Visualizing Cluster-specific Genes from Single-cell Transcriptomics Data Using Association Plots

Visualizing single-cell transcriptomics data in an informative way is a major challenge in biological data analysis. Clustering of cells is a prominent analysis step and the results are usually visualized in a planar embedding of the cells using methods like PCA, t-SNE, or UMAP. Given a cluster of cells, one frequently searches for the genes highly expressed specifically in that cluster. At this point, visualization is usually replaced by studying a list of differentially expressed genes. Association Plots are derived from correspondence analysis and constitute a planar visualization of the features which characterize a given cluster of observations. We have adapted Association Plots to address the challenge of visualizing cluster-specific genes in large single-cell data sets. Our method is made available as a free R package called APL. We demonstrate the application of APL and Association Plots to single-cell RNA-seq data on two example data sets. First, we present how to delineate novel marker genes using Association Plots with the example of Peripheral Blood Mononuclear Cell data. Second, we show how to apply Association Plots for annotating cell clusters to known cell types using Association Plots and a predefined list of marker genes. To do this we will use data from the human cell atlas of fetal gene expression. Results from Association Plots will also be compared to methods for deriving differentially expressed genes, and we will show the integration of APL with Gene Ontology Enrichment

The universe dynamics in the tachyon cosmology with non-minimal coupling to matter

Recently, the tachyon cosmology has been represented as dark energy model to support the current acceleration of the universe without phantom crossing. In this paper, we study the dynamics of the tachyon cosmology in which the field plays the role of tachyon field and also non--minimally coupled to the matter lagrangian. The model shows current universe acceleration and also phantom crossing in the future. Two cosmological tests are also performed to validate the model; the difference in the distance modulus and the model independent Cosmological Redshift Drift (CRD) test.Comment: 14 pages, 11 figure

Cerebral venous sinus thrombosis due to vaccine-induced immune thrombotic thrombocytopenia in middle-income countries

Background: Adenovirus-based COVID-19 vaccines are extensively used in low- and middle-income countries (LMICs). Remarkably, cases of cerebral venous sinus thrombosis due to vaccine-induced immune thrombotic thrombocytopenia (CVST-VITT) have rarely been reported from LMICs. Aims: We studied the frequency, manifestations, treatment, and outcomes of CVST-VITT in LMICs. Methods: We report data from an international registry on CVST after COVID-19 vaccination. VITT was classified according to the Pavord criteria. We compared CVST-VITT cases from LMICs to cases from high-income countries (HICs). Results: Until August 2022, 228 CVST cases were reported, of which 63 were from LMICs (all middle-income countries [MICs]: Brazil, China, India, Iran, Mexico, Pakistan, Turkey). Of these 63, 32 (51%) met the VITT criteria, compared to 103 of 165 (62%) from HICs. Only 5 of the 32 (16%) CVST-VITT cases from MICs had definite VITT, mostly because anti-platelet factor 4 antibodies were often not tested. The median age was 26 (interquartile range [IQR] 20–37) versus 47 (IQR 32–58) years, and the proportion of women was 25 of 32 (78%) versus 77 of 103 (75%) in MICs versus HICs, respectively. Patients from MICs were diagnosed later than patients from HICs (1/32 [3%] vs. 65/103 [63%] diagnosed before May 2021). Clinical manifestations, including intracranial hemorrhage, were largely similar as was intravenous immunoglobulin use. In-hospital mortality was lower in MICs (7/31 [23%, 95% confidence interval (CI) 11–40]) than in HICs (44/102 [43%, 95% CI 34–53], p = 0.039). Conclusions: The number of CVST-VITT cases reported from LMICs was small despite the widespread use of adenoviral vaccines. Clinical manifestations and treatment of CVST-VITT cases were largely similar in MICs and HICs, while mortality was lower in patients from MICs.</p

Sex differences in cerebral venous sinus thrombosis after adenoviral vaccination against COVID-19

Introduction: Cerebral venous sinus thrombosis associated with vaccine-induced immune thrombotic thrombocytopenia (CVST-VITT) is a severe disease with high mortality. There are few data on sex differences in CVST-VITT. The aim of our study was to investigate the differences in presentation, treatment, clinical course, complications, and outcome of CVST-VITT between women and men. Patients and methods: We used data from an ongoing international registry on CVST-VITT. VITT was diagnosed according to the Pavord criteria. We compared the characteristics of CVST-VITT in women and men. Results: Of 133 patients with possible, probable, or definite CVST-VITT, 102 (77%) were women. Women were slightly younger [median age 42 (IQR 28–54) vs 45 (28–56)], presented more often with coma (26% vs 10%) and had a lower platelet count at presentation [median (IQR) 50x109/L (28–79) vs 68 (30–125)] than men. The nadir platelet count was lower in women [median (IQR) 34 (19–62) vs 53 (20–92)]. More women received endovascular treatment than men (15% vs 6%). Rates of treatment with intravenous immunoglobulins were similar (63% vs 66%), as were new venous thromboembolic events (14% vs 14%) and major bleeding complications (30% vs 20%). Rates of good functional outcome (modified Rankin Scale 0-2, 42% vs 45%) and in-hospital death (39% vs 41%) did not differ. Discussion and conclusions: Three quarters of CVST-VITT patients in this study were women. Women were more severely affected at presentation, but clinical course and outcome did not differ between women and men. VITT-specific treatments were overall similar, but more women received endovascular treatment.</p

Optical coherence tomography angiography in choroidal melanoma and nevus

Fariba Ghassemi,1,2 Reza Mirshahi,1,2 Kaveh Fadakar,1,2 Siamak Sabour3 1Retina &amp; Vitreous Service, 2Eye Research Center, Farabi Eye Hospital, Tehran University of Medical Sciences, 3Safety Promotion and Injury Prevention Research Centre, Department of Clinical Epidemiology, Shahid Beheshti University of Medical Sciences, Tehran, Iran Synopsis: In optical coherence tomography angiography, the choroidal vascular flow rate in choroidal melanoma is significantly lower than that in choroidal nevus.Objective: The objective of this study was to describe the choriocapillaris and retinal features imaged by optical coherence tomography angiography (OCTA) in eyes with choroidal nevus from small malignant choroidal melanoma.Methods: In this retrospective, noninvasive, observational study, 11 patients diagnosed with small choroidal mass (five with choroidal nevus and six with malignant melanoma) who underwent dilated fundus examination, ocular ultrasonography and OCTA images were compared.Results: In choroidal nevus of all patients, OCTA demonstrated a hyporeflective mass with no significant deformity of choroidal vasculature and an intact retinal pigment epithelium (RPE)&ndash;Bruch&rsquo;s membrane complex. The flow void mass was surrounded by an intense vascular rim named as surface microvasculature (SMV) that had an approximately similar flow rate median of 63.68 mm2 (60.42&ndash;67.62 mm2), comparable with the median of the contralateral normal eye of 61.77 mm2 (60.42&ndash;64.53 mm2; P&gt;0.09) for nevi. OCTA showed an obscured Bruch&rsquo;s membrane&ndash;RPE&ndash;Bruch&rsquo;s membrane complex and outer retinal layer in choroidal melanomas. Choriocapillaris flow rate over the melanomas was 55.73% (41.93%&ndash;60.82%), and the corresponding normal areas had a flow area of 62.75% (61.99%&ndash;63.10%; P=0.01). A flow rate difference between choroidal melanoma and nevus was significant (P=0.006). Axial and peripheral feeding vessels were more dilated and tortuous compared with benign nevi.Conclusion: Decreased flow rate of SMV of choroidal melanoma cases compared with nevi was a significant finding. Detection of characteristic vascular features of choroidal melanoma by OCTA could make OCTA an assuring diagnostic modality to differentiate malignant lesions. Keywords: melanoma, choroidal nevus, OCT, OCTA, uveal melanom

Practice patterns and influence of allograft nephrectomy in pediatric kidney re- transplantation: A pediatric nephrology research consortium study

IntroductionThere are no guidelines regarding management of failed pediatric renal transplants.Materials & MethodsWe performed a first of its kind multicenter study assessing prevalence of transplant nephrectomy, patient characteristics, and outcomes in pediatric renal transplant recipients with graft failure from January 1, 2006, to December 31, 2016.ResultsFourteen centers contributed data on 186 pediatric recipients with failed transplants. The 76 recipients that underwent transplant nephrectomy were not significantly different from the 110 without nephrectomy in donor or recipient demographics. Fifty- three percent of graft nephrectomies were within a year of transplant. Graft tenderness prompted transplant nephrectomy in 91% (P < .001). Patients that underwent nephrectomy were more likely to have a prior diagnosis of rejection within 3 months (43% vs 29%; P = .04). Nephrectomy of allografts did not affect time to re- listing, donor source at re- transplant but significantly decreased time to (P = .009) and incidence (P = .0002) of complete cessation of immunosuppression post- graft failure. Following transplant nephrectomy, recipients were significantly more likely to have rejection after re- transplant (18% vs 7%; P = .03) and multiple rejections in first year after re- transplant (7% vs 1%; P = .03).ConclusionsPractices pertaining to failed renal allografts are inconsistent- 40% of failed pediatric renal allografts underwent nephrectomy. Graft tenderness frequently prompted transplant nephrectomy. There is no apparent benefit to graft nephrectomy related to sensitization; but timing / frequency of immunosuppression withdrawal is significantly different with slightly increased risk for rejection following re- transplant.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/169276/1/petr13974.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/169276/2/petr13974_am.pd