From scenario to roadmap: Design and evaluation of a web-based participatory watershed planning system for optimizing multistage implementation plans of management practices under stepwise investment.

Planning multistage implementation plans, or roadmaps, based on the spatial distribution of a best management practice (BMP) scenario is essential for achieving watershed management goals under realistic conditions, such as stepwise investment plans that involve multiple stakeholders, including investors, economic and environmental beneficiaries. The state-of-the-art BMP roadmap optimization method can address this need for optimization but is over-specialized and complex to non-expert stakeholders. This study designed a user-friendly web-based participatory watershed planning system to assist a diverse group of stakeholders in reaching a consensus on optimal roadmaps. The participatory process of stakeholders includes iteratively proposing stepwise investment constraints, submitting roadmap optimization tasks, analyzing spatiotemporal results from multiple perspectives, and selecting preferred roadmaps. The proposed system design separates the participatory process of non-expert stakeholders from the specialized modeling process of constructing simulation-optimization tools for BMP roadmaps, which is done in advance by professional modelers and encapsulated as webservices on the server side. The webservices expose a small set of essential parameters to lower barriers to use. The interactive participatory process is presented to stakeholders through web browsers with an easy-to-use interface. The system design was evaluated by implementing an agricultural watershed planning system for soil erosion reduction and conducting a role-playing experiment involving three groups of stakeholders with different standpoints in proposing investment constraints. The experimental results show that the optimal roadmap sets exhibit progressive improvements across three-round optimizations started by different stakeholders, effectively capturing the varying perspectives of stakeholders and facilitating consensus-building among them. The idea of system design and example implementation can serve as a valuable reference for developing related user-friendly environmental decision support systems.

Tumor mutation burden in Chinese cancer patients and the underlying driving pathways of high tumor mutation burden across different cancer types.

BACKGROUND: Tumor mutation burden (TMB) has an important association with immunotherapy responses. TMB in the Chinese population has not been well established. Finding differences between the Chinese and Caucasian populations and elucidating the underlying biological mechanisms of high TMB might help develop more precise and effective means for TMB and immunotherapy response prediction. METHODS: Chinese cancer patients fresh tissue (n=2,177), formalin-fixed, paraffin-embed (FFPE) specimens (n=3,294), and pleural fluid (n=189) were profiled using a 295- or 520-gene next-generation sequencing (NGS) panel. The association of the TMB status with a series of molecular features and biological pathways was determined using bootstrapping. RESULTS: TMB, measured by 295- or 520-cancer-related gene panels, was correlated with whole-exome sequencing (WES) TMB based on the in silico simulation in The Cancer Genome Atlas cohort. The median TMB of our data was slightly higher than that from the Foundation Medicine Inc. (FMI) dataset. TMB was also slightly different within the same cancer type between the Chinese and Caucasian population. We discovered that the underlying pathways of TMB status varied greatly and sometimes had an opposite association with TMB across different cancer types. Moreover, we developed a 23-gene and a 16-gene signature to predict TMB prediction for lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC), respectively, indicating a histology-specific mechanism for driving high-TMB in lung cancer. CONCLUSIONS: TMB varies among different ethnic populations. Our findings extend the knowledge of the underlying biological mechanisms for high TMB and might be helpful for developing more precise and accessible TMB assessment panels and algorithms in more cancer types.

[Comparing the responses of radial growth between Quercus mongolica and Phellodendron amurense to climate change in Xiaoxing'an Mountains, China.] / å°å ´å®‰å²­è’™å¤æ Žå’Œé»„è èå¾„å‘ç”Ÿé•¿å¯¹æ°”å€™å˜åŒ–çš„å“åº”æ¯”è¾ƒ.

Quercus mongolica and Phellodendron amurense are two important broad-leaved species in temperate forests of Northeast China. It is critical to explore their responses to climate change for supporting management, protection, and restoration of the broad-leaved forest in Northeast China under the future climate change scenario. Three sampling sites along a longitude gradient, Heilun, Tieli and Yichun, were set up in the Xiaoxing'an Mountains. Dendrochronological methods were used to establish standard chronologies for Q. mongolica and P. amurense. Correlation analyses were conducted between these chronologies and local climatic factors to establish the spatial and temporal variations in growth-climate relationship of Q. mongolica and P. amurense. The results showed that the radial growth of P. amurense was sensitive to temperature, while that of Q. mongolica was limi-ted by both temperature and precipitation. The temperature sensitivities of these two species were different. High spring temperature inhibited the radial growth of Q. mongolica, but promoted that of P. amurense. The limiting effect of high maximum temperature in summer on radial growth of Q. mongolica was significantly higher than that of P. amurense. With the increases of longitude (water availability), the correlation coefficients between radial growth of Q. mongolica and precipitation gradually weakened, while P. amurense didn't change. The physiological characteristics of those tree species was the key factors affecting their growth-climate relationship. With the significant warming since the 1976, the growth trend of P. amurense increased, whilst that of Q. mongolica decreased. Deteriorated drought stress caused by warming and difference in the species' ability to cope with water deficits might be the main reasons for different responses of two species, and for the divergence phenomenon occurring for Q. mongolica. If warming continues or worsens in the future, the growth of Q. mongolica may decline due to the intensified drought stress, while that of P. amurense may be less affected or be slightly enhanced.

Characterization of CIb1 gene promoter from silkworm, Bombyx mori.

The hemolymph chymotrypsin inhibitor b1 (CIb1) of silkworm, Bombyx mori, plays an important role in innate immunity. In order to study its encoding gene CIb1, five heterogeneous promoter fragments of 844 bp, 682 bp, 516 bp, 312 bp and 82 bp in length were cloned from genomic DNA of the p50 silkworm strain. Characterization of the CIb1 promoter was performed in vitro using the firefly luciferase gene as reporter. The results showed that CIb1 promoter fragments have transcription activities in the B. mori ovary-derived BmN cell line. The 82 bp fragment (-72 to +10 nt) containing the eukaryotic core promoter elements revealed a basic transcription activity. The Bm1 element, upstream the transcription initiation site, showed a positive regulation function to the CIb1 promoter. CIb1 promoter-like fragments from the genomic DNA of the tetra hybrid silkworm SujuxMinghu provided a natural deletion model for the study of the CIb1 promoter. In vitro analysis indicated that the 132 bp fragment from -517 nt to -386 nt upstream of the transcription initiation site strongly suppressed the transcription activity of the CIb1 promoter, suggesting that the 132 bp fragment harbours strong negative cis-acting elements. Infection of Bombyx mori nucleopolyhedrovirus (BmNPV) increased the activity of the CIb1 promoter, having provided another evidence to the function of CIb1 in the innate immunity of silkworm.

Characterization of a late gene, ORF60 from Bombyx mori nucleopolyhedrovirus.

Open reading frame 60 of Bombyx mori nucleopolyhedrovirus (Bm60) is located between 56,673 and 57,479 bp in the BmNPV genome which encodes 268 amino acid residues with predicted molecular weight of 31.0 kDa. Bm60 and its homologues have been identified in 11 completely sequenced lepidopteran NPVs. The transcript of Bm60 was detected by RT-PCR at 18-72 h post-infection (p.i.), while the corresponding protein could be detected at 24-72 h p.i. in BmNPV-infected BmN cells by Western blot analysis using a polyclonal antibody against Bm60. The expression of Bm60 was inhibited in the presence of Ara-c, an inhibitor of viral DNA synthesis. These results together indicated that Bm60 was a late gene. The size of Bm60 product was found to be a 31 kDa in BmNPV-infected BmN cells, consistent with predicted molecular weight. Immunofluoresence analysis showed that the Bm60 product was first detected in the cytoplasm at 24 h p.i and also located in nucleus during later infection. In conclusion, the available data suggest that Bm60 is a functional ORF of BmNPV and encodes a 31kDa protein expressed in the later stage of infection cycle.

[In vitro purging effect of CD3AK/iNOS on leukemia cells].

BACKGROUND & OBJECTIVE: LAK cells have been applied to purge minimal residual leukemia cells in allogeneic hematopoietic stem cell transplantation(AHSCT) in clinic practice. CD3AK cells belong to T lymphocytes activated by anti-CD3McAb. This study was to construct nitric oxide donor CD3AK/iNOS through transfecting inducible nitric oxide synthase (iNOS) gene into human CD3AK cells by retroviral vector, and investigate the cytotoxic activity of CD3AK/iNOS to leukemia cell lines K562 and K562/ADM. METHODS: The amphotropic packaging cell line PA317 transfected with iNOS gene was cultivated to obtain viral supernatant. Human peripheral blood mononuclear cells (PBMNCs) were isolated and activated by anti-CD3McAb and low dose of interleukin-2 (IL-2). CD3AK cells were incubated with viral supernatant. The amount of nitric oxide (NO) and the activity of iNOS in the cultured supernatant of CD3AK/iNOS were evaluated. The cytotoxic activities of CD3AK/iNOS and CD3AK cells to K562 and K562/ADM cells were evaluated by MTT assay. RESULTS: The contents of NO excreted by CD3AK/iNOS and CD3AK cells were (378.60+/-41.57) micromol/L and (98.07+/-22.31) micromol/L, respectively (P<0.001); the activities of iNOS synthesized by CD3AK/iNOS and CD3AK cells were (20.77+/-2.49) U/ml and (9.81+/-1.96) U/ml, respectively (P<0.001). The cytotoxic activities of CD3AK/iNOS cells to K562 and K562/ADM cells were significantly stronger than those of CD3AK [(64.85+/-18.13)% vs. (45.66+/-17.46)%, P<0.05; (63.80+/-9.93)% vs. (47.85+/-12.01)%, P<0.05]. CONCLUSIONS: The content of NO and activity of iNOS synthesized and excreted by CD3AK/iNOS cells are largely increased compared with those of CD3AK cells. CD3AK/iNOS cells have more significant cytotoxic activity to K562 and K562/ADM cells than CD3AK cells, but its cytotoxic activities to K562 and K562/ADM cells are similar.

[Purging effects of CD3AK/iNOS in vitro on primary leukemic cells from chronic myeloid leukemia patients].

To investigate the purging effect of CD3AK/iNOS on primary leukemic cells from chronic myeloid leukemia patients in vitro, amphotropic packaging cell line PA317 transfected with the whole length of iNOS gene was cultivated, amplified and screened by G418. The viral titer was determined by the NIH3T3 cells. Human peripheral blood mononuclear cells were isolated and activated by anti-CD3 monoclonal antibody in vitro. CD3AK cells were incubated with viral supernatant and selected by G418. Resistant clones were assayed for iNOS gene expression by RT-RCR. The content of nitric oxide and the activity of iNOS in the culture supernatant of CD3AK/iNOS were evaluated by the method of Griess. After BMMNC or PBMNC from CML patients were co-cultured with CD3AK/iNOS, CD3AK/Neo and CD3AK/iNOS respectively, the expression of bcr/abl fusion gene was detected by serial dilution semi-quantitative net RT-PCR assay. The results showed that anti-G418 positive packaging cell line PA317 transfected with the whole length of iNOS gene clones could stably synthesize and excrete recombinant retroviral vectors. The titer of recombinant retroviral vectors was 1.0 x 10(5) CFU/ml. After being transfected by recombinant retroviral supernatant, the iNOS cDNA was expressed in CD3AK/iNOS. The content of NO and activity of iNOS that synthesized and excreted by CD3AK/iNOS were notably increased, compared with those of CD3AK. There were statistically significant differences in NO content and iNOS activity between two groups. After BMMNC or PBMNC from CML patients were co-cultured with CD3AK/iNOS, CD3AK/Neo and CD3AK/iNOS respectively, the expression of bcr/abl fusion gene in all of them was down-regulated by serial dilution semi-quantitative RT-PCR assay. It is concluded that construction of CD3AK/iNOS can markedly increase the content of NO and the activity of iNOS, which can be more efficient in in vitro purging leukemia cells for autologous hematopoietic stem cell transplantation.

[Chronomodulated chemotherapy of oxaliplatin, 5-fluorouracil and folinic acid for advanced gastric cancer].

OBJECTIVE: The combination of oxaliplatin (L-OHP), 5-fluorouracil (5-Fu) and folinic acid (FA), being one of the effective regimens for advanced gastric cancer, is used in form of chronomodulated chemotherapy for advanced gastric cancer to investigate its efficacy and safety. METHODS: Twenty-six patients received a 4-day chronomodulated infusion of L-OHP, 5-Fu and FA. L-OHP (25 mg.m(-2).d(-1)) infused from 10:00 am to 22:00 pm, and followed by 5-Fu (600 mg.m(-2).d(-1)) and FA (300 mg.m(-2).d(-1)) from 22:00 pm to 10:00 am for 4 days using a multichannel programmable pump, every 2 weeks as an cycle for at least 2 cycles. RESULTS: Twenty-six patients with previously untreated advanced gastric cancer were eligible. Two complete and 13 partial remissions were observed with an overall response rate of 57.7%. Stable disease was observed in 6 patients (23.1%) and progressive disease in five (19.2%). Four of these patients underwent surgery. The median remission time was 3.5 months and time to tumor progression (TTP) was 4.5 months. The median overall survival time was 8 months. A total of 80 cycles were given without any grade 4 toxicity observed, but grade 3 thrombocytopenia (1.3%) and mucositis (1.3%) in one patient, two grade 3 neutropenia (2.5%) and nausea/vomiting (2.5%) in 2. CONCLUSION: Chronomodulated intravenous chemotherapy of oxaliplatin, 5-fluorouracil and folinic acid is effective and safe in the treatment of advanced gastric cancer.

Study on Bombyx mori silk treated by oxygen plasma.

Study of the morphology, aggregation structure and properties of Bombyx mori silk treated by low temperature oxygen plasma showed that slight flutes appeared on the surface of Bombyx mori silk fiber and that its surface structure changed after plasma treatment. The conformation also changed and crystalline degree decreased. The stannic filling rate of treated fiber was improved. Because of etching, the weight of the fiber decreased but the breaking strength changed little after short-time treatment.

[Effect of IL-6/sIL-6R on ex vivo expansion of human cord blood derived CD34+ cells].

BACKGROUND & OBJECTIVE: Hematopoietic stem cells (HSC) have the ability of regeneration, differentiation, and reconstructing hematopoietic function, and it is widely used in many fields such as hematopoietic stem cell transplantation, immune therapy, gene therapy and so on. Human cord blood (CB) is abundant of HSC. But a single collection of CB has only a limited amount of HCS and cannot fit the clinical and research use. Thus ex vivo expansion of human CB derived HSC is important. We know that there are some cytokines, which can synergize for enhancing the expansion of CB derived CD34(+) cells in vitro. Currently, some experiments have discovered that IL-6/sIL-6R or its chimera can enhance the ex vivo expansion of CD34(+)gp130+IL-6R- subpopulation. This study was designed to observe the effect of IL-6/sIL-6R on the ex vivo expansion of human CB derived CD34(+) cells, and explore the optimal cytokine combinations. METHODS: Human CB derived CD34(+) cells were isolated by Mini MACS and cultured in ex vivo liquid media in the presence of different cytokine cocktails for 7 or 14 days. After cultured on the seventh or the fourteenth day, the total number of the cultured cells were counted, the ratio of the CD34(+) cell were assayed by flow cytometry (FCM) and the number of it were calculated, and CFU-GM were cultured, then the effects of different cytokine combinations on the ex vivo expansion of CD34(+) cells were compared. In line with the different cytokine cocktails, our experiment divided into five groups: (A) control,(B) SCF,(C) IL-6/sIL-6R+SCF,(D) IL-6/sIL-6R+SCF+FL,and (E) SCF+FL. RESULTS: After cultured in vitro for 7 or 14 days, (1) the number of CD34(+) cells descended apparently in groups A and B; (2) the number of nucleated cells and CD34(+) cells after cultural on the seventh or the fourteenth day increased 7.1+/-2.4 folds, 39.0+/-14.0 folds; 1.8+/-0.7 folds, 4.8+/-2.4 folds, respectively in group C; 16.5+/-5.7 folds, 110.0+/-28.0 folds; 3.5+/-1.5 folds, 10.2+/-4.2 folds in Group D; 17.3+/-3.8 folds, 104.0+/-21.0 folds; 3.6+/-2.1folds, 8.4+/-3.5 folds in Group E. The expansion effects of group C, D, and E were all superior to the group A or B (P< 0.01). The expansion effects of group D and E were superior to group C (P< 0.01). But there was no difference between group D and E (P >0.05); (3) Adding the concentration of sIL-6R to 400 ng/ml, the number of nucleated and CD34(+) cells increased 24.0+/-4.8 folds and 5.6+/-1.2 folds in group D after cultured for seven days superior to group E (P< 0.05). CONCLUSION: IL-6/sIL-6R, SCF, FL can synergize for enhancing the ex vivo expansion of human CB derived CD34(+) cells. But this synergetic effect depends on the concentration of sIL-6R.