Toward a generalizable machine learning workflow for neurodegenerative disease staging with focus on neurofibrillary tangles.

Machine learning (ML) has increasingly been used to assist and expand current practices in neuropathology. However, generating large imaging datasets with quality labels is challenging in fields which demand high levels of expertise. Further complicating matters is the often seen disagreement between experts in neuropathology-related tasks, both at the case level and at a more granular level. Neurofibrillary tangles (NFTs) are a hallmark pathological feature of Alzheimer disease, and are associated with disease progression which warrants further investigation and granular quantification at a scale not currently accessible in routine human assessment. In this work, we first provide a baseline of annotator/rater agreement for the tasks of Braak NFT staging between experts and NFT detection using both experts and novices in neuropathology. We use a whole-slide-image (WSI) cohort of neuropathology cases from Emory University Hospital immunohistochemically stained for Tau. We develop a workflow for gathering annotations of the early stage formation of NFTs (Pre-NFTs) and mature intracellular (iNFTs) and show ML models can be trained to learn annotator nuances for the task of NFT detection in WSIs. We utilize a model-assisted-labeling approach and demonstrate ML models can be used to aid in labeling large datasets efficiently. We also show these models can be used to extract case-level features, which predict Braak NFT stages comparable to expert human raters, and do so at scale. This study provides a generalizable workflow for various pathology and related fields, and also provides a technique for accomplishing a high-level neuropathology task with limited human annotations.

Cerebral Microbleeds and Intracranial Hemorrhages in Adult Patients on Extracorporeal Membrane Oxygenation-Autopsy Study.

Current studies lack robust information on the prevalence and associated factors of cerebral microbleeds in patients who underwent extracorporeal membrane oxygenation. DESIGN: Retrospective analysis. SETTING: We reviewed patients who underwent (extracorporeal membrane oxygenation) and subsequent brain autopsy with gross and microscopic examinations from January 2009 to December 2018 from a single tertiary center. PATIENTS: Twenty-five extracorporeal membrane oxygenation patients (median age, 53 yr; interquartile range, 36-61 yr; 17 women and 8 men) underwent brain autopsy. INTERVENTIONS: Descriptive analysis of neuropathologic findings. Cerebral microbleed was defined as a small focus (< 10 mm diameter) of accumulation of blood product in the brain tissue. Macrohemorrhage was defined as any of the grossly identifiable epidural, subdural, subarachnoid, or intraparenchymal hemorrhages larger than 10 mm. MEASUREMENT AND MAIN RESULTS: Of 25 (22 venoarterial extracorporeal membrane oxygenation; three venovenous extracorporeal membrane oxygenation), 15 patients (60%) were found to have cerebral microbleeds, whereas 13 (52%) had macrohemorrhages, of whom five (20%) had both. Overall, 92% of brains demonstrated the presence of either cerebral microbleeds or macrohemorrhages after extracorporeal membrane oxygenation support. Of the patients with cerebral microbleeds, lobar cerebral microbleeds (80%) occurred more frequently than deep cerebral microbleeds (60%), with 40% of patients having both types. The cases of macrohemorrhages consisted of one epidural (8%), two subdural (15%), and 10 subarachnoid hemorrhages (77%). In univariate analyses, the presence of macrohemorrhages was significantly associated with the presence of cerebral microbleeds (p = 0.03) with odds ratio of 0.13 (CI, 0.02-0.82). Age, sex, extracorporeal membrane oxygenation duration, extracorporeal membrane oxygenation type, use of aspirin or dialysis during extracorporeal membrane oxygenation support, bloodstream infections, hemoglobin, platelets, and coagulopathy profiles were not associated with cerebral microbleeds. CONCLUSIONS: In patients with postmortem neuropathologic evaluation, 92% sustained acute cerebral microbleeds or macrohemorrhages after extracorporeal membrane oxygenation support. Cerebral microbleeds were commonly present in the majority of extracorporeal membrane oxygenation nonsurvivors. Further research is necessary to study the long-term sequelae, such as cognitive outcome of extracorporeal membrane oxygenation-associated cerebral microbleeds in extracorporeal membrane oxygenation survivors.

Multiple Neurodegenerative Pathologies in an Alzheimer's Disease Patient Treated with Fornical Deep Brain Stimulation.

As an established treatment for movement disorders, deep brain stimulation (DBS) has been adapted for the treatment of Alzheimer's disease (AD) by modulating fornix activity. Although it is generally regarded as a safe intervention in patients over 65 years of age, the complex neurophysiology and interconnection within circuits connected to the fornix warrants a careful ongoing evaluation of the true benefit and risk potential of DBS on slowing cognitive decline in AD patients. Here we report on a patient who died long after being implanted with a DBS device who donated her brain for neuropathologic study. The autopsy confirmed multiple proteinopathies including AD-related change, diffuse neocortical Lewy body disease, TDP-43 proteinopathy, and a nonspecific tauopathy. We discuss the possible mechanisms of these overlapping neurodegenerative disorders and caution that future studies of DBS for AD will need to take these findings into consideration.

Clinically Silent Brain Injury and Perioperative Neurological Events in Patients With Left Ventricular Assist Device: A Brain Autopsy Study.

Current studies underestimate the prevalence of brain injury in patients with left ventricular assist devices (LVADs), as CT scans are not sensitive in detecting cerebral ischemia. Using postmortem neuropathological evaluation, we sought to characterize the types and risk factors of brain injury in LVAD patients. We reviewed 24 LVAD patients who underwent brain autopsy with gross and microscopic examinations from 1993 through 2019 at a single tertiary center. Patients who expired less than 7 days after implantation or who underwent explantation more than 7 days before death were excluded. Our study demonstrated that all LVAD nonsurvivors developed brain injury. The most common brain injury was hemorrhage (71%), followed by infarct (42%) and hypoxic ischemic brain injury (HIBI) (33%), and 10 patients (42%) presented with more than 1 brain injury. Cerebral microbleeds (CMBs) and intracranial hemorrhage were present in 33% and 42%, respectively. In those with intracranial hemorrhage, subarachnoid hemorrhage (25%) and intracerebral hemorrhage (25%) were more common than subdural hematoma (4%). Intracranial hemorrhage was associated with driveline infection (P = 0.047), and HIBI was associated with prior history of chronic obstructive pulmonary disease (P = 0.037). Fourteen (60%) had clinically silent brain injury with 65% of hemorrhages and 70% of infarcts being silent. However, the impact of silent brain injury on neurologic outcome and mortality remains unclear. Standardized neurologic monitoring and surveillance are recommended to better detect these clinically silent brain injury.

Acute Brain Injury in Infant Venoarterial Extracorporeal Membrane Oxygenation: An Autopsy Study.

OBJECTIVES: Characterization of the types and timing of acute brain injury in infant autopsy patients after extracorporeal membrane oxygenation. DESIGN: Retrospective cohort study. SETTING: Single tertiary-care center. PATIENTS: Infants supported on extracorporeal membrane oxygenation. MEASUREMENTS AND MAIN RESULTS: Clinical and pathologic records were reviewed for infant extracorporeal membrane oxygenation patients who had undergone brain autopsy in a single center between January 2009 and December 2018. Twenty-four patients supported on venoarterial extracorporeal membrane oxygenation had postmortem examination with brain autopsy. Median age at extracorporeal membrane oxygenation initiation was 82 days (interquartile range, 11-263 d), median age at time of death was 20 weeks (interquartile range, 5-44 wk), and median extracorporeal membrane oxygenation support duration was 108 hours (interquartile range, 35-366 hr). The most common acute brain injury found at autopsy was hypoxic-ischemic brain injury (58%) followed by intracranial hemorrhage (29%). The most common types of intracranial hemorrhage were intracerebral (17%), subarachnoid (17%), and subdural (8%). Only five infants (21%) did not have acute brain injury. Correlates of acute brain injury included low preextracorporeal membrane oxygenation oxygen saturation as well as elevated liver enzymes, total bilirubin, and lactate on days 1 and 3 of extracorporeal membrane oxygenation. Gestational age, Apgar scores, birth weight, extracorporeal membrane oxygenation duration, anticoagulation therapy, and renal and hepatic impairments were not associated with acute brain injury. CONCLUSIONS: Acute brain injury was observed in 79% of autopsies conducted in infants supported on extracorporeal membrane oxygenation. Hypoxic-ischemic brain injury was the most common type of brain injury (58%), and further associations with preextracorporeal membrane oxygenation acute brain injury require additional exploration.

Publisher Correction: Shared proteomic effects of cerebral atherosclerosis and Alzheimer's disease on the human brain.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Shared proteomic effects of cerebral atherosclerosis and Alzheimer's disease on the human brain.

Cerebral atherosclerosis contributes to dementia via unclear processes. We performed proteomic sequencing of dorsolateral prefrontal cortex in 438 older individuals and found associations between cerebral atherosclerosis and reduced synaptic signaling and between RNA splicing and increased oligodendrocyte development and myelination. Consistently, single-cell RNA sequencing showed cerebral atherosclerosis associated with higher oligodendrocyte abundance. A subset of proteins and modules associated with cerebral atherosclerosis was also associated with Alzheimer's disease, suggesting shared mechanisms.

Large-scale proteomic analysis of Alzheimer's disease brain and cerebrospinal fluid reveals early changes in energy metabolism associated with microglia and astrocyte activation.

Our understanding of Alzheimer's disease (AD) pathophysiology remains incomplete. Here we used quantitative mass spectrometry and coexpression network analysis to conduct the largest proteomic study thus far on AD. A protein network module linked to sugar metabolism emerged as one of the modules most significantly associated with AD pathology and cognitive impairment. This module was enriched in AD genetic risk factors and in microglia and astrocyte protein markers associated with an anti-inflammatory state, suggesting that the biological functions it represents serve a protective role in AD. Proteins from this module were elevated in cerebrospinal fluid in early stages of the disease. In this study of >2,000 brains and nearly 400 cerebrospinal fluid samples by quantitative proteomics, we identify proteins and biological processes in AD brains that may serve as therapeutic targets and fluid biomarkers for the disease.

Intraneural perineurioma in neurofibromatosis type 2 with molecular analysis.

Intraneural perineuriomas are rare benign neoplasms. The gene associated with neurofibromatosis 2 (NF2) is located on chromosome 22q12, and mutations in NF2 are commonly seen in soft tissue perineuriomas. However, an association between NF2 mutations and intraneural perineuriomas (INPs) has not been well established. We present a 20-year-old male with NF2, multiple schwannomas and an intraneural perineurioma in the radial nerve at the spiral groove. Sequencing of NF2, SMARCB1, and LZTR1 was performed and demonstrated loss of the long arm of chromosome 22 including NF2, SMARCB1, and LZTR1, and a constitutional NF2:c.(-4577_-854)_(45-185)del alteration. We review the literature supporting two mutually exclusive pathways involving NF2 and TRAF7 mutations that lead to the development of INPs.

Understanding Characteristics of Acute Brain Injury in Adult Extracorporeal Membrane Oxygenation: An Autopsy Study.

OBJECTIVES: Current studies lack information on characteristics of acute brain injury in patients with extracorporeal membrane oxygenation. We sought to characterize the types, timing, and risk factors of acute brain injury in extracorporeal membrane oxygenation. DESIGN: Retrospective analysis. SETTING: We reviewed the extracorporeal membrane oxygenation patients who had undergone brain autopsy with gross and microscopic examinations from January 2009 to December 2018 from a single tertiary center. PATIENTS: Twenty-five patients (median age 53 yr) had postmortem brain autopsy. INTERVENTIONS: Description and analysis of neuropathologic findings. MEASUREMENT AND MAIN RESULTS: Of 25, 22 had venoarterial extracorporeal membrane oxygenation (88%) (nine cardiac arrest; 13 cardiogenic shock) and three had venovenous extracorporeal membrane oxygenation cannulation (12%). The median extracorporeal membrane oxygenation support time was 96 hours (interquartile range, 26-181 hr). The most common acute brain injury was hypoxic-ischemic brain injury (44%), followed by intracranial hemorrhage (24%), and ischemic infarct (16%). Subarachnoid hemorrhage (20%) was the most common type of intracranial hemorrhage, followed by intracerebral hemorrhage (8%), and subdural hemorrhage (4%). Only eight patients (32%) were without acute brain injury after extracorporeal membrane oxygenation. The most common involved location for hypoxic-ischemic brain injury was cerebral cortices (82%) and cerebellum (55%). The pattern of ischemic infarct was territorial in cerebral cortices. The risk factors for acute brain injury included hypertension history (11 vs 1; p = 0.01), preextracorporeal membrane oxygenation antiplatelet use (7 vs 0; p = 0.03), and a higher day 1 lactate level (10.0 vs 5.1; p = 0.02). Patients with hypoxic-ischemic brain injury had more hypertension (8 vs 4; p = 0.047), a higher day 1 lactate level (12.6 vs 5.8; p = 0.02), and a lower pH level (7.09 vs 7.24; p = 0.027). Extracorporeal membrane oxygenation duration, cannulation methods, hemoglobin level, coma, renal impairment, and hepatic impairment were not associated with acute brain injury. CONCLUSIONS: In the population who underwent postmortem neuropathologic evaluation, 68% of extracorporeal membrane oxygenation nonsurvivors developed acute brain injury. Hypoxic-ischemic brain injury was the most common type of injury suggesting that patients sustained acute brain injury as a consequence of cardiogenic shock and cardiac arrest. Further research with a systematic neurologic monitoring is necessary to define the timing of acute brain injury in patients with extracorporeal membrane oxygenation.

Neuropathological findings in comatose patients with venoarterial extracorporeal membrane oxygenation.

We sought to describe the relation between neuropathology and clinical information including neurological examination and electroencephalogram findings in extracorporeal membrane oxygenation. We reviewed the patients who had undergone brain autopsy from November 2017 through December 2018. Four patients with neuromonitoring had post mortem examination with brain autopsy. The median age was 56, and all had venoarterial extracorporeal membrane oxygenation cannulation. There was no known acute neurologic injury prior to extracorporeal membrane oxygenation. While on extracorporeal membrane oxygenation, all were persistently comatose off sedation. Continuous encephalogram was done on all four, all of which showed delta frequency with absent reactivity. In Case 1, the pathological evaluation demonstrated small infarcts in cerebral cortices. In Case 2, it showed cortical microhemorrhages and chronic microinfarcts in basal ganglia. In Cases 3 and 4, the neuropathological assessment demonstrated diffuse hypoxic-ischemic brain injury. The clinical presentation was consistent with the widespread neuropathologic injury in two cases (Cases 3 and 4) but not in the other two (Cases 1 and 2). While "poor neurological status" was provided in the end-of-life discussion in all four, only two had significant brain injuries. There is limited understanding about brain injury in extracorporeal membrane oxygenation. Extrapolations related to prognostication from experience in other brain injury needs to be approached cautiously.

Acute Invasive Fungal Rhinosinusitis: Frozen Section Histomorphology and Diagnosis with PAS Stain.

Acute invasive fungal rhinosinusitis (AIFRS) is a fulminant infection in immunocompromised patients requiring rapid diagnosis (DX), frequently made on frozen section (FS) of sinonasal biopsies, followed by prompt surgical debridement. However, FS interpretation is often difficult and DX sometimes not possible. In this study we sought to characterize reasons for misinterpretation and methods to improve diagnostic accuracy. The FS slides from 271 biopsies of suspected AIFRS in a 16-year period were reviewed and the morphologic features evaluated for their utility in DX. Recurring specific patterns of necrosis were identified, which to our knowledge have not been described in the literature. Although they provide strong evidence for AIFRS, identifying fungus consistently in necrotic tissue is essential for DX. Clues to identifying fungus and pitfalls in misidentification were identified, but even with expert knowledge of these, a gap in accurate DX remained. The key to FS DX of AIFRS is to improve fungus identification in necrotic tissues. Methods had been sought in the past to stain fungus at FS without consistent success. The Periodic Acid Schiff's Reaction for Fungi was modified by our histopathology department for use on frozen tissue (PASF-fs) resulting in effective staining of the fungus. It stained fungus on all 62 positive slides when applied retrospectively over hematoxylin and eosin (H&E) stained FSs and used prospectively at FS for DX. Although knowledge of histologic morphology on FS is important, the crucial value of this study is the novel use of PASF-fs to identify fungus in the DX of AIFRS.

Frozen Section as a Rapid and Accurate Method for Diagnosing Acute Invasive Fungal Rhinosinusitis.

Objective Identify methods to improve the frozen-section diagnosis of acute invasive fungal rhinosinusitis. Study Design Biopsies with frozen section for suspected acute invasive fungal rhinosinusitis were reviewed to identify causes for missed diagnoses and evaluate methods for potential improvement. Setting All aspects of the study were performed at the Penn State Milton S. Hershey Medical Center. Subjects and Methods All frozen sections performed for suspected acute invasive fungal rhinosinusitis between 2006 through 2017 were reviewed with their diagnoses compared to the final diagnoses. Sensitivity and specificity were determined for each biopsy specimen to evaluate the diagnostic method and for each patient for its effectiveness on outcome. Causes for frozen-section failures in diagnosis were identified. A periodic acid-Schiff stain for fungus (PASF) was modified for use on frozen tissue (PASF-fs) and applied both retrospectively and prospectively to frozen sections to determine its ability to identify undetected fungus and improve diagnostic sensitivity. Results Of 63 biopsies positive for acute invasive fungal rhinosinusitis, 51 were diagnosed on frozen section, while 61 were identified by including the novel PASF-fs stain, reducing the failure rate from 19% to 3%. Of 41 cases that were positive, 34 were diagnosed on frozen section. Of the 7 that were not, 5 were identified by including the PASF-fs, reducing the failure rate from 17% to 5%. Conclusions Frozen section interpretation of biopsies for suspected acute invasive fungal rhinosinusitis using a PASF-fs stain should enable a rapid and accurate diagnosis with improved outcomes by shortening the time to surgery.

Non-sustained microvolt level T-wave alternans in congenital long QT syndrome types 1 and 2.

BACKGROUND: Patients with long QT syndrome (LQTS) are predisposed to polymorphic ventricular tachycardia (VT) during adrenergic stimulation. Microvolt T-wave alternans (MTWA) is linked to vulnerability to VT in structural heart disease. The prevalence of non-sustained MTWA (NS-MTWA) in LQTS is unknown. METHODS: 31 LQT1, 42 LQT2, and 80 controls underwent MTWA testing during exercise. MTWA tests were classified per standardized criteria, and re-analyzed according to the modified criteria to account for NS-MTWA. RESULTS: LQT1 and LQT2 patients had a significantly higher frequency of late NS-MTWA (26% and 12%) compared to controls (0%). There was no significant difference between the groups with respect to sustained and early NS-MTWA. Late NS-MTWA was significantly associated with QTc. CONCLUSION: LQT1 and LQT2 patients had a higher prevalence of late NS-MTWA during exercise than matched controls. NS-MTWA likely reflects transient adrenergically mediated dispersion of repolarization, and could be a marker of arrhythmic risk in LQTS.

In vivo strains in the femur of the Virginia opossum (Didelphis virginiana) during terrestrial locomotion: testing hypotheses of evolutionary shifts in mammalian bone loading and design.

Terrestrial locomotion can impose substantial loads on vertebrate limbs. Previous studies have shown that limb bones from cursorial species of eutherian mammals experience high bending loads with minimal torsion, whereas the limb bones of non-avian reptiles (and amphibians) exhibit considerable torsion in addition to bending. It has been hypothesized that these differences in loading regime are related to the difference in limb posture between upright mammals and sprawling reptiles, and that the loading patterns observed in non-avian reptiles may be ancestral for tetrapod vertebrates. To evaluate whether non-cursorial mammals show loading patterns more similar to those of sprawling lineages, we measured in vivo strains in the femur during terrestrial locomotion of the Virginia opossum (Didelphis virginiana), a marsupial that uses more crouched limb posture than most mammals from which bone strains have been recorded, and which belongs to a clade phylogenetically between reptiles and the eutherian mammals studied previously. The presence of substantial torsion in the femur of opossums, similar to non-avian reptiles, would suggest that this loading regime likely reflects an ancestral condition for tetrapod limb bone design. Strain recordings indicate the presence of both bending and appreciable torsion (shear strain: 419.1 ± 212.8 µÎµ) in the opossum femur, with planar strain analyses showing neutral axis orientations that placed the lateral aspect of the femur in tension at the time of peak strains. Such mediolateral bending was unexpected for a mammal running with near-parasagittal limb kinematics. Shear strains were similar in magnitude to peak compressive axial strains, with opossum femora experiencing similar bending loads but higher levels of torsion compared with most previously studied mammals. Analyses of peak femoral strains led to estimated safety factor ranges of 5.1-7.2 in bending and 5.5-7.3 in torsion, somewhat higher than typical mammalian values for bending, but approaching typical reptilian values for shear. Loading patterns of opossum limb bones therefore appear intermediate in some respects between those of eutherian mammals and non-avian reptiles, providing further support for hypotheses that high torsion and elevated limb bone safety factors may represent persistent ancestral conditions in the evolution of tetrapod limb bone loading and design.