage to the published MCPH4 locus on chromosome 15q21.1. Sequencing of coding exons of candidate genes in the interval identified a nonconservative amino acid change in a highly conserved residue of the centrosomal protein CEP152. The affected children in these two families were both homozygous for this missense variant. The third affected child was compound heterozygous for the missense mutation plus a second, premature-termination mutation truncating a third of the protein and preventing its localization to centrosomes in transfected cells. CEP152 is the putative mammalian ortholog of Drosphila asterless, mutations in which affect mitosis in the fly. Published data from zebrafish are also consistent with a role of CEP152 in centrosome function. By RT-PCR, CEP152 is expressed in the embryonic mouse brain, similar to other MCPH genes. Like some other MCPH genes, CEP152 shows signatures of positive selection in the human lineage. CEP152 is a strong candidate for the causal gene underlying MCPH4 and may be an important gene in the evolution of human brain size.

Small molecule inhibitors of PCNA/PIP-box interaction suppress translesion DNA synthesis.

Proliferating cell nuclear antigen (PCNA) is an essential component for DNA replication and DNA damage response. Numerous proteins interact with PCNA through their short sequence called the PIP-box to be promoted to their respective functions. PCNA supports translesion DNA synthesis (TLS) by interacting with TLS polymerases through PIP-box interaction. Previously, we found a novel small molecule inhibitor of the PCNA/PIP-box interaction, T2AA, which inhibits DNA replication in cells. In this study, we created T2AA analogues and characterized them extensively for TLS inhibition. Compounds that inhibited biochemical PCNA/PIP-box interaction at an IC50 <5 µM inhibited cellular DNA replication at 10 µM as measured by BrdU incorporation. In cells lacking nucleotide-excision repair activity, PCNA inhibitors inhibited reactivation of a reporter plasmid that was globally damaged by cisplatin, suggesting that the inhibitors blocked the TLS that allows replication of the plasmid. PCNA inhibitors increased γH2AX induction and cell viability reduction mediated by cisplatin. Taken together, these findings suggest that inhibitors of PCNA/PIP-box interaction could chemosensitize cells to cisplatin by inhibiting TLS.

Mutation in the gene encoding ubiquitin ligase LRSAM1 in patients with Charcot-Marie-Tooth disease.

Charcot-Marie-Tooth disease (CMT) represents a family of related sensorimotor neuropathies. We studied a large family from a rural eastern Canadian community, with multiple individuals suffering from a condition clinically most similar to autosomal recessive axonal CMT, or AR-CMT2. Homozygosity mapping with high-density SNP genotyping of six affected individuals from the family excluded 23 known genes for various subtypes of CMT and instead identified a single homozygous region on chromosome 9, at 122,423,730-129,841,977 Mbp, shared identical by state in all six affected individuals. A homozygous pathogenic variant was identified in the gene encoding leucine rich repeat and sterile alpha motif 1 (LRSAM1) by direct DNA sequencing of genes within the region in affected DNA samples. The single nucleotide change mutates an intronic consensus acceptor splicing site from AG to AA. Direct analysis of RNA from patient blood demonstrated aberrant splicing of the affected exon, causing an obligatory frameshift and premature truncation of the protein. Western blotting of immortalized cells from a homozygous patient showed complete absence of detectable protein, consistent with the splice site defect. LRSAM1 plays a role in membrane vesicle fusion during viral maturation and for proper adhesion of neuronal cells in culture. Other ubiquitin ligases play documented roles in neurodegenerative diseases. LRSAM1 is a strong candidate for the causal gene for the genetic disorder in our kindred.

CAR T-cell Design-dependent Remodeling of the Brain Tumor Immune Microenvironment Modulates Tumor-associated Macrophages and Anti-glioma Activity.

Understanding the intricate dynamics between adoptively transferred immune cells and the brain tumor immune microenvironment (TIME) is crucial for the development of effective T cell-based immunotherapies. In this study, we investigated the influence of the TIME and chimeric antigen receptor (CAR) design on the anti-glioma activity of B7-H3-specific CAR T-cells. Using an immunocompetent glioma model, we evaluated a panel of seven fully murine B7-H3 CARs with variations in transmembrane, costimulatory, and activation domains. We then investigated changes in the TIME following CAR T-cell therapy using high-dimensional flow cytometry and single-cell RNA sequencing. Our results show that five out of six B7-H3 CARs with single costimulatory domains demonstrated robust functionality in vitro. However, these CARs had significantly varied levels of antitumor activity in vivo. To enhance therapeutic effectiveness and persistence, we incorporated 41BB and CD28 costimulation through transgenic expression of 41BBL on CD28-based CAR T-cells. This CAR design was associated with significantly improved anti-glioma efficacy in vitro but did not result in similar improvements in vivo. Analysis of the TIME revealed that CAR T-cell therapy influenced the composition of the TIME, with the recruitment and activation of distinct macrophage and endogenous T-cell subsets crucial for successful antitumor responses. Indeed, complete brain macrophage depletion using a CSF1R inhibitor abrogated CAR T-cell antitumor activity. In sum, our study highlights the critical role of CAR design and its modulation of the TIME in mediating the efficacy of adoptive immunotherapy for high-grade glioma. SIGNIFICANCE: CAR T-cell immunotherapies hold great potential for treating brain cancers; however, they are hindered by a challenging immune environment that dampens their effectiveness. In this study, we show that the CAR design influences the makeup of the immune environment in brain tumors, underscoring the need to target specific immune components to improve CAR T-cell performance, and highlighting the significance of using models with functional immune systems to optimize this therapy.

Epilepsy surgery in children with genetic etiologies: A prospective evaluation of current practices and outcomes.

OBJECTIVE: This study assesses current practices and outcomes of epilepsy surgery in children with a genetic etiology. It explores the pre-surgical workup, types of surgeries, and post-surgical outcomes in a broad array of disorders. METHODS: Patients ≤18 years who completed epilepsy surgery and had a known genetic etiology prior to surgical intervention were extrapolated from the Pediatric Epilepsy Research Consortium (PERC) surgery database, across 18 US centers. Data were assessed univariably by neuroimaging and EEG results, genetic group (structural gene, other gene, chromosomal), and curative intent. Outcomes were based on a modified International League Against Epilepsy (ILAE) outcome score. RESULTS: Of 81 children with genetic epilepsy, 72 % had daily seizures when referred for surgery evaluation, which occurred a median of 2.2 years (IQR 0.3, 5.2) after developing drug resistance. Following surgery, 68 % of subjects had >50 % seizure reduction, with 33 % achieving seizure freedom [median follow-up 11 months (IQR 6, 17). Seizure freedom was most common in the monogenic structural group, but significant palliation was present across all groups. Presence of a single EEG focus was associated with a greater likelihood of seizure freedom (p=0.02). SIGNIFICANCE: There are meaningful seizure reductions following epilepsy surgery in the majority of children with a genetic etiology, even in the absence of a single structural lesion and across a broad spectrum of genetic causes. These findings highlight the need for expedited referral for epilepsy surgery and support of a broadened view of which children may benefit from epilepsy surgery, even when the intent is palliative.

Language level predicts perceptual categorization of complex reversible events in children.

Language plays a well-documented role in perceptual object categorization, but little is known about its role in the categorization of complex events. We explored this here with a perspective from age or developmentally appropriate language capacities in neurotypical children between the ages of two and four years (N = 21), and from delayed language development in a clinical group of children (N = 20), whose verbal mental ages (VMA) often fell far below their chronological ages (CAs). All participants watched two demonstrations of a series of transitive events (e.g. tiger jumps over a girl). The toy agents were then moved out of sight, and participants had to act out the same event type, based on a different tiger and girl that were selected among two distractors. We aimed to determine how mastery of this task relates to CA in the neurotypical group, and whether task performance in the clinical group was predicted by VMA and a standardized measure of grammatical comprehension. Results from a series of logistic mixed-effect regression models showed that neurotypical children start to perform correctly on this task with a chance of around 50% during their third year of CA but reach ceiling performance only during their fourth. A similar pattern emerged for VMA in the clinical group, despite a wide range of CAs and diagnoses. In addition, grammatical comprehension predicted performance. These patterns suggest that language competence plays a role in the perceptual categorization and encoding of complex reversible events.

Haploinsufficiency of the lysosomal sialidase NEU1 results in a model of pleomorphic rhabdomyosarcoma in mice.

Rhabdomyosarcoma, the most common pediatric sarcoma, has no effective treatment for the pleomorphic subtype. Still, what triggers transformation into this aggressive phenotype remains poorly understood. Here we used Ptch1+/-/ETV7TG/+/- mice with enhanced incidence of rhabdomyosarcoma to generate a model of pleomorphic rhabdomyosarcoma driven by haploinsufficiency of the lysosomal sialidase neuraminidase 1. These tumors share mostly features of embryonal and some of alveolar rhabdomyosarcoma. Mechanistically, we show that the transforming pathway is increased lysosomal exocytosis downstream of reduced neuraminidase 1, exemplified by the redistribution of the lysosomal associated membrane protein 1 at the plasma membrane of tumor and stromal cells. Here we exploit this unique feature for single cell analysis and define heterogeneous populations of exocytic, only partially differentiated cells that force tumors to pleomorphism and promote a fibrotic microenvironment. These data together with the identification of an adipogenic signature shared by human rhabdomyosarcoma, and likely fueling the tumor's metabolism, make this model of pleomorphic rhabdomyosarcoma ideal for diagnostic and therapeutic studies.