Bateshay4765

It is a growing trend among researchers to make their data publicly available for experimental reproducibility and data reusability. Sharing data with fellow researchers helps in increasing the visibility of the work. On the other hand, there are researchers who are inhibited by the lack of data resources. To overcome this challenge, many repositories and knowledge bases have been established to date to ease data sharing. Further, in the past two decades, there has been an exponential increase in the number of datasets added to these dataset repositories. However, most of these repositories are domain-specific, and none of them can recommend datasets to researchers/users. Naturally, it is challenging for a researcher to keep track of all the relevant repositories for potential use. Thus, a dataset recommender system that recommends datasets to a researcher based on previous publications can enhance their productivity and expedite further research. This work adopts an information retrieval (IR) paradigm for dae that this system will further promote data sharing, offset the researchers' workload in identifying the right dataset and increase the reusability of biomedical datasets. Database URL http//genestudy.org/recommends/#/.Single-cell RNA sequencing (scRNA-seq) provides a powerful tool to determine expression patterns of thousands of individual cells. However, the analysis of scRNA-seq data remains a computational challenge due to the high technical noise such as the presence of dropout events that lead to a large proportion of zeros for expressed genes. Taking into account the cell heterogeneity and the relationship between dropout rate and expected expression level, we present a cell sub-population based bounded low-rank (PBLR) method to impute the dropouts of scRNA-seq data. Through application to both simulated and real scRNA-seq datasets, PBLR is shown to be effective in recovering dropout events, and it can dramatically improve the low-dimensional representation and the recovery of gene‒gene relationships masked by dropout events compared to several state-of-the-art methods. Moreover, PBLR also detects accurate and robust cell sub-populations automatically, shedding light on its flexibility and generality for scRNA-seq data analysis.Fanconi anemia (FA) is a disorder of DNA repair that manifests as bone marrow (BM) failure. The lack of accurate murine models of FA has refocused efforts toward differentiation of patient-derived induced pluripotent stem cells (IPSCs) to hematopoietic progenitor cells (HPCs). However, an intact FA DNA repair pathway is required for efficient IPSC derivation, hindering these efforts. To overcome this barrier, we used inducible complementation of FANCA-deficient IPSCs, which permitted robust maintenance of IPSCs. Modulation of FANCA during directed differentiation to HPCs enabled the production of FANCA-deficient human HPCs that recapitulated FA genotoxicity and hematopoietic phenotypes relative to isogenic FANCA-expressing HPCs. FANCA-deficient human HPCs underwent accelerated terminal differentiation driven by activation of p53/p21. We identified growth arrest specific 6 (GAS6) as a novel target of activated p53 in FANCA-deficient HPCs and modulate GAS6 signaling to rescue hematopoiesis in FANCA-deficient cells. This study validates our strategy to derive a sustainable, highly faithful human model of FA, uncovers a mechanism of HPC exhaustion in FA, and advances toward future cell therapy in FA.The prognosis of patients with relapsed or refractory (R/R) diffuse large B-cell lymphoma (DLBCL) is poor. Chimeric antigen receptor (CAR) T-cell therapy has been approved for R/R DLBCL after 2 prior lines of therapy based on data from single-arm phase 2 trials, with complete responses (CRs) in 40% to 60% of patients. However, a direct comparison with other treatments is not available and, moreover, its true efficacy in real-world patients is unknown. In this single center, retrospective, observational study of 215 patients, we compared outcomes in patients treated with CAR T-cell therapy (n = 69) with a historical population treated with alternate therapies (n = 146). Patients treated with CAR T cell vs alternate therapies demonstrated a CR rate of 52% vs 22% (P less then .001), median progression-free survival (PFS) of 5.2 vs 2.3 months (P = .01), and median overall survival (OS) of 19.3 vs 6.5 months (P = .006), and this advantage appeared to persist irrespective of the number of lines of prior therapy. After adjusting for unfavorable pretreatment disease characteristics, superior overall response rate in the CAR T cohort remained significant; however, differences in PFS and OS between cohorts did not. selleckchem In addition, patients who responded to alternate therapies demonstrated prolonged remissions comparable to those who responded to CAR T therapy. We contend that in select clinical scenarios alternate therapies may be as efficacious as CAR T therapy; thus, additional study is warranted, ideally with randomized prospective trials.Engineered T-cell therapies have demonstrated impressive clinical responses in patients with hematologic malignancies. Despite this efficacy, many patients have a transient persistence of T cells, which can be correlated with transient clinical response. Translational data on T cells from pediatric cancer patients shows a progressive decline in chimeric antigen receptor (CAR) suitability with cumulative chemotherapy regardless of regimen. We investigated the effects of chemotherapy on surviving T cells in vitro, describing residual deficits unique to each agent including mitochondrial damage and metabolic alterations. In the case of cyclophosphamide but not doxorubicin or cytarabine, these effects could be reversed with N-acetylcysteine. Specifically, we observed that surviving T cells could be stimulated, expanded, and transduced with CARs with preserved short-term cytolytic function but at far lower numbers and with residual metabolic deficits. These data have implications for understanding the effects of chemotherapy on mature T cells later collected for adoptive cell therapy, as chemotherapy-exposed T cells may have lingering dysfunction that affects ex vivo adoptive cell therapy manufacturing techniques and, ultimately, clinical efficacy.