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1.
Cortex ; 180: 18-34, 2024 Sep 11.
Article in English | MEDLINE | ID: mdl-39305720

ABSTRACT

There are recognized neuroimaging regions of interest in typical Alzheimer's disease which have been used to track disease progression and aid prognostication. However, there is a need for validated baseline imaging markers to predict clinical decline in atypical Alzheimer's Disease. We aimed to address this need by producing models from baseline imaging features using penalized regression and evaluating their predictive performance on various clinical measures. Baseline multimodal imaging data, in combination with clinical testing data at two time points from 46 atypical Alzheimer's Disease patients with a diagnosis of logopenic progressive aphasia (N = 24) or posterior cortical atrophy (N = 22), were used to generate our models. An additional 15 patients (logopenic progressive aphasia = 7, posterior cortical atrophy = 8), whose data were not used in our original analysis, were used to test our models. Patients underwent MRI, FDG-PET and Tau-PET imaging and a full neurologic battery at two time points. The Schaefer functional atlas was used to extract network-based and regional gray matter volume or PET SUVR values from baseline imaging. Penalized regression (Elastic Net) was used to create models to predict scores on testing at Time 2 while controlling for baseline performance, education, age, and sex. In addition, we created models using clinical or Meta Region of Interested (ROI) data to serve as comparisons. We found the degree of baseline involvement on neuroimaging was predictive of future performance on cognitive testing while controlling for the above measures on all three imaging modalities. In many cases, model predictability improved with the addition of network-based neuroimaging data to clinical data. We also found our network-based models performed superiorly to the comparison models comprised of only clinical or a Meta ROI score. Creating predictive models from imaging studies at a baseline time point that are agnostic to clinical diagnosis as we have described could prove invaluable in both the clinical and research setting, particularly in the development and implementation of future disease modifying therapies.

3.
Brain Commun ; 6(4): fcae227, 2024.
Article in English | MEDLINE | ID: mdl-39086629

ABSTRACT

Electrophysiologic disturbances due to neurodegenerative disorders such as Alzheimer's disease and Lewy Body disease are detectable by scalp EEG and can serve as a functional measure of disease severity. Traditional quantitative methods of EEG analysis often require an a-priori selection of clinically meaningful EEG features and are susceptible to bias, limiting the clinical utility of routine EEGs in the diagnosis and management of neurodegenerative disorders. We present a data-driven tensor decomposition approach to extract the top 6 spectral and spatial features representing commonly known sources of EEG activity during eyes-closed wakefulness. As part of their neurologic evaluation at Mayo Clinic, 11 001 patients underwent 12 176 routine, standard 10-20 scalp EEG studies. From these raw EEGs, we developed an algorithm based on posterior alpha activity and eye movement to automatically select awake-eyes-closed epochs and estimated average spectral power density (SPD) between 1 and 45 Hz for each channel. We then created a three-dimensional (3D) tensor (record × channel × frequency) and applied a canonical polyadic decomposition to extract the top six factors. We further identified an independent cohort of patients meeting consensus criteria for mild cognitive impairment (30) or dementia (39) due to Alzheimer's disease and dementia with Lewy Bodies (31) and similarly aged cognitively normal controls (36). We evaluated the ability of the six factors in differentiating these subgroups using a Naïve Bayes classification approach and assessed for linear associations between factor loadings and Kokmen short test of mental status scores, fluorodeoxyglucose (FDG) PET uptake ratios and CSF Alzheimer's Disease biomarker measures. Factors represented biologically meaningful brain activities including posterior alpha rhythm, anterior delta/theta rhythms and centroparietal beta, which correlated with patient age and EEG dysrhythmia grade. These factors were also able to distinguish patients from controls with a moderate to high degree of accuracy (Area Under the Curve (AUC) 0.59-0.91) and Alzheimer's disease dementia from dementia with Lewy Bodies (AUC 0.61). Furthermore, relevant EEG features correlated with cognitive test performance, PET metabolism and CSF AB42 measures in the Alzheimer's subgroup. This study demonstrates that data-driven approaches can extract biologically meaningful features from population-level clinical EEGs without artefact rejection or a-priori selection of channels or frequency bands. With continued development, such data-driven methods may improve the clinical utility of EEG in memory care by assisting in early identification of mild cognitive impairment and differentiating between different neurodegenerative causes of cognitive impairment.

4.
Commun Biol ; 7(1): 919, 2024 Jul 30.
Article in English | MEDLINE | ID: mdl-39079981

ABSTRACT

Retinoblastoma are childhood eye tumors arising from retinal precursor cells. Two distinct retinoblastoma subtypes with different clinical behavior have been described based on gene expression and methylation profiling. Using consensus clustering of DNA methylation analysis from 61 retinoblastomas, we identify a MYCN-driven cluster of subtype 2 retinoblastomas characterized by DNA hypomethylation and high expression of genes involved in protein synthesis. Subtype 2 retinoblastomas outside the MYCN-driven cluster are characterized by high expression of genes from mesodermal development, including NKX2-5. Knockdown of MYCN expression in retinoblastoma cell models causes growth arrest and reactivates a subtype 1-specific photoreceptor signature. These molecular changes suggest that removing the driving force of MYCN oncogenic activity rescues molecular circuitry driving subtype 1 biology. The MYCN-RB gene signature generated from the cell models better identifies MYCN-driven retinoblastoma than MYCN amplification and can identify cases that may benefit from MYCN-targeted therapy. MYCN drives tumor progression in a molecularly defined retinoblastoma subgroup, and inhibiting MYCN activity could restore a more differentiated and less aggressive tumor biology.


Subject(s)
N-Myc Proto-Oncogene Protein , Retinoblastoma , Humans , Retinoblastoma/genetics , Retinoblastoma/pathology , N-Myc Proto-Oncogene Protein/genetics , N-Myc Proto-Oncogene Protein/metabolism , DNA Methylation , Retinal Neoplasms/genetics , Retinal Neoplasms/pathology , Retinal Neoplasms/metabolism , Gene Expression Regulation, Neoplastic , Cell Line, Tumor , Cell Dedifferentiation/genetics , Female , Male , Child, Preschool
5.
Brain Commun ; 6(4): fcae183, 2024.
Article in English | MEDLINE | ID: mdl-39021510

ABSTRACT

Predominant limbic degeneration has been associated with various underlying aetiologies and an older age, predominant impairment of episodic memory and slow clinical progression. However, the neurological syndrome associated with predominant limbic degeneration is not defined. This endeavour is critical to distinguish such a syndrome from those originating from neocortical degeneration, which may differ in underlying aetiology, disease course and therapeutic needs. We propose a set of clinical criteria for a limbic-predominant amnestic neurodegenerative syndrome that is highly associated with limbic-predominant age-related TDP-43 encephalopathy but also other pathologic entities. The criteria incorporate core, standard and advanced features, including older age at evaluation, mild clinical syndrome, disproportionate hippocampal atrophy, impaired semantic memory, limbic hypometabolism, absence of neocortical degeneration and low likelihood of neocortical tau, with degrees of certainty (highest, high, moderate and low). We operationalized this set of criteria using clinical, imaging and biomarker data to validate its associations with clinical and pathologic outcomes. We screened autopsied patients from Mayo Clinic and Alzheimer's Disease Neuroimaging Initiative cohorts and applied the criteria to those with an antemortem predominant amnestic syndrome (Mayo, n = 165; Alzheimer's Disease Neuroimaging Initiative, n = 53) and who had Alzheimer's disease neuropathological change, limbic-predominant age-related TDP-43 encephalopathy or both pathologies at autopsy. These neuropathology-defined groups accounted for 35, 37 and 4% of cases in the Mayo cohort, respectively, and 30, 22 and 9% of cases in the Alzheimer's Disease Neuroimaging Initiative cohort, respectively. The criteria effectively categorized these cases, with Alzheimer's disease having the lowest likelihoods, limbic-predominant age-related TDP-43 encephalopathy patients having the highest likelihoods and patients with both pathologies having intermediate likelihoods. A logistic regression using the criteria features as predictors of TDP-43 achieved a balanced accuracy of 74.6% in the Mayo cohort, and out-of-sample predictions in an external cohort achieved a balanced accuracy of 73.3%. Patients with high likelihoods had a milder and slower clinical course and more severe temporo-limbic degeneration compared to those with low likelihoods. Stratifying patients with both Alzheimer's disease neuropathological change and limbic-predominant age-related TDP-43 encephalopathy from the Mayo cohort according to their likelihoods revealed that those with higher likelihoods had more temporo-limbic degeneration and a slower rate of decline and those with lower likelihoods had more lateral temporo-parietal degeneration and a faster rate of decline. The implementation of criteria for a limbic-predominant amnestic neurodegenerative syndrome has implications to disambiguate the different aetiologies of progressive amnestic presentations in older age and guide diagnosis, prognosis, treatment and clinical trials.

7.
Sci Rep ; 14(1): 17464, 2024 07 29.
Article in English | MEDLINE | ID: mdl-39075097

ABSTRACT

Digital quantification of gait can be used to measure aging- and disease-related decline in mobility. Gait performance also predicts prognosis, disease progression, and response to therapies. Most gait analysis systems require large amounts of space, resources, and expertise to implement and are not widely accessible. Thus, there is a need for a portable system that accurately characterizes gait. Here, depth video from two portable cameras accurately reconstructed gait metrics comparable to those reported by a pressure-sensitive walkway. 392 research participants walked across a four-meter pressure-sensitive walkway while depth video was recorded. Gait speed, cadence, and step and stride durations and lengths strongly correlated (r > 0.9) between modalities, with root-mean-squared-errors (RMSE) of 0.04 m/s, 2.3 steps/min, 0.03 s, and 0.05-0.08 m for speed, cadence, step/stride duration, and step/stride length, respectively. Step, stance, and double support durations (gait cycle percentage) significantly correlated (r > 0.6) between modalities, with 5% RMSE for step and stance and 10% RMSE for double support. In an exploratory analysis, gait speed from both modalities significantly related to healthy, mild, moderate, or severe categorizations of Charleson Comorbidity Indices (ANOVA, Tukey's HSD, p < 0.0125). These findings demonstrate the viability of using depth video to expand access to quantitative gait assessments.


Subject(s)
Gait Analysis , Gait , Humans , Male , Female , Gait/physiology , Middle Aged , Gait Analysis/methods , Gait Analysis/instrumentation , Adult , Video Recording/methods , Aged , Walking/physiology , Pressure , Walking Speed/physiology , Motion Capture
8.
Acta Neuropathol ; 147(1): 95, 2024 06 07.
Article in English | MEDLINE | ID: mdl-38847845

ABSTRACT

The non-WNT/non-SHH (Grp3/Grp4) medulloblastomas (MBs) include eight second-generation subgroups (SGS; I-VIII) each with distinct molecular and clinical characteristics. Recently, we also identified two prognostically relevant transcriptome subtypes within each SGS MB, which are associated with unique gene expression signatures and signaling pathways. These prognostic subsets may be in connection to the intra-tumoral cell landscape that underlies SGS MB clinical-molecular diversity. Here, we performed a deconvolution analysis of the Grp3/Grp4 MB bulk RNA profiles using the previously identified single-cell RNA-seq reference dataset and focusing on variability in the cellular composition of SGS MB. RNA deconvolution analysis of the Grp3/Grp4 MB disclosed the subgroup-specific neoplastic cell subpopulations. Neuronally differentiated axodendritic GP3-C1 and glutamatergic GP4-C1 subpopulations were distributed within Grp3- and Grp4-associated SGS MB, respectively. Progenitor GP3-B2 subpopulation was prominent in aggressive SGS II MB, whereas photoreceptor/visual perception GP3/4-C2 cell content was typical for SGS III/IV MB. The current study also revealed significant variability in the proportions of cell subpopulations between clinically relevant SGS MB transcriptome subtypes, where unfavorable cohorts were enriched with cell cycle and progenitor-like cell subpopulations and, vice versa, favorable subtypes were composed of neuronally differentiated cell fractions predominantly. A higher than median proportion of proliferating and progenitor cell subpopulations conferred the shortest survival of the Grp3 and Grp 4 MB, and similar survival associations were identified for all SGS MB except SGS IV MB. In summary, the recently identified clinically relevant Grp3/Grp4 MB transcriptome subtypes are composed of different cell populations. Future studies should aim to validate the prognostic and therapeutic role of the identified Grp3/Grp4 MB inter-tumoral cellular heterogeneity. The application of the single-cell techniques on each SGS MB separately could help to clarify the clinical significance of subgroup-specific variability in tumor cell content and its relation with prognostic transcriptome signatures identified before.


Subject(s)
Cerebellar Neoplasms , Medulloblastoma , Transcriptome , Humans , Medulloblastoma/genetics , Medulloblastoma/pathology , Medulloblastoma/metabolism , Cerebellar Neoplasms/genetics , Cerebellar Neoplasms/pathology , Cerebellar Neoplasms/metabolism , Cell Proliferation/genetics , Male , Child , Female , Child, Preschool , Adolescent , Prognosis
9.
Mayo Clin Proc ; 99(8): 1284-1296, 2024 Aug.
Article in English | MEDLINE | ID: mdl-38935019

ABSTRACT

OBJECTIVE: To evaluate the performance of Alzheimer disease (AD) cerebrospinal fluid (CSF) biomarkers in a tertiary neurology clinic setting with high frequency of non-AD cases, including normal pressure hydrocephalus (NPH). METHODS: There were 534 patients who underwent AD CSF biomarkers (Roche Elecsys Aß42, p-Tau181, total-Tau) from April 1, 2020, through April 23, 2021. A behavioral neurologist blinded to CSF results assigned a clinical diagnosis retrospectively on the basis of consensus criteria, and a neuroradiologist blinded to the diagnosis and CSF studies graded brain magnetic resonance images for indicators of CSF dynamics disorders. Associations between biomarkers, diagnoses, and imaging were assessed by χ2, analysis of covariance, and linear regression methods. RESULTS: Median age at time of testing was 67 years (range, 19 to 96 years), median symptom duration was 2 years (range, 0.4 to 28 years), and median Short Test of Mental Status score was 30 (range, 0 to 38). Clinical diagnoses significantly correlated with different CSF biomarker values (χ2=208.3; P=10e-4). p-Tau181/Aß42 ratios above 0.023 positively correlated with Alzheimer dementia (more than individual measures). This ratio also had the best performance for differentiating Alzheimer dementia from NPH (area under the curve, 0.869). Imaging markers supportive of CSF dynamics disorders correlated with low Aß42, p-Tau181, and total-Tau. CONCLUSION: In a heterogeneous clinical population, abnormal p-Tau181/Aß42 ratios (>0.023) have the strongest association with Alzheimer dementia and probably represent a comorbid AD pathologic component in persons clearly matching non-AD neurodegenerative syndromes. Altered CSF dynamics were associated with lower concentrations of AD CSF biomarkers regardless of clinical diagnosis, but the ratio compensates for these changes. In the appropriate clinical setting, an isolated abnormal Aß42 should prompt consideration of NPH.


Subject(s)
Alzheimer Disease , Amyloid beta-Peptides , Biomarkers , tau Proteins , Humans , Alzheimer Disease/cerebrospinal fluid , Alzheimer Disease/diagnosis , Biomarkers/cerebrospinal fluid , Aged , Male , Female , Middle Aged , Amyloid beta-Peptides/cerebrospinal fluid , tau Proteins/cerebrospinal fluid , Aged, 80 and over , Adult , Retrospective Studies , Peptide Fragments/cerebrospinal fluid , Hydrocephalus, Normal Pressure/cerebrospinal fluid , Hydrocephalus, Normal Pressure/diagnosis , Tertiary Care Centers , Young Adult , Magnetic Resonance Imaging/methods
10.
JMIR AI ; 3: e52054, 2024 Mar 15.
Article in English | MEDLINE | ID: mdl-38875581

ABSTRACT

BACKGROUND: Large curated data sets are required to leverage speech-based tools in health care. These are costly to produce, resulting in increased interest in data sharing. As speech can potentially identify speakers (ie, voiceprints), sharing recordings raises privacy concerns. This is especially relevant when working with patient data protected under the Health Insurance Portability and Accountability Act. OBJECTIVE: We aimed to determine the reidentification risk for speech recordings, without reference to demographics or metadata, in clinical data sets considering both the size of the search space (ie, the number of comparisons that must be considered when reidentifying) and the nature of the speech recording (ie, the type of speech task). METHODS: Using a state-of-the-art speaker identification model, we modeled an adversarial attack scenario in which an adversary uses a large data set of identified speech (hereafter, the known set) to reidentify as many unknown speakers in a shared data set (hereafter, the unknown set) as possible. We first considered the effect of search space size by attempting reidentification with various sizes of known and unknown sets using VoxCeleb, a data set with recordings of natural, connected speech from >7000 healthy speakers. We then repeated these tests with different types of recordings in each set to examine whether the nature of a speech recording influences reidentification risk. For these tests, we used our clinical data set composed of recordings of elicited speech tasks from 941 speakers. RESULTS: We found that the risk was inversely related to the number of comparisons an adversary must consider (ie, the search space), with a positive linear correlation between the number of false acceptances (FAs) and the number of comparisons (r=0.69; P<.001). The true acceptances (TAs) stayed relatively stable, and the ratio between FAs and TAs rose from 0.02 at 1 × 105 comparisons to 1.41 at 6 × 106 comparisons, with a near 1:1 ratio at the midpoint of 3 × 106 comparisons. In effect, risk was high for a small search space but dropped as the search space grew. We also found that the nature of a speech recording influenced reidentification risk, with nonconnected speech (eg, vowel prolongation: FA/TA=98.5; alternating motion rate: FA/TA=8) being harder to identify than connected speech (eg, sentence repetition: FA/TA=0.54) in cross-task conditions. The inverse was mostly true in within-task conditions, with the FA/TA ratio for vowel prolongation and alternating motion rate dropping to 0.39 and 1.17, respectively. CONCLUSIONS: Our findings suggest that speaker identification models can be used to reidentify participants in specific circumstances, but in practice, the reidentification risk appears small. The variation in risk due to search space size and type of speech task provides actionable recommendations to further increase participant privacy and considerations for policy regarding public release of speech recordings.

11.
Mol Cancer ; 23(1): 123, 2024 Jun 07.
Article in English | MEDLINE | ID: mdl-38849845

ABSTRACT

BACKGROUND: Pediatric-type diffuse high-grade glioma (pHGG) is the most frequent malignant brain tumor in children and can be subclassified into multiple entities. Fusion genes activating the MET receptor tyrosine kinase often occur in infant-type hemispheric glioma (IHG) but also in other pHGG and are associated with devastating morbidity and mortality. METHODS: To identify new treatment options, we established and characterized two novel orthotopic mouse models harboring distinct MET fusions. These included an immunocompetent, murine allograft model and patient-derived orthotopic xenografts (PDOX) from a MET-fusion IHG patient who failed conventional therapy and targeted therapy with cabozantinib. With these models, we analyzed the efficacy and pharmacokinetic properties of three MET inhibitors, capmatinib, crizotinib and cabozantinib, alone or combined with radiotherapy. RESULTS: Capmatinib showed superior brain pharmacokinetic properties and greater in vitro and in vivo efficacy than cabozantinib or crizotinib in both models. The PDOX models recapitulated the poor efficacy of cabozantinib experienced by the patient. In contrast, capmatinib extended survival and induced long-term progression-free survival when combined with radiotherapy in two complementary mouse models. Capmatinib treatment increased radiation-induced DNA double-strand breaks and delayed their repair. CONCLUSIONS: We comprehensively investigated the combination of MET inhibition and radiotherapy as a novel treatment option for MET-driven pHGG. Our seminal preclinical data package includes pharmacokinetic characterization, recapitulation of clinical outcomes, coinciding results from multiple complementing in vivo studies, and insights into molecular mechanism underlying increased efficacy. Taken together, we demonstrate the groundbreaking efficacy of capmatinib and radiation as a highly promising concept for future clinical trials.


Subject(s)
Brain Neoplasms , Glioma , Proto-Oncogene Proteins c-met , Xenograft Model Antitumor Assays , Animals , Humans , Glioma/pathology , Glioma/drug therapy , Glioma/genetics , Glioma/therapy , Proto-Oncogene Proteins c-met/antagonists & inhibitors , Proto-Oncogene Proteins c-met/genetics , Proto-Oncogene Proteins c-met/metabolism , Mice , Brain Neoplasms/pathology , Brain Neoplasms/drug therapy , Brain Neoplasms/genetics , Brain Neoplasms/radiotherapy , Benzamides/pharmacology , Benzamides/therapeutic use , Cell Line, Tumor , Oncogene Proteins, Fusion/genetics , Oncogene Proteins, Fusion/metabolism , Female , Protein Kinase Inhibitors/pharmacology , Protein Kinase Inhibitors/therapeutic use , Pyridines/pharmacology , Pyridines/therapeutic use , Crizotinib/pharmacology , Crizotinib/therapeutic use , Disease Models, Animal , Child , Neoplasm Grading , Anilides/pharmacology , Imidazoles , Triazines
12.
Med Sci Sports Exerc ; 56(10): 1867-1881, 2024 Oct 01.
Article in English | MEDLINE | ID: mdl-38768014

ABSTRACT

PURPOSE: Chronic, high-altitude hypoxic exposure increases the risk of high-altitude pulmonary hypertension (PH). Emerging evidence shows maternal exercise may improve offspring resistance to disease throughout life. The purpose of this study is to determine if maternal exercise mitigates chronic hypoxic-induced changes in the offspring indicative of high-altitude PH development. METHODS: Female adult C57BL/6J mice were randomly allocated to nonexercise or exercise conditions. Exercise consisted of voluntary running wheel exercise for 4 wk during the perinatal period. Three days after birth, the pups remained at low altitude (normoxia) or were exposed to hypobaric hypoxia of 450 mm Hg to simulate ~4500 m of altitude exposure until 8 wk of age. The study consisted of four groups: hypoxia + nonexercise pregnancy, hypoxia + exercise, or the respective normoxia conditions (normoxia + nonexercise or normoxia + exercise). Offspring body size, motor function, right ventricular systolic pressure (RVSP), and cardiopulmonary morphology were assessed after 8 wk in normoxia or hypoxia. RESULTS: Both hypoxic groups had smaller body sizes, reduced motor function, increased hematocrit, RVSP, muscularization in medium-sized pulmonary arteries, as well as right ventricular hypertrophy and contractility compared with the normoxic groups ( P < 0.05). CONCLUSIONS: Chronic hypoxia simulating 4500 m attenuated growth, lowered motor function, and elicited PH development. Voluntary maternal exercise did not significantly decrease RVSP in the offspring, which aligned with a lack of effect to attenuate abnormal body size and cardiopulmonary development due to chronic hypoxia. These findings are preliminary in nature, and more powered studies through larger group sizes are required to generalize the results to the population.


Subject(s)
Hypertension, Pulmonary , Hypoxia , Mice, Inbred C57BL , Physical Conditioning, Animal , Vascular Remodeling , Animals , Vascular Remodeling/physiology , Hypertension, Pulmonary/physiopathology , Hypertension, Pulmonary/etiology , Female , Physical Conditioning, Animal/physiology , Pregnancy , Hypoxia/physiopathology , Prenatal Exposure Delayed Effects , Pulmonary Artery/physiopathology , Mice , Altitude Sickness/physiopathology , Male
13.
Neurocase ; 30(1): 1-7, 2024 02.
Article in English | MEDLINE | ID: mdl-38758704

ABSTRACT

A research participant was monitored over nearly two decades at Mayo Clinic, undergoing annual neurologic assessments, neuropsychological tests, and multimodal imaging. Initially, he was cognitively normal but developed symptoms consistent with Posterior Cortical Atrophy (PCA) during the study. Early tests indicated mild, yet normal-range declines in language and visuospatial skills. FDG-PET scans revealed increased metabolism in posterior brain regions long before symptoms appeared. Advanced analysis using a novel in-house machine-learning tool predicted concurrent Alzheimer's disease and dementia with Lewy bodies. Autopsy confirmed a mixed neurodegenerative condition with significant Alzheimer's pathology and dense neocortical Lewy bodies. This case underscores the value of longitudinal imaging in predicting complex neurodegenerative diseases, offering vital insights into the early neurocognitive changes associated with PCA and dementia with Lewy bodies.


Subject(s)
Atrophy , Lewy Body Disease , Positron-Emission Tomography , Humans , Lewy Body Disease/pathology , Lewy Body Disease/metabolism , Lewy Body Disease/diagnostic imaging , Male , Atrophy/pathology , Cerebral Cortex/pathology , Cerebral Cortex/diagnostic imaging , Cerebral Cortex/metabolism , Aged , Alzheimer Disease/pathology , Alzheimer Disease/metabolism , Alzheimer Disease/diagnostic imaging , Prodromal Symptoms , Neuropsychological Tests
14.
Nucleic Acids Res ; 52(W1): W287-W293, 2024 Jul 05.
Article in English | MEDLINE | ID: mdl-38747351

ABSTRACT

The PSIRED Workbench is a long established and popular bioinformatics web service offering a wide range of machine learning based analyses for characterizing protein structure and function. In this paper we provide an update of the recent additions and developments to the webserver, with a focus on new Deep Learning based methods. We briefly discuss some trends in server usage since the publication of AlphaFold2 and we give an overview of some upcoming developments for the service. The PSIPRED Workbench is available at http://bioinf.cs.ucl.ac.uk/psipred.


Subject(s)
Deep Learning , Proteins , Software , Proteins/chemistry , Proteins/genetics , Internet , Protein Conformation , Computational Biology/methods , Sequence Analysis, Protein/methods
15.
J Nucl Med ; 65(7): 1122-1128, 2024 Jul 01.
Article in English | MEDLINE | ID: mdl-38782458

ABSTRACT

The widespread deposition of amyloid-ß (Aß) plaques in late-stage Alzheimer disease is well defined and confirmed by in vivo PET. However, there are discrepancies between which regions contribute to the earliest topographic Aß deposition within the neocortex. Methods: This study investigated Aß signals in the perithreshold SUV ratio range using Pittsburgh compound B (PiB) PET in a population-based study cross-sectionally and longitudinally. PiB PET scans from 1,088 participants determined the early patterns of PiB loading in the neocortex. Results: Early-stage Aß loading is seen first in the temporal, cingulate, and occipital regions. Regional early deposition patterns are similar in both apolipoprotein ε4 carriers and noncarriers. Clustering analysis shows groups with different patterns of early amyloid deposition. Conclusion: These findings of initial Aß deposition patterns may be of significance for diagnostics and understanding the development of Alzheimer disease phenotypes.


Subject(s)
Alzheimer Disease , Amyloid beta-Peptides , Neocortex , Positron-Emission Tomography , Thiazoles , Humans , Neocortex/diagnostic imaging , Neocortex/metabolism , Amyloid beta-Peptides/metabolism , Male , Female , Aged , Alzheimer Disease/diagnostic imaging , Alzheimer Disease/metabolism , Aniline Compounds , Middle Aged , Aged, 80 and over , Cross-Sectional Studies , Longitudinal Studies , Radiopharmaceuticals
16.
Sci Data ; 11(1): 432, 2024 May 01.
Article in English | MEDLINE | ID: mdl-38693191

ABSTRACT

The genus Clostridium is a large and diverse group within the Bacillota (formerly Firmicutes), whose members can encode useful complex traits such as solvent production, gas-fermentation, and lignocellulose breakdown. We describe 270 genome sequences of solventogenic clostridia from a comprehensive industrial strain collection assembled by Professor David Jones that includes 194 C. beijerinckii, 57 C. saccharobutylicum, 4 C. saccharoperbutylacetonicum, 5 C. butyricum, 7 C. acetobutylicum, and 3 C. tetanomorphum genomes. We report methods, analyses and characterization for phylogeny, key attributes, core biosynthetic genes, secondary metabolites, plasmids, prophage/CRISPR diversity, cellulosomes and quorum sensing for the 6 species. The expanded genomic data described here will facilitate engineering of solvent-producing clostridia as well as non-model microorganisms with innately desirable traits. Sequences could be applied in conventional platform biocatalysts such as yeast or Escherichia coli for enhanced chemical production. Recently, gene sequences from this collection were used to engineer Clostridium autoethanogenum, a gas-fermenting autotrophic acetogen, for continuous acetone or isopropanol production, as well as butanol, butanoic acid, hexanol and hexanoic acid production.


Subject(s)
Clostridium , Genome, Bacterial , Phylogeny , Clostridium/genetics , Solvents , Fermentation
17.
Neurology ; 102(11): e209497, 2024 Jun 11.
Article in English | MEDLINE | ID: mdl-38759131

ABSTRACT

Large language models (LLMs) are advanced artificial intelligence (AI) systems that excel in recognizing and generating human-like language, possibly serving as valuable tools for neurology-related information tasks. Although LLMs have shown remarkable potential in various areas, their performance in the dynamic environment of daily clinical practice remains uncertain. This article outlines multiple limitations and challenges of using LLMs in clinical settings that need to be addressed, including limited clinical reasoning, variable reliability and accuracy, reproducibility bias, self-serving bias, sponsorship bias, and potential for exacerbating health care disparities. These challenges are further compounded by practical business considerations and infrastructure requirements, including associated costs. To overcome these hurdles and harness the potential of LLMs effectively, this article includes considerations for health care organizations, researchers, and neurologists contemplating the use of LLMs in clinical practice. It is essential for health care organizations to cultivate a culture that welcomes AI solutions and aligns them seamlessly with health care operations. Clear objectives and business plans should guide the selection of AI solutions, ensuring they meet organizational needs and budget considerations. Engaging both clinical and nonclinical stakeholders can help secure necessary resources, foster trust, and ensure the long-term sustainability of AI implementations. Testing, validation, training, and ongoing monitoring are pivotal for successful integration. For neurologists, safeguarding patient data privacy is paramount. Seeking guidance from institutional information technology resources for informed, compliant decisions, and remaining vigilant against biases in LLM outputs are essential practices in responsible and unbiased utilization of AI tools. In research, obtaining institutional review board approval is crucial when dealing with patient data, even if deidentified, to ensure ethical use. Compliance with established guidelines like SPIRIT-AI, MI-CLAIM, and CONSORT-AI is necessary to maintain consistency and mitigate biases in AI research. In summary, the integration of LLMs into clinical neurology offers immense promise while presenting formidable challenges. Awareness of these considerations is vital for harnessing the potential of AI in neurologic care effectively and enhancing patient care quality and safety. The article serves as a guide for health care organizations, researchers, and neurologists navigating this transformative landscape.


Subject(s)
Artificial Intelligence , Neurology , Humans , Neurology/standards , Quality of Health Care
18.
JAMA Neurol ; 81(6): 619-629, 2024 Jun 01.
Article in English | MEDLINE | ID: mdl-38619853

ABSTRACT

Importance: Factors associated with clinical heterogeneity in Alzheimer disease (AD) lay along a continuum hypothesized to associate with tangle distribution and are relevant for understanding glial activation considerations in therapeutic advancement. Objectives: To examine clinicopathologic and neuroimaging characteristics of disease heterogeneity in AD along a quantitative continuum using the corticolimbic index (CLix) to account for individuality of spatially distributed tangles found at autopsy. Design, Setting, and Participants: This cross-sectional study was a retrospective medical record review performed on the Florida Autopsied Multiethnic (FLAME) cohort accessioned from 1991 to 2020. Data were analyzed from December 2022 to December 2023. Structural magnetic resonance imaging (MRI) and tau positron emission tomography (PET) were evaluated in an independent neuroimaging group. The FLAME cohort includes 2809 autopsied individuals; included in this study were neuropathologically diagnosed AD cases (FLAME-AD). A digital pathology subgroup of FLAME-AD cases was derived for glial activation analyses. Main Outcomes and Measures: Clinicopathologic factors of heterogeneity that inform patient history and neuropathologic evaluation of AD; CLix score (lower, relative cortical predominance/hippocampal sparing vs higher, relative cortical sparing/limbic predominant cases); neuroimaging measures (ie, structural MRI and tau-PET). Results: Of the 2809 autopsied individuals in the FLAME cohort, 1361 neuropathologically diagnosed AD cases were evaluated. A digital pathology subgroup included 60 FLAME-AD cases. The independent neuroimaging group included 93 cases. Among the 1361 FLAME-AD cases, 633 were male (47%; median [range] age at death, 81 [54-96] years) and 728 were female (53%; median [range] age at death, 81 [53-102] years). A younger symptomatic onset (Spearman ρ = 0.39, P < .001) and faster decline on the Mini-Mental State Examination (Spearman ρ = 0.27; P < .001) correlated with a lower CLix score in FLAME-AD series. Cases with a nonamnestic syndrome had lower CLix scores (median [IQR], 13 [9-18]) vs not (median [IQR], 21 [15-27]; P < .001). Hippocampal MRI volume (Spearman ρ = -0.45; P < .001) and flortaucipir tau-PET uptake in posterior cingulate and precuneus cortex (Spearman ρ = -0.74; P < .001) inversely correlated with CLix score. Although AD cases with a CLix score less than 10 had higher cortical tangle count, we found lower percentage of CD68-activated microglia/macrophage burden (median [IQR], 0.46% [0.32%-0.75%]) compared with cases with a CLix score of 10 to 30 (median [IQR], 0.75% [0.51%-0.98%]) and on par with a CLix score of 30 or greater (median [IQR], 0.40% [0.32%-0.57%]; P = .02). Conclusions and Relevance: Findings show that AD heterogeneity exists along a continuum of corticolimbic tangle distribution. Reduced CD68 burden may signify an underappreciated association between tau accumulation and microglia/macrophages activation that should be considered in personalized therapy for immune dysregulation.


Subject(s)
Alzheimer Disease , Magnetic Resonance Imaging , Neuroglia , Positron-Emission Tomography , Humans , Alzheimer Disease/diagnostic imaging , Alzheimer Disease/pathology , Alzheimer Disease/metabolism , Male , Female , Aged , Aged, 80 and over , Neuroglia/pathology , Neuroglia/metabolism , Cross-Sectional Studies , Retrospective Studies , Neurofibrillary Tangles/pathology , tau Proteins/metabolism , Middle Aged , Neuroimaging , Cohort Studies , Brain/diagnostic imaging , Brain/pathology , Brain/metabolism , Autopsy
19.
JAMA Netw Open ; 7(4): e244266, 2024 Apr 01.
Article in English | MEDLINE | ID: mdl-38558141

ABSTRACT

Importance: Frontotemporal lobar degeneration (FTLD) is relatively rare, behavioral and motor symptoms increase travel burden, and standard neuropsychological tests are not sensitive to early-stage disease. Remote smartphone-based cognitive assessments could mitigate these barriers to trial recruitment and success, but no such tools are validated for FTLD. Objective: To evaluate the reliability and validity of smartphone-based cognitive measures for remote FTLD evaluations. Design, Setting, and Participants: In this cohort study conducted from January 10, 2019, to July 31, 2023, controls and participants with FTLD performed smartphone application (app)-based executive functioning tasks and an associative memory task 3 times over 2 weeks. Observational research participants were enrolled through 18 centers of a North American FTLD research consortium (ALLFTD) and were asked to complete the tests remotely using their own smartphones. Of 1163 eligible individuals (enrolled in parent studies), 360 were enrolled in the present study; 364 refused and 439 were excluded. Participants were divided into discovery (n = 258) and validation (n = 102) cohorts. Among 329 participants with data available on disease stage, 195 were asymptomatic or had preclinical FTLD (59.3%), 66 had prodromal FTLD (20.1%), and 68 had symptomatic FTLD (20.7%) with a range of clinical syndromes. Exposure: Participants completed standard in-clinic measures and remotely administered ALLFTD mobile app (app) smartphone tests. Main Outcomes and Measures: Internal consistency, test-retest reliability, association of smartphone tests with criterion standard clinical measures, and diagnostic accuracy. Results: In the 360 participants (mean [SD] age, 54.0 [15.4] years; 209 [58.1%] women), smartphone tests showed moderate-to-excellent reliability (intraclass correlation coefficients, 0.77-0.95). Validity was supported by association of smartphones tests with disease severity (r range, 0.38-0.59), criterion-standard neuropsychological tests (r range, 0.40-0.66), and brain volume (standardized ß range, 0.34-0.50). Smartphone tests accurately differentiated individuals with dementia from controls (area under the curve [AUC], 0.93 [95% CI, 0.90-0.96]) and were more sensitive to early symptoms (AUC, 0.82 [95% CI, 0.76-0.88]) than the Montreal Cognitive Assessment (AUC, 0.68 [95% CI, 0.59-0.78]) (z of comparison, -2.49 [95% CI, -0.19 to -0.02]; P = .01). Reliability and validity findings were highly similar in the discovery and validation cohorts. Preclinical participants who carried pathogenic variants performed significantly worse than noncarrier family controls on 3 app tasks (eg, 2-back ß = -0.49 [95% CI, -0.72 to -0.25]; P < .001) but not a composite of traditional neuropsychological measures (ß = -0.14 [95% CI, -0.42 to 0.14]; P = .32). Conclusions and Relevance: The findings of this cohort study suggest that smartphones could offer a feasible, reliable, valid, and scalable solution for remote evaluations of FTLD and may improve early detection. Smartphone assessments should be considered as a complementary approach to traditional in-person trial designs. Future research should validate these results in diverse populations and evaluate the utility of these tests for longitudinal monitoring.


Subject(s)
Frontotemporal Dementia , Frontotemporal Lobar Degeneration , Adult , Aged , Female , Humans , Male , Middle Aged , Cohort Studies , Frontotemporal Dementia/diagnosis , Frontotemporal Lobar Degeneration/diagnosis , Frontotemporal Lobar Degeneration/pathology , Frontotemporal Lobar Degeneration/psychology , Neuropsychological Tests , Reproducibility of Results , Smartphone , Clinical Trials as Topic
20.
World Neurosurg ; 186: e622-e629, 2024 06.
Article in English | MEDLINE | ID: mdl-38604534

ABSTRACT

BACKGROUND: Many patients with idiopathic normal pressure hydrocephalus (iNPH) have medical comorbidities requiring anticoagulation that could negatively impact outcomes. This study evaluated the safety of ventriculoperitoneal shunt placement in iNPH patients on systemic anticoagulation versus those not on anticoagulation. METHODS: Patients >60 years of age with iNPH who underwent shunting between 2018 and 2022 were retrospectively reviewed. Baseline demographics, comorbidities (quantified by modified frailty index and Charlson comorbidity index), anticoagulant/antiplatelet agent use (other than aspirin), operative details, and complications were collected. Outcomes of interest were the occurrence of postoperative hemorrhage and overdrainage. RESULTS: A total of 234 patients were included in the study (mean age 75.22 ± 6.04 years; 66.7% male); 36 were on anticoagulation/antiplatelet therapy (excluding aspirin). This included 6 on Warfarin, 19 on direct Xa inhibitors, 10 on Clopidogrel, and 1 on both Clopidogrel and Warfarin. Notably, 70% of patients (164/234) used aspirin alone or combined with anticoagulation or clopidogrel. Baseline modified frailty index was similar between groups, but those on anticoagulant/antiplatelet therapy had a higher mean Charlson comorbidity index (2.67 ± 1.87 vs. 1.75 ± 1.84; P = 0.001). Patients on anticoagulants were more likely to experience tract hemorrhage (11.1 vs. 2.5%; P = 0.03), with no significant difference in the rates of intraventricular hemorrhage or overdrainage-related subdural fluid collection. CONCLUSIONS: Anticoagulant and antiplatelet agents are common in the iNPH population, and patients on these agents experienced higher rates of tract hemorrhage following ventriculoperitoneal shunt placement; however, overall hemorrhagic complication rates were similar.


Subject(s)
Anticoagulants , Hydrocephalus, Normal Pressure , Platelet Aggregation Inhibitors , Ventriculoperitoneal Shunt , Humans , Ventriculoperitoneal Shunt/adverse effects , Female , Hydrocephalus, Normal Pressure/surgery , Male , Aged , Anticoagulants/therapeutic use , Anticoagulants/adverse effects , Retrospective Studies , Aged, 80 and over , Platelet Aggregation Inhibitors/therapeutic use , Platelet Aggregation Inhibitors/adverse effects , Postoperative Hemorrhage/epidemiology
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