A longitudinal evaluation of personalized intrinsic network topography and cognitive decline in Parkinson's disease.

Resting state functional magnetic resonance imaging (R-fMRI) offers insight into how synchrony within and between brain networks is altered in disease states. Individual and disease-related variability in intrinsic connectivity networks may influence our interpretation of R-fMRI data. We used a personalized approach designed to account for individual variation in the spatial location of correlation maxima to evaluate R-fMRI differences between Parkinson's disease (PD) patients who showed cognitive decline, those who remained cognitively stable and cognitively stable controls. We compared fMRI data from these participant groups, studied at baseline and 18 months later, using both network-based statistics (NBS) and calculations of mean inter- and intra-network connectivity within pre-defined functional networks. The NBS analysis showed that PD participants who remained cognitively stable showed exclusively (at baseline) or predominantly (at follow-up) increased intra-network connectivity, whereas decliners showed exclusively reduced intra-network and inter- (ventral attention and default mode) connectivity, in comparison with the control group. Evaluation of mean connectivity between all regions of interest (ROIs) within a priori networks showed that decliners had consistently reduced inter-network connectivity for ventral attention, somatomotor, visual and striatal networks and reduced intra-network connectivity for ventral attention network to striatum and cerebellum. These findings suggest that specific functional connectivity covariance patterns differentiate PD cognitive subtypes and may predict cognitive decline. Further, increased intra and inter-network synchrony may support cognitive function in the face of PD-related network disruptions.

Using in vivo functional and structural connectivity to predict chronic stroke aphasia deficits.

Focal brain damage caused by stroke can result in aphasia and advances in cognitive neuroscience suggest that impairment may be associated with network-level disorder rather than just circumscribed cortical damage. Several studies have shown meaningful relationships between brain-behaviour using lesions; however, only a handful of studies have incorporated in vivo structural and functional connectivity. Patients with chronic post-stroke aphasia were assessed with structural (n = 68) and functional (n = 39) MRI to assess whether predicting performance can be improved with multiple modalities and if additional variance can be explained compared to lesion models alone. These neural measurements were used to construct models to predict four key language-cognitive factors: (i) phonology; (ii) semantics; (iii) executive function; and (iv) fluency. Our results showed that each factor (except executive ability) could be significantly related to each neural measurement alone; however, structural and functional connectivity models did not explain additional variance above the lesion models. We did find evidence that the structural and functional predictors may be linked to the core lesion sites. First, the predictive functional connectivity features were found to be located within functional resting-state networks identified in healthy controls, suggesting that the result might reflect functionally specific reorganization (damage to a node within a network can result in disruption to the entire network). Second, predictive structural connectivity features were located within core lesion sites, suggesting that multimodal information may be redundant in prediction modelling. In addition, we observed that the optimum sparsity within the regularized regression models differed for each behavioural component and across different imaging features, suggesting that future studies should consider optimizing hyperparameters related to sparsity per target. Together, the results indicate that the observed network-level disruption was predicted by the lesion alone and does not significantly improve model performance in predicting the profile of language impairment.

Bipartite functional fractionation within the neural system for social cognition supports the psychological continuity of self versus other.

Research of social neuroscience establishes that regions in the brain's default-mode network (DN) and semantic network (SN) are engaged by socio-cognitive tasks. Research of the human connectome shows that DN and SN regions are both situated at the transmodal end of a cortical gradient but differ in their loci along this gradient. Here we integrated these 2 bodies of research, used the psychological continuity of self versus other as a "test-case," and used functional magnetic resonance imaging to investigate whether these 2 networks would encode social concepts differently. We found a robust dissociation between the DN and SN-while both networks contained sufficient information for decoding broad-stroke distinction of social categories, the DN carried more generalizable information for cross-classifying across social distance and emotive valence than did the SN. We also found that the overarching distinction of self versus other was a principal divider of the representational space while social distance was an auxiliary factor (subdivision, nested within the principal dimension), and this representational landscape was more manifested in the DN than in the SN. Taken together, our findings demonstrate how insights from connectome research can benefit social neuroscience and have implications for clarifying the 2 networks' differential contributions to social cognition.

Child-oriented word associations improve models of early word learning.

How words are associated within the linguistic environment conveys semantic content; however, different contexts induce different linguistic patterns. For instance, it is well known that adults speak differently to children than to other adults. We present results from a new word association study in which adult participants were instructed to produce either unconstrained or child-oriented responses to each cue, where cues included 672 nouns, verbs, adjectives, and other word forms from the McArthur-Bates Communicative Development Inventory (CDI; Fenson et al., 2006). Child-oriented responses consisted of higher frequency words with fewer letters, earlier ages of acquisition, and higher contextual diversity. Furthermore, the correlations among the responses generated for each pair of cues differed between unconstrained (adult-oriented) and child-oriented responses, suggesting that child-oriented associations imply different semantic structure. A comparison of growth models guided by a semantic network structure revealed that child-oriented associations are more predictive of early lexical growth. Additionally, relative to a growth model based on a corpus of naturalistic child-directed speech, the child-oriented associations explain added unique variance to lexical growth. Thus, these new child-oriented word association norms provide novel insight into the semantic context of young children and early lexical development.

Interpretations of meaningful and ambiguous hand gestures in autistic and non-autistic adults: A norming study.

Gestures are ubiquitous in human communication, and a growing but inconsistent body of research suggests that people with autism spectrum disorder (ASD) may process co-speech gestures differently from neurotypical individuals. To facilitate research on this topic, we created a database of 162 gesture videos that have been normed for comprehensibility by both autistic and non-autistic raters. These videos portray an actor performing silent gestures that range from highly meaningful (e.g., iconic gestures) to ambiguous or meaningless. Each video was rated for meaningfulness and given a one-word descriptor by 40 autistic and 40 non-autistic adults, and analyses were conducted to assess the level of within- and across-group agreement. Across gestures, the meaningfulness ratings provided by raters with and without ASD correlated at r > 0.90, indicating a very high level of agreement. Overall, autistic raters produced a more diverse set of verbal labels for each gesture than did non-autistic raters. However, measures of within-gesture semantic similarity among the responses provided by each group did not differ, suggesting that increased variability within the ASD group may have occurred at the lexical rather than semantic level. This study is the first to compare gesture naming between autistic and non-autistic individuals, and the resulting dataset is the first gesture stimulus set for which both groups were equally represented in the norming process. This database also has broad applicability to other areas of research related to gesture processing and comprehension. The video database and accompanying norming data are available on the Open Science Framework.

Finding Distributed Needles in Neural Haystacks.

The human cortex encodes information in complex networks that can be anatomically dispersed and variable in their microstructure across individuals. Using simulations with neural network models, we show that contemporary statistical methods for functional brain imaging-including univariate contrast, searchlight multivariate pattern classification, and whole-brain decoding with L1 or L2 regularization-each have critical and complementary blind spots under these conditions. We then introduce the sparse-overlapping-sets (SOS) LASSO-a whole-brain multivariate approach that exploits structured sparsity to find network-distributed information-and show in simulation that it captures the advantages of other approaches while avoiding their limitations. When applied to fMRI data to find neural responses that discriminate visually presented faces from other visual stimuli, each method yields a different result, but existing approaches all support the canonical view that face perception engages localized areas in posterior occipital and temporal regions. In contrast, SOS LASSO uncovers a network spanning all four lobes of the brain. The result cannot reflect spurious selection of out-of-system areas because decoding accuracy remains exceedingly high even when canonical face and place systems are removed from the dataset. When used to discriminate visual scenes from other stimuli, the same approach reveals a localized signal consistent with other methods-illustrating that SOS LASSO can detect both widely distributed and localized representational structure. Thus, structured sparsity can provide an unbiased method for testing claims of functional localization. For faces and possibly other domains, such decoding may reveal representations more widely distributed than previously suspected.SIGNIFICANCE STATEMENT Brain systems represent information as patterns of activation over neural populations connected in networks that can be widely distributed anatomically, variable across individuals, and intermingled with other networks. We show that four widespread statistical approaches to functional brain imaging have critical blind spots in this scenario and use simulations with neural network models to illustrate why. We then introduce a new approach designed specifically to find radically distributed representations in neural networks. In simulation and in fMRI data collected in the well studied domain of face perception, the new approach discovers extensive signal missed by the other methods-suggesting that prior functional imaging work may have significantly underestimated the degree to which neurocognitive representations are distributed and variable across individuals.

Metal Oxide Laser Ionization Mass Spectrometry Imaging (MOLI MSI) Using Cerium(IV) Oxide.

Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) is a powerful technique for spatially resolved metabolomics. A variation on MALDI, termed metal oxide laser ionization (MOLI), capitalizes on the unique property of cerium(IV) oxide (CeO2) to induce laser-catalyzed fatty acyl cleavage from lipids and has been utilized for bacterial identification. In this study, we present the development and utilization of CeO2 as an MSI catalyst. The method was developed using a MALDI TOF instrument in negative ion mode, equipped with a high frequency laser. Instrument parameters for MOLI MS fatty acid catalysis with CeO2 were optimized with phospholipid standards and fatty acid catalysis was confirmed using lipid extracts from reference bacterial strains, and sample preparation was optimized using mouse brain tissue. MOLI MSI was applied to the imaging of normal mouse brain revealing differentiable fatty acyl pools in myelinated and nonmyelinated regions. Similarly, MOLI MSI showed distinct fatty acyl composition in tumor regions of a patient derived xenograft mouse model of glioblastoma. To assess the potential of MOLI MSI to detect pathogens directly from tissue, a pseudoinfection model was prepared by spotting Escherichia coli lipid extracts on mouse brain tissue sections and imaged by MOLI MSI. The spotted regions were molecularly resolved from the supporting mouse brain tissue by the diagnostic odd-chained fatty acids and reflected control bacterial MOLI MS signatures. We describe MOLI MSI for the first time and highlight its potential for spatially resolved fatty acyl analysis, characterization of fatty acyl composition in tumors, and its potential for pathogen detection directly from tissue.

Efficient protease based purification of recombinant matrix metalloprotease-1 in E. coli.

MMP1 is an essential enzyme for tissue remodeling both in normal and pathological states. We report a method of purifying activated human MMP1 in E. coli without using urea or 4-Aminophenylmercuric acetate (APMA). Instead, a non-ionic detergent, Triton X-100, was used in the lysis buffer to solubilize MMP1 followed by the protease activities of both trypsin and MMP1 to digest E. coli proteins and activate pro-MMP1. Identity of activated MMP1 was confirmed by Western blot using anti-human MMP1 antibodies, whereas the mass was determined to be 43 kD using matrix assisted laser desorption ionization time-of-flight mass spectrometry (MALDI TOF-MS). Collagen and gelatin degradation by purified MMP1 were confirmed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS PAGE) of degraded FITC-labeled type-1 collagen and gelatin zymogram. Broad-spectrum protease activity of purified MMP1 was also confirmed by lysis of native E. coli proteins. Inexpensive high throughput purification of recombinant human MMP1 in E. coli will enable easier MMP1 production for diverse applications.

Strain-level Staphylococcus differentiation by CeO2-metal oxide laser ionization mass spectrometry fatty acid profiling.

BACKGROUND: The Staphylococcus genus is composed of 44 species, with S. aureus being the most pathogenic. Isolates of S. aureus are generally susceptible to ß-lactam antibiotics, but extensive use of this class of drugs has led to increasing emergence of resistant strains. Increased occurrence of coagulase-negative staphylococci as well as S. aureus infections, some with resistance to multiple classes of antibiotics, has driven the necessity for innovative options for treatment and infection control. Despite these increasing needs, current methods still only possess species-level capabilities and require secondary testing to determine antibiotic resistance. This study describes the use of metal oxide laser ionization mass spectrometry fatty acid (FA) profiling as a rapid, simultaneous Staphylococcus identification and antibiotic resistance determination method. RESULTS: Principal component analysis was used to classify 50 Staphyloccocus isolates. Leave-one-spectrum-out cross-validation indicated 100 % correct assignment at the species and strain level. Fuzzy rule building expert system classification and self-optimizing partial least squares discriminant analysis, with more rigorous evaluations, also consistently achieved greater than 94 and 84 % accuracy, respectively. Preliminary analysis differentiating MRSA from MSSA demonstrated the feasibility of simultaneous determination of strain identification and antibiotic resistance. CONCLUSION: The utility of CeO2-MOLI MS FA profiling coupled with multivariate statistical analysis for performing strain-level differentiation of various Staphylococcus species proved to be a fast and reliable tool for identification. The simultaneous strain-level detection and antibiotic resistance determination achieved with this method should greatly improve outcomes and reduce clinical costs for therapeutic management and infection control.

Identification of bacteria by fatty acid profiling with direct analysis in real time mass spectrometry.

RATIONALE: Bacterial fatty acid profiling is a well-established technique for bacterial identification. Current methods involving esterification and gas chromatography/mass spectrometry (GC/MS) or matrix-assisted laser desorption/ionization (MALDI) analysis are effective, but there are potential benefits to be gained by investigating ambient ionization methods that can provide rapid analysis without derivatization or additional sample handling. METHODS: Lipid extracts from colonies of five Gram-positive and five Gram-negative pathogenic bacteria were analyzed by Direct Analysis in Real Time (DART) ionization coupled with a time-of-flight mass spectrometer. Fatty acid profiles were obtained from the negative-ion DART mass spectra without additional derivatization or sample preparation. RESULTS: Fatty acid profiles obtained from the deprotonated molecules [M - H](-) were found to be highly species-specific and reproducible. Leave-one-out cross validation (LOOCV) for principal component analysis (PCA) showed 100% correct classification accuracy. CONCLUSIONS: The results of this preliminary feasibility study show good precision and accuracy, and the fatty acid patterns are clearly distinctive for each of the ten species examined. The speed and ease of analysis and the high classification accuracy for this initial study indicate that DART is an effective method for bacterial fatty acid profiling.

Decoding semantic representations in mind and brain.

A key goal for cognitive neuroscience is to understand the neurocognitive systems that support semantic memory. Recent multivariate analyses of neuroimaging data have contributed greatly to this effort, but the rapid development of these novel approaches has made it difficult to track the diversity of findings and to understand how and why they sometimes lead to contradictory conclusions. We address this challenge by reviewing cognitive theories of semantic representation and their neural instantiation. We then consider contemporary approaches to neural decoding and assess which types of representation each can possibly detect. The analysis suggests why the results are heterogeneous and identifies crucial links between cognitive theory, data collection, and analysis that can help to better connect neuroimaging to mechanistic theories of semantic cognition.

φX216, a P2-like bacteriophage with broad Burkholderia pseudomallei and B. mallei strain infectivity.

BACKGROUND: Burkholderia pseudomallei and B. mallei are closely related Category B Select Agents of bioterrorism and the causative agents of the diseases melioidosis and glanders, respectively. Rapid phage-based diagnostic tools would greatly benefit early recognition and treatment of these diseases. There is extensive strain-to-strain variation in B. pseudomallei genome content due in part to the presence or absence of integrated prophages. Several phages have previously been isolated from B. pseudomallei lysogens, for example φK96243, φ1026b and φ52237. RESULTS: We have isolated a P2-like bacteriophage, φX216, which infects 78% of all B. pseudomallei strains tested. φX216 also infects B. mallei, but not other Burkholderia species, including the closely related B. thailandensis and B. oklahomensis. The nature of the φX216 host receptor remains unclear but evidence indicates that in B. mallei φX216 uses lipopolysaccharide O-antigen but a different receptor in B. pseudomallei. The 37,637 bp genome of φX216 encodes 47 predicted open reading frames and shares 99.8% pairwise identity and an identical strain host range with bacteriophage φ52237. Closely related P2-like prophages appear to be widely distributed among B. pseudomallei strains but both φX216 and φ52237 readily infect prophage carrying strains. CONCLUSIONS: The broad strain infectivity and high specificity for B. pseudomallei and B. mallei indicate that φX216 will provide a good platform for the development of phage-based diagnostics for these bacteria.

High Predictive Accuracy of Negative Schizotypy With Acoustic Measures.

Negative schizotypal traits potentially can be digitally phenotyped using objective vocal analysis. Prior attempts have shown mixed success in this regard, potentially because acoustic analysis has relied on small, constrained feature sets. We employed machine learning to (a) optimize and cross-validate predictive models of self-reported negative schizotypy using a large acoustic feature set, (b) evaluate model performance as a function of sex and speaking task, (c) understand potential mechanisms underlying negative schizotypal traits by evaluating the key acoustic features within these models, and (d) examine model performance in its convergence with clinical symptoms and cognitive functioning. Accuracy was good (> 80%) and was improved by considering speaking task and sex. However, the features identified as most predictive of negative schizotypal traits were generally not considered critical to their conceptual definitions. Implications for validating and implementing digital phenotyping to understand and quantify negative schizotypy are discussed.

Mass Spectrometry and Microbial Diagnostics in the Clinical Laboratory.

Over the past decade, matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry has revolutionized the practice of clinical microbiology and infectious disease diagnostics. Rapid advancement has occurred through the development and implementation of mass spectrometric protein profiling technologies that are widely available. Ease of sample preparation, rapid turnaround times, and high throughput accuracy have accelerated acceptance within the clinical laboratory. New mass spectrometric technologies centered on multiple microbial diagnostic markers are in development. Such new applications, reviewed in this article and on the near horizon, stand to greatly enhance the capabilities and utility for improved mass spectrometric microbial identification and patient care.

Characterizing the early vocabulary profiles of preverbal and minimally verbal children with autism spectrum disorder.

LAY ABSTRACT: Although preverbal and minimally verbal children with autism spectrum disorder represent a significant portion of the autism spectrum disorder population, we have a limited understanding of and characterization of them. Although it is a given that their lexical profiles contain fewer words, it is important to determine whether (a) the words preverbal and minimally verbal children with autism spectrum disorder produce are similar to the first words typically developing children produce or (b) there are unique features of the limited words that preverbal and minimally verbal children with autism spectrum disorder produce. The current study compared the early word profiles of preverbal and minimally verbal children with autism spectrum disorder to vocabulary-matched typically developing toddlers. Children with autism spectrum disorder produced proportionally more verbs than typically developing toddlers. Also, children with autism spectrum disorder produced proportionally more action and food words, while typically developing toddlers produced proportionally more animal words, animal sounds and sound effects, and people words. Children with autism spectrum disorder also produced "mommy" and "daddy" at lower rates. Our findings identified several areas of overlap in early word learning; however, our findings also point to differences that may be connected to core weaknesses in social communication (i.e. people words). The findings highlight words and categories that could serve as useful targets for communication intervention with preverbal and minimally verbal children with autism spectrum disorder.

Evidence for a deep, distributed and dynamic code for animacy in human ventral anterior temporal cortex.

How does the human brain encode semantic information about objects? This paper reconciles two seemingly contradictory views. The first proposes that local neural populations independently encode semantic features; the second, that semantic representations arise as a dynamic distributed code that changes radically with stimulus processing. Combining simulations with a well-known neural network model of semantic memory, multivariate pattern classification, and human electrocorticography, we find that both views are partially correct: information about the animacy of a depicted stimulus is distributed across ventral temporal cortex in a dynamic code possessing feature-like elements posteriorly but with elements that change rapidly and nonlinearly in anterior regions. This pattern is consistent with the view that anterior temporal lobes serve as a deep cross-modal 'hub' in an interactive semantic network, and more generally suggests that tertiary association cortices may adopt dynamic distributed codes difficult to detect with common brain imaging methods.

Validating Biobehavioral Technologies for Use in Clinical Psychiatry.

The last decade has witnessed the development of sophisticated biobehavioral and genetic, ambulatory, and other measures that promise unprecedented insight into psychiatric disorders. As yet, clinical sciences have struggled with implementing these objective measures and they have yet to move beyond "proof of concept." In part, this struggle reflects a traditional, and conceptually flawed, application of traditional psychometrics (i.e., reliability and validity) for evaluating them. This paper focuses on "resolution," concerning the degree to which changes in a signal can be detected and quantified, which is central to measurement evaluation in informatics, engineering, computational and biomedical sciences. We define and discuss resolution in terms of traditional reliability and validity evaluation for psychiatric measures, then highlight its importance in a study using acoustic features to predict self-injurious thoughts/behaviors (SITB). This study involved tracking natural language and self-reported symptoms in 124 psychiatric patients: (a) over 5-14 recording sessions, collected using a smart phone application, and (b) during a clinical interview. Importantly, the scope of these measures varied as a function of time (minutes, weeks) and spatial setting (i.e., smart phone vs. interview). Regarding reliability, acoustic features were temporally unstable until we specified the level of temporal/spatial resolution. Regarding validity, accuracy based on machine learning of acoustic features predicting SITB varied as a function of resolution. High accuracy was achieved (i.e., ~87%), but only when the acoustic and SITB measures were "temporally-matched" in resolution was the model generalizable to new data. Unlocking the potential of biobehavioral technologies for clinical psychiatry will require careful consideration of resolution.

Enhanced matrix-assisted laser desorption/ionization time-of-flight mass spectrometric analysis of bacteriophage major capsid proteins with beta-mercaptoethanol pretreatment.

Bacteriophage (phage) proteins have been analyzed previously with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). However, analysis of phage major capsid proteins (MCPs) has been limited by the ability to reproducibly generate ions from MCP monomers. While the acidic conditions of MALDI-TOF MS sample preparation have been shown to aid in disassembly of some phage capsids, many require further treatment to successfully liberate MCP monomers. The findings presented here suggest that beta-mercaptoethanol reduction of the disulfide bonds linking phage MCPs prior to mass spectrometric analysis results in significantly increased MALDI-TOF MS sensitivity and reproducibility of Yersinia pestis-specific phage protein profiles.

Current Perspective: 3D Spheroid Models Utilizing Human-Based Cells for Investigating Metabolism-Dependent Drug-Induced Liver Injury.

Drug-induced liver injury (DILI) remains a leading cause for the withdrawal of approved drugs. This has significant financial implications for pharmaceutical companies, places increasing strain on global health services, and causes harm to patients. For these reasons, it is essential that in-vitro liver models are capable of detecting DILI-positive compounds and their underlying mechanisms, prior to their approval and administration to patients or volunteers in clinical trials. Metabolism-dependent DILI is an important mechanism of drug-induced toxicity, which often involves the CYP450 family of enzymes, and is associated with the production of a chemically reactive metabolite and/or inefficient removal and accumulation of potentially toxic compounds. Unfortunately, many of the traditional in-vitro liver models fall short of their in-vivo counterparts, failing to recapitulate the mature hepatocyte phenotype, becoming metabolically incompetent, and lacking the longevity to investigate and detect metabolism-dependent DILI and those associated with chronic and repeat dosing regimens. Nevertheless, evidence is gathering to indicate that growing cells in 3D formats can increase the complexity of these models, promoting a more mature-hepatocyte phenotype and increasing their longevity, in vitro. This review will discuss the use of 3D in vitro models, namely spheroids, organoids, and perfusion-based systems to establish suitable liver models to investigate metabolism-dependent DILI.

Machine learning for suicidology: A practical review of exploratory and hypothesis-driven approaches.

Machine learning is being used to discover models to predict the progression from suicidal ideation to action in clinical populations. While quantifiable improvements in prediction accuracy have been achieved over theory-driven efforts, models discovered through machine learning continue to fall short of clinical relevance. Thus, the value of machine learning for reaching this objective is hotly contested. We agree that machine learning, treated as a "black box" approach antithetical to theory-building, will not discover clinically relevant models of suicide. However, such models may be developed through deliberate synthesis of data- and theory-driven approaches. By providing an accessible overview of essential concepts and common methods, we highlight how generalizable models and scientific insight may be obtained by incorporating prior knowledge and expectations to machine learning research, drawing examples from suicidology. We then discuss challenges investigators will face when using machine learning to discover models of low prevalence outcomes, such as suicide.