Biomedical subjects

Yushan Liu

Publications and source records attributed to Yushan Liu.

11 recordsLinked to original sources

PubMed2026

Segzoo: a turnkey system that summarizes genome annotations.

MOTIVATION: Segmentation and automated genome annotation (SAGA) techniques, such as Segway and ChromHMM, assign labels to every part of the genome, identifying similar patterns across multiple genomic input signals. Inferring biological meaning in these patterns remains challenging. Doing so requires a time-consuming process of manually downloading reference data, running multiple analysis methods, and interpreting many individual results. RESULTS: To simplify these tasks, we developed the turnkey system Segzoo. As input, Segzoo only requires a genome annotation file in browser extensible data (BED) format. It automatically downloads the rest of the data required for comparisons. Segzoo performs analyses using these data and summarizes results in a single visualization. AVAILABILITY AND IMPLEMENTATION: The source code for Python ≥ 3.7 on Linux is freely available for download at https://github.com/hoffmangroup/segzoo under the GNU General Public License (GPL) version 2. Segzoo is also available in the Bioconda package segzoo: https://anaconda.org/bioconda/segzoo. We have deposited in Zenodo the version of the Segzoo source which produced the results in this article (https://doi.org/10.5281/zenodo.10988775), other code and data used to produce the results (https://doi.org/10.5281/zenodo.10477083), and the results (https://doi.org/10.5281/zenodo.10477106).

Software↗

PubMed2006

Investigation of novel incineration technology for hospital waste.

Conventional incineration systems for hospital waste (HW) emit large amounts of particulate matter (PM) and heavy metals, as well as dioxins, due to the large excess air ratio. Additionally, the final process residues--bottom and fly ashes containing high levels of heavy metals and dioxins--also constitute a serious environmental problem. These issues faced by HW incineration processes are very similar to those confronted by conventional municipal solid waste (MSW) incinerators. In our previous work, we developed a novel technology integrating drying, pyrolysis, gasification, combustion, and ash vitrification (DPGCV) in one step, which successfully solved these issues in MSW incineration. In this study, many experiments are carried out to investigate the feasibility of employing the DPGCV technology to solve the issues faced by HW incineration processes, although there was no MSW incinerator used as a HW incinerator till now. Experiments were conducted in an industrial HW incineration plant with a capacity of 24 tons per day (TPD), located in Zhenzhou, Henan Province. Results illustrated that this DPGCV technology successfully solved these issues as confronted by the conventional HW incinerators and achieved the expected results for HW incineration as it did for MSW incineration. The outstanding performance of this DPGCV technology is due to the fact that the primary chamber acted as both gasifier for organic matter and vitrifying reactor for ashes, and the secondary chamber acted as a gas combustor.

Dioxins↗

PubMed2006

Induction of allospecific tolerance by immature dendritic cells genetically modified to express soluble TNF receptor.

The ability of dendritic cells (DC) to initiate immune responses or induce immune tolerance is strictly dependent on their maturation state. TNF-alpha plays a pivotal role in the differentiation and maturation of DC. Blockade of TNF-alpha action may arrest DC in an immature state, prolonging their window of tolerogenic opportunity. Immature DC (imDC) were transfected with recombinant adenovirus to express soluble TNF-alpha receptor type I (sTNFRI), a specific inhibitor of TNF-alpha. The capacity of sTNFRI gene-modified imDC (DC-sTNFRI) to induce immune tolerance was analyzed. sTNFRI expression renders imDC resistant to maturation induction and impairs their capacity to migrate or present Ag. This process leads to induction of allogeneic T cell hyporesponsiveness and the generation of IL-10-producing T regulatory-like cells. In vivo pretreatment of transplant recipients with DC-sTNFRI induces long-term survival of cardiac allografts in 50% of cases, and leads to a substantial increase in the generation of microchimerism and T regulatory cell numbers. Thus, blockade of TNF-alpha action by sTNFRI genetic modification can inhibit the maturation of DC and potentiate the in vivo capacity of imDC to induce donor-specific immune tolerance and prolong allograft survival.

Animals↗

PubMed2006

An estimator of number of species from quadrat sampling.

We consider the problem of estimating the number of distinct species S in a study area from the recorded presence or absence of species in each of a sample of quadrats. A generalized jackknife estimator of S is derived, along with an estimate of its variance. It is compared with the jackknife estimator for S proposed by Heltshe and Forrester and the empirical Bayes estimator of Mingoti and Meeden. We show that the empirical Bayes estimator has the form of a generalized jackknife estimator under a specific model for species distribution. We compare the new estimators of S to the empirical Bayes estimator via simulation. We characterize circumstances under which each is superior.

Analysis of Variance↗

PubMed2005

Novel incineration technology integrated with drying, pyrolysis, gasification, and combustion of MSW and ashes vitrification.

The conventional mass burn systems for municipal solid waste (MSW) emit large amount of acidic gases and dioxins as well as heavy metals due to the large excess air ratio. Additionally, the final process residues, bottom ash with potential leachability of heavy metals and fly ash with high level of heavy metals and dioxins, also constitute a major environmental problem. To deal with these issues more effectively, a novel MSW incineration technology was developed in this study. MSW drying, pyrolysis, gasification, incineration, and ash vitrification were achieved as a spectrum of combustion by the same equipment (primary chamber) in one step. In practice, the primary chamber of this technology actually acted as both gasifier for organic matter and vitrifying reactor for ashes, and the combustion process was mainly completed in the secondary chamber. Experiments were carried outto examine its characteristics in an industrial MSW incineration plant, located in Taiyuan, with a capability of 100 tons per day (TPD). Results showed that (1) the pyrolysis, gasification, and vitrification processes in the primary chamber presented good behaviors resulting in effluent gases with high contents of combustibles (e.g., CO and CH4) and bottom ash with a low loss-on-ignition (L.o.l), low leachability of heavy metals, and low toxicity of cyanide and fluoride. The vitrified bottom ash was benign to its environment and required no further processing for its potential applications. (2) Low stack emissions of dioxins (0.076 ng of TEQ m(-3)), heavy metals (ranging from 0.013 to 0.033 mg m(-3)), and other air pollutants were achieved. This new technology could effectively dispose Chinese MSW with a low calorific value and high water content; additionally, it also had a low capital and operating costs compared with the imported systems.

Air Pollutants↗

PubMed2005

Simplified technique for heterotopic vascularized cervical heart transplantation in mice.

Technical problems have limited the widespread use of mouse vascularized heart transplantation as a medical research tool. In this report, we describe a simplified method for performing heterotopic cervical transplantation by the cuff technique. The right pulmonary artery of the donor heart is equipped with a 22-gauge cuff. The aortic arch is isolated and transected at the level of the brachiocephalic artery. After proximally ligating the inferior vena cava with 9-0 silk, the residual blood vessels and lungs are ligated proximally and then carefully transected. The carotid artery is then everted over the Teflon cuff. Using this modified procedure, the operation from harvesting the donor heart to skin closure of the recipient mouse can be completed within 35 min. This simplified method for mouse heart transplantation was shown to have a high success rate, and is practical for use in transplantation immunology research.

Animals↗

PubMed2004

Functional expression and characterization of four novel neurotoxins from sea anemone Anthopleura sp.

The genes of four novel neurotoxins, named Hk2a, Hk7a, Hk8a, and Hk16a, were obtained from sea anemone Anthopleura sp. All four neurotoxins were composed of 47 amino acid residues and the variable residues among them were found in positions 14, 22, 25, and 37. To study their activities, the four toxins fused to the Escherichia coli thioredoxin were overexpressed by BL21 (DE3), cleaved off from the fusion partner, purified, and characterized with MALDI-TOF and CD assays. Contractile force studies of isolated SD atria indicated that rHk2a had the strongest and rHk7a the longest heart stimulation effect. Consequently, the Arg14, a highly conserved residue in various sea anemone neurotoxins, can be inferred to contribute to the duration but not the intensity of contraction-stimulating activity. Our work renders useful information to studies of sea anemone neurotoxins, especially to the clarification of the function of the disputative Arg14.

Amino Acid Sequence↗

PubMed2004

Effective induction of immune tolerance by portal venous infusion with IL-10 gene-modified immature dendritic cells leading to prolongation of allograft survival.

Dendritic cells (DC) not only initiate T cell responses, but are also involved in the induction of tolerance. The functional properties of DC are strictly dependent on their state of maturation. It has been shown that immature DC can induce immune tolerance and prolong allograft survival. Interleukin-10 (IL-10) is an important immunosuppressive cytokine which inhibits maturation and function of DC. In order to improve the tolerogenicity of DC, we and others showed that adenovirus vectors can effectively mediate IL-10 genetic modification of DC, and IL-10 genetic modification can inhibit MHC II, B7.2, and CD40 expression, IL-12 secretion and the T cell stimulatory capacity of DC. The primary aim of this study is to examine the in vivo effects of this approach on allograft survival in a murine cardiac allograft transplantation model. To our surprise,we observed that infusion of immature DC genetically modified to express IL-10 (DC-IL-10) via the tail vein could not prolong allograft survival in the recipients, but shortened their survival. More interestingly, portal venous infusion of DC-IL-10 markedly prolonged allograft survival. The diverse effects of DC-IL-10 infusion through different routes may be due to the different immune responses to alloantigens in recipients that received DC-IL-10 via either the portal or the tail vein. Decreased cytotoxicity, polarization of Th2 response, poor T cell stimulating activity of liver DC and enhanced incidence of donor DC in the recipients may contribute to the more efficient prolongation of allograft survival observed after portal venous infusion of DC-IL-10. These results suggest that portal venous infusion may be an effective approach for immature DC to induce immune tolerance or hyporesponsiveness against donor antigens, and prolong allograft survival.

Animals↗

PubMed2003

Anti-ICAM-1 antibody and CTLA-4Ig synergistically enhance immature dendritic cells to induce donor-specific immune tolerance in vivo.

Immature dendritic cells (DC) have been demonstrated to induce T-cell hyporesponsiveness in vitro and immune tolerance in vivo. However, immature DC (iDC) may become mature once infused in vivo, thus limiting the prolongation of the allograft survival. Considering that mature DC express high level of B7, intercellular adhesion molecule-1 (ICAM-1), and T-cell activation needs costimulation signals provided by DC, we selected anti-ICAM-1 mAb and cytotoxic T lymphocyte antigen-4Ig fusion protein (CTLA-4Ig) for in vivo administration to block costimulation pathways in order to further improve the efficacy of iDC to induce immune tolerance. Seven days before allogeneic cardiac transplantations, the recipients were intravenously (i.v.) pretreated of donor-derived iDC with or without simultaneous injections of anti-ICAM-1 mAb and CTLA-4Ig. CTLA-4Ig or anti-ICAM-1 mAb administration alone resulted in significant prolongation of cardiac allograft survival induced by iDC. When used simultaneously, CTLA-4Ig and anti-ICAM-1 mAb induced permanent allografts acceptance even in 90% recipients. The recipients could keep the skin alive for a longer time in the donor-specific second transplantation, but no effect was observed on the skin from C3H third-party mice. The efficient induction of donor-specific tolerance observed above may be related to the more potent inhibition of donor-specific T-cell responses including cytotoxicity activity, Th1 cytokines production, and alloantibody production by the combined use of anti-ICAM-1 mAb and CTLA-4Ig. Our data suggest that anti-ICAM-1 antibody and CTLA-4Ig can synergistically enhance iDC to induce donor-specific immune tolerance in vivo.

Abatacept↗

PubMed2003

Blockade of CD40 pathway enhances the induction of immune tolerance by immature dendritic cells genetically modified to express cytotoxic T lymphocyte antigen 4 immunoglobulin.

BACKGROUND: Immature dendritic cells (DCs) have the tolerogenic potential to induce alloantigen-specific immune tolerance. Cytotoxic T lymphocyte antigen 4 immunoglobulin (CTLA4Ig) gene-modified immature DCs have been shown to maintain their tolerogenicity and prolong allograft survival to some extent. We investigated whether blockade of CD40 pathway by anti-CD40 ligand (L) monoclonal antibody (mAb) could enhance the immune tolerance induction by immature DCs genetically modified to express CTLA4Ig (DC-CTLA4Ig). METHODS: The tolerogenic properties of DC-CTLA4Ig were analyzed. In the vascularized heterotopic heart transplantation murine model, 2 x 10(6) DC-CTLA4Ig were infused intravenously into recipients, with or without a concomitant administration of anti-CD40L mAb 7 days before transplantation. Host responses to donor alloantigen were quantified by mixed leukocyte reaction and CTL assays. Donor major histocompatibility complex class II (Iab) expression in recipient lymph nodes was detected posttransplantation by semiquantitative reverse transcriptase-polymerase chain reaction. RESULTS: The allostimulatory activity of DC-CTLA4Ig was reduced. DC-CTLA4Ig also induced alloantigen-specific T-cell hyporesponsiveness and polarized T helper 2 cytokine production. Pretreatment of the recipients with DC-CTLA4Ig modestly prolonged allograft survival, without long-term allograft acceptance. Combined administration of DC-CTLA4Ig and anti-CD40L mAb significantly prolonged cardiac allograft survival, with long-term (>100 days) survival of 50% of the allografts in the pretreated recipients. More potent donor-specific inhibition of immune response against alloantigens and increased microchimerism were observed in these recipients. CONCLUSIONS: Blockade of CD40 pathway with anti-CD40L mAb potentiates the tolerogenic potential of DC-CTLA4Ig and enhances the induction of antigen-specific immune tolerance more effectively.

Abatacept↗

PubMed2002

[Cadaver renal transplantation and multivariate analysis for graft survival: a clinical review of 2 016 cases].

OBJECTIVE: To review kidney transplantation in the center and analyze the risk factors affecting long-term allograft survival. METHODS: Thirty-two relative variables were analyzed with SAS statistical software. Using Log-rank method, we investigated influence of these variables on short-and long-term survival of grafts. Kaplan-Meier analysis was used to estimate the 1-, 3-, 5-, 10-years graft survival rates and half-life. Proportional hazards regression analysis (Cox model) was used to assess and rank the relative risk of potential variables. RESULTS: The 1-, 3-, 5-, 10-years graft survival rates were 83%, 75%, 66% and 48%. After excluding the patients died with functioning grafts, the 1-, 3-, 5-, 10 years grafts survival rate increased to 89%, 82%, 75% and 69%, respectively. The mean half-life was 8.78 +/- 0.14 and 14.09 +/- 0.20 years, respectively. By Log-rank analysis, factors affecting short- and long-term graft survival were identified as: renal function, duration of graft function became normal, cold-ischemia time, presence of acute rejection, delayed graft function, immunosuppressive regimen, complication, infection, anti-rejection therapy. Cox model multivariate analysis showed that there were 18 factors affecting graft survival. CONCLUSIONS: New immunosuppressive agents not only significantly increase short-term graft survival, but also have the better long-term outcome tendency. Making assurance to get high quality donor organ and minimizing the death with graft function may be the most feasible way to prolong graft survival at present.

Adult↗