Identification of immune cell infiltration and biomarkers in Alzheimer's disease and COVID-19 by integrated bioinformatics analysis and machine learning (preprint)

Background: Since its emergence in late 2019, COVID-19 has become a global epidemic, resulting in numerous infections, including a significant number of critically ill patients. Several studies have suggested a possible link between Alzheimer's disease (AD) and COVID-19. For instance, a Mendelian randomization study has proposed a causal relationship between Alzheimer's disease and COVID-19 in the pathogenic mechanism. However, there are limited studies exploring the common pathogenic genes and immune infiltration between the two. Therefore, we conducted this study to identify key genes in COVID-19 associated with Alzheimer's disease, evaluate their correlation with immune cell characteristics and metabolic pathways, and investigate potential novel biomarkers. Methods: Transcriptome analyses were used to identify common biomolecular markers of AD and COVID-19. Differential expression analysis and weighted gene co-expression network analysis (WGCNA) were performed on gene chip datasets (GSE213313, GSE5281, and GSE63060) from AD and COVID-19 patients to identify genes associated with both conditions. Common pathogenic molecular mechanisms were identified through Gene Ontology (GO) enrichment analyses. The core genes were then identified using machine learning methods. Subsequently, we evaluated the relationship between these core genes and common immune cells and metabolic pathways. Finally, our findings were validated through single-cell analysis. Results: The study identified 484 common differentially expressed genes (DEGs) by taking the intersection of genes between AD and COVID-19. The black module, containing 132 genes, showed the highest association between the two diseases according to WGCNA. GO enrichment analysis revealed that these genes mainly affect inflammation, cytokines, immune-related functions, and signaling pathways related to metal ions and cellular response to viruses. Additionally, a machine learning approach identified eight core genes. We identified links between these genes and immune cells and also found a strong association between EIF3H and oxidative phosphorylation. In addition, these results were further validated by single-cell analysis. Conclusion: This study identifies potential shared genes, signaling pathways, immune-related alterations, and changes in metabolic pathways that may collectively contribute to the pathogenesis of COVID-19 and Alzheimer's disease. These findings provide new targets for the diagnosis and treatment of both diseases.

The Effectiveness of Socially Assistive Robots in Improving Children’s Pain and Negative Affectivity during Needle-based Invasive Treatment: A Systematic Review and Meta-analysis (preprint)

Background The ability of socially assistive robots (SARs) to treat dementia and Alzheimer’s disease has been verified. Currently, to increase the range of their application, there is an increasing amount of interest in using SARs to relieve pain and negative emotions among children in routine medical settings. However, there is little consensus regarding the use of these robots. Objective This study aimed to evaluate the effect of SARs on pain and negative affectivity among children undergoing invasive needle-based procedures. Design This study was a systematic review and meta-analysis of randomized controlled trials that was conducted in accordance with the Cochrane Handbook guidelines. Methods The PubMed, Embase, EBSCO, Web of Science, Cochrane Library, Embase, CNKI, and WanFang databases were searched from inception to January 2024 to identify relevant randomized controlled trials (RCTs). We used the Cochrane Risk of Bias tool 2.0 (RoB2.0) to assess the risk of bias among the included studies, and we used RevMan 6.3 software to conduct the meta-analysis. The Grading of Recommendations, Assessment, Development, and Evaluation (GRADE) framework was used to assess the quality of the evidence. Results Ten RCTs involving 815 pediatric subjects were selected for this review and reported outcomes related to pain and emotions during IV placement, port needle insertion, flu vaccination, blood sampling, and dental treatment. Children undergoing needle-related procedures with SARs reported less anxiety (SMD= -0.36; 95% CI= -0.64, -0.09; P = 0.01) and fewer distressed avoidance behaviors (SMD= -0.67; 95% CI= -1.04, -0.30; P = 0.0004) than did those receiving typical care. There were nonsignificant differences between these groups in terms of in pain (SMD = -0.02; 95% CI = − 0.81, 0.78; P = 0.97) and fear (SMD = 0.38; 95% CI= -0.06, 0.82; P = 0.09). The results of exploratory subgroup analyses revealed no statistically significant differences based on the intervention type of robots or anesthetic use. Conclusions The use of SARs is a promising intervention method for alleviating anxiety and distress among children undergoing needle-related procedures. However, additional high-quality randomized controlled trials are needed to further validate these conclusions. Registrations The protocol of this study has been registered in the database PROSPERO (registration ID: CRD42023413279).

Real-word immunogenicity of a recombinant subunit COVID-19 vaccine and effectiveness against omicron infection: a prospective, multi-centre, longitudinal cohort study in Alzheimer's disease patients (preprint)

Introduction Vaccination is an essential strategy against COVID-19 in the current era of emerging variants. This study evaluates the real-world immunogenicity and effectiveness of the recombinant subunit COVID-19 vaccine (Zifivax) in Alzheimer's disease (AD) patients.Methods 249 AD patients were enrolled in a multicentre, longitudinal cohort study. Levels of RBD-IgG, neutralization antibody activity, and cytokines were identified to evaluate the immune responses. Clinical outcomes were assessed within one month following Omicron infection..Results Following three doses, the vaccine induced a robust immune response, elevating neutralizing antibodies and activating T-cells. AD patients exhibited significantly higher humoral immune responses compared to unvaccinated counterparts. Following Omicron infection, unvaccinated patients experienced higher levels of Th1/Th2-type cytokines than vaccinated individuals. Vaccination correlated with increased survival rates and extended survival times after infection..Discussion The findings highlight the vaccine's efficacy in reducing severe illness, and preventing death in AD patients facing Omicron infection.

No clear evidence for relationships of Apolipoprotein E genotype with measures of common infections in three UK cohorts (preprint)

APOE genotype is the strongest genetic risk factor for late onset Alzheimer's disease, with the ϵ2 and ϵ4 alleles decreasing and increasing risk relative to the ϵ3 allele, respectively. Although evidence has been conflicting, several common infections have been associated with Alzheimer's disease risk, and interactions by APOE ϵ4 carriage have also been reported. Nevertheless, to date, no study has examined relationships between APOE genotype and measures of multiple common infections among large population-based studies. We investigated associations of APOE ϵ2 and ϵ4 carriage (i.e. non-carrier vs carrier) with serostatus and antibody titers to 14 common pathogens — encompassing herpesviruses, human polyomaviruses, C.trachomatis , H.pylori , and T.gondii — in three population—based cohorts (UK Biobank, National Survey of Health and Development, Southall and Brent Revisited). Pathogen serostatus was derived using validated antibody cut-offs for relevant antigens and included as an outcome assessing previous infection. Antibody titers were dichotomised among the seropositive subset for each antigen and included as binary outcomes assessing recent immunological responses. We conducted analyses in each cohort using mixed-models, including age, sex and genetic principal components as fixed-effects, and genetic relatedness as a random-effect. In secondary analyses, we additionally assessed i) relationships of APOE ϵ2 and ϵ4 dosage (i.e. number of copies of the allele of interest), and ii) relationships of APOE genotype with continuous antibody titers (rank-based inverse normal transformed). Findings were meta-analysed across cohorts (n=10,059) using random-effects models and corrected for multiple tests using the false discovery rate. We found no clear evidence of relationships between APOE genotype and serostatus or antibody titers to any pathogen, with no strong associations observed in any of our analyses following multiple testing correction. Investigations of APOE genotypes with the clinical manifestations of these pathogens, as well as expanding to include other viruses such as SARS-CoV-2, would also be warranted.

Viral Infections, a Trigger and Risk Factor of Alzheimer’s Disease? (preprint)

Alzheimer’s Disease (AD), a progressive and debilitating condition, is reported to be the most common type of dementia, with at least 55 million people believed to be currently affected. Many causation hypotheses of AD exist, yet the intriguing link between viral infection and its possible contribution to the known etiology of AD has become an attractive focal point of research for the field and a challenging study task. In this review, we will explore the historical perspective and milestones that led the field to investigate the viral connection to AD. Specifically, several viruses such as Herpes Simplex Virus 1 (HSV-1), Zika virus (ZIKV), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), along with several others mentioned, include the various viruses presently considered within the field. We delve into the strong evidence implicating these viruses in the development of AD. We will also extend beyond these mere associations by carefully analyzing the potential mechanisms by which viruses may contribute to AD pathology. This includes but is not limited to direct neuronal infections, dysregulation of immune responses, and the impact on protein processing. Controversies and challenges of the viral-AD relationship emerge as we tease out these potential mechanisms considered. Looking forward, we emphasize the future directions the field should take to tackle the remaining unanswered questions and the glaring research gaps that persist. Overall, this review aims to provide a comprehensive survey of the past, present, and future of the potential link between viral infections and their association with AD development.

Plasma proteomic evidence for increased Alzheimer's disease-related brain pathology after SARS-CoV-2 infection (preprint)

Viral infections have been linked to an increased risk for dementia. We investigated whether SARS-CoV-2 infection increases preclinical brain pathology associated with Alzheimer's disease (AD) by comparing changes in plasma biomarkers in UK Biobank participants with and without prior SARS-CoV-2 infection. We discovered an association between SARS-CoV-2 infection and reduced plasma A{beta}42:A{beta}40 concentration ratio. In older participants, SARS-CoV-2 infection was associated with both lower plasma A{beta}42 and higher plasma pTau-181. These biomarker changes, which have been associated with beta-amyloid accumulation and prodromal AD, were associated with increased brain imaging signatures of AD, poorer cognitive scores, and worse assessments of overall health and appeared to be greater in participants who had been hospitalised with COVID-19. Protein biomarker risk scores for other diseases were also raised among individuals who had past SARS-CoV-2 infections. Our data provide support for the hypothesis that viral infections can accelerate prodromal AD pathology and highlight biomarker profiles indicative of an increased risk of dementia and systemic diseases after SARS-CoV-2 infection, particularly in older people.

COVID-19 symptoms are attenuated in atopic dermatitis patients treated with dupilumab Short running title: Reduced COVID-19 symptoms in dupilumab-treated AD (preprint)

Background: In the SARS-CoV-2/COVID-19 pandemic, we need to understand the impact of immunomodulatory medications on COVID-19 symptom severity in patients with inflammatory diseases, including the Type 2/Th2 polarized skin disease, atopic dermatitis/AD. Since it is believed that Type 1/Th1immunity controls viral infections, and that there is a Th1/Th2 counter-regulation, we hypothesized that Th2 targeting with the IL-4Rα-antagonist, dupilumab, in patients with moderate-to-severe AD rebalances Th1/Th2 axis, potentially leading to attenuated COVID-19 symptoms. Methods: : 1,237 moderate-to-severe AD patients in the Icahn School of Medicine at Mount Sinai Department of Dermatology were enrolled in a registry. Patients were screened for COVID-19-related symptoms and assigned a severity score (asymptomatic[0]-fatal[5]). Scores were compared among 3 treatment groups: dupilumab (n=632), other systemic treatments (n=107), and limited/no treatment (n=498). Demographic and comorbid covariates were adjusted by multivariate logistic regression models. Results: : The dupilumab-treated group showed reduced incidence and severity of COVID-19 symptoms versus other treatment groups. Dupilumab-treated patients were less likely to experience moderate-to-severe symptoms versus patients on other systemics (p=0.01) and on limited/no treatment (p=0.04), and less likely to experience any symptoms versus patients on other systemics (p=0.01). This effect was seen in our entire cohort and in the subgroup of patients with verified COVID-19 or high-risk exposure. Conclusions: : Patients on dupilumab experienced less severe COVID-19 manifestations and lesser symptoms compared to patients on other systemics and on limited/no treatment. These results suggest that Th2 modulation with dupilumab may have a protective effect on anti-viral immune response in AD patients.

Long COVID Disability Burden in US Adults: YLDs and NIH Funding Relative to Other Conditions (preprint)

BackgroundLong COVID (LC) is novel, debilitating and likely chronic. Yet, scant data exist about its disability burden to guide scientific research and public health planning. We estimated Long COVIDs non-fatal disease burden in US adults and its FY2024 actual: burden-commensurate research funding from the National Institutes of Health (NIH) relative to other conditions, and biological sex. MethodsWe present YLDs/100,000 for 70 NIH Research, Condition, and Disease Categories (RCDCs). Prevalence of disabling Long COVID was obtained from cross sectional surveys of representative samples of US adults, from September 2022 to August 2023. Disabling Long COVID was defined as incident symptoms persisting more than 3 months post-COVID, that significantly compromise daily activities. We calculated burden-commensurate funding for the top YLD conditions and for female vs. male dominant conditions. FindingsDisabling Long COVID was reported by 1.5% (n= 10,401) of n=757,580 respondents: Compared to the overall sample, those with disabling LC disproportionately identify as female (64.4% vs. 51.4%) and experiencing disability (80.8% vs. 52.9%) anxiety (57.5% vs. 23.8%) and depression (51.3% vs.18.5%). It ranked in the top 25% of YLDs at 320/100,000, between Alzheimers (279.4/100,000) and asthma (355.7/100,000) but received just 10% of its actual: YLD-commensurate funding. Only 5 conditions received less actual: burden: commensurate funding, including Myalgic Encephalitis/Chronic Fatigue Syndrome (<1%), another post-viral, female-dominant condition. InterpretationLC has debilitated 3.8 million (weighted frequency) US adults. Research funding for it, like other female dominant conditions, lags behind its disability burden. Research in ContextEvidence before this study - We analyzed Long-COVIDs (LC) non-fatal disease burden in the US--represented by YLD (years lived with disability= prevalence x disability weight) -- and National Institutes of Health (NIH) research 2024 funding relative to other conditions. We searched PubMed through 11/28/2023 for Long COVID prevalence (US), and Long COVID disability and disease burden (not US-specific). The keywords "years lived with disability" + "COVID" yielded n= 38 articles (11/29/23); but most referenced "disability-adjusted life years" (DALYs) in other countries. Similarly, "disease burden" + Long COVID yielded 23 papers, but no US YLD data. See Supplement 1 for meta-analyses, systematic reviews and US studies of Long COVID prevalence and impact. We instead sourced YLD data from the US Census Bureaus Household Pulse Survey (HPS) and the Institute for Health Metrics and Evaluation (IHME) /Global Burden of Disease (GBD) Long COVID Study Group. The HPS queries adults about Long COVID-related symptoms and their impact on daily activities. We applied the IHME/GBDs estimated Long COVID disability weight of 0.21 and harmonized it with our LC case definition from the HPS data in consultation with IHME/GBD researchers. To harmonize IHME/GBD disability weights for non-LC diseases/conditions with the NIHs terminology, we consulted with NIH staff. LC definition and measurement affects prevalence and burden estimates; our use of high-quality data sources and transparency in reporting how they were applied reduces the risk of biased assumptions. Added value of this study- Long COVID is a chronic debilitating condition. While there is ample research on COVIDs acute illness and loss of life, there are no population-based data on its disability burden. We provide that data. To guide scientific research and public health planning, we report YLDs associated with disabling Long COVID (i.e., symptoms significantly limit activity), and; compare it to other conditions YLDs, NIH funding, and female-vs. male-dominance. It ranked in the top 25% of YLDs at 320/100,000, between Alzheimers (279.4/100,000) and asthma (355.7/100,000) but received just 10% of its YLD-commensurate funding. Only 5 conditions received less burden-commensurate funding; 3/5 were female-dominant, including Myalgic Encephalitis/Chronic Fatigue Syndrome (ME/CFS) at <1%, another post-viral condition that shares significant overlap with Long COVID. Overall, median funding/YLD was >= 5 times greater for male-vs. female-dominant conditions. Implications of all the available evidence-Nearly 4 million US adults (weighted frequency) live with disabling Long COVID. They disproportionately identify as female and as having a disability, anxiety and depression. Yet NIH funding for diagnostic and treatment research for Long COVID hasnt kept pace with its disability burden.

A Span-based Model for Extracting Overlapping PICO Entities from RCT Publications (preprint)

Objectives Extraction of PICO (Populations, Interventions, Comparison, and Outcomes) entities is fundamental to evidence retrieval. We present a novel method PICOX to extract overlapping PICO entities. Materials and Methods PICOX first identifies entities by assessing whether a word marks the beginning or conclusion of an entity. Then it uses a multi-label classifier to assign one or more PICO labels to a span candidate. PICOX was evaluated using one of the best-performing baselines, EBM-NLP, and three more datasets, i.e., PICO-Corpus, and RCT publications on Alzheimer's Disease or COVID-19, using entity-level precision, recall, and F1 scores. Results PICOX achieved superior precision, recall, and F1 scores across the board, with the micro F1 score improving from 45.05 to 50.87 (p << 0.01). On the PICO-Corpus, PICOX obtained higher recall and F1 scores than the baseline and improved the micro recall score from 56.66 to 67.33. On the COVID-19 dataset, PICOX also outperformed the baseline and improved the micro F1 score from 77.10 to 80.32. On the AD dataset, PICOX demonstrated comparable F1 scores with higher precision when compared to the baseline. Conclusion PICOX excels in identifying overlapping entities and consistently surpasses a leading baseline across multiple datasets. Ablation studies reveal that its data augmentation strategy effectively minimizes false positives and improves precision.

Disentangling the relationship between cancer mortality and COVID-19 (preprint)

Several countries have reported that deaths with a primary code of cancer did not rise during COVID-19 pandemic waves compared to baseline pre-pandemic levels. This is in apparent conflict with findings from cohort studies where cancer has been identified as a risk factor for COVID-19 mortality. Here we further elucidate the relationship between cancer mortality and COVID-19 on a population level in the US by testing the impact of death certificate coding changes during the pandemic and leveraging heterogeneity in pandemic intensity across US states. We computed excess mortality from weekly deaths during 2014-2020 nationally and for three states with distinct COVID-19 wave timing (NY, TX, and CA). We compared pandemic-related mortality patterns from underlying and multiple causes (MC) death data for six types of cancer and high-risk chronic conditions such as diabetes and Alzheimers. Any coding change should be captured in MC data. Nationally in 2020, we found only modest excess MC cancer mortality ([~]12,000 deaths), representing a 2% elevation over baseline. Mortality elevation was measurably higher for less deadly cancers (breast, colorectal, and hematologic, 2-5%) than cancers with a poor 5-year survival (lung and pancreatic, 0-1%). In comparison, there was substantial elevation in MC deaths from diabetes (39%) and Alzheimers (31%). Homing in on the intense spring 2020 COVID-19 wave in NY, mortality elevation was 2-15% for cancer and 126% and 55% for diabetes and Alzheimers, respectively. Simulations based on a demographic model indicate that differences in life expectancy for these conditions, along with the age and size of the at-risk populations, largely explain the observed differences in excess mortality during the COVID-19 pandemic. In conclusion, we found limited elevation in cancer mortality during COVID-19 waves, even after considering coding changes. Our demographic model predicted low expected excess mortality in populations living with certain types of cancer, even if cancer is a risk factor for COVID-19 fatality risk, due to competing mortality risk. We also find a moderate increase in excess mortality from blood cancers, aligned with other types of observational studies. While our study concentrates on the immediate consequences of the COVID-19 pandemic on cancer mortality, further research should consider the pandemic impact on hospitalizations, delayed diagnosis/treatment and risk of Long COVID in cancer patients.

Neuropathological assessment of the olfactory bulb and tract in individuals with COVID-19 (preprint)

The majority of patients with Parkinson disease (PD) experience a loss in their sense of smell and accumulate insoluble alpha-synuclein aggregates in their olfactory bulbs (OB). Subjects affected by a SARS-CoV-2-linked illness (COVID-19) frequently experience hyposmia. We previously hypothesized that alpha-synuclein and tau misprocessing could occur following host responses to microbial triggers. Using semiquantitative measurements of immunohistochemical signals, we examined OB and olfactory tract specimens collected serially at autopsies between 2020 and 2023. Deceased subjects comprised 50 adults, which included COVID19+ patients (n=22), individuals with Lewy body disease (e.g., PD and dementia with Lewy bodies (DLB; n=6)), Alzheimer disease (AD; n=3), other non-synucleinopathy-linked degenerative diseases (e.g., progressive supranuclear palsy (PSP; n=2) and multisystem atrophy (MSA; n=1)). Further, we included neurologically healthy controls (HCO; n=9) and those with an inflammation-rich brain disorder as neurological controls (NCO; n=7). When probing for inflammatory changes focusing on anterior olfactory nuclei (AON) using anti-CD68 immunostaining, scores were consistently elevated in NCO and AD cases. In contrast, inflammation on average was not significantly altered in COVID19+ patients relative to controls, although anti-CD68 reactivity in their OB and tracts declined with progression in age. Mild-to-moderate increases in phospho-alpha-Syn and phospho-tau signals were detected in the AON of tauopathy- and synucleinopathy-afflicted brains, respectively, consistent with mixed pathology, as described by others. Lastly, when both sides were available for comparison in our case series, we saw no asymmetry in the degree of pathology of the left versus right OB and tracts. We concluded from our autopsy series that after a fatal course of COVID-19, microscopic changes, when present, in the rostral, intracranial portion of the olfactory circuitry generally reflected neurodegenerative processes seen elsewhere in the brain. In general, inflammation correlated best with the degree of Alzheimer's-linked tauopathy and declined with progression of age in COVID19+ patients.

Stereotypic persistent B cell receptor clonotypes in Alzheimer's Disease (preprint)

We constructed in silico B cell receptor (BCR) repertoires using peripheral blood (PB) samples collected from 44 Alzheimer's Disease (AD) patients at baseline and 37 patients at follow-up. For the control group (CG), we used BCR repertoire data from the chronologically collected PB samples of 55 healthy volunteers vaccinated with the SARS-CoV2 mRNA vaccine. AD patients shared 3,983 stereotypic BCR clonotypes not found in CG, and their degree of overlap between patient pairs were significantly higher than that of CG pairs, even with the SAS-CoV2 spike protein triggering a concerted BCR response. Many stereotypic AD patient-specific BCR clonotypes co-existed in more than four patients and persisted throughout the two sampling points. One of these BCR clonotypes encoded an antibody reactive to the A{beta}42 peptide. Our findings strongly suggest that AD patients are exposed to common (auto)antigens associated with disease pathology, and that their BCR repertoire signatures have high diagnostic potential.

SARS-CoV-2 Spike amyloid fibrils specifically and selectively accelerates amyloid fibril formation of human prion protein and the amyloid β peptide (preprint)

An increasing number of reports suggest an association between COVID-19 infection and initiation or acceleration of neurodegenerative diseases including Alzheimer's disease (AD) and Creutzfeldt-Jakob disease (CJD). Both these diseases and several other neurodegenerative diseases are caused by conversion of human proteins into a misfolded, aggregated amyloid fibril state. The fibril formation process is self-perpetuating by seeded conversion from preformed fibril seeds. We recently described a plausible mechanism for amyloid fibril formation of SARS-CoV-2 spike protein. Spike-protein formed amyloid fibrils upon cleavage by neutrophil elastase, abundant in the inflammatory response to COVID-19 infection. We here provide evidence of significant Spike-amyloid fibril seeded acceleration of amyloid formation of CJD associated human prion protein (HuPrP) using an in vitro conversion assay. By seeding the HuPrP conversion assay with other in vitro generated disease associated amyloid fibrils we demonstrate that this is not a general effect but a specific feature of spike-amyloid fibrils. We also showed that the amyloid fibril formation of AD associated A{beta}1-42 was accelerated by Spike-amyloid fibril seeds. Of seven different 20-amino acid long peptides, Spike532 (532NLVKNKCVNFNFNGLTGTGV551) was most efficient in seeding HuPrP and Spike601 (601GTNTSNQVAVLYQDVNCTEV620) was most effective in seeding A{beta}1-42, suggesting substrate dependent selectivity of the cross-seeding activity. Albeit purely in vitro, our data suggest that cross-seeding by Spike-amyloid fibrils can be implicated in the increasing number of reports of CJD, AD, and possibly other neurodegenerative diseases in the wake of COVID-19.

Impact of age and sex on neuroinflammation following SARS-CoV-2 infection in a murine model (preprint)

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the etiological agent for the worldwide COVID-19 pandemic, is known to infect people of all ages and both sexes. Senior populations have the greatest risk of severe disease, and sexual dimorphism in clinical outcomes has been reported in COVID-19. SARS-CoV-2 infection in humans can cause damage to multiple organ systems, including the brain. Neurological symptoms are widely observed in patients with COVID-19, with many survivors suffering from persistent neurological and cognitive impairment, potentially accelerating Alzheimer's disease. The present study aims to investigate the impact of age and sex on the neuroinflammatory response to SARS-CoV-2 infection using a mouse model. Wild-type C57BL/6 mice were inoculated, by intranasal route, with SARS-CoV-2 lineage B.1.351 variant known to infect mice. Older animals and in particular males exhibited a significantly greater weight loss starting at 4 dpi. In addition, male animals exhibited higher viral RNA loads and higher titers of infectious virus in the lung, which was particularly evident in males at 16 months of age. Notably, no viral RNA was detected in the brains of infected mice, regardless of age or sex. Nevertheless, expression of IL-6, TNF-, and CCL-2 in the lung and brain was increased with viral infection. An unbiased brain RNA-seq/transcriptomic analysis showed that SARS-CoV-2 infection caused significant changes in gene expression profiles in the brain, with innate immunity, defense response to virus, cerebravascular and neuronal functions, as the major molecular networks affected. The data presented in this study show that SARS-CoV-2 infection triggers a neuroinflammatory response despite the lack of detectable virus in the brain. Age and sex have a modifying effect on this pathogenic process. Aberrant activation of innate immune response, disruption of blood-brain barrier and endothelial cell integrity, and supression of neuronal activity and axonogenesis underlie the impact of SARS-CoV-2 infection on the brain. Understanding the role of these affected pathways in SARS-CoV-2 pathogenesis helps identify appropriate points of therapeutic interventions to alleviate neurological dysfunction observed during COVID-19.

The Human Microglia Atlas (HuMicA) Unravels Changes in Homeostatic and Disease-Associated Microglia Subsets across Neurodegenerative Conditions (preprint)

Dysregulated microglia activation, leading to neuroinflammation, is currently considered to be of major relevance in the development and progression of neurodegenerative diseases. The initial M1/M2 dual activation classification for microglia is now considered outdated. Even the "disease-associated microglia" (DAM) phenotype, firstly described in mice, has proven insufficient to precisely represent the multitude of microglia phenotypes in pathology. In this study, we have constructed a transcriptomic atlas of human brain immune cells by integrating single-nucleus (sn)RNA-seq datasets from multiple neurodegenerative conditions. Sixteen datasets were included, comprising 295 samples from patients with Alzheimer's disease, autism spectrum disorder, epilepsy, multiple sclerosis, Lewy body diseases, COVID-19, and healthy controls. The integrated Human Microglia Atlas (HuMicA) dataset included 60,557 nuclei and revealed 11 microglial subpopulations distributed across all pathological and healthy conditions. Among these, we identified four different homeostatic clusters as well as pathological phenotypes. These included two stages of early and late activation of the DAM phenotype and the disease-inflammatory macrophage (DIM) phenotype, which was recently described in mice, and is also present in human microglia, as indicated by our analysis. The high versatility of microglia is evident through changes in subset distribution across various pathologies, suggesting their contribution to the establishment of pathological phenotypes. Our analysis showed overall depletion of four substates of homeostatic microglia, and expansion of niche subpopulations within the DAM and DIM spectrum across distinct neurodegenerative pathologies. The HuMicA is an invaluable resource tool used to support further advances in the study of microglia biology through healthy and disease settings.

Invariant Scattering Transform for Medical Imaging (preprint)

Invariant scattering transform introduces new area of research that merges the signal processing with deep learning for computer vision. Nowadays, Deep Learning algorithms are able to solve a variety of problems in medical sector. Medical images are used to detect diseases brain cancer or tumor, Alzheimer's disease, breast cancer, Parkinson's disease and many others. During pandemic back in 2020, machine learning and deep learning has played a critical role to detect COVID-19 which included mutation analysis, prediction, diagnosis and decision making. Medical images like X-ray, MRI known as magnetic resonance imaging, CT scans are used for detecting diseases. There is another method in deep learning for medical imaging which is scattering transform. It builds useful signal representation for image classification. It is a wavelet technique; which is impactful for medical image classification problems. This research article discusses scattering transform as the efficient system for medical image analysis where it's figured by scattering the signal information implemented in a deep convolutional network. A step by step case study is manifested at this research work.

Navigating the Complexities of Dementia Care: The Lived Experiences of Black American Family Caregivers.

Black American individuals have a higher rate of Alzheimer's disease and related dementias (ADRD) diagnoses compared to other racial/ethnic groups, and their family caregiver population is expected to increase rapidly over the next 2 decades. The current study aimed to explore Black American women's experiences caring for family members with ADRD. An interpretative phenomenology approach was used to gain a deeper understanding of the caregiving experiences of Black American women. Participants in the study were all Black American married women aged 63 to 81 years (mean = 71.3 years, SD = 6.6 years). Key themes that emerged from the study included: (a) Family Care Obligation, (b) Caregiving Journey, (c) Prioritizing Health Concerns, (d) Coping Behaviors, and (e) Support Needs and Challenges. Family caregivers require ongoing support, education, and guidance. Implications for nursing practice include focusing on family assessments, increased education and awareness, and collaboration with interdisciplinary teams to provide the best resources. [Journal of Gerontological Nursing, 49(6), 19-26.].

The functional and structural changes in the hippocampus of COVID-19 patients.

Since the hippocampus is predominantly susceptible to injuries caused by COVID-19, there are increasing data indicating the likelihood of post-infection memory loss and quickening neurodegenerative disorders, such as Alzheimer's disease. This is due to the fact that the hippocampus has imperative functions in spatial and episodic memory as well as learning. COVID-19 activates microglia in the hippocampus and induces a CNS cytokine storm, leading to loss of hippocampal neurogenesis. The functional and structural changes in the hippocampus of COVID-19 patients can explain neuronal degeneration and reduced neurogenesis in the human hippocampus. This will open a window to explain memory and cognitive dysfunctions in "long COVID" through the resultant loss of hippocampal neurogenesis.

Cellular Metabolism: A Fundamental Component of Degeneration in the Nervous System.

It is estimated that, at minimum, 500 million individuals suffer from cellular metabolic dysfunction, such as diabetes mellitus (DM), throughout the world. Even more concerning is the knowledge that metabolic disease is intimately tied to neurodegenerative disorders, affecting both the central and peripheral nervous systems as well as leading to dementia, the seventh leading cause of death. New and innovative therapeutic strategies that address cellular metabolism, apoptosis, autophagy, and pyroptosis, the mechanistic target of rapamycin (mTOR), AMP activated protein kinase (AMPK), growth factor signaling with erythropoietin (EPO), and risk factors such as the apolipoprotein E (APOE-ε4) gene and coronavirus disease 2019 (COVID-19) can offer valuable insights for the clinical care and treatment of neurodegenerative disorders impacted by cellular metabolic disease. Critical insight into and modulation of these complex pathways are required since mTOR signaling pathways, such as AMPK activation, can improve memory retention in Alzheimer's disease (AD) and DM, promote healthy aging, facilitate clearance of ß-amyloid (Aß) and tau in the brain, and control inflammation, but also may lead to cognitive loss and long-COVID syndrome through mechanisms that can include oxidative stress, mitochondrial dysfunction, cytokine release, and APOE-ε4 if pathways such as autophagy and other mechanisms of programmed cell death are left unchecked.

Proteomic landscape of astrocytes and pericytes infected with HIV/SARS-CoV-2 mono/co-infection, impacting on neurological complications (preprint)

Background Although most individuals recover from coronavirus disease 2019 (COVID-19) within a few weeks, some people continue to experience a wide range of symptoms known as post-acute sequelae of SARS-CoV-2 (PASC) or long COVID. Majority of patients with PASC develop neurological disorders like brain fog, fatigue, mood swings, sleep disorders, loss of smell and test among others collectively called neuro-PASC. While the people living with HIV (PWH) do not have a higher risk of developing severe disease and mortality/morbidity due to COVID-19. As a large section of PWH suffered from HIV-associated neurocognitive disorders (HAND), it is essential to understand the impact of neuro-PASC on people with HAND. In pursuit of this, we infected HIV/SARS-CoV-2 alone or together in primary human astrocytes and pericytes and performed proteomics to understand the impact of co-infection in the central nervous system.Methods Primary human astrocytes and pericytes were infected with SARS-CoV-2 or HIV or HIV + SARS-CoV-2. The concentration of HIV and SARS-CoV-2 genomic RNA in the culture supernatant was quantified using reverse transcriptase quantitative real time polymerase chain reaction (RT-qPCR). This was followed by a quantitative proteomics analysis of mock, HIV, SARS-CoV-2, and HIV + SARS-CoV-2 infected astrocytes and pericytes to understand the impact of the virus in CNS cell types.Results Both healthy and HIV-infected astrocytes and pericytes support abortive/low level of SARS-CoV-2 replication. In both mono-infected and co-infected cells, we observe a modest increase in the expression of SARS-CoV-2 host cell entry factors (ACE2, TMPRSS2, NRP1, and TRIM28) and inflammatory mediators (IL-6, TNF-α, IL-1β and IL-18). Quantitative proteomic analysis has identified uniquely regulated pathways in mock vs SARS-CoV-2, mock vs HIV + SARS-CoV-2, and HIV vs HIV + SARS-CoV-2 infected astrocytes and pericytes. The gene set enrichment analysis revealed that the top ten enriched pathways are linked to several neurodegenerative disorders, including Alzheimer's disease, Parkinson's disease, Huntington's disease, and amyotrophic lateral sclerosis.Conclusions Our study emphasizes the significance of long-term monitoring of patients co-infected with HIV and SARS-CoV-2 to detect and understand the development of neurological abnormalities. By unraveling the molecular mechanisms involved, we can identify potential targets for future therapeutic interventions.