Single-nucleus and spatial transcriptomic profiling of human temporal cortex and white matter reveals novel associations with AD pathology.

Alzheimer's disease (AD) is a neurodegenerative disorder with complex pathological manifestations and is the leading cause of cognitive decline and dementia in elderly individuals. A major goal in AD research is to identify new therapeutic pathways by studying the molecular and cellular changes in the disease, either downstream or upstream of the pathological hallmarks. In this study, we present a comprehensive investigation of cellular heterogeneity from the temporal cortex region of 40 individuals, comprising healthy donors and individuals with differing tau and amyloid burden. Using single-nucleus transcriptome analysis of 430,271 nuclei from both gray and white matter of these individuals, we identified cell type-specific subclusters in both neuronal and glial cell types with varying degrees of association with AD pathology. In particular, these associations are present in layer specific glutamatergic (excitatory) neuronal types, along with GABAergic (inhibitory) neurons and glial subtypes. These associations were observed in early as well as late pathological progression. We extended this analysis by performing multiplexed in situ hybridization using the CARTANA platform, capturing 155 genes in 13 individuals with varying levels of tau pathology. By modeling the spatial distribution of these genes and their associations with the pathology, we not only replicated key findings from our snRNA data analysis, but also identified a set of cell type-specific genes that show selective enrichment or depletion near pathological inclusions. Together, our findings allow us to prioritize specific cell types and pathways for targeted interventions at various stages of pathological progression in AD.

Distinct microglial transcriptomic signatures within the hippocampus.

Microglia, the resident immune cells of the brain, are crucial in the development of the nervous system. Recent evidence demonstrates that microglia modulate adult hippocampal neurogenesis by inhibiting cell proliferation of neural precursors and survival both in vitro and in vivo, thus maintaining a balance between cell division and cell death in the neural stem cell pool. There are increasing reports suggesting these microglia found in neurogenic niches differ from their counterparts in non-neurogenic areas. Here, we present evidence that hippocampal microglia exhibit transcriptomic heterogeneity, with some cells expressing genes associated with neurogenesis. By comprehensively profiling myeloid lineage cells in the hippocampus using single cell RNA-sequencing, we have uncovered a small, yet distinct population of microglia which exhibit depletion in genes associated with homeostatic microglia and enrichment of genes associated with phagocytosis. Intriguingly, this population also expresses a gene signature with substantial overlap with previously characterized phenotypes, including disease associated microglia (DAM), a particularly unique and compelling microglial state.

Multicellular communities are perturbed in the aging human brain and Alzheimer's disease.

The role of different cell types and their interactions in Alzheimer's disease (AD) is a complex and open question. Here, we pursued this question by assembling a high-resolution cellular map of the aging frontal cortex using single-nucleus RNA sequencing of 24 individuals with a range of clinicopathologic characteristics. We used this map to infer the neocortical cellular architecture of 638 individuals profiled by bulk RNA sequencing, providing the sample size necessary for identifying statistically robust associations. We uncovered diverse cell populations associated with AD, including a somatostatin inhibitory neuronal subtype and oligodendroglial states. We further identified a network of multicellular communities, each composed of coordinated subpopulations of neuronal, glial and endothelial cells, and we found that two of these communities are altered in AD. Finally, we used mediation analyses to prioritize cellular changes that might contribute to cognitive decline. Thus, our deconstruction of the aging neocortex provides a roadmap for evaluating the cellular microenvironments underlying AD and dementia.

A cellular taxonomy of the adult human spinal cord.

The mammalian spinal cord functions as a community of cell types for sensory processing, autonomic control, and movement. While animal models have advanced our understanding of spinal cellular diversity, characterizing human biology directly is important to uncover specialized features of basic function and human pathology. Here, we present a cellular taxonomy of the adult human spinal cord using single-nucleus RNA sequencing with spatial transcriptomics and antibody validation. We identified 29 glial clusters and 35 neuronal clusters, organized principally by anatomical location. To demonstrate the relevance of this resource to human disease, we analyzed spinal motoneurons, which degenerate in amyotrophic lateral sclerosis (ALS) and other diseases. We found that compared with other spinal neurons, human motoneurons are defined by genes related to cell size, cytoskeletal structure, and ALS, suggesting a specialized molecular repertoire underlying their selective vulnerability. We include a web resource to facilitate further investigations into human spinal cord biology.

Cell type-specific changes identified by single-cell transcriptomics in Alzheimer's disease.

The rapid advancement of single-cell transcriptomics in neurology has allowed for profiling of post-mortem human brain tissue across multiple diseases. Over the past 3 years, several studies have examined tissue from donors with and without diagnoses of Alzheimer's disease, highlighting key changes in cell type composition and molecular signatures associated with pathology and, in some cases, cognitive decline. Although all of these studies have generated single-cell/nucleus RNA-seq or ATAC-seq data from the full array of major cell classes in the brain, they have each focused on changes in specific cell types. Here, we synthesize the main findings from these studies and contextualize them in the overall space of large-scale omics studies of Alzheimer's disease. Finally, we touch upon new horizons in the field, in particular advancements in high-resolution spatial interrogation of tissue and multi-modal efforts-and how they are likely to further advance mechanistic and target-selection studies on Alzheimer's disease.

Effectiveness of Tranexamic Acid in Reducing Postoperative Blood Loss in Patients Undergoing Off-Pump Coronary Artery Bypass Grafting.

Background Off-pump coronary artery bypass grafting (OP-CABG) is an accepted surgical option in treating ischemic heart disease and has proven safer than traditional on-pump CABG in terms of reducing perioperative bleeding, coagulopathy, avoiding cardiopulmonary bypass machine and its related morbidity. However, there is evidence that shows the risk of bleeding in OP-CABG due to surgical trauma, heart manipulations, and heparin-protamine exposure. We aim to evaluate the effectiveness of tranexamic acid (TxA) in reducing blood loss and related perioperative complications in patients undergoing OP-CABG. Method An individual matched cohort study was conducted at a cardiac centre over a period of one year. We enrolled a total of 60 patients undergoing OPCABG in our study. The basic strategy was to enroll every possible intervention patient until the desired sample size (30 in each group) was achieved and then to select and enroll controls, using a prospective individual matching strategy. Preoperative cardiac risk evaluation was done using the European System for Cardiac Operative Risk Evaluation II (EuroSCORE II) in both groups. The intervention group (I) received TxA 10 mg/kg over 10 minutes at the time of induction while the control group (C) did not receive any TxA. Postoperative blood loss was measured by observing chest drain output 24 hourly till the chest drain tube was removed. Perioperative complications were also recorded. Results Demographics and baseline characteristics were comparable among groups (p > 0.05). The mean volume of postoperative blood loss in the I group at 24 hours and 48 hours were 352.67 ml and 86.83 ml, respectively. On the other hand, in the C group, the mean volume of postoperative blood loss was 602.00 ml and 166.3 ml. The data showed a statistically significant difference in the postoperative chest drainage output between the groups (unpaired t-test, p < 0.05) and exhibiting a significant reduction in postoperative blood loss in the I group. However, there was no significant difference in blood transfusion requirements in both of the groups (Mann Whitney U test, p > 0.05). The mean duration of postoperative complications, inotropic support, intermittent positive pressure ventilation, intensive care, and hospital stay were also comparable depicting no significant effect of TxA on reducing the perioperative morbidity. Conclusion This study showed the significance of TxA in reducing bleeding in the postoperative period in patients undergoing OP-CABG.

Pneumothorax Following Bougie-guided Intubation in a Difficult Airway: A Report of Two Cases.

Patients coming for atlantoaxial dislocation surgery represent a unique subset of difficult intubation. In addition to having restricted neck movements, excessive movements at the neck joint during intubation must be avoided to avoid further compression. In view of the anticipated difficult intubation, adjuncts or introducers may be required to aid intubation, the most commonly used being bougies. Complications are known to occur with the use of bougies but fortunately the incidences are far and few. The most dreaded of these is pneumothorax, secondary to trauma by the bougie. The use of an adult bougie for pediatric intubations could possibly increase the risk of the same. Here, we report two incidences of pneumothorax after bougie-guided intubation.

Early detection of cryostorage tank failure using a weight-based monitoring system.

PURPOSE: To study the relationship between liquid nitrogen loss and temperature in cryostorage dewars and develop an early-warning alarm for impending tank failure. METHODS: Cryostorage dewars were placed on custom-engineered scales, and weight and temperature data were continuously monitored in the setting of slow, medium, and fast rate-loss of LN2 to simulate three scenarios of tank failure. RESULTS: LN2 Tank weights and temperatures were continuously monitored and recorded, with a calculated alarm trigger set at 10% weight loss and temperature of - 185 °C. With an intact tank, a 10% loss in LN2 occurred in 4.2-4.9 days. Warming to - 185 °C occurred in 37.8-43.7 days, over 30 days after the weight-based alarm was triggered. Full evaporation of LN2 required ~ 36.8 days. For the medium rate-loss simulation, a 10% loss in LN2 occurred in 0.8 h. Warming to - 185 °C occurred in 3.7-4.8 h, approximately 3 h after the weight-based alarm was triggered. For the fast rate-loss simulation, a 10% weight loss occurred within 15 s, and tanks were depleted in under 3 min. Tank temperatures began to rise immediately and at a relatively constant rate of 43.9 °C/h and 51.6 °C/h. Temperature alarms would have sounded within 0.37 and 0.06 h after the breech. CONCLUSIONS: This study demonstrates that a weight-based alarm system can detect tank failures prior to a temperature-based system. Weight-based monitoring could serve as a redundant safety mechanism for added protection of cryopreserved reproductive tissues.

Clustering and Candidate Motif Detection in Exosomal miRNAs by Application of Machine Learning Algorithms.

BACKGROUND: The clustering pattern and motifs give immense information about any biological data. An application of machine learning algorithms for clustering and candidate motif detection in miRNAs derived from exosomes is depicted in this paper. Recent progress in the field of exosome research and more particularly regarding exosomal miRNAs has led much bioinformatic-based research to come into existence. The information on clustering pattern and candidate motifs in miRNAs of exosomal origin would help in analyzing existing, as well as newly discovered miRNAs within exosomes. Along with obtaining clustering pattern and candidate motifs in exosomal miRNAs, this work also elaborates the usefulness of the machine learning algorithms that can be efficiently used and executed on various programming languages/platforms. RESULT: Data were clustered and sequence candidate motifs were detected successfully. The results were compared and validated with some available web tools such as 'BLASTN' and 'MEME suite'. CONCLUSION: The machine learning algorithms for aforementioned objectives were applied successfully. This work elaborated utility of machine learning algorithms and language platforms to achieve the tasks of clustering and candidate motif detection in exosomal miRNAs. With the information on mentioned objectives, deeper insight would be gained for analyses of newly discovered miRNAs in exosomes which are considered to be circulating biomarkers. In addition, the execution of machine learning algorithms on various language platforms gives more flexibility to users to try multiple iterations according to their requirements. This approach can be applied to other biological data-mining tasks as well.

Rapid preimplantation genetic screening using a handheld, nanopore-based DNA sequencer.

OBJECTIVE: To determine if a handheld, nanopore-based DNA sequencer can be used for rapid preimplantation genetic screening (PGS). DESIGN: Laboratory study. SETTING: Academic medical center. PATIENT(S): Amplified genomic DNA from euploid and aneuploid trophectoderm biopsy samples (n=9) that was also tested using traditional next generation sequencing (NGS). INTERVENTION(S): Short-read DNA library preparation and nanopore-based sequencing using a hand-held MinION sequencer. MAIN OUTCOME MEASURE(S): Comparison of cytogenetic testing result from NGS and nanopore-based sequencing and the time required for library preparation and sequencing. RESULT(S): Multiplexed short-read DNA library preparation was completed in 45 minutes. Sequencing on a single sample was completed within 20 minutes and 5 samples were simultaneously sequenced in under 2 hours. Whole-chromosome aneuploidy screening results obtained from nanopore-based sequencing were identical to those obtained using NGS. CONCLUSION(S): Here we report the first application of nanopore-based sequencing for PGS on trophectoderm biopsy samples using a novel rapid multiplxed short-read nanopore sequencing library preparation protocol. Sequencing for aneuploidy screening could be performed on a single sample in 20 minutes and on 5 samples, simultaneously, within 2 hours. Overall, nanopore sequencing is a promising tool to perform rapid PGS onsite, enabling same day testing and embryo transfer, thus obviating the need for complex, large and expensive DNA sequencers or embryo freezing.

Efficacy and Safety of Using Air Versus Alkalinized 2% Lignocaine for Inflating Endotracheal Tube Cuff and Its Pressure Effects on Incidence of Postoperative Coughing and Sore Throat.

BACKGROUND AND OBJECTIVE: We wished to compare the endotracheal tube (ETT) cuff pressure inflated with air or alkalinized lignocaine during anesthesia and evaluate clinical symptoms such as coughing and sore throat (postoperative sore throat [POST]) following tracheal extubation. MATERIALS AND METHODS: This was a prospective randomized controlled study conducted in a tertiary care set up over a period of 1 year. We included 100 patients in age group of 18-65 years posted for elective surgeries of duration more than 90 min under general anesthesia with N2O-O2 mixture. Patients were randomized using computer-generated randomization table into air and lignocaine group. The ETT cuff was inflated with air or alkalinized lignocaine (2% lignocaine with 7.5% sodium bicarbonate, in the proportions of 19.0:1.0 ml) to the volume that prevented air leak using cuff pressure manometer. After extubation, an independent observer blinded to study group recorded the presence or absence of coughing and POST at immediately, 1 h and 24 h postoperatively. RESULTS: Demographic data, baseline characteristics (American Society of Anesthesiologists grade, intracuff volume/cuff pressure at start of surgery), and duration of anesthesia were comparable among study groups (P > 0.05). Cuff pressure and volume achieved in the end of surgery were much higher in air group as compared to lignocaine group (P < 0.05). Incidence of coughing and POST at immediately, 1 h and 24 h postoperatively was significantly higher in air group compared to lignocaine group. Impact of duration of anesthesia on rise in cuff pressure was significantly higher in air group and its effect on cuff-induced laryngotracheal morbidity was significant in both air and lignocaine group. CONCLUSION: This study showed the significance of use of alkalinized 2% lignocaine in prevention of rise of cuff pressure and incidence of coughing and POST. Duration of anesthesia has also a significant effect on incidence of postoperative trachea-laryngeal morbidity.

A study of partial pressure of arterial carbon dioxide and end-tidal carbon dioxide correlation in intraoperative and postoperative period in neurosurgical patients.

BACKGROUND AND AIM: Monitoring carbon dioxide (CO2) is of utmost importance in neurosurgical patients. It is measured by partial pressure of arterial CO2 (PaCO2) and end-tidal CO2 (ETCO2). We aimed to study the correlation between PaCO2 and ETCO2 in neurosurgical patients in the intraoperative and postoperative period on mechanical ventilation in Postanesthesia Care Unit (PACU). METHODOLOGY: This was prospective observational study done at tertiary care teaching public hospital over a period of 1 year. We studied 30 patients undergoing elective craniotomy intraoperatively and in the postoperative period on mechanical ventilation for 24 h. Serial measurement of ETCO2 and PaCO2 at baseline, hourly intraoperatively and every 6 hourly in the PACU were studied. Data analysis was done using SPSS software version 20. RESULTS: The mean PaCO2-ETCO2 gradient intraoperatively over 4 h is 3.331 ± 2.856 and postoperatively over 24 h is 2.779 ± 2.932 and lies in 95% confidence interval. There was statistically significant correlation between PaCO2 and ETCO2 intraoperatively baseline, 1 h, 2 h, 3 h, and 4 h with Pearson's correlation coefficients of 0.799, 0.522, 0582, 0.439, and 0.547, respectively (P < 0.05). In PACU at baseline, 6 h, 12 h, 18 h, and 24 h Pearson's correlation coefficients were. 534, -0.032, 0.522, 0.242, 0.592, and 0.547, respectively, which are highly significant at three instances (P < 0.01). CONCLUSION: ETCO2 correlates PaCO2 with acceptable accuracy in neurosurgical patients in the intraoperative and postoperative period on mechanical ventilation in Intensive Care Unit. Thus, continuous and noninvasive ETCO2 can be used as a reliable guide to estimate arterial PCO2 during neurosurgical procedures and in PACU.

Mining SNPs in extracellular vesicular transcriptome of Trypanosoma cruzi: a step closer to early diagnosis of neglected Chagas disease.

One of the newest and strongest members of intercellular communicators, the Extracellular vesicles (EVs) and their enclosed RNAs; Extracellular RNAs (exRNAs) have been acknowledged as putative biomarkers and therapeutic targets for various diseases. Although a very deep insight has not been possible into the physiology of these vesicles, they are believed to be involved in cell-to-cell communication and host-pathogen interactions. EVs might be significantly helpful in discovering biomarkers for possible target identification as well as prognostics, diagnostics and developing vaccines. In recent studies, highly bioactive EVs have drawn attention of parasitologists for being able to communicate between different cells and having likeliness of reflecting both source and target environments. Next-generation sequencing (NGS) has eased the way to have a deeper insight into these vesicles and their roles in various diseases. This article arises from bioinformatics-based analysis and predictive data mining of transcriptomic (RNA-Seq) data of EVs, derived from different life stages of Trypanosoma cruzi; a causing agent of neglected Chagas disease. Variants (Single Nucleotide Polymorphisms (SNPs)) were mined from Extracellular vesicular transcriptomic data and functionally analyzed using different bioinformatics based approaches. Functional analysis showed the association of these variants with various important factors like Trans-Sialidase (TS), Alpha Tubulin, P-Type H+-ATPase, etc. which, in turn, are associated with disease in different ways. Some of the 'candidate SNPs' were found to be stage-specific, which strengthens the probability of finding stage-specific biomarkers. These results may lead to a better understanding of Chagas disease, and improved knowledge may provide further development of the biomarkers for prognosis, diagnosis and drug development for treating Chagas disease.