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.

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.

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.

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.

MetaUniDec: High-Throughput Deconvolution of Native Mass Spectra.

The expansion of native mass spectrometry (MS) methods for both academic and industrial applications has created a substantial need for analysis of large native MS datasets. Existing software tools are poorly suited for high-throughput deconvolution of native electrospray mass spectra from intact proteins and protein complexes. The UniDec Bayesian deconvolution algorithm is uniquely well suited for high-throughput analysis due to its speed and robustness but was previously tailored towards individual spectra. Here, we optimized UniDec for deconvolution, analysis, and visualization of large data sets. This new module, MetaUniDec, centers around a hierarchical data format 5 (HDF5) format for storing datasets that significantly improves speed, portability, and file size. It also includes code optimizations to improve speed and a new graphical user interface for visualization, interaction, and analysis of data. To demonstrate the utility of MetaUniDec, we applied the software to analyze automated collision voltage ramps with a small bacterial heme protein and large lipoprotein nanodiscs. Upon increasing collisional activation, bacterial heme-nitric oxide/oxygen binding (H-NOX) protein shows a discrete loss of bound heme, and nanodiscs show a continuous loss of lipids and charge. By using MetaUniDec to track changes in peak area or mass as a function of collision voltage, we explore the energetic profile of collisional activation in an ultra-high mass range Orbitrap mass spectrometer. Graphical abstract ᅟ.

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.

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.

Heat treatments modify the tribological properties of nickel boron coatings.

The effects of annealing temperature on the tribological properties of electroless nickel-boron coatings have been investigated. The coatings were annealed in a tube furnace under a flow (0.0094 N m(3)/min) of oxygen gas at temperatures of 250, 400, 550, and 700 °C for 3 h. Using scanning electron microscopy, images of the annealed coatings documented changes in surface morphology. From this it was seen that the higher annealing temperatures produced marked changes, moving from the nodular structure of nickel-boron coatings to a flaked surface morphology. The chemical effect of the annealing temperature was studied via X-ray photoelectron spectroscopy (XPS) and Raman spectroscopy. The XPS data indicated that after annealing at the temperatures of 550 and 700 °C, an accumulation of boron oxide species could be seen at the surface as well as a complete loss of nickel signal. An analysis of Raman spectra collected across the surface further identified the predominant species to be boric acid. The tribological response of the coatings was studied with a pin-on-disk tribometer with 440C stainless steel balls run against the coatings in ambient air. It was seen that the as received sample and the sample annealed at 250 °C samples exhibited modest friction properties, while the 400 °C sample had increased friction due to wear debris from the ball. The 550 and 700 °C samples showed remarkably low friction coefficients between 0.06 and 0.08, attributable to the presence of boric acid. The wear tracks were analyzed using scanning white light interferometry and from this data wear rates were obtained for the coatings ranging from 10(-8) to 10(-7) mm(3)/Nm.

Mutations in a novel serine protease PRSS56 in families with nanophthalmos.

PURPOSE: Nanophthalmos is a rare genetic ocular disorder in which the eyes of affected individuals are abnormally small. Patients suffer from severe hyperopia as a result of their markedly reduced axial lengths, but otherwise are capable of seeing well unlike other more general forms of microphthalmia. To date one gene for nanophthalmos has been identified, encoding the membrane-type frizzled related protein MFRP. Identification of additional genes for nanophthalmos will improve our understanding of normal developmental regulation of eye growth. METHODS: We ascertained a cohort of families from eastern Canada and Mexico with familial nanophthalmos. We performed high density microsatellite and high density single nucleotide polymorphism (SNP) genotyping to identify potential chromosomal regions of linkage. We sequenced coding regions of genes in the linked interval by traditional PCR-based Sanger capillary electrophoresis methods. We cloned and sequenced a novel cDNA from a putative causal gene to verify gene structure. RESULTS: We identified a linked locus on chromosome 2q37 with a peak logarithm (base 10) of odds (LOD) score of 4.7. Sequencing of coding exons of all genes in the region identified multiple segregating variants in one gene, recently annotated as serine protease gene (PRSS56), coding for a predicted trypsin serine protease-like protein. One of our families was homozygous for a predicted pathogenic missense mutation, one family was compound heterozygous for two predicted pathogenic missense mutations, and one family was compound heterozygous for a predicted pathogenic missense mutation plus a frameshift leading to obligatory truncation of the predicted protein. The PRSS56 gene structure in public databases is based on a virtual transcript assembled from overlapping incomplete cDNA clones; we have now validated the structure of a full-length transcript from embryonic mouse brain RNA. CONCLUSIONS: PRSS56 is a good candidate for the causal gene for nanophthalmos in our families.

Effect of fluorocarbon molecules confined between sliding self-mated PTFE surfaces.

We report on the frictional response and atomic process that occur when molecular fluorocarbon molecules of varying lengths are sheared between two polytetrafluoroethylene (PTFE) surfaces. The thicknesses of the molecular layers are also varied. The approach is classical molecular dynamics simulations using a reactive bond-order potential parametrized for fluorocarbons. The results indicate that the presence of the molecules has a significant impact on the measured friction and wear of the surfaces, and that this impact depends on the nature of the fluorocarbon molecules and the thickness of the molecular film. The molecular mechanisms responsible for these differences are presented.

Re-examining the home disadvantage in professional ice hockey.

Occurrence of the home disadvantage in professional ice hockey was examined by analyzing shootout data from 2005 through 2008. Results indicated that teams involved in shootouts playing at their home arenas did not lose significantly more games at home than on the road. Results did not support the hypotheses that emphasize the roles of physical contact and diffusion of responsibility in accounting for past failures to find the home disadvantage in professional ice hockey.

Interfacial reactivity of Au, Pd, and Pt on BiI3 (001): implications for electrode selection.

Understanding the contact-semiconductor interface is important in determining the performance of a semiconductor device. This study investigated the contact chemistry of BiI(3) single crystal with Au, Pd, and Pt electrodes using X-ray photoelectron spectroscopy (XPS), a technique widely used to probe the interfacial chemistry of many materials. Chemical reactions were identified on the BiI(3) surface for the case of Pd and Pt contacts, while Au showed no reactivity with BiI(3). The difference in reactivities correlated with different surface morphologies of the contact on the BiI(3) surface, which was evidenced by atomic force microscopy (AFM) characterization. The dark resistivity of the BiI(3) crystal with above contact materials was measured by I-V characterization. The highest resistivity was obtained when Au was employed as the contact. These results suggest that Au is better than Pd and Pt as the contact material for BiI(3) single crystal.

Mutations in origin recognition complex gene ORC4 cause Meier-Gorlin syndrome.

Meier-Gorlin syndrome is a rare autosomal recessive genetic condition whose primary clinical hallmarks include small stature, small external ears and small or absent patellae. Using marker-assisted mapping in multiple families from a founder population and traditional coding exon sequencing of positional candidate genes, we identified three different mutations in the gene encoding ORC4, a component of the eukaryotic origin recognition complex, in five individuals with Meier-Gorlin syndrome. In two such individuals that were negative for mutations in ORC4, we found potential mutations in ORC1 and CDT1, two other genes involved in origin recognition. ORC4 is well conserved in eukaryotes, and the yeast equivalent of the human ORC4 missense mutation was shown to be pathogenic in functional assays of cell growth. This is the first report, to our knowledge, of a germline mutation in any gene of the origin recognition complex in a vertebrate organism.

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.

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.

The role of water in modifying friction within MoS2 sliding interfaces.

To explore the environmental dependence of friction for solid lubricants containing molybdenum disulfide (MoS(2)), we have investigated friction on the basal plane of single-crystal MoS(2) with atomic force microscopy (AFM) as a function of relative humidity (RH) and tip composition. For both a bare Si(3)N(4) tip and a MoS(2)-coated tip, changes in interfacial friction are observed with increasing relative humidity, however, with markedly different behaviors. For sliding contacts involving bare Si(3)N(4) tips, the friction coefficient is observed to increase with increasing RH, from 0% to the point of water saturation. For Si(3)N(4) tips precoated with MoS(2) particles, friction appears to be relatively insensitive to increasing RH in the range of 0-40%. However, above 40% RH, a drastic increase in friction is observed and is accompanied by evidence for interfacial wear provided in images of the basal plane following the friction measurements. A comparison to the tribological properties of the basal plane of highly oriented pyrolytic graphite (HOPG) using identical probe tips highlights the unique character of self-mated MoS(2) interfaces.

Distinguishing microbial genome fragments based on their composition: evolutionary and comparative genomic perspectives.

It is well known that patterns of nucleotide composition vary within and among genomes, although the reasons why these variations exist are not completely understood. Between-genome compositional variation has been exploited to assign environmental shotgun sequences to their most likely originating genomes, whereas within-genome variation has been used to identify recently acquired genetic material such as pathogenicity islands. Recent sequence assignment techniques have achieved high levels of accuracy on artificial data sets, but the relative difficulty of distinguishing lineages with varying degrees of relatedness, and different types of genomic sequence, has not been examined in depth. We investigated the compositional differences in a set of 774 sequenced microbial genomes, finding rapid divergence among closely related genomes, but also convergence of compositional patterns among genomes with similar habitats. Support vector machines were then used to distinguish all pairs of genomes based on genome fragments 500 nucleotides in length. The nearly 300,000 accuracy scores obtained from these trials were used to construct general models of distinguishability versus taxonomic and compositional indices of genomic divergence. Unusual genome pairs were evident from their large residuals relative to the fitted model, and we identified several factors including genome reduction, putative lateral genetic transfer, and habitat convergence that influence the distinguishability of genomes. The positional, compositional, and functional context of a fragment within a genome has a strong influence on its likelihood of correct classification, but in a way that depends on the taxonomic and ecological similarity of the comparator genome.

Reproducing the manual annotation of multiple sequence alignments using a SVM classifier.

MOTIVATION: Aligning protein sequences with the best possible accuracy requires sophisticated algorithms. Since the optimal alignment is not guaranteed to be the correct one, it is expected that even the best alignment will contain sites that do not respect the assumption of positional homology. Because formulating rules to identify these sites is difficult, it is common practice to manually remove them. Although considered necessary in some cases, manual editing is time consuming and not reproducible. We present here an automated editing method based on the classification of 'valid' and 'invalid' sites. RESULTS: A support vector machine (SVM) classifier is trained to reproduce the decisions made during manual editing with an accuracy of 95.0%. This implies that manual editing can be made reproducible and applied to large-scale analyses. We further demonstrate that it is possible to retrain/extend the training of the classifier by providing examples of multiple sequence alignment (MSA) annotation. Near optimal training can be achieved with only 1000 annotated sites, or roughly three samples of protein sequence alignments. AVAILABILITY: This method is implemented in the software MANUEL, licensed under the GPL. A web-based application for single and batch job is available at http://fester.cs.dal.ca/manuel. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.