LRcell: detecting the source of differential expression at the sub-cell-type level from bulk RNA-seq data.

Given most tissues are consist of abundant and diverse (sub-)cell types, an important yet unaddressed problem in bulk RNA-seq analysis is to identify at which (sub-)cell type(s) the differential expression occurs. Single-cell RNA-sequencing (scRNA-seq) technologies can answer the question, but they are often labor-intensive and cost-prohibitive. Here, we present LRcell, a computational method aiming to identify specific (sub-)cell type(s) that drives the changes observed in a bulk RNA-seq experiment. In addition, LRcell provides pre-embedded marker genes computed from putative scRNA-seq experiments as options to execute the analyses. We conduct a simulation study to demonstrate the effectiveness and reliability of LRcell. Using three different real datasets, we show that LRcell successfully identifies known cell types involved in psychiatric disorders. Applying LRcell to bulk RNA-seq results can produce a hypothesis on which (sub-)cell type(s) contributes to the differential expression. LRcell is complementary to cell type deconvolution methods.

Obesity during preclinical Alzheimer's disease development exacerbates brain metabolic decline.

Alzheimer's disease (AD) is the most common form of dementia. Obesity in middle age increases AD risk and severity, which is alarming given that obesity prevalence peaks at middle age and obesity rates are accelerating worldwide. Midlife, but not late-life obesity increases AD risk, suggesting that this interaction is specific to preclinical AD. AD pathology begins in middle age, with accumulation of amyloid beta (Aß), hyperphosphorylated tau, metabolic decline, and neuroinflammation occurring decades before cognitive symptoms appear. We used a transcriptomic discovery approach in young adult (6.5 months old) male and female TgF344-AD rats that overexpress mutant human amyloid precursor protein and presenilin-1 and wild-type (WT) controls to determine whether inducing obesity with a high-fat/high-sugar "Western" diet during preclinical AD increases brain metabolic dysfunction in dorsal hippocampus (dHC), a brain region vulnerable to the effects of obesity and early AD. Analyses of dHC gene expression data showed dysregulated mitochondrial and neurotransmission pathways, and up-regulated genes involved in cholesterol synthesis. Western diet amplified the number of genes that were different between AD and WT rats and added pathways involved in noradrenergic signaling, dysregulated inhibition of cholesterol synthesis, and decreased intracellular lipid transporters. Importantly, the Western diet impaired dHC-dependent spatial working memory in AD but not WT rats, confirming that the dietary intervention accelerated cognitive decline. To examine later consequences of early transcriptional dysregulation, we measured dHC monoamine levels in older (13 months old) AD and WT rats of both sexes after long-term chow or Western diet consumption. Norepinephrine (NE) abundance was significantly decreased in AD rats, NE turnover was increased, and the Western diet attenuated the AD-induced increases in turnover. Collectively, these findings indicate obesity during prodromal AD impairs memory, potentiates AD-induced metabolic decline likely leading to an overproduction of cholesterol, and interferes with compensatory increases in NE transmission.

Prevalence of bradyarrhythmias needing pacing in COVID-19.

BACKGROUND: The Sars-Cov-2 infection is a multisystem illness that can affect the cardiovascular system. Tachyarrhythmias have been reported but the prevalence of bradyarrhythmia is unclear. Cases have been described of transient high-degree atrioventricular (AV) block in COVID-19 that were managed conservatively. METHOD: A database of all patients requiring temporary or permanent pacing in two linked cardiac centers was used to compare the number of procedures required during the first year of the pandemic compared to the corresponding period a year earlier. The database was cross-referenced with a database of all patients testing positive for Sars-Cov-2 infection in both institutions to identify patients who required temporary or permanent pacing during COVID-19. RESULTS: The number of novel pacemaker implants was lower during the COVID-19 pandemic than the same period the previous year (540 vs. 629, respectively), with a similar proportion of high-degree AV block (38.3% vs. 33.2%, respectively, p = .069). Four patients with the Sars-Cov-2 infection had a pacemaker implanted for high-degree AV block, two for sinus node dysfunction. Of this cohort of six patients, two succumbed to the COVID-19 illness and one from non-COVID sepsis. Device interrogation demonstrated a sustained pacing requirement in all cases. CONCLUSION: High-degree AV block remained unaltered in prevalence during the COVID-19 pandemic. There was no evidence of transient high-degree AV block in patients with the Sars-Cov-2 infection. Our experience suggests that all clinically significant bradyarrhythmia should be treated by pacing according to usual protocols regardless of the COVID status.

Prolonged QT predicts prognosis in COVID-19.

BACKGROUND: Coronavirus disease-2019 (COVID-19) causes severe illness and multi-organ dysfunction. An abnormal electrocardiogram is associated with poor outcome, and QT prolongation during the illness has been linked to pharmacological effects. This study sought to investigate the effects of the COVID-19 illness on the corrected QT interval (QTc). METHOD: For 293 consecutive patients admitted to our hospital via the emergency department for COVID-19 between 01/03/20 -18/05/20, demographic data, laboratory findings, admission electrocardiograph and clinical observations were compared in those who survived and those who died within 6 weeks. Hospital records were reviewed for prior electrocardiograms for comparison with those recorded on presentation with COVID-19. RESULTS: Patients who died were older than survivors (82 vs 69.8 years, p < 0.001), more likely to have cancer (22.3% vs 13.1%, p = 0.034), dementia (25.6% vs 10.7%, p = 0.034) and ischemic heart disease (27.8% vs 10.7%, p < 0.001). Deceased patients exhibited higher levels of C-reactive protein (244.6 mg/L vs 146.5 mg/L, p < 0.01), troponin (1982.4 ng/L vs 413.4 ng/L, p = 0.017), with a significantly longer QTc interval (461.1 ms vs 449.3 ms, p = 0.007). Pre-COVID electrocardiograms were located for 172 patients; the QTc recorded on presentation with COVID-19 was longer than the prior measurement in both groups, but was more prolonged in the deceased group (448.4 ms vs 472.9 ms, pre-COVID vs COVID, p < 0.01). Multivariate Cox-regression analysis revealed age, C-reactive protein and prolonged QTc of >455 ms (males) and >465 ms (females) (p = 0.028, HR 1.49 [1.04-2.13]), as predictors of mortality. QTc prolongation beyond these dichotomy limits was associated with increased mortality risk (p = 0.0027, HR 1.78 [1.2-2.6]). CONCLUSION: QTc prolongation occurs in COVID-19 illness and is associated with poor outcome.

GAGA factor maintains nucleosome-free regions and has a role in RNA polymerase II recruitment to promoters.

Previous studies have shown that GAGA Factor (GAF) is enriched on promoters with paused RNA Polymerase II (Pol II), but its genome-wide function and mechanism of action remain largely uncharacterized. We assayed the levels of transcriptionally-engaged polymerase using global run-on sequencing (GRO-seq) in control and GAF-RNAi Drosophila S2 cells and found promoter-proximal polymerase was significantly reduced on a large subset of paused promoters where GAF occupancy was reduced by knock down. These promoters show a dramatic increase in nucleosome occupancy upon GAF depletion. These results, in conjunction with previous studies showing that GAF directly interacts with nucleosome remodelers, strongly support a model where GAF directs nucleosome displacement at the promoter and thereby allows the entry Pol II to the promoter and pause sites. This action of GAF on nucleosomes is at least partially independent of paused Pol II because intergenic GAF binding sites with little or no Pol II also show GAF-dependent nucleosome displacement. In addition, the insulator factor BEAF, the BEAF-interacting protein Chriz, and the transcription factor M1BP are strikingly enriched on those GAF-associated genes where pausing is unaffected by knock down, suggesting insulators or the alternative promoter-associated factor M1BP protect a subset of GAF-bound paused genes from GAF knock-down effects. Thus, GAF binding at promoters can lead to the local displacement of nucleosomes, but this activity can be restricted or compensated for when insulator protein or M1BP complexes also reside at GAF bound promoters.

Gene × Environment Determinants of Stress- and Anxiety-Related Disorders.

The burgeoning field of gene-by-environment (G×E) interactions has revealed fascinating biological insights, particularly in the realm of stress-, anxiety-, and depression-related disorders. In this review we present an integrated view of the study of G×E interactions in stress and anxiety disorders, including the evolution of genetic association studies from genetic epidemiology to contemporary large-scale genome-wide association studies and G×E studies. We convey the importance of consortia efforts and collaboration to gain the large sample sizes needed to move the field forward. Finally, we discuss several robust and well-reproduced G×E interactions and demonstrate how epidemiological identification of G×E interactions has naturally led to a plethora of basic research elucidating the mechanisms of high-impact genetic variants.

Impaired thrombolysis: a novel cardiovascular risk factor in end-stage renal disease.

AIMS: End-stage renal disease (ESRD) patients have an excess cardiovascular risk, above that predicted by traditional risk factor models. Prothrombotic status may contribute to this increased risk. Global thrombotic status assessment, including measurement of occlusion time (OT) and thrombolytic status, may identify vulnerable patients. Our aim was to assess overall thrombotic status in ESRD and relate this to cardiovascular risk. METHODS AND RESULTS: Thrombotic and thrombolytic status of ESRD patients (n = 216) on haemodialysis was assessed using the Global Thrombosis Test. This novel, near-patient test measures the time required to form (OT) and time required to lyse (lysis time, LT) an occlusive platelet thrombus. Patients were followed-up for 276 ± 166 days for major adverse cardiovascular events (MACE, composite of cardiovascular death, non-fatal MI, or stroke). Peripheral arterial or arterio-venous fistula thrombosis was a secondary endpoint. Occlusion time was reduced (491 ± 177 vs. 378 ± 96 s, P < 0.001) and endogenous thrombolysis was impaired (LT median 1820 vs.1053 s, P < 0.001) in ESRD compared with normal subjects. LT ≥ 3000 s occurred in 42% of ESRD patients, and none of the controls. Impaired endogenous thrombolysis (LT ≥ 3000 s) was strongly associated MACE (HR = 4.25, 95% CI = 1.58-11.46, P = 0.004), non-fatal MI and stroke (HR = 14.28, 95% CI = 1.86-109.90, P = 0.01), and peripheral thrombosis (HR = 9.08, 95% CI = 2.08-39.75, P = 0.003). No association was found between OT and MACE. CONCLUSION: Impaired endogenous thrombolysis is a novel risk factor in ESRD, strongly associated with cardiovascular events.

Intraaortic balloon pump use in high-risk percutaneous coronary intervention.

PURPOSE OF REVIEW: Despite the long-term availability and clinical usage of intraaortic balloon pump (IABP) counterpulsation, there is a paucity of randomized trial evidence for its use. Here, we will review the latest evidence for its usage in different clinical settings. RECENT FINDINGS: There have been decades of nonrandomized and observational data available, but only in the last 3 years has there been availability of randomized evidence for IABP use in acute myocardial infarction (AMI) with cardiogenic shock, ST elevation acute coronary syndromes (STE-ACS) without shock and high-risk percutaneous coronary intervention (PCI) cohorts. SUMMARY: To the surprise of many, despite the sound physiological benefits achieved by the use of IABP counterpulsation in these situations, all the recent trials did not achieve the primary endpoint, although there is a trend towards long-term benefit with its use. This may alter its elective use in practice and may lead to changes in current guidance and possibly increase the focus on other mechanical circulatory devices. Despite the neutral primary endpoints in these recent trials, there is a signal that a subset of the population may benefit by elective IABP use and get good haemodynamic support, thus suggesting, in our view, that further understanding and research are required to gain maximum physiological benefit from this device and to aid decision making for an individualized, patient-centred approach.

Clinically significant thrombosis in pediatric heart transplant recipients during their waiting period.

Thrombosis is a serious complication of heart failure for which available data on pediatric patients are scarce. This report describes the frequency and risk factors of clinically significant thrombosis (CST) for children awaiting transplantation. A retrospective study analyzed a cohort of heart recipients with CST, defined by the presence of intracardiac thrombus by imaging, explant pathology, or symptomatic clinical event. Among the 123 patients in the study, 56 % were male and 44 % had congenital heart disease. The median age at transplantation was 6.6 years (range 0-30 years). The prevalence of CST was 12.2 % (15/123), and its incidence was 32.7 events per 100 patient-years. The thromboembolic event frequencies were 2.4 % and 6.5 events per 100 patient-years. The median interval from listing to CST was eight days (range 0-113 days). The median wait-list duration was 31 days (range 8-169 days) in the CST group versus 51 days (range 0-1,743 days) in the non-CST group. Inpatient status was statistically associated with CST (14 of 15 subjects were inpatients, p = 0.03). Inotropic support (p = 0.068) and United Network for Organ Sharing (UNOS) status 1 (p = 0.061) approached significance. Clinically significant thrombosis was common in this end-stage heart failure population. Until randomized clinical trial data are available, it may be reasonable to consider anticoagulation for children admitted with decompensated heart failure and listed as UNOS status 1.

Dysregulation of Prefrontal Oligodendrocyte Lineage Cells Across Mouse Models of Adversity and Human Major Depressive Disorder Oligodendrocyte dysregulation in mouse models of stress and MDD.

Animal models of adversity have yielded few molecular mechanisms that translate to human stress-related diseases like major depressive disorder (MDD). We congruently analyze publicly available bulk-tissue transcriptomic data from prefrontal cortex (PFC) in multiple mouse models of adversity and in MDD. We apply strategies, to quantify cell-type specific enrichment from bulk-tissue transcriptomics, utilizing reference single cell RNA sequencing datasets. These analyses reveal conserved patterns of oligodendrocyte (OL) dysregulation across animal experiments, including susceptibility to social defeat, acute cocaine withdrawal, chronic unpredictable stress, early life stress, and adolescent social isolation. Using unbiased methodologies, we further identify a dysregulation of layer 6 neurons that associate with deficits in goal-directed behavior after social isolation. Human post-mortem brains with MDD show similar OL transcriptome changes in Brodmann Areas 8/9 in both male and female patients. This work assesses cell type involvement in an unbiased manner from differential expression analyses across animal models of adversity and human MDD and finds a common signature of OL dysfunction in the frontal cortex.

The Use and Efficacy of FFR-CT: Real-World Multicenter Audit of Clinical Data With Cost Analysis.

BACKGROUND: Fractional flow reserve-computed tomography (FFR-CT) is endorsed by UK and U.S. chest pain guidelines, but its clinical effectiveness and cost benefit in real-world practice are unknown. OBJECTIVES: The purpose of this study was to audit the use of FFR-CT in clinical practice against England's National Institute for Health and Care Excellence guidance and assess its diagnostic accuracy and cost. METHODS: A multicenter audit was undertaken covering the 3 years when FFR-CT was centrally funded in England. For coronary computed tomographic angiograms (CCTAs) submitted for FFR-CT analysis, centers provided data on symptoms, CCTA and FFR-CT findings, and subsequent management. Audit standards included using FFR-CT only in patients with stable chest pain and equivocal stenosis (50%-69%). Diagnostic accuracy was evaluated against invasive FFR, when performed. Follow-up for nonfatal myocardial infarction and all-cause mortality was undertaken. The cost of an FFR-CT strategy was compared to alternative stress imaging pathways using cost analysis modeling. RESULTS: A total of 2,298 CCTAs from 12 centers underwent FFR-CT analysis. Stable chest pain was the main symptom in 77%, and 40% had equivocal stenosis. Positive and negative predictive values of FFR-CT were 49% and 76%, respectively. A total of 46 events (2%) occurred over a mean follow-up period of 17 months; FFR-CT (cutoff: 0.80) was not predictive. The FFR-CT strategy costs £2,102 per patient compared with an average of £1,411 for stress imaging. CONCLUSIONS: In clinical practice, the National Institute for Health and Care Excellence criteria for using FFR-CT were met in three-fourths of patients for symptoms and 40% for stenosis. FFR-CT had a low positive predictive value, making its use potentially more expensive than conventional stress imaging strategies.

Temporary transvenous pacing: endangered skill.

BACKGROUND: Temporary cardiac pacing although is an essential requirement for core medical training (CMT) in UK, there are no defined training measures and guidelines available as to who should perform this. METHODS: We conducted an anonymous survey of 300 non-cardiology medical registrars regarding their individual ability, experience and training received in temporary pacing wire (TPW) insertion. RESULTS: A total of 202 (67%) responses were received. 61% (123) had not performed any TPW insertion before becoming a registrar. Only 18% (38) felt confident in inserting a TPW unsupervised and only 14 (7%) had ever received any formal training. The majority, 169 (84%), did not feel that their on-call consultant general physician would be able to perform the procedure. CONCLUSION: This survey shows that general medical registrars lack a major life-saving skill that is required as part of CMT. Thus, there is now an urgent clinical governance need to either formally train physicians or abandon the concept and practice of general internal medicine-led temporary pacing, and devolve this to cardiologists.

Comparative evaluation of dimension and surface detail accuracy of models produced by three different rapid prototype techniques.

Rapid prototyping (RP) is a technology that produces physical models by selectively solidifying ultra violet (UV) sensitive liquid resin using a laser beam. These models can be formed using various techniques. A study was undertaken to compare the dimensional accuracy and surface details of three prototype models with a 3D STL (standard template library) image. In this study the STL file was used to produce three different rapid prototype models namely; model 1-fused deposition model (FDM) using ABS (acrylonitrile butadiene styrene), model 2-Polyjet using a clear resin and model 3-a 3 dimensional printing using a composite material. Measurements were made at various anatomical points. For surface detail reproductions the models were subjected to scanning electron microscopy analysis. The dimensions of the model created by Polyjet were closest to the 3D STL virtual image followed by the 3DP model and FDM. SEM analysis showed uniform smooth surface on Polyjet model with adequate surface details.

Coronary Caverns: Spontaneous Recanalized Chronic Total Occlusion With Multiple Microchannels.

Spontaneous chronic total occlusion recanalization is rare. It has scarcely been described previously and with minimal visual detail. Optical coherence tomography permitted comprehensive visualization of the microchannels in this case, seldom seen previously. With Thrombolysis in Myocardial Infarction 3 flow in the affected vessel via these patent channels, optimal medical therapy may be an appropriate strategy.

Medium-Term Outcomes in COVID-19.

COVID-19 causes severe illness that results in morbidity and mortality. Electrocardiographic features, including QT prolongation, have been associated with poor acute outcomes; data on the medium-term outcomes remain scarce. This study evaluated the 1-year outcomes of patients who survived the acute COVID-19 infection. Methods and Materials: Data of the 159 patients who survived the COVID-19 illness during the first wave (1 March 2020−18 May 2020) were collected. Patient demographics, laboratory findings and electrocardiography data were evaluated. Patients who subsequently died within 1-year of the index illness were compared to those who remained well. Results: Of the 159 patients who had survived the index illness, 28 (17.6%) subsequently perished within 1-year. In comparison to the patients that were alive after 1-year, the deceased were older (68 vs. 83 years, p < 0.01) and equally male (60.4% vs. 53.6%, p = 0.68), with a similar proportion of hypertension (59.5% vs. 57.1%, p = 0.68), diabetes (25.2% vs. 39.2%, p = 0.096) and ischaemic heart disease (11.5% vs. 7.1%, p = 0.54). The QTc interval for the alive and deceased patients shortened by a similar degree from the illness to post-COVID (−26 ± 33.5 vs. −20.6 ± 30.04 milliseconds, p = 0.5); the post-COVID R-R interval was longer in the alive patients compared to the deceased (818.9 ± 169.3 vs. 761.1 ± 61.2 ms, p = 0.02). A multivariate Cox regression analysis revealed that age (HR1.098 [1.045−1.153], p < 0.01), diabetes (HR3.972 [1.47−10.8], p < 0.01) and the post-COVID R-R interval (HR0.993 [0.989−0.996], p < 0.01) were associated with 1-year mortality. Conclusions: The COVID-19-associated mortality risk extends to the post-COVID period. The QTc does recover following the acute illness and is not associated with outcomes; the R-R interval is a predictor of 1-year mortality.

Cluster Analysis of Clozapine Consumer Perspectives and Comparison to Consumers on Other Antipsychotics.

Despite its unique efficacy, clozapine remains underutilized in the United States. Perceptions about clozapine and barriers to its use have been examined among prescribers, but insufficiently studied among consumers. We surveyed 211 antipsychotic consumers (86 on clozapine and 125 on other antipsychotics) on their medication-related perspectives in a public hospital system in Atlanta, Georgia, USA. In contrast to their previous regimen, 72% of clozapine consumers reported they were more satisfied with clozapine. When compared with consumers taking other antipsychotics, clozapine consumers reported more side effects but did not differ on other measures of satisfaction or efficacy. We found Caucasians to be overrepresented among clozapine, as compared to other antipsychotic consumers. Side effects most strongly associated with poor safety ratings were sedation, limb jerking, and dizziness when standing. However, clozapine was only rated less safe by consumers who experienced more than one of these side effects. We used an unsupervised clustering approach to identify three major groups of clozapine consumers. Cluster A (19%) had the lowest safety ratings, aversion to blood work, and a high rate of side effects that associate with lower safety ratings. Cluster B (25%) experienced more hospitalizations and reported satisfaction with clozapine that correlated with efficacy ratings, irrespective of safety ratings. Cluster C (56%) experienced fewer hospitalizations, fewer previous drug trials, greater educational attainment, lower rates of smoking, and rated clozapine more highly. This work identifies common side effects that influence the subjective safety of clozapine and suggests that attitudes toward clozapine depend on context-specific factors.

Genomic updates in understanding PTSD.

Twin studies as well as more recent genetics-based heritability analyses demonstrate that up to 40 to 50% of the variance in predicting PTSD following trauma is heritable. However, most of the specific gene pathways and mechanism that mediate risk vs. resilience for PTSD following trauma exposure have yet to be elucidated. This review will examine the latest results from large scale Genome-wide association studies as well as other approaches aimed at understanding mechanisms of development of and recovery from PTSD.

Dynamic Patterns of Threat-Associated Gene Expression in the Amygdala and Blood.

Stress and trauma profoundly influence psychiatric biobehavioral outcomes. The identification of treatment and biomarker targets would be accelerated by a broad understanding of the biological responses to these events. The goal of this study was to determine genes responsive to auditory fear conditioning (FC), a well-characterized amygdala-dependent rodent model of threat-exposure, in the presence or absence of prior stress history, providing insight into the physiological processes underlying response to trauma. RNA-sequencing was performed in blood and amygdala from mice that underwent fear conditioning with (Immo+FC) and without (FC) prior immobilization stress, a paradigm that induces HPA axis, and behavioral stress sensitization. In the amygdala, 607 genes were regulated by FC vs. home-cage (HC) controls, and 516 genes differed in stress-sensitized mice (Immo+FC vs. FC). In the former, we observed an enhancement of specific biological processes involved in learning and synaptic transmission, and in the latter processes associated with cell proliferation and the cellular response to drugs. In the blood of stress-sensitized animals, 468 genes were dynamically regulated when compared to FC, and were enriched for the biological pathways of inflammation and cytokine signaling. This study identified genes and pathways that respond to threat in the amygdala and blood of mice with and without a prior stress history and reveals the impact of stress history on subsequent inflammation. Future studies will be needed to examine the role of these dynamically regulated genes may play in human clinical stress and trauma-related disorders.

Performance and exhaust emission characteristics of variable compression ratio diesel engine fuelled with esters of crude rice bran oil.

As a substitute to petroleum-derived diesel, biodiesel has high potential as a renewable and environment friendly energy source. For petroleum importing countries the choice of feedstock for biodiesel production within the geographical region is a major influential factor. Crude rice bran oil is found to be good and viable feedstock for biodiesel production. A two step esterification is carried out for higher free fatty acid crude rice bran oil. Blends of 10, 20 and 40 % by vol. crude rice bran biodiesel are tested in a variable compression ratio diesel engine at compression ratio 15, 16, 17 and 18. Engine performance and exhaust emission parameters are examined. Cylinder pressure-crank angle variation is also plotted. The increase in compression ratio from 15 to 18 resulted in 18.6 % decrease in brake specific fuel consumption and 14.66 % increase in brake thermal efficiency on an average. Cylinder pressure increases by 15 % when compression ratio is increased. Carbon monoxide emission decreased by 22.27 %, hydrocarbon decreased by 38.4 %, carbon dioxide increased by 17.43 % and oxides of nitrogen as NOx emission increased by 22.76 % on an average when compression ratio is increased from 15 to 18. The blends of crude rice bran biodiesel show better results than diesel with increase in compression ratio.