Data_Sheet_1_Development and validation of a risk prediction model for incident liver cancer.docx

ObjectiveWe aimed to develop and validate a risk prediction model for liver cancer based on routinely available risk factors using the data from UK Biobank prospective cohort study.MethodsThis analysis included 359,489 participants (2,894,807 person-years) without a previous diagnosis of cancer. We used the Fine-Gray regression model to predict the incident risk of liver cancer, accounting for the competing risk of all-cause death. Model discrimination and calibration were validated internally. Decision curve analysis was conducted to quantify the clinical utility of the model. Nomogram was built based on regression coefficients.ResultsGood discrimination performance of the model was observed in both development and validation datasets, with an area under the curve (95% confidence interval) for 5-year risk of 0.782 (0.748–0.816) and 0.771 (0.702–0.840) respectively. The calibration showed fine agreement between observed and predicted risks. The model yielded higher positive net benefits in the decision curve analysis than considering either all participants as being at high or low risk, which indicated good clinical utility.ConclusionA new risk prediction model for liver cancer composed of routinely available risk factors was developed. The model had good discrimination, calibration and clinical utility, which may help with the screening and management of liver cancer for general population in the public health field.</p

Decay of the VSV-G-pseudotyped HIV-1 in resting CD4 T cells.

<p>(A) Resting CD4 T cells were purified by negative depletion, rested overnight, and then pre-stimulated with anti-CD3/CD28 beads for 1 hour and infected with HIV-1(VSV-G) (552 ng p24 per million cells) (A1). Cells were also infected without pre-stimulation (A2 to A5) and then stimulated with anti-CD3/CD28 beads at 2 hours, day 1, day 3, or day 5 post infection to initiate viral replication. The p24 release was measured following anti-CD3/CD28 stimulation (marked as day “0” on the X-axis of each panel). (B) is a repeat of (A) in the same donor, using HIV-1_NL4-3 (Wt) (552 ng p24 per million cells).</p

Direct and Indirect Effects of UV-B Exposure on Litter Decomposition: A Meta-Analysis

<div><p>Ultraviolet-B (UV-B) exposure in the course of litter decomposition may have a direct effect on decomposition rates via changing states of photodegradation or decomposer constitution in litter while UV-B exposure during growth periods may alter chemical compositions and physical properties of plants. Consequently, these changes will indirectly affect subsequent litter decomposition processes in soil. Although studies are available on both the positive and negative effects (including no observable effects) of UV-B exposure on litter decomposition, a comprehensive analysis leading to an adequate understanding remains unresolved. Using data from 93 studies across six biomes, this introductory meta-analysis found that elevated UV-B directly increased litter decomposition rates by 7% and indirectly by 12% while attenuated UV-B directly decreased litter decomposition rates by 23% and indirectly increased litter decomposition rates by 7%. However, neither positive nor negative effects were statistically significant. Woody plant litter decomposition seemed more sensitive to UV-B than herbaceous plant litter except under conditions of indirect effects of elevated UV-B. Furthermore, levels of UV-B intensity significantly affected litter decomposition response to UV-B (<i>P</i><0.05). UV-B effects on litter decomposition were to a large degree compounded by climatic factors (e.g., MAP and MAT) (<i>P</i><0.05) and litter chemistry (e.g., lignin content) (<i>P</i><0.01). Results suggest these factors likely have a bearing on masking the important role of UV-B on litter decomposition. No significant differences in UV-B effects on litter decomposition were found between study types (field experiment vs. laboratory incubation), litter forms (leaf vs. needle), and decay duration. Indirect effects of elevated UV-B on litter decomposition significantly increased with decay duration (<i>P</i><0.001). Additionally, relatively small changes in UV-B exposure intensity (30%) had significant direct effects on litter decomposition (<i>P</i><0.05). The intent of this meta-analysis was to improve our understanding of the overall effects of UV-B on litter decomposition.</p> </div

Different effects of dynasore on the replication of HIV-1(VSV-G) and Wt in a human T cell, Rev-CEM.

<p>(A) Rev-CEM, a Rev-dependent GFP indicator cell, was pretreated for 30 minutes with 80 µM, 8 µM, or 0.8 µM dynasore, respectively, or treated with 0.1% DMSO as a control. Cells were subsequently infected with HIV-1(VSV-G) in the presence of dynasore for 2 hours. Following infection, cells were washed three times with medium, and then cultured in the absence of dynasore. Viral replication was monitored by flow cytometry analysis of HIV-dependent GFP expression at 48 hours (20,000 cells analyzed per sample). Propidum iodide (PI) was added into the cell suspension prior to flow cytometry. Viable cells were gated (R1) based on low PI staining and cell size (FSC). GFP expression within the viable cell population (R1) was measured. Both the GFP percentage (%) and mean intensity (M) were shown. (B) is an identical experiment using HIV-1_NL4-3 (Wt). For the 80 µM dynasore treatment, another three-independent infections with each virus were performed. The averages from the three-independent experiments are: 15.05%±0.21 (VSV-G), 10.11%±0.06 (VSV-G plus 80 µM dynasore), <i>p</i> = 0.0003; 2.94%±0.39 (Wt), 2.84%±0.30 (Wt plus 80 µM dynasore), <i>p</i> = 0.38.</p

The HIV envelope but not VSV-G is capable of mediating latent infection of resting CD4 T cells.

<p>Resting CD4 T cells were purified from the peripheral blood by negative depletion. Cells were unstimulated (A) or activated with magnetic beads conjugated with antibodies against the human CD3 and CD28 receptors (two beads per cell) for 1 day (B), and then analyzed for cell cycle progression using 7-AAD, PY staining to confirm sufficient T cell activation following stimulation. (C) In CD3/CD28 pre-stimulated CD4 T cells, a higher than Wt level of viral replication was observed in cells infected with HIV-1(VSV-G). One million cells were infected with 25 ng (p24) of HIV-1_NL4-3 (wt) or the VSV-G pseudotyped virus (VSV-G). (D) In resting CD4 T cells that were not pre-stimulated, only the Wt but not the VSV-G pseudotyped HIV-1 replicated following T cell activation at day 5. Cells were infected with 25 ng (p24) of both viruses, incubated for 5 days, and then activated with anti-CD3/CD28 beads. (E) and (F) were a repeat of (C) and (D) in another donor, with AZT (50 µM) added at day 1 and day 5 post infection, respectively, to limit viral replication to a single cycle.</p

Comparison of viral DNA synthesis in CEM-SS cells infected with either HIV-1(VSV-G) or HIV-1_NL4-3.

<p>Cells were infected with an equal TCID₅₀ dose of HIV-1(VSV-G) or HIV-1_NL4-3 (Wt) (1.27×10⁵ TCID_50/Rev-CEM per million cells). Following infection for 2 hours, cell-free viruses were washed away. Total cellular DNA was extracted from cells, and then amplified by real-time PCR to measure the synthesis of full-length HIV-1 DNA (2 hours post infection) (A) and 2-LTR circles at later time points (6 and 12 hours post infection) (B). The relative ratios of 2-LTR circles at 12 hours and HIV-1 DNA at 2 hours were plotted (C).</p

Image_1_Label-free LC-MS/MS proteomics analyses reveal CLIC1 as a predictive biomarker for bladder cancer staging and prognosis.tif

IntroductionBladder cancer (BC) is a significant carcinoma of the urinary system that has a high incidence of morbidity and death owing to the challenges in accurately identifying people with early-stage BC and the lack of effective treatment options for those with advanced BC. Thus, there is a need to define new markers of prognosis and prediction.MethodsIn this study, we have performed a comprehensive proteomics experiment by label-free quantitative proteomics to compare the proteome changes in the serum of normal people and bladder cancer patients—the successful quantification of 2064 Quantifiable proteins in total. A quantitative analysis was conducted to determine the extent of changes in protein species' relative intensity and reproducibility. There were 43 upregulated proteins and 36 downregulated proteins discovered in non-muscle invasive bladder cancer and normal individuals. Sixty-four of these proteins were elevated, and 51 were downregulated in muscle-invasive and non-muscle-invasive bladder cancer, respectively. Functional roles of differentially expressed proteins were annotated using Gene Ontology (GO) and Clusters of Orthologous Groups of Proteins (COG). To analyze the functions and pathways enriched by differentially expressed proteins, GO enrichment analysis, protein domain analysis, and KEGG pathway analysis were performed. The proteome differences were examined and visualized using radar plots, heat maps, bubble plots, and Venn diagrams.ResultsAs a result of combining the Venn diagram with protein-protein interactions (PPIs), Chloride intracellular channel 1 (CLIC1) was identified as the primary protein. Using the Gene Set Cancer Analysis (GSCA) website, the influence of CLIC1 on immune infiltration was analyzed. A negative correlation between CD8 naive and CLIC1 levels was found. For validation, immunohistochemical (IHC), qPCR, and western blotting (WB) were performed.Further, we found that CLIC1 was associated with a poor prognosis of bladder cancer in survival analysis.DiscussionOur research screened CLIC1 as a tumor-promoting protein in bladder cancer for the first time using serum mass spectrometry. And CLIC1 associated with tumor stage, and immune infiltrate. The prognostic biomarker and therapeutic target CLIC1 may be new for bladder cancer patients.</p

DataSheet_2_Label-free LC-MS/MS proteomics analyses reveal CLIC1 as a predictive biomarker for bladder cancer staging and prognosis.zip

IntroductionBladder cancer (BC) is a significant carcinoma of the urinary system that has a high incidence of morbidity and death owing to the challenges in accurately identifying people with early-stage BC and the lack of effective treatment options for those with advanced BC. Thus, there is a need to define new markers of prognosis and prediction.MethodsIn this study, we have performed a comprehensive proteomics experiment by label-free quantitative proteomics to compare the proteome changes in the serum of normal people and bladder cancer patients—the successful quantification of 2064 Quantifiable proteins in total. A quantitative analysis was conducted to determine the extent of changes in protein species' relative intensity and reproducibility. There were 43 upregulated proteins and 36 downregulated proteins discovered in non-muscle invasive bladder cancer and normal individuals. Sixty-four of these proteins were elevated, and 51 were downregulated in muscle-invasive and non-muscle-invasive bladder cancer, respectively. Functional roles of differentially expressed proteins were annotated using Gene Ontology (GO) and Clusters of Orthologous Groups of Proteins (COG). To analyze the functions and pathways enriched by differentially expressed proteins, GO enrichment analysis, protein domain analysis, and KEGG pathway analysis were performed. The proteome differences were examined and visualized using radar plots, heat maps, bubble plots, and Venn diagrams.ResultsAs a result of combining the Venn diagram with protein-protein interactions (PPIs), Chloride intracellular channel 1 (CLIC1) was identified as the primary protein. Using the Gene Set Cancer Analysis (GSCA) website, the influence of CLIC1 on immune infiltration was analyzed. A negative correlation between CD8 naive and CLIC1 levels was found. For validation, immunohistochemical (IHC), qPCR, and western blotting (WB) were performed.Further, we found that CLIC1 was associated with a poor prognosis of bladder cancer in survival analysis.DiscussionOur research screened CLIC1 as a tumor-promoting protein in bladder cancer for the first time using serum mass spectrometry. And CLIC1 associated with tumor stage, and immune infiltrate. The prognostic biomarker and therapeutic target CLIC1 may be new for bladder cancer patients.</p

Untransformed response ratios pertaining to UV-B effects on litter decomposition.

<p>Direct effects of elevated UV-B (a) and attenuated UV-B (b) as well as indirect effects of elevated UV-B (c) and attenuated UV-B (d) on litter decomposition. Dots with error bars denote the overall mean response ratio with a 95% CI. Wood denotes litter from woody plants; herbaceous denotes litter from herbaceous plants. Lab. denotes the study was carried out in a laboratory; field denotes the study was carried out in the field.</p

Measurement of viral entry and DNA synthesis following HIV-1(VSV-G) infection of resting CD4 T cells.

<p>(A) Resting or pre-activated (CD3/CD28 beads, two beads per cell) CD4 T cells (1×10⁶) were infected with 200 ng of Nef-luciferase-tagged HIV-1_NL4-3 (Wt) or HIV-1(VSV-G) for 2 hours. Infected cells were washed three times and then used to measure luciferase activity in live cells. As a control, CEM-SS cells were identically infected with the Nef-luciferase-tagged HIV-1(VSV-G). Uninfected cells were identically treated and measured for luciferase activities. (B) Resting or pre-activated (overnight PHA plus IL-2 treatment) CD4 T cells (1×10⁶) were infected with 200 ng of HIV-1_NL4-3 (Wt) or HIV-1(VSV-G) in 0.5 ml for 2 hours. Following infection, cells were treated with TrypLE (Invitrogen) for 2 minutes at 37°C and then washed an additional three times with medium. Cells were pelleted and subsequently lysed for p24 ELISA. (C to E) Resting CD4 T cells were infected with an equal TCID₅₀ dose of HIV-1_NL4-3 (Wt) or HIV-1(VSV-G) (2.53×10⁵ TCID_50/Rev-CEM per million cells). Following infection for 2 hours, cell-free viruses were washed away. Cells were cultured for 5 days and then activated with anti-CD3/CD28 beads. (C) A measurement of p24 release confirmed that only the Wt virus but not HIV-1(VSV-G) replicated following CD3/CD28 stimulation. (D, E) Total cellular DNA from infected cells was extracted at different time points, and then amplified with real-time PCR for HIV late DNA (D) or 2-LTR-circles (E). (F, G) is a repeat of (D, E) on another donor using an equal p24 level of Wt and HIV-1(VSV-G) to infect resting T cells. Total cellular DNA was extracted from infected cells at different time points and PCR-amplified for HIV late DNA (F) or 1-LTR circles (G), along with the β-actin pseudogene as a control.</p