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Background and Aims: Refractory celiac disease type II (RCDII) is characterized by a clonally expanded aberrant cell population in the small intestine. The role of other tissue-resident immune subsets in RCDII is unknown. Here, we characterized CD8 and CD4 T cells in RCDII duodenum at the single-cell level and in situ. Methods: We applied mass cytometry on CD45+ duodenal cells derived from intestinal biopsies (n = 23) and blood samples (n = 20) from RCDII patients and controls. Additionally, we analyzed intestinal biopsies from celiac disease (n = 11) and RCDI (n = 2) patients. We performed single-cell RNA-sequencing on CD45+ duodenal cells derived from a RCDII patient, immunofluorescence staining for in situ analysis and flow cytometry for phenotyping of RCDII aberrant and CD8 T cells. Results: Compared to healthy controls, we observed that CD27+PD-1+ memory CD8αβ cells and CD4 T regulatories (Tregs) were more abundant in RCDII duodenum (CD8 ∗∗0.0029; CD4 ∗∗∗0.0001). The CD27+PD-1+ memory CD8αβ cells expressed the tissue-resident marker CD69, immunoregulatory markers (TIGIT, HAVCR2, TNFRSF9), NKG2A, were enriched for activated pathways and displayed cytotoxic gene signatures (NKG7, PRF1, GZMA). The absence of CD103 accords with their localization in the lamina propria as determined by in situ analysis. The CD25+FoxP3+CD27+CD127dim/- CD4 Tregs expressed IL1R2 and IL32 and costimulatory molecules (TNFSRS4, ICOS and TNFRSF18) and resided in the lamina propria as well. Flow cytometry confirmed the presence of the inhibitory receptor NKG2A on expanded duodenal CD8 T cells and HLA-E, the ligand for NKG2A, on expanded aberrant cells. Conclusion: RCDII is characterized by the simultaneous presence of an activated CD27+PD-1+ memory CD8αβ T cell subset and CD4 Tregs, suggesting that checkpoint blockade with anti-NKG2A/PD-1 and/or anticytotoxic T lymphocyte antigen 4 may be an attractive treatment option.

Introduction: Single-cell RNA sequencing (scRNA-seq) and single-nucleus RNA sequencing (snRNA-seq) provide valuable insights into the cellular states of kidney cells. However, the annotation of cell types often requires extensive domain expertise and time-consuming manual curation, limiting scalability and generalizability. To facilitate this process, we tested the performance of five supervised classification methods for automatic cell type annotation. Results: We analyzed publicly available sc/snRNA-seq datasets from five expert-annotated studies, comprising 62,120 cells from 79 kidney biopsy samples. Datasets were integrated by harmonizing cell type annotations across studies. Five different supervised machine learning algorithms (support vector machines, random forests, multilayer perceptrons, k-nearest neighbors, and extreme gradient boosting) were applied to automatically annotate cell types using four training datasets and one testing dataset. Performance metrics, including accuracy (F1 score) and rejection rates, were evaluated. All five machine learning algorithms demonstrated high accuracies, with a median F1 score of 0.94 and a median rejection rate of 1.8 %. The algorithms performed equally well across different datasets and successfully rejected cell types that were not present in the training data. However, F1 scores were lower when models trained primarily on scRNA-seq data were tested on snRNA-seq data. Conclusions: Despite limitations including the number of biopsy samples, our findings demonstrate that machine learning algorithms can accurately annotate a wide range of adult kidney cell types in scRNA-seq/snRNA-seq data. This approach has the potential to standardize cell type annotation and facilitate further research on cellular mechanisms underlying kidney disease.

Abstract Different dosing strategies exist to initiate warfarin, most commonly fixed warfarin dosing (FWD), clinical warfarin dosing (CWD), and genetic‐guided warfarin dosing (GWD). Landmark trials have shown GWD to be superior when compared to FWD in the EU‐PACT trial or CWD in the GIFT trial. COAG trial did not show differences between GWD and CWD. We aim to compare the anticoagulation quality outcomes of CWD and FWD. This is a prospective cohort study with a retrospective comparator. Recruited subjects in the CWD (prospective) arm were initiated on warfarin according to the clinical dosing component of the algorithm published in www.warfarindosing.org. The primary efficacy outcome was the percentage time in the therapeutic range (PTTR) from day 3 to 6 till day 28 to 35. The study enrolled 122 and 123 patients in the CWD and FWD, respectively. The PTTR did not differ statistically between CWD and FWD (62.2 ± 26.2% vs. 58 ± 25.4%, p = 0.2). There was also no difference between both arms in the percentage of visits with extreme subtherapeutic international normalized ratio (INR) (4; 7.7 ± 14.7% vs. 7.5 ± 12.4%, p = 0.92). We conclude that CWD did not improve the anticoagulation quality parameters compared to the FWD method.

BackgroundAcute coronary syndrome (ACS) remains a risk factor for heart failure (HF). Therefore, we aimed to assess the cardioprotective role of sodium–glucose cotransporter-2 (SGLT2) inhibitors post-ACS in patients with acute HF (AHF) and diabetes.MethodsWe conducted a retrospective observational cohort study employing propensity score matching. This study involved patients with diabetes admitted with ACS complicated by AHF, defined as either new clinical HF requiring diuretics during the index admission or having an ejection fraction (EF) of

The spread of fake news among Arabic media including social media represents a great challenge to the integrity of information and the trust of the public in it. In this paper, we introduce a comprehensive deep-learning framework, named ArabFake, that goes beyond the binary classification on Arabic fake news detection. ArabFake, built over MARBERTv2 (a state-of-the-art model for multi-dialectal Arabic tweets), proficiently address the complexity of the Arabic language while performing three unified tasks which are fake news detection, content categorization and its risk assessment. The framework promotes efficiency and performance both by enabling multi-task learning through shared knowledge representation across tasks. In order to facilitate development and evaluation, we present the ArabFake Dataset consisting of 2,495 manually labelled news items with labels that are verified by experts regarding fake news categories and risk levels. ArabFake demonstrates robust performance, achieving an F1 score of 94.12% for fake news detection, 84.92% for categorization, and 88.91% for risk zone assessment, highlighting its reliability and effectiveness across multiple tasks. We improve interpretability and extract insight into manipulative techniques by integrating valence scoring as part of the framework that emphasizes misleading linguistic cues used to disseminate fake news within the produced image. The results show that ArabFake is a holistic Arabic fake news detection framework that has practical implications on news organizations and fact checking projects.

Most regulatory elements, especially enhancer sequences, are cell population-specific. One could even argue that a distinct set of regulatory elements is what defines a cell population. However, discovering which non-coding regions of the DNA are essential in which context, and as a result, which genes are expressed, is a difficult task. Some computational models tackle this problem by predicting gene expression directly from the genomic sequence. These models are currently limited to predicting bulk measurements and mainly make tissue-specific predictions. Here, we present a model that leverages single-cell RNA-sequencing data to predict gene expression. We show that cell population-specific models outperform tissue-specific models, especially when the expression profile of a cell population and the corresponding tissue are dissimilar. Further, we show that our model can prioritize GWAS variants and learn motifs of transcription factor binding sites. We envision that our model can be useful for delineating cell population-specific regulatory elements.

Abstract With the number of cells measured in single-cell RNA sequencing (scRNA-seq) datasets increasing exponentially and concurrent increased sparsity due to more zero counts being measured for many genes, we demonstrate here that downstream analyses on binary-based gene expression give similar results as count-based analyses. Moreover, a binary representation scales up to ~ 50-fold more cells that can be analyzed using the same computational resources. We also highlight the possibilities provided by binarized scRNA-seq data. Development of specialized tools for bit-aware implementations of downstream analytical tasks will enable a more fine-grained resolution of biological heterogeneity.

Abstract Background Dyslipidemia is recognized as one of the risk factors of cardiovascular diseases (CVDs), type 2 diabetes mellitus (T2DM), and non‐alcoholic fatty liver disease (NAFLD). Objective The study aimed to investigate the association between selected single nucleotide polymorphisms (SNPs) with dyslipidemia and increased susceptibility risks of CVD, NAFLD, and/or T2DM in dyslipidemia patients in comparison with healthy control individuals from the Qatar genome project. Methods A community‐based cross‐sectional study was conducted among 2933 adults (859 dyslipidemia patients and 2074 healthy control individuals) from April to December 2021 to investigate the association between 331 selected SNPs with dyslipidemia and increased susceptibility risks of CVD, NAFLD and/or T2DM, and covariates. Results The genotypic frequencies of six SNPs were found to be significantly different in dyslipidemia patients subjects compared to the control group among males and females. In males, three SNPs were found to be significant, the rs11172113 in over‐dominant model, the rs646776 in recessive and over‐dominant models, and the rs1111875 in dominant model. On the other hand, two SNPs were found to be significant in females, including rs2954029 in recessive model, and rs1801251 in dominant and recessive models. The rs17514846 SNP was found for dominant and over‐dominant models among males and only the dominant model for females. We found that the six SNPs linked to gender type had an influence in relation to disease susceptibility. When controlling for the four covariates (gender, obesity, hypertension, and diabetes), the difference between dyslipidemia and the control group remained significant for the six variants. Finally, males were three times more likely to have dyslipidemia in comparison with females, hypertension was two times more likely to be present in the dyslipidemia group, and diabetes was six times more likely to be in the dyslipidemia group. Conclusion The current investigation provides evidence of association for a common SNP to coronary heart disease and suggests a sex‐dependent effect and encourage potential therapeutic applications.

In this paper, the problem of autonomous optimal absolute orbit keeping for a satellite mission in Low Earth Orbit using electric propulsion is considered. The main peculiarity of the approach is to support small satellite missions in which the platform is equipped with a single thruster nozzle that provides acceleration on a single direction at a time. This constraint implies that an attitude maneuver is necessary before or during each thrusting arc to direct the nozzle into the desired direction. In this context, an attitude guidance algorithm specific for the orbit maneuver has been developed. A Model Predictive Control scheme is proposed, where the attitude kinematics are coupled with the orbital dynamics in order to obtain the optimal guidance profiles in terms of satellite state, reference attitude, and thrust magnitude. The proposed control scheme is developed exploiting formation flying techniques where the reference orbit is that of a virtual spacecraft that the main satellite is required to rendezvous with. In addition to the controller design, the closed-loop configuration is presented supported by numerical simulations. The efficacy of the proposed autonomous orbit-keeping approach is shown in several application scenarios.

Transcatheter aortic valve replacement (TAVR) is a treatment option for patients with asymptomatic severe aortic stenosis who are candidates for a bioprosthesis across the entire spectrum of risk. TAVR carries a risk for thrombotic and bleeding events, focusing on the importance of defining the optimal antithrombotic regimen. Patients undergoing TAVR are mostly elderly and have many comorbidities such as atrial fibrillation (AF) requiring oral anticoagulants (OACs) or coronary artery disease requiring antiplatelet agents. After TAVR among patients without baseline indications for OAC, recent data suggest dual-antiplatelet therapy is associated with an increased risk for bleeding events, particularly early postprocedure compared with single-antiplatelet therapy with aspirin. The risk of leaflet thrombosis in patients undergoing TAVR raised concern about the use of OAC in patients without an initial indication for anticoagulation therapy. Although it showed effectiveness in modulating thrombus formation at the valve level, the bleeding hazard has shown to be unacceptably high, and the net benefit of combining antiplatelet and OAC therapy is unproven. For patients with indications for the use of long-term OAC, such as those with AF, adding antiplatelet therapy increases bleeding events. A favorable effect of new OAC agents over Vitamin K antagonists is debatable. Overall, single-antiplatelet therapy and OAC appear to be reasonable strategies in patients without and with indications for concurrent anticoagulation, respectively. This article aims to review the available published studies and recommendations in the literature regarding the use of antithrombotic therapy post-TAVR.

Background & Aims: Refractory celiac disease type II (RCDII) is a rare indolent lymphoma in the small intestine characterized by a clonally expanded intraepithelial intracellular CD3+surfaceCD3-CD7+CD56- aberrant cell population. However, RCDII pathogenesis is ill-defined. Here, we aimed at single-cell characterization of the innate and adaptive immune system in RCDII. Methods: Paired small intestinal and blood samples from 12 RCDII patients and 6 healthy controls were assessed by single-cell mass cytometry with a 39–cell surface marker antibody panel, designed to capture heterogeneity of the innate and adaptive immune system. A second single-cell mass cytometry panel that included transcription factors and immune checkpoints was used for analysis of paired samples from 5 RCDII patients. Single-cell RNA sequencing analysis was performed on duodenal samples from 2 RCDII patients. Finally, we developed a 40-marker imaging mass cytometry antibody panel to evaluate cell–cell interactions in duodenal biopsy specimens of RCDII patients. Results: We provide evidence for intertumoral and intratumoral cell heterogeneity within the duodenal and peripheral aberrant cell population present in RCDII. Phenotypic discrepancy was observed between peripheral and duodenal aberrant cells. In addition, we observed that part of the aberrant cell population proliferated and observed co-localization of aberrant cells with CD163+ antigen-presenting cells (APCs) in situ. In addition, we observed phenotypic discrepancy between peripheral and duodenal aberrant cells. Conclusions: Novel high-dimensional single-cell technologies show substantial intertumoral and intratumoral heterogeneity in the aberrant cell population in RCDII. This may underlie variability in refractory disease status between patients and responsiveness to therapy, pointing to the need for personalized therapy in RCDII based on patient-specific immune profiles.

The characteristic endogenous circadian rhythm of plasma glucocorticoid concentrations is made up from an underlying ultradian pulsatile secretory pattern. Recent evidence has indicated that this ultradian cortisol pulsatility is crucial for normal emotional response in man. In this study, we investigate the anatomical transcriptional and cell type signature of brain regions sensitive to a loss of ultradian rhythmicity in the context of emotional processing. We combine human cell type and transcriptomic atlas data of high spatial resolution with functional magnetic resonance imaging (fMRI) data. We show that the loss of cortisol ultradian rhythm alters emotional processing response in cortical brain areas that are characterized by transcriptional and cellular profiles of GABAergic function. We find that two previously identified key components of rapid non-genomic GC signaling – the ANXA1 gene and retrograde endocannabinoid signaling – show most significant differential expression (q = 3.99e−10) and enrichment (fold enrichment = 5.56, q = 9.09e−4). Our results further indicate that specific cell types, including a specific NPY-expressing GABAergic neuronal cell type, and specific G protein signaling cascades underly the cerebral effects of a loss of ultradian cortisol rhythm. Our results provide a biological mechanistic underpinning of our fMRI findings, indicating specific cell types and cascades as a target for manipulation in future experimental studies.

Abstract Chronic myelogenous leukemia is a myeloproliferative neoplasm characterized by the BCR‐ABL1 fusion gene and the development of the Philadelphia chromosome, which leads to an increase in granulocytes and bone marrow myeloid precursors in the blood, it can lead to many possible complications depending on the disease stage at the time of diagnosis. The Morel‐Lavallée lesion (MLL) is a closed traumatic soft‐tissue degloving injury, that results from the separation of the hypodermis from the underlying fascia, with resultant hemo‐lymphatic fluid collection between the tissue layers. We report a case of a 48‐year‐old male patient, with no chronic illnesses, who presented with 2 weeks history of posterior chest wall pain and swelling. Initial investigation showed a white blood cell count of 364.4 × 103/μl. Bone marrow pathology report findings were consistent with chronic myeloid leukemia (CML), and the BCR‐ABL test came positive. CT chest with contrast showed a large chest wall lesion, suggestive of a Morel‐Lavallee lesion. Ultrasound‐guided aspiration of the lesion yielded 20 mm of fluid from the thick hematoma. Histopathology of the fluid showed Necrotic debris with mixed inflammation. Patient's condition improved, and he was discharged on Dasatinib with follow‐up in hematology and surgery clinics.

Single-cell omics (SCO) has revolutionized the way and the level of resolution by which life science research is conducted, not only impacting our understanding of fundamental cell biology but also providing novel solutions in cutting-edge medical research. The rapid development of single-cell technologies has been accompanied by the active development of data analysis methods, resulting in a plethora of new analysis tools and strategies every year. Such a rapid development of SCO methods and tools poses several challenges in standardization, benchmarking, computational resources and training. These challenges are in line with the activities of ELIXIR, the European coordinated infrastructure for life science data. Here, we describe the current landscape of and the main challenges in SCO data, and propose the creation of the ELIXIR SCO Community to coordinate the efforts in order to best serve SCO researchers in Europe and beyond. The Community will build on top of national experiences and pave the way towards integrated long-term solutions for SCO research.

Classification methods for scRNA-seq data are limited in their ability to learn from multiple datasets simultaneously. Here the authors present scHPL, a hierarchical progressive learning method that automatically finds relationships between cell populations across multiple datasets and constructs a classification tree.

Chronic intestinal inflammation underlies inflammatory bowel disease (IBD). Previous studies indicated alterations in the cellular immune system; however, it has been challenging to interrogate the role of all immune cell subsets simultaneously. Therefore, we aimed to identify immune cell types associated with inflammation in IBD using high-dimensional mass cytometry. We analyzed 188 intestinal biopsies and paired blood samples of newly-diagnosed, treatment-naive patients (n=42) and controls (n=26) in two independent cohorts. We applied mass cytometry (36-antibody panel) to resolve single cells and analyzed the data with unbiased Hierarchical-SNE. In addition, imaging-mass cytometry (IMC) was performed to reveal the spatial distribution of the immune subsets in the tissue. We identified 44 distinct immune subsets. Correlation network analysis identified a network of inflammation-associated subsets, including HLA-DR+CD38+ EM CD4+ T cells, T regulatory-like cells, PD1+ EM CD8+ T cells, neutrophils, CD27+ TCRγδ cells and NK cells. All disease-associated subsets were validated in a second cohort. This network was abundant in a subset of patients, independent of IBD subtype, severity or intestinal location. Putative disease-associated CD4+ T cells were detectable in blood. Finally, imaging-mass cytometry revealed the spatial colocalization of neutrophils, memory CD4+ T cells and myeloid cells in the inflamed intestine. Our study indicates that a cellular network of both innate and adaptive immune cells colocalizes in inflamed biopsies from a subset of patients. These results contribute to dissecting disease heterogeneity and may guide the development of targeted therapeutics in IBD.

Alternative RNA splicing varies across the brain. Its mapping at single cell resolution is unclear. Here, the authors provide a spatial and single-cell splicing atlas reporting brain region- and cell type-specific expression of different isoforms in the postnatal mouse brain.

Abstract The recent boom in microfluidics and combinatorial indexing strategies, combined with low sequencing costs, has empowered single-cell sequencing technology. Thousands—or even millions—of cells analyzed in a single experiment amount to a data revolution in single-cell biology and pose unique data science problems. Here, we outline eleven challenges that will be central to bringing this emerging field of single-cell data science forward. For each challenge, we highlight motivating research questions, review prior work, and formulate open problems. This compendium is for established researchers, newcomers, and students alike, highlighting interesting and rewarding problems for the coming years.

Cortical atrophy is a common manifestation in Parkinson’s disease (PD), particularly in advanced stages of the disease. To elucidate the molecular underpinnings of cortical thickness changes in PD, we performed an integrated analysis of brain-wide healthy transcriptomic data from the Allen Human Brain Atlas and patterns of cortical thickness based on T1-weighted anatomical MRI data of 149 PD patients and 369 controls. For this purpose, we used partial least squares regression to identify gene expression patterns correlated with cortical thickness changes. In addition, we identified gene expression patterns underlying the relationship between cortical thickness and clinical domains of PD. Our results show that genes whose expression in the healthy brain is associated with cortical thickness changes in PD are enriched in biological pathways related to sumoylation, regulation of mitotic cell cycle, mitochondrial translation, DNA damage responses, and ER-Golgi traffic. The associated pathways were highly related to each other and all belong to cellular maintenance mechanisms. The expression of genes within most pathways was negatively correlated with cortical thickness changes, showing higher expression in regions associated with decreased cortical thickness (atrophy). On the other hand, sumoylation pathways were positively correlated with cortical thickness changes, showing higher expression in regions with increased cortical thickness (hypertrophy). Our findings suggest that alterations in the balanced interplay of these mechanisms play a role in changes of cortical thickness in PD and possibly influence motor and cognitive functions.

Abstract Background Single-cell transcriptomics is rapidly advancing our understanding of the cellular composition of complex tissues and organisms. A major limitation in most analysis pipelines is the reliance on manual annotations to determine cell identities, which are time-consuming and irreproducible. The exponential growth in the number of cells and samples has prompted the adaptation and development of supervised classification methods for automatic cell identification. Results Here, we benchmarked 22 classification methods that automatically assign cell identities including single-cell-specific and general-purpose classifiers. The performance of the methods is evaluated using 27 publicly available single-cell RNA sequencing datasets of different sizes, technologies, species, and levels of complexity. We use 2 experimental setups to evaluate the performance of each method for within dataset predictions (intra-dataset) and across datasets (inter-dataset) based on accuracy, percentage of unclassified cells, and computation time. We further evaluate the methods’ sensitivity to the input features, number of cells per population, and their performance across different annotation levels and datasets. We find that most classifiers perform well on a variety of datasets with decreased accuracy for complex datasets with overlapping classes or deep annotations. The general-purpose support vector machine classifier has overall the best performance across the different experiments. Conclusions We present a comprehensive evaluation of automatic cell identification methods for single-cell RNA sequencing data. All the code used for the evaluation is available on GitHub (https://github.com/tabdelaal/scRNAseq_Benchmark). Additionally, we provide a Snakemake workflow to facilitate the benchmarking and to support the extension of new methods and new datasets.

The biological mechanisms underlying inter-individual differences in human stress reactivity remain poorly understood. We aimed to identify the molecular underpinning of aberrant neural stress sensitivity in individuals at risk for schizophrenia. Linking mRNA expression data from the Allen Human Brain Atlas to task-based fMRI revealed 201 differentially expressed genes in cortex-specific brain regions differentially activated by stress in individuals with low (healthy siblings of schizophrenia patients) or high (healthy controls) stress sensitivity. These genes are associated with stress-related psychiatric disorders (e.g. schizophrenia and anxiety) and include markers for specific neuronal populations (e.g. ADCYAP1, GABRB1, SSTR1, and TNFRSF12A), neurotransmitter receptors (e.g. GRIN3A, SSTR1, GABRB1, and HTR1E), and signaling factors that interact with the corticosteroid receptor and hypothalamic-pituitary-adrenal axis (e.g. ADCYAP1, IGSF11, and PKIA). Overall, the identified genes potentially underlie altered stress reactivity in individuals at risk for schizophrenia and other psychiatric disorders and play a role in mounting an adaptive stress response in at-risk individuals, making them potentially druggable targets for stress-related diseases.

The power of single-cell RNA sequencing (scRNA-seq) in detecting cell heterogeneity or developmental process is becoming more and more evident every day. The granularity of this knowledge is further propelled when combining two batches of scRNA-seq into a single large dataset. This strategy is however hampered by technical differences between these batches. Typically, these batch effects are resolved by matching similar cells across the different batches. Current approaches, however, do not take into account that we can constrain this matching further as cells can also be matched on their cell type identity. We use an auto-encoder to embed two batches in the same space such that cells are matched. To accomplish this, we use a loss function that preserves: (1) cell-cell distances within each of the two batches, as well as (2) cell-cell distances between two batches when the cells are of the same cell-type. The cell-type guidance is unsupervised, i.e., a cell-type is defined as a cluster in the original batch. We evaluated the performance of our cluster-guided batch alignment (CBA) using pancreas and mouse cell atlas datasets, against six state-of-the-art single cell alignment methods: Seurat v3, BBKNN, Scanorama, Harmony, LIGER, and BERMUDA. Compared to other approaches, CBA preserves the cluster separation in the original datasets while still being able to align the two datasets. We confirm that this separation is biologically meaningful by identifying relevant differential expression of genes for these preserved clusters.

Background Iron deficiency anaemia (IDA) is a major health issues and common type of nutritional deficiency worldwide. For IDA treatment, intravenous (IV) iron is a useful therapy. Objective To determine the efficacy and cost-effectiveness (CE) of intravenous (IV) Ferric Carboxymaltose (FCM) versus IV Iron Sucrose (IS) in treating IDA. Data sources Electronic medical record i.e. Cerner® system. Target population Adults patients with iron deficiency anaemia. Time horizon A 12-month period (01/01/2018–31/12/2018). Perspective Hamad Medical Corporation (HMC, a public hospital). Intervention IV Ferric Carboxymaltose versus IV Iron Sucrose. Outcome measures With regard to responses to treatment i.e., efficacy of treatment with FCM & IS in IDA patients, hemoglobin (Hgb), ferritin, and transferrin saturation (TSAT) levels were the primary outcomes. Additionally, the researchers also collected levels of iron, platelet, white blood cell (WBC), red blood cell (RBC), mean corpuscular hemoglobin (MCH), and mean corpuscular volume (MCV). The costs i.e. resources consumed (obtained from NCCCR-HMC) and the CE of FCM versus IS were the secondary outcomes. Results of base-case analysis There was a significant improvement in Hgb, RBC and MCH levels in the IS group than the FCM group. The overall cost of IS therapy was significantly higher than FCM. The medication cost for FCM was approximately 6.5 times higher than IS, nonetheless, it is cheaper in terms of bed cost and nursing cost. The cost effectiveness (CE) ratio illustrated that FCM and IS were significantly different in terms of Hgb, ferritin and MCH levels. Further, Incremental Cost Effectiveness Ratio (ICER) indicated that further justifications and decisions need to be made for FCM when using Hgb, iron, TSAT, MCH and MCV levels as surrogate outcomes. Results of sensitivity analysis Not applicable. Limitations The study did not consider the clinical or humanistic outcome. Conclusions The higher cost of FCM versus IS can be offset by savings in healthcare personnel time and bed space. ICER indicated that further justifications and decisions need to be made for FCM when using Hgb, iron, TSAT, MCH and MCV levels as surrogate outcomes.

Cancers are characterized by extensive heterogeneity that occurs intratumorally, between lesions, and across patients. To study cancer as a complex biological system, multidimensional analyses of the tumor microenvironment are paramount. Single-cell technologies such as flow cytometry, mass cytometry, or single-cell RNA-sequencing have revolutionized our ability to characterize individual cells in great detail and, with that, shed light on the complexity of cancer microenvironments. However, a key limitation of these single-cell technologies is the lack of information on spatial context and multicellular interactions. Investigating spatial contexts of cells requires the incorporation of tissue-based techniques such as multiparameter immunofluorescence, imaging mass cytometry, or in situ detection of transcripts. In this Review, we describe the rise of multidimensional single-cell technologies and provide an overview of their strengths and weaknesses. In addition, we discuss the integration of transcriptomic, genomic, epigenomic, proteomic, and spatially-resolved data in the context of human cancers. Lastly, we will deliberate on how the integration of multi-omics data will help to shed light on the complex role of cell types present within the human tumor microenvironment, and how such system-wide approaches may pave the way toward more effective therapies for the treatment of cancer.

The utilization of fermented foods with health-promoting properties is becoming more popular around the world. Consequently, kefir, a fermented milk beverage made from kefir grains, was shown in numerous studies to be a probiotic product providing significant health benefits. Herein, we assessed the antibacterial and antifungal potential of kefir against a variety of pathogenic bacteria and fungi. This study also showed the effectiveness of kefir in healing wounds in human gastric epithelial cells (GES-1) by (80.78%) compared with control (55.75%) within 48 h. The quantitative polymerase chain reaction (qPCR) results of kefir-treated HCV- or HBV- infected cells found that 200 µg/mL of kefir can eliminate 92.36% of HCV and 75.71% of HBV relative to the untreated infected cells, whereas 800 µg/mL (the highest concentration) completely eradicated HCV and HBV. Moreover, the estimated IC50 values of kefir, at which HCV and HBV were eradicated by 50%, were 63.84 ± 5.81 µg/mL and 224.02 ± 14.36 µg/mL, correspondingly. Kefir can significantly suppress the elevation of TNF-α and upregulate IL-10 and INF-γ in both treated HCV- and HBV-infected cells. High-performance liquid chromatography (HPLC) and gas chromatography-mass spectrometry (GC-MS) analysis of kefir revealed the presence of numerous active metabolites which mainly contribute to the antimicrobial, antiviral, and immunomodulatory activities. This study demonstrated, for the first time, the anti-HBV efficacy of kefir while also illustrating the immunomodulatory impact in the treated HBV-infected cells. Accordingly, kefir represents a potent antiviral agent against both viral hepatitis C and B, as well as having antimicrobial and wound healing potential.

The depletion of fossil fuels have seriously encouraged extensive search for alternative renewable resources. Among these resources are the use of biodiesel (highly expensive, low yield) and the blending of waste cooking oil (WCO) with light diesel oil (LDO). The present paper undertakes an experimental investigation to study the effects of varying the blending ratio of WCO/LDO on the flame characteristics, combustor efficiency, and exhaust emissions. This blending ratio is varied from 0% to 100%. For any particular blend, the equivalence ratio is varied from 0.6 to 1.05. The experiments are conducted inside a water cooled, cylindrical, combustor fitted with a coaxially mounted waste oil burner. The measurements include the inflame and exhaust mean gas temperatures and the dry volumetric species concentrations (CO, NOx, CxHy and O2) at the combustor exit. The present results indicate that the blending ratio should not exceed 20% to ensure acceptable combustor efficiency and lower emissions. Keywords: Waste cooking oil (WCO), Swirled burner, Combustor, Inflame thermal contouring map, Exhaust emissions, Equivalence ratio, Blended fuel oils

Abstract Imaging genetics deals with relationships between genetic variation and imaging variables, often in a disease context. The complex relationships between brain volumes and genetic variants have been explored with both dimension reduction methods and model-based approaches. However, these models usually do not make use of the extensive knowledge of the spatio-anatomical patterns of gene activity. We present a method for integrating genetic markers (single nucleotide polymorphisms) and imaging features, which is based on a causal model and, at the same time, uses the power of dimension reduction. We use structural equation models to find latent variables that explain brain volume changes in a disease context, and which are in turn affected by genetic variants. We make use of publicly available spatial transcriptome data from the Allen Human Brain Atlas to specify the model structure, which reduces noise and improves interpretability. The model is tested in a simulation setting and applied on a case study of the Alzheimer’s Disease Neuroimaging Initiative.

Several studies have analyzed gene expression profiles in the substantia nigra to better understand the pathological mechanisms causing Parkinson’s disease (PD). However, the concordance between the identified gene signatures in these individual studies was generally low. This might have been caused by a change in cell type composition as loss of dopaminergic neurons in the substantia nigra pars compacta is a hallmark of PD. Through an extensive meta-analysis of nine previously published microarray studies, we demonstrated that a big proportion of the detected differentially expressed genes was indeed caused by cyto-architectural alterations due to the heterogeneity in the neurodegenerative stage and/or technical artefacts. After correcting for cell composition, we identified a common signature that deregulated the previously unreported ammonium transport, as well as known biological processes such as bioenergetic pathways, response to proteotoxic stress, and immune response. By integrating with protein interaction data, we shortlisted a set of key genes, such as LRRK2, PINK1, PRKN, and FBXO7, known to be related to PD, others with compelling evidence for their role in neurodegeneration, such as GSK3β, WWOX, and VPC, and novel potential players in the PD pathogenesis. Together, these data show the importance of accounting for cyto-architecture in these analyses and highlight the contribution of multiple cell types and novel processes to PD pathology, providing potential new targets for drug development.

The maintenance of pancreatic islet architecture is crucial for proper β-cell function. We previously reported that disruption of human islet integrity could result in altered β-cell identity. Here we combine β-cell lineage tracing and single-cell transcriptomics to investigate the mechanisms underlying this process in primary human islet cells. Using drug-induced ER stress and cytoskeleton modification models, we demonstrate that altering the islet structure triggers an unfolding protein response that causes the downregulation of β-cell maturity genes. Collectively, our findings illustrate the close relationship between endoplasmic reticulum homeostasis and β-cell phenotype, and strengthen the concept of altered β-cell identity as a mechanism underlying the loss of functional β-cell mass.

Thrombotic disease represents a rare manifestation of leprosy. In this study, we report the case of an external jugular vein thrombosis associated with tuberculoid leprosy in a 23-year-old male patient. The patient presented with a 3-month history of painful cord-like swelling on the left side of the neck and a nearly 3-week history of skin lesions on the left cheek and right leg. Physical examination revealed cord-like, tender swelling on the left lateral aspect of the neck overlying the sternocleidomastoid muscle, and a hypopigmented, hypoaesthetic 6×7 cm lesion with an irregular margin on the left cheek. A Doppler ultrasound examination of the jugular vein showed thrombosis of the left external jugular vein. Three-dimensional reconstruction of the computed tomography scan showed the enlarged and enhanced left external jugular vein, as well as 1 of its tributaries, and the thickened skin patch. A skin punch biopsy from the left cheek lesion revealed granulomatous inflammation with occasional peri-adnexal granulomas, consistent with the clinical impression of tuberculoid leprosy. A diagnosis of leprosy with external jugular vein thrombosis was established. Anticoagulation therapy was initiated, and the patient was referred to an infectious disease clinic for treatment with anti-leprosy medications.

The human fetal immune system must protect the infant against the sudden exposure to a large variety of pathogens upon birth. While it is known that the fetal immune system develops in sequential waves, relatively little is known about the composition of the innate and adaptive immune system in the tissues. Here, we applied high-dimensional mass cytometry to profile the immune system in human fetal liver, spleen, and intestine. With Hierarchical Stochastic Neighbor Embedding (HSNE) we distinguished 177 distinct immune cell clusters, including both previously identified and novel cell clusters. PCA analysis indicated substantial differences between the compositions of the immune system in the different organs. Through dual t-SNE we identified tissue-specific cell clusters, which were found both in the innate and adaptive compartment. To determine the spatial location of tissue-specific subsets we developed a 31-antibody panel to reveal both the immune compartment and surrounding stromal elements through analysis of snap-frozen tissue samples with imaging mass cytometry. Imaging mass cytometry reconstructed the tissue architecture and allowed both the characterization and determination of the location of the various immune cell clusters within the tissue context. Moreover, it further underpinned the distinctness of the immune system in the tissues. Thus, our results provide evidence for early compartmentalization of the adaptive and innate immune compartment in fetal spleen, liver, and intestine. Together, our data provide a unique and comprehensive overview of the composition and organization of the human fetal immune system in several tissues.