bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparing methods of cellular segmentation in prefrontal and primary visual cortices in Alzheimer’s disease
Authors: McKendell Alec K , McDonough Elizabeth , Lowery Lisa , Abate Samantha , Meyer Daniel , Luebke Jennifer , Hof Patrick R , Varghese Merina 
Published: January 2025

AbstractBackgroundIn Alzheimer’s disease (AD), specific brain regions become vulnerable to pathology while others remain resilient. New methods of imaging such as highly multiplexed immunofluorescence (MxIF) provide an abundance of spatial information, while analytical techniques like machine learning (ML) can address questions of cellular contributors to this regional vulnerability.MethodWe performed MxIF staining for 26 markers and compared postmortem human samples from an AD‐susceptible brain area, the prefrontal cortex (PFC, Brodmann’s areas 9, 10 or 46) to an AD‐resilient brain area, the primary visual cortex (V1, area 17). Subjects included AD (n = 3, clinical dementia rating CDR 3, Thal stages 3‐4, Braak stages V‐VI), mild cognitive impairment (n = 4, CDR 0.5, Thal stages 1‐3, Braak stages I‐V), and age‐matched healthy controls (n = 5, CDR 0, Thal stages 0‐1, Braak stages I‐II), including both females and males. We first used a custom Fiji plugin that leverages iterative ML to segment the images via DAPI or HUD signals. For the DAPI segmentation, ML subsequently classifies the cell type based on relevant channels. The second method used QuPath to segment exclusively using DAPI signal followed by cell‐type classifications. Segmentations and classifications in QuPath used static thresholds.ResultUsing Fiji for HUD segmentation and filtering by the presence of nuclei, we found a decrease specifically in layer 5 PFC neurons from CDR 0 to CDR 0.5. Surprisingly, this decrease did not hold in QuPath when segmenting first using DAPI. Both methods found an increase in GFAP‐expressing astrocytes primarily in layer 1. However, the pan‐astrocyte marker ALDH1L1 showed an inverse relationship, with higher density found in layers 2 through 6. Both findings held true regardless of brain region or CDR. Finally, in addition to the white matter, both methods found an increase in oligodendrocytes (MBP+, MBP+/HUD+) within layer 4 of V1 and driven by CDR 0.5.ConclusionComparisons between the image analysis modalities demonstrate that the method by which cells are segmented and classified can impact the interpretation of MxIF data. Combining knowledge of disease biology with a deeper understanding of when and how to use these techniques will improve data precision.
Single‐nucleus RNA sequencing reveals hippocampal cell type‐specific transcriptional alterations in Alzheimer’s‐linked ACE variant R1284Q knock‐in mice
Authors: Salvo Miranda A , Cuddy Leah K , Chandra Sidhanth , Ramakrishnan Abhirami , Piehl Natalie , Watson Thomas J , Gate David , Popovic Jelena , Prokopenko Dmitry , Tanzi Rudolph E. , Vassar Robert J. 
Published: January 2025

AbstractBackgroundAngiotensin‐converting enzyme (ACE) is a validated risk locus for developing late‐onset Alzheimer’s disease (LOAD). ACE1 controls blood pressure through the renin‐angiotensin system (RAS), but it is also present and acts locally in the brain. Hypertension is associated with an increased risk for developing AD, and people taking select RAS‐targeting therapeutics have reduced incidence of AD. The ACE variant rs4980 (R1284Q murine mutation) was discovered in LOAD families through WGS. Our group previously showed that ACE1 R1284Q caused age‐associated hippocampal neurodegeneration and gliosis in mutant knock‐in (KI) mice, which was more aggressive in females. Importantly, these phenotypes were rescued by treatment with anti‐hypertensive drugs. Our previous study showed that ACE1 R1284Q caused neuron death in mice, however the mechanism is still unknown. This work aims to identify vulnerable hippocampal cell populations and pathways which might clarify the mechanism of ACE1 R1284Q‐mediated neurodegeneration.MethodSingle nuclei were extracted from 30mg of flash‐frozen hippocampi from 6‐, and 12‐month‐old R1284Q ACE+/+ (WT) and ACEKI/KI (KI) and processed using 10X Genomics 3’ Dual‐Index chemistry. Libraries were sequenced using the NovaSeq 6000. Preprocessing, quality control, and integration was performed on reads before subjecting them to cluster, differential expression, and pathway analyses.ResultTogether, the samples were represented by 143,000 nuclei in 23 clusters encompassing all neuronal and glial populations in the hippocampus. We identified the expression of every RAS component, excluding renin, in the hippocampus. Notably, inhibitory and excitatory neurons had the most differentially expressed genes (DEGs) in 12‐month KI samples compared to controls. Additionally, 12‐month KI females had upregulated microglial C1q genes compared to males.ConclusionWe found expression of RAS genes in the hippocampus, which to our knowledge has not yet been characterized by single‐nucleus RNA sequencing. Furthermore, inhibitory neuron transcriptomes are the most affected in 12‐month KI mice, suggesting altered neuron communication that may lead to neuron loss. Additionally, we identified sex‐specific differences in 12‐month KI female microglia, which may explain the more aggressive gliosis seen in female KIs compared to males. Future directions include performing ingenuity pathway analysis to identify upstream regulators of DEGs and experimental perturbations to test our hypotheses.
Herpesviruses infections associations in people with young onset dementia – Herpes simplex infection appears to be relevant
Authors: Hosseini Akram A. , Maple Peter A.C , Tanasescu Radu , Gran Bruno 
Published: January 2025

AbstractBackgroundEarly Onset Alzheimer’s Disease (EOAD) is thought to result from a combination of environmental, genetic, and lifestyle factors. Herpesvirus infections may contribute to the development of EOAD and the objective of our study is to identify potential associations between herpes virus infections and the risk of developing EOAD.MethodAmyloid‐status Alzheimer’s disease was diagnosed based on clinical history and ATN criteria, determined by the measuring the Amyloidß42:40 ratio, tau, and 181‐Phospho‐tau in the cerebrospinal fluid. EOAD was defined as the onset of symptoms before the age of 65. Antibodies to herpesviruses were detected in patients’ sera using commercially available enzyme immunoassays. The following markers were tested: cytomegalovirus IgG, total (HSV1/HSV2) herpes simplex virus IgG, IgM and IgA, and varicella‐zoster virus (VZV) IgG. The Mann‐Whitney U test and the Fisher’s exact test assessed differences in population and categorized data, with statistical significance set at p<0.05.ResultSera from 20 individuals with Amyloid‐status EOAD and 20 age‐ and sex‐matched healthy controls (HCs) were tested. There were 13 females and seven males in the EOAD and HCs groups with a mean age of 60.4 years and 60.7 years, respectively. All individuals were VZV IgG seropositive with geometric mean levels of 967 mIU/ml and 827 mIU/ml in EOAD and HCs, respectively. The seroprevalences of CMV IgG were 45.0% and 35.0% in EOAD and HCs, respectively. The geometric mean CMV IgG levels were significantly higher (p = 0.029) in EOAD (678 Paul Ehrlich International units/ml) versus HCs (380 Paul Ehrlich International units/ml). The seroprevalences of HSV IgG were 90.0% in EOAD and 65.0% in HCs (difference not significant). Total HSV IgG levels were similar in EOAD (geometric mean level = 594 EU/ml) and HCs (geometric mean level = 640 EU/ml). Two individuals with EOAD and none in the HCs group showed evidence of HSV reactivation.ConclusionThe sample sets tested are small; however, testing is ongoing. Currently, it appears that individuals with EOAD have higher levels of CMV IgG compared to healthy controls.
Analysing the Genetic Mosaic of Relapsing Remitting vs Clinically isolated syndrome Multiple Sclerosis: A Bioinformatics Perspective on Subtype‐Specific Variations
Authors: Bhonsale Aman Milind , Varma Ishita , Subhedar Atharva , Khankar Shreya , Chandak Snehal , Suryawanshi Mahima , Mast Siddhali , Lalotra Tapesh , Phadke Parth , Pakhmode Sarthak , Tripathi Satyendra , Deshmukh Vishwajit , Patil Ashlesh 
Published: January 2025

AbstractBackgroundMultiple Sclerosis (MS) is a chronic, etiologically complex disease of the central nervous system (CNS) characterized by inflammation, demyelination, and neuronal damage. MS has seven categories based on disease course. Seventy to eighty percent of individuals with MS initially develop a clinical pattern with periodic relapses and remissions, called relapsing‐remitting MS (RRMS). Clinically isolated syndrome (CIS) refers to a single clinical inflammatory attack on the CNS. Evidence suggests that CD8+ T cells play a substantial role in MS pathophysiology. In this bioinformatic study, we aim to identify specific genes and pathways up‐regulated or down‐regulated in CD8+ T cells of RRMS and CIS subtypes.MethodThe GSE19285 dataset on the Gene Expression Omnibus (GEO) consists of the whole transcriptome of sorted T cells (CD8+) from treatment‐naive MS patients. Age‐matched sampling maintained uniformity. Data analysis used GEO2R with the Benjamini & Hochberg method (False discovery rate, padj < 0.05), and log fold change threshold greater than 1.5 or less than 1.5. We explored genetic profiles in immune cells, comparing RR (n = 17, age 30.76±7.05 years), CIS (n = 17, age 30.76±6.90 years), and healthy controls (n = 17, age 30.71±7.09 years). Gene pathway and protein‐protein interaction analyses of differentially expressed genes used the STRING platform.ResultThe study revealed upregulation of TRBV4‐2 gene in CD8+ cells of RRMS patients compared to healthy controls, while several genes, including AATK, PPP1R14C and TRIM36, were downregulated in RRMS. Two genes, DACT1 and CD4, were identified as upregulated in CD8+ cells, while several genes, including MYOM2, AATK, GPR27, LOC105370088, TRR‐ACG1‐2, KIR2DL3, and SIGLEC10, were downregulated in CIS compared to healthy controls. Additionally, CD4, DACT1, and CYBRD1 genes were up‐regulated in CIS compared to RRMS.ConclusionIn RRMS, TRIM36’s role in proteostasis and neurodegeneration is highlighted, with protein‐protein interaction analysis showing dysfunctional ubiquitination. Altered antigen processing and presentation in CIS compared to healthy individuals and RRMS suggest differences in pathophysiology in this subtype. Furthermore, recent study has suggested CYBRD1 as a potential MS biomarker.
Fit for purpose high‐throughput absolute quantitation of chimeric aducanumab in mouse cortex and plasma
Authors: Doud Emma H. , Haynes Kathryn A , Santos Diogo Francisco Silva , Mosley Amber L. , Quinney Sara K , Rizzo Stacey J Sukoff , Territo Paul R 
Published: January 2025

AbstractBackgroundAlthough pharmacokinetics and pharmacodynamics of biotherapeutics are commonly studied through ELISAs; however, the extremely strong binding of modern antibody‐based therapeutics result in background, inability of secondary antibody binding, and nonlinear response curves. The selectivity and specificity imparted through the use of liquid chromatography‐targeted mass spectrometry (LC‐MS/MS) allows for absolute quantitation of chosen peptides. For MODEL‐AD, here we present a high‐throughput workflow for absolute quantification of chimeric aducanumab from cortex and plasma of 5XFAD mice.MethodsA targeted MS assay for quantitation of aducanumab was designed utilizing guidelines described by the National Cancer Institute’s Clinical Proteomic Tumor Analysis Consortium. Proteotryptic peptides unique for chimeric aducanumab were selected, and stable isotope versions were purchased as spike in controls. Given that aducanumab was present in mouse cortex at very low levels, a high sensitivity and high throughput methodology was optimized with Protein A enrichment, reduction, alkylation, trypsin digestion, loading samples onto Evotips using an AssayMap Bravo (Agilent). Evosep LC was paired with a Lumos Tribrid orbitrap (Thermo Fisher Scientific) and data were analyzed in Skyline (MacCoss lab) with a concentration curve of pure protein in matrix normalized to spike in stable isotope labeled peptides.ResultsThe three tryptic peptides used for quantitation of aducanumab had lower limits of detection and quantification of 1‐500 Amol pure peptide on column and 2‐5 ng aducanumab/uL in plasma and 0.225 ng/ug brain homogenate. This assay was sensitive and linear over 1 to 500,000 Amol range with high reproducibility (CV 3‐10%). Using a protein A purification, the lower limit of quantification was decreased by 100 fold. This assay was micronized for 96 sample formats, where a single plate could be analyzed in 48‐72 hours.ConclusionsAlthough unique peptides will vary, we anticipate this general workflow will allow for quantitation of AD focused biotherapeutics. As part of the open science framework, this methodology will be made available to the broader research community to facilitate broad application.
Intranasally Administered EVs from hiPSC‐derived NSCs Alter the Transcriptomic Profile of Activated Microglia and Conserve Brain Function in an Alzheimer’s Model
Authors: Madhu Leelavathi N , Kodali Maheedhar , Upadhya Raghavendra , Rao Shama , Shuai Bing , Somayaji Yogish , Attaluri Sahithi , Kirmani Maha , Gupta Shreyan , Maness Nathaniel , Rao Xiaolan , Cai James , Shetty Ashok K 
Published: January 2025

AbstractBackgroundCurrent treatments for Alzheimer’s disease (AD) lack disease‐modifying interventions. Hence, novel therapies capable of restraining AD progression and maintaining better brain function for extended periods after the initial diagnosis have great significance. Extracellular vesicles (EVs) from human induced pluripotent stem cell (hiPSC)‐derived neural stem cells (NSCs) are attractive in this context due to their robust antiinflammatory properties.MethodThree‐month‐old 5x familial AD (5xFAD) mice received IN administration of hiPSC‐NSC‐EVs (∼30 billion EVs) or the vehicle (weekly for two weeks). Seventy‐two hours later, a cohort of mice was euthanized, fresh microglia were isolated from the brain, and the expression of genes linked to DAM and NLRP3‐inflammasome signaling was examined via scRNA‐sequencing. Another cohort of 5xFAD mice was investigated for cognitive and mood function commencing one‐month post‐EV/Veh administration and euthanized two months post‐EV/Veh administration to assess the effects on long‐term progressive increases in neuroinflammation, amyloid‐beta plaques, and phosphorylated tau (p‐tau).ResultMicroglia in all brain regions, including plaque‐associated microglia, internalized hiPSC‐NSC‐EVs entering the brain. Single‐cell RNA sequencing at 72 hours post‐EV administration revealed microglia with transcriptomic changes indicative of diminished activation. Multiple genes linked to disease‐associated microglia, NOD‐, LRR‐ and pyrin domain‐containing protein 3 (NLRP3)‐inflammasome and interferon‐1 signaling displayed reduced expression. Adding hiPSC‐NSC‐EVs to cultured human microglia challenged with amyloid‐beta oligomers also resulted in similar effects. Furthermore, the modulatory effects of hiPSC‐NSC‐EVs on microglia in the hippocampus persisted even two months post‐EV treatment, evidenced by reductions in microglial clusters and inflammasome complexes, concentrations of mediators, and end products of NLRP3 inflammasome activation, the expression of genes and proteins involved in p38/mitogen‐activated protein kinase hyperactivation, and proteins linked to activation of interferon‐1 signaling. The hippocampus also exhibited reduced amyloid‐beta plaques and p‐tau. Such modulatory effects of hiPSC‐NSC‐EVs also led to better cognitive and mood function.ConclusionEarly hiPSC‐NSC‐EV intervention in AD can maintain better brain function by reducing adverse neuroinflammatory signaling cascades, amyloid‐beta plaque load, and p‐tau.Supported by a grant from the National Institute for Aging (1RF1AG074256‐01A1 to A.K.S.)
Association between Long COVID and neuropsychological outcomes in a Brazilian Cohort: preliminary results
Authors: Senger Joana Emilia , Machado Luiza Santos , Silveira Maiele Dornelles , da Silva Ana Paula Bornes , Ferrari‐Souza João Pedro , de Bastiani Marco Antônio , Povala Guilherme , Borelli Wyllians Vendramini , de Mello Guilherme Bastos , da Ros João Pedro Uglione , Jotz Arthur Viana , Kadan Matheus Fakhri , Radaelli Graciane , Pascoal Tharick A. , Matushita Cristina Sebastião , Soder Ricardo Benardi , Schumacher‐Schuh Artur Francisco , Souza Diogo O. , Lourenco Mychael V. , de Paula de Paula Faria Daniele , Coutinho Artur Martins , da Costa Jaderson Costa , de Souza Débora Guerini , Zimmer Eduardo R. 
Published: January 2025

AbstractBackgroundCOVID‐19 pandemic has brought long‐lasting social, emotional, and cognitive consequences. Long COVID is characterized by a myriad of symptoms and complications that persist long after the infection, including cognitive decline and mental health impairment. This study aims to investigate depressive symptoms and cognitive performance stratified by sex and group in adults with and without long COVID.MethodCommunity‐dwelling individuals from Porto Alegre, Brazil, were divided into control and long COVID groups. We recruited 49 individuals, aged >50 years. Individuals were evaluated with the mini mental state examination (MMSE), Clock Drawing Test, Trail Making Test (TMT‐B), Wechsler Memory Scale (WMS‐R) and PHQ‐9 scale of depressive symptoms. A regression model was conducted stratified by sex, age and group. PHQ‐9 was used as an interaction of the same variables. Data were analyzed using R, considering p‐value < 0.05.ResultA total of 49 individuals (59.8 ± 8.06 mean years of age, 63.3% females), having high education (>11 years of study) were included. The control group was comprised of 18 individuals (36.73%) and the long COVID group had 31 individuals (63.26%). The Long COVID group had a worse performance in WMS‐A (p <0.011) and WMS‐B (p <0.03) in the immediate test and WSM‐B recall (p <0.02). The PHQ‐9 test differed between groups, with long COVID individuals presenting depressive symptoms (p <0.003). We also found an interaction of long COVID and PHQ‐9 impacting on the TMT‐ B test (p <0.03).ConclusionPreliminary results showed that long COVID induced impairment in executive functions, specifically in working memory and episodic memory scores. Additionally, there was an impact of depressive symptoms in the relationship between group and TMT‐B scores. Participants with depressive symptoms had worsened cognitive performance on the regression analysis. A larger sample should corroborate these findings and provide further insights into the long COVID cognitive impact.
Clinical and neuropathological differences in dementia and the correlation between the sexes
Authors: Socher Karen L R , Justo Alberto Fernando Oliveira , Rodriguez Roberta Diehl , Leite Renata Elaine Paraizo , Jacob‐Filho Wilson , Pasquallucci Carlos Augusto , Nitrini Ricardo , Grinberg Lea T. , Suemoto Claudia Kimie , Brucki Sonia Maria Dozzi 
Published: January 2025

AbstractBackgroundThe study of dementia and its differences between the sexes is widely investigated, mainly in Alzheimer’s disease. However, most studies on dementia are not carried out in a multiethnic population. Here we analyze demographic data, clinical symptoms, and neuropathological characteristics of a large mixed Brazilian sample.MethodThe Biobank for Aging Studies has a unique collection of brain samples that we selected over 50 years of age. All were examined for the presence of dementia pathology according to internationally accepted criteria for pathological staging and diagnosis. All cases have a complete semi‐structured interview carried out to obtain sociodemographic data, lifestyle, past medical history, and the presence of cognitive impairment (CI) was defined according to the Clinical Dementia Rating Scale (CDR≥0.5).ResultOf the 1,611 cases included, 801 were men and 811 were women. Regarding ethnicity, 65.2% were identified by family members as white for both groups. Regarding differences between sexes, women were older, less literate and had greater cognitive impairment in the CDR and Sum of Boxes (p>0.001). The neuropathological findings showed a sample of women with a lower percentage (48.9%) of initial Braak stages and a higher percentage (51.3%) of Braak stage ≥III (p>0.001). Higher prevalence of moderate and frequent CERAD score (p>0.001), as well as TDP‐43 proteinopathy. Concerning other pathologies such as Lewy Body Diseases, Lacunar Infarction, Arteriosclerosis, and Cerebral Amyloid Angiopathy, no significance was found. When analyzing sex and clinical symptoms using a multivariate linear regression model, there was significance for both the final CDR score and the sum of the boxes. The association of neuropathological and clinical findings through logistic regression with adjustment for age and education, there is a tendency for women to present more symptoms, regardless of the subtype of neuropathological lesion. For Alzheimer’s disease pathology, there was statistical significance with the clinical pathology and continuous staging with prevalence in women, as well as in the presence of TDP‐43 pathology and hyaline arteriosclerosis in vascular pathology.ConclusionSex in the neuropathology of dementia plays an important role in cognitive symptoms, highlighting the need to consider it in future prevention and treatment strategies.
The Alzheimer’s Disease Sequencing Project: Progress and Update
Authors: Pericak‐Vance Margaret A 
Published: January 2025

AbstractIn response to the National Alzheimer’s Project Act (NAPA) in 2012 the National Institute on Aging (NIA) commenced a new genetics initiative (the Alzheimer’s Disease Sequencing Project [ADSP]) to understand the genetic architecture of Alzheimer’s Disease and Related Dementias (AD/ADRD). The ADSP has three main goals 1) To Identify new genes and genetic variations that contribute to increased risk for or protection against AD/ADRD, 2) to provide insight as to how these genes and variations impact AD/ADRD, 3) to identify potential avenues or approaches to translate genetic results into therapeutic targets. The ADSP has led the field in global inclusion and diversity with the goal of universal success in the treatment and prevention of AD/ADRD. The most recent release of over 36,000 genomes from over 40 cohorts worldwide is evidence to this effect. This first presentation will be a brief introduction and overview of the structure, growth, and progress of the ADSP.