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Whole brain encoding.
No full textEncoding model performance in all face-selective voxels. Ventral view of the remaining two subjects for dVAE (left), VAE (center) and VGG-face (right). (EPS)</p
Lyssavirus M proteins’ sequences were compared.
No full textThe protein sequences of lyssavirus M were compared and analyzed with ESPript 3.0 online software (https://espript.ibcp.fr/ESPript/cgi-bin/ESPript.cgi). (TIF)</p
Primer sequence of Q- PCR.
No full textColorectal cancer (CRC) is a major cause of cancer mortality and a serious health problem worldwide. Mononuclear phagocytes are the main immune cells in the tumor microenvironment of CRC with remarkable plasticity, and current studies show that macrophages are closely related to tumor progression, invasion and dissemination. To understand the immunological function of mononuclear phagocytes comprehensively and deeply, we use single-cell RNA sequencing and classify mononuclear phagocytes in CRC into 6 different subsets, and characterize the heterogeneity of each subset. We find that tissue inhibitor of metalloproteinases (TIMPs) involved in the differentiation of proinflammatory and anti-inflammatory mononuclear phagocytes. Trajectory of circulating monocytes differentiation into tumor-associated macrophages (TAMs) and the dynamic changes at levels of transcription factor (TF) regulons during differentiation were revealed. We also find that C5 subset, characterized by activation of lipid metabolism, is in the terminal state of differentiation, and that the abundance of C5 subset is negatively correlated with CRC patients’ prognosis. Our findings advance the understanding of circulating monocytes’ differentiation into macrophages, identify a new subset associated with CRC prognosis, and reveal a set of TF regulons regulating mononuclear phagocytes differentiation, which are expected to be potential therapeutic targets for reversing immunosuppressive tumor microenvironment.</div
Unique characteristics of immunosuppressive cluster C5.
No full text(A). UMAP plots of mononuclear phagocytes in CRC with treatment-naïve (left) and treated with PC (right). Cells are colored by clusters. (B). Bar plot showed proportion of different clusters in CRC with treatment-naïve and treated with PC. (C). UMAP plots of mononuclear phagocytes in CRC before chemotherapy (left) and after chemotherapy (right). Cells are colored by clusters. (D). Bar plot showed proportion of different clusters in CRC before and after chemotherapy. (E). Violin plots showed expression levels of LILRB4 (top) and CD274 (bottom) in each cluster. (F). Dot plot showed metabolism activity of different clusters. (G). Pairwise Pearson’s correlation for infiltration patterns of ten major cell types in TCGA CRC cohort.</p
pntd.0011961.t006 - Quantitative PCR as a marker for preemptive therapy and its role in therapeutic control in <i>Trypanosoma cruzi</i>/HIV coinfection
No full textpntd.0011961.t006 - Quantitative PCR as a marker for preemptive therapy and its role in therapeutic control in Trypanosoma cruzi/HIV coinfectio
Reagent List.
No full textBackgroundCD4+ T cells play a central role in control of L. donovani infection, through IFN-γ production required for activation of macrophages and killing of intracellular parasites. Impaired control of parasites can in part be explained by hampered CD4+ T cells effector functions in visceral leishmaniasis (VL) patients. In a recent studies that defined transcriptional signatures for CD4+ T cells from active VL patients, we found that expression of the IL-7 receptor alpha chain (IL-7Rα; CD127) was downregulated, compared to CD4+ T cells from endemic controls (ECs). Since IL-7 signaling is critical for the survival and homeostatic maintenance of CD4+ T cells, we investigated this signaling pathway in VL patients, relative to ECs.MethodsCD4+ T cells were enriched from peripheral blood collected from VL patients and EC subjects and expression of IL7 and IL7RA mRNA was measured by real time qPCR. IL-7 signaling potential and surface expression of CD127 and CD132 on CD4+ T cell was analyzed by multicolor flow cytometry. Plasma levels of soluble IL-7 and sIL-7Rα were measured by ELISA.ResultTranscriptional profiling data sets generated previously from our group showed lower IL7RA mRNA expression in VL CD4+ T cells as compared to EC. A significant reduction was, however not seen when assessing IL7RA mRNA by RT-qPCR. Yet, the levels of soluble IL-7Rα (sIL-7Rα) were reduced in plasma of VL patients compared to ECs. Furthermore, the levels of soluble IL-7 were higher in plasma from VL patients compared to ECs. Interestingly, expression of the IL-7Rα protein was higher on VL patient CD4+ T cells as compared to EC, with activated CD38+ CD4+ T cells showing higher surface expression of IL-7Rα compared to CD38- CD4+ T cells in VL patients. CD4+ T cells from VL patients had higher signaling potential baseline and after stimulation with recombinant human IL-7 (rhIL-7) compared to EC, as measured by phosphorylation of STAT5 (pSTAT5). Interestingly, it was the CD38 negative cells that had the highest level of pSTAT5 in VL patient CD4+ T cells after IL-7 stimulation. Thus, despite unaltered or potentially lowered IL7RA mRNA expression by CD4+ T cells from VL patients, the surface expression of the IL-7Rα was higher compared to EC and increased pSTAT5 was seen following exposure to rhIL-7. Accordingly, IL-7 signaling appears to be functional and even enhanced in VL CD4+ T cells and cannot explain the impaired effector function of VL CD4+ T cells. The enhanced plasma IL-7 may serve as part of homeostatic feedback mechanism regulating IL7RA expression in CD4+ T cells.</div
Simulation parameters and SBI training.
No full textBiophysically detailed neural models are a powerful technique to study neural dynamics in health and disease with a growing number of established and openly available models. A major challenge in the use of such models is that parameter inference is an inherently difficult and unsolved problem. Identifying unique parameter distributions that can account for observed neural dynamics, and differences across experimental conditions, is essential to their meaningful use. Recently, simulation based inference (SBI) has been proposed as an approach to perform Bayesian inference to estimate parameters in detailed neural models. SBI overcomes the challenge of not having access to a likelihood function, which has severely limited inference methods in such models, by leveraging advances in deep learning to perform density estimation. While the substantial methodological advancements offered by SBI are promising, their use in large scale biophysically detailed models is challenging and methods for doing so have not been established, particularly when inferring parameters that can account for time series waveforms. We provide guidelines and considerations on how SBI can be applied to estimate time series waveforms in biophysically detailed neural models starting with a simplified example and extending to specific applications to common MEG/EEG waveforms using the the large scale neural modeling framework of the Human Neocortical Neurosolver. Specifically, we describe how to estimate and compare results from example oscillatory and event related potential simulations. We also describe how diagnostics can be used to assess the quality and uniqueness of the posterior estimates. The methods described provide a principled foundation to guide future applications of SBI in a wide variety of applications that use detailed models to study neural dynamics.</div
The enhancement performance of different methods on the OceanDark [33] dataset is compared with three randomly selected photos from the dataset.
No full textThe enhancement performance of different methods on the OceanDark [33] dataset is compared with three randomly selected photos from the dataset.</p
The overall flowchart of the proposed method, first the input image is color corrected in the color correction module, then the output image is taken for processing in the contrast enhancement and visibility enhancement modules respectively, and finally the two outputs are made as inputs to the multi-task fusion module for processing to get the final result.
No full textThe overall flowchart of the proposed method, first the input image is color corrected in the color correction module, then the output image is taken for processing in the contrast enhancement and visibility enhancement modules respectively, and finally the two outputs are made as inputs to the multi-task fusion module for processing to get the final result.</p
Region-specific probability of habitat suitability uncertainty maps.
No full textUncertainty in ensemble projections of queen snapper occurrence in the A) west, B) northeast, and C) southeast region of Puerto Rico. The map layer used to generate this figure is from NOAA National Centers for Environmental Information and provided without restriction by the U.S. Government.</p