diff --git a/_bibliography/pubs.bib b/_bibliography/pubs.bib index 2509fb9..1e69623 100644 --- a/_bibliography/pubs.bib +++ b/_bibliography/pubs.bib @@ -1288,7 +1288,7 @@ @Article{ Creixell2023 this kinase signaling, AXL and YAP form a positive feedback loop that sustains drug tolerant persister cells. Altogether, this work demonstrates an approach for dissecting signaling regulators by which AXL drives erlotinib resistance-associated phenotypic changes.}, - journal = {Submitted} + journal = {bioRxiv [Preprint]} } @Article{ Peyton2023, @@ -1375,7 +1375,7 @@ @Article{ Hung2024 day = 5, preprint = {https://biorxiv.org/cgi/content/short/2024.07.05.602272v1}, abstract = {Tensor factorization is a dimensionality reduction method applied to multidimensional arrays. These methods are useful for identifying patterns within a variety of biomedical datasets due to their ability to preserve the organizational structure of experiments and therefore aid in generating meaningful insights. However, missing data in the datasets being analyzed can impose challenges. Tensor factorization can be performed with some level of missing data and reconstruct a complete tensor. However, while tensor methods may impute these missing values, the choice of fitting algorithm may influence the fidelity of these imputations. Previous approaches, based on alternating least squares with prefilled values or direct optimization, suffer from introduced bias or slow computational performance. In this study, we propose that censored least squares can better handle missing values with data structured in tensor form. We ran censored least squares on four different biological datasets and compared its performance against alternating least squares with prefilled values and direct optimization. We used the error of imputation and the ability to infer masked values to benchmark their missing data performance. Censored least squares appeared best suited for the analysis of high-dimensional biological data by accuracy and convergence metrics across several studies.}, - journal = {Submitted} + journal = {bioRxiv [Preprint]} } @Article{ Abraham2024, @@ -1416,16 +1416,18 @@ @Article{ Movassaghi2024 day = 18, abstract = {Voltammetry is widely used to detect and quantify oxidizable or reducible species in complex environments. The neurotransmitter serotonin epitomizes an analyte that is challenging to detect in situ due to low concentrations and co-existing similarly structured analytes and interferents. We developed rapid-pulse voltammetry for brain neurotransmitter monitoring due to the high information content in non-background-subtracted faradaic and non-faradic current responses at each pulse step. Here, we illustrate how Bayesian optimization can be used to hone searches for optimized rapid pulse waveforms in prohibitively large combinatorial spaces. Our machine-learning-guided workflow outperformed random and human-guided waveform designs and is tunable a priori to enable selective analyte detection. We interpreted the black box optimizer to gain insights into the logic of machine-learning-guided waveform design. Our approach is straightforward and generalizable for a variety of single and multi-analyte problems requiring optimized electrochemical waveform solutions.}, preprint = {https://doi.org/10.26434/chemrxiv-2024-xq474}, - journal = {Submitted} + journal = {chemRxiv [Preprint]} } @Article{ Kojima2024, year = {2024}, - author = {Hidenobu Kojima, Thomas A Morinelli, Yue Wang, Jackson L Chin, Aaron S Meyer, Yi-Chu Kao, Kentaro Kadono, Siyuan Yao, Taylor Torgerson, Kenneth J Dery, Adil Bhat, Elaine F Reed, Fady M Kaldas, Dirk J van der Windt, Douglas G Farmer, Jerzy W Kupiec}, + author = {Hidenobu Kojima and Thomas A Morinelli and Yue Wang and Jackson L Chin and Aaron S Meyer and Yi-Chu Kao and Kentaro Kadono and Siyuan Yao and Taylor Torgerson and Kenneth J Dery and Adil Bhat and Elaine F Reed and Fady M Kaldas and Dirk J van der Windt and Douglas G Farmer and Jerzy W Kupiec}, title = {Group 1 innate lymphoid cells protect liver transplants from ischemia-reperfusion injury via an interferon-γ-mediated pathway}, keywords = {immunology, transplantation}, month = {December}, - day = 27, - abstract = {Innate lymphoid cells (ILCs) regulate tissue inflammatory responses. However, it remains unknown whether ILCs are involved in orthotopic liver transplantation (OLT). We dissected roles of ILCs in early liver graft injury due to ischemia and reperfusion (IR). In a murine OLT model, WT liver grafts suffered significantly higher IR injury (IRI) in Rag2-γc double knockout (DKO) than Rag2 KO recipients, in association with downregulation of group 1 ILCs genes, including IFN-γ. Consistently, group 1 ILCs depletion or IFN-γ neutralization in Rag2 KO recipients increased the severity of IRI. Meanwhile, IFN-γ treatment reduced liver graft injury in Rag2-γc DKO recipients. A protective role of donor ILCs was documented by using Rag2-γc DKO or anti-NK1.1 treated WT donors. In vitro, low-dose IFN-γ protected hepatocytes from TNF-α-induced cell death with upregulated c-FLIP expression and suppressed caspase-8 activation. Treatment of liver grafts with low-dose IFN-γ during cold preservation increased c-FLIP expression and alleviated graft injury in WT recipients. In human liver transplants, c-FLIP levels were positively correlated with IFN-γ in pre-transplant liver biopsies. Of note, enhanced c-FLIP reduced post-transplant caspase-8 activation, IRI gradings, and early allograft dysfunction. Our translational study reveals a novel cytoprotective function of group 1 ILCs in OLTs by IFN-γ-mediated pathway.}, - journal = {American Journal of Transplantation (accepted)} + day = 28, + url = {https://www.sciencedirect.com/science/article/abs/pii/S1600613524007937}, + doi = {10.1016/j.ajt.2024.11.035}, + abstract = {As important immune regulatory cells, whether innate lymphoid cells (ILCs) are involved in liver transplantation (LT) remains unclear. In a murine orthotopic LT model, we dissected roles of ILCs in liver ischemia-reperfusion injury (IRI). Wild type (WT) grafts suffered significantly higher IRI in Rag2-γc double knockout (DKO) than Rag2 KO recipients, in association with downregulation of group 1 ILCs genes, including IFN-γ. Antibody-mediated ILC depletion or IFN-γ neutralization in Rag2 KO recipients increased, while IFN-γ treatment in DKO recipients reduced, liver graft injuries. At the donor side, grafts from DKO mice or anti-NK1.1-treated WT mice suffered significantly higher IRI, while grafts treated with IFN-γ during cold preservation decreased IRI. Thus, both recipient and donor group 1 ILCs protect liver grafts from IRI. Low-dose IFN-γ upregulated c-FLIP expression in vitro and in vivo, and protected hepatocytes from inflammatory cell death. In human liver graft biopsies, single-cell RNA-sequencing analysis revealed group 1 ILCs produce IFN-γ. The c-FLIP levels were positively correlated with IFN-γ in pre-transplant biopsies. Grafts with higher c-FLIP were associated with lower caspase-8 activation, IRI gradings, and frequency of early allograft dysfunction post-LT. Our study reveals a novel IFN-γ-mediated cytoprotective role of group 1 ILCs in LT.}, + journal = {American Journal of Transplantation} }