We present an integrated stand-alone software package named KaKs_Calculator 2.0 as an updated version. It incorporates 17 methods for the calculation of nonsynonymous and synonymous substitution rates; among them, we ...We present an integrated stand-alone software package named KaKs_Calculator 2.0 as an updated version. It incorporates 17 methods for the calculation of nonsynonymous and synonymous substitution rates; among them, we added our modified versions of several widely used methods as the gamma series including y-NG, y-LWL, ）,-MLWL, y-LPB, y-MLPB, y-YN and y-MYN, which have been demonstrated to perform better under certain conditions than their original forms and are not implemented in the previous version. The package is readily used for the identification of positively selected sites based on a sliding window across the sequences of interests in 5＇ to 3＇ direction of protein-coding sequences, and have improved the overall performance on sequence analysis for evolution studies. A toolbox, including C＋＋ and Java source code and executable files on both Windows and Linux platforms together with a user instruction, is downloadable from the website for academic purpose at https：//sourceforge.net/projects/kakscalculator2/.展开更多
Objective: To explore cell death and apoptosis in rat hippocampal neurons at different time points after ischemia, hypoxia and reperfusion injury and to elucidate time window characteristics in ischemia neuronal injur...Objective: To explore cell death and apoptosis in rat hippocampal neurons at different time points after ischemia, hypoxia and reperfusion injury and to elucidate time window characteristics in ischemia neuronal injury. Methods: Hippocampal neurons were obtained from rat embryo and were cultured in vitro. The ischemia and reperfusion of cultured rat hippocampal neurons were simulated by oxygen-glucose deprivation (OGD) and recovery. OGD at different time points ((0.25) h to (3.0) h) and then the same recovery (24 h) were prepared. Annexin (V-PI) staining and flow cytometry examined neuron death and apoptosis at different time after injury. Results: After OGD and recovery, both necrosis and apoptosis were observed. At different times after OGD, there were statistically significant differences in neuron necrosis rate (P<(0.05)), but not in apoptosis rate (P>(0.05)). At recovery, survival rate of hippocampal neurons further decreased while apoptosis rate increased. Furthermore, apoptosis rates of different time differed greatly (P<(0.05)). Apoptosis rate gradually increased with significant difference among those of different time points (P<(0.05)). However, 2 h after ischemia, apoptosis rate decreased markedly. Conclusions: Apoptosis is an important pathway of delayed neuron death. The therapeutic time window should be within 2 h after cerebral ischemia and hypoxia.展开更多
We report here geochemical data, U-Pb zircon ages, and Hf isotopes for the high-Mg diorites (HMDs), Nb-enriched basaltic porphyrys (NEBPs) and plagiogranites (PLAGs) in the Pingshui segment of the Jiangshan-Shaoxing s...We report here geochemical data, U-Pb zircon ages, and Hf isotopes for the high-Mg diorites (HMDs), Nb-enriched basaltic porphyrys (NEBPs) and plagiogranites (PLAGs) in the Pingshui segment of the Jiangshan-Shaoxing suture zone. The HMDs are characterized by high Mg# (>60), high Na and LREE contents, depletion of HREE and HFSE, and pronounced positive εNd(t) values of 7.0 to 7.7, similar to some adakitic high-Mg andesites. The NEBPs are relatively Na-rich (Na2O/K2O>6) and display high abundances of P2O5 (～1.00%), TiO2 (～3.08%) and HFSE (e.g., Nb=9.53–10.27 ppm). Their Nd isotopic compositions (εNd(t)=6.8–8.0) are comparable to those of the HMDs. The PLAGs are metaluminous (A/CNK=0.84–0.89) and sodic (Na2O/K2O>10). Their depletion in HFSE (e.g., Nb, Ta) is consistent with “SSZ-type” plagiogranite. Zircon LA-ICP-MS U-Pb dating yields an age of 932±7 Ma for the HMD, 916±6 Ma for the NEBP, and 902±5 Ma for the PLAG, respectively, indicating that they were products of early Neoproterozoic magmatism. The PLAGs exhibit relatively high zircon Hf isotopes and positive εHf(t) values of 11.0 to 16.2, consistent with their Nd isotopic data (εNd(t)=7.5–8.4). Such features are similar to those of oceanic plagiogranites in ophiolites and distinct from those of crust-derived granites. The PLAGs were most likely derived from partial melting of subducted oceanic crust in an active continental margin. Considering these results in the context of the regional geology, we suggest that a slab window in the subducting oceanic crust between the Yangtze Block and Cathaysia Block was possibly the principal cause for the unique arc magmatism in the area. The upwelling asthenosphere below the slab window may have provided significant thermodynamic conditions.展开更多
Objective To estimate the feasibility and the efficacy of early extubation and sequential non-invasive mechanical ventilation (MV) in chronic obstructive pulmonary disease (COPD) with exacerbated hypercapnic respirat...Objective To estimate the feasibility and the efficacy of early extubation and sequential non-invasive mechanical ventilation (MV) in chronic obstructive pulmonary disease (COPD) with exacerbated hypercapnic respiratory failure.Methods Twenty-two intubated COPD patients with severe hypercapnic respiratory failure due to pulmonary infection (pneumonia or purulent bronchitis) were involved in the study. At the time of pulmonary infection control window (PIC window) appeared, when pulmonary infection had been significantly controlled (resolution of fever and decrease in purulent sputum, radiographic infiltrations, and leukocytosis) after the antibiotic and the comprehensive therapy, the early extubation was conducted and followed by non-invasive MV via facial mask immediately in 11 cases (study group). Other 11 COPD cases with similar clinical characteristics who continuously received invasive MV after PIC window were recruited as control group.Results All patients had similar clinical characteristics and gas exchange before treatment, as well as the initiating time and all indices at the time of the PIC window. For study group and control group, the duration of invasive MV was (7.1±2.9) vs (23.0±14.0) days, respectively, P<0.01. The total duration of ventilatory support was (13±7) vs (23±14) days, respectively, P<0.05. The incidence of ventilator associated pneumonia (VAP) were 0/11 vs 6/11, respectively, P<0.01. The duration of intensive care unit (ICU) stay was (13±7) vs (26±14) days, respectively, P<0.05. Conclusions In COPD patients requiring intubation and MV for pulmonary infection and hypercapnic respiratory failure, early extubation followed by non-invasive MV initiated at the point of PIC window significantly decreases the invasive and total durations of ventilatory support, the risk of VAP, and the duration of ICU stay.展开更多
In this study, we established a Wistar rat model of right middle cerebral artery occlusion and observed pathological imaging changes （T2-weighted imaging [T2WI], T2FLAIR, and diffusion-weighted imaging [DWI]） follow...In this study, we established a Wistar rat model of right middle cerebral artery occlusion and observed pathological imaging changes （T2-weighted imaging [T2WI], T2FLAIR, and diffusion-weighted imaging [DWI]） following cerebral infarction. The pathological changes were divided into three phases： early cerebral infarction, middle cerebral infarction, and late cerebral infarction. In the early cerebral infarction phase （less than 2 hours post-infarction）, there was evidence of intracellular edema, which improved after reperfusion. This improvement was defined as the ischemic penumbra. In this phase, a high DWI signal and a low apparent diffusion coefficient were observed in the right basal ganglia region. By contrast, there were no abnormal T2WI and T2FLAIR signals. For the middle cerebral infarction phase （2-4 hours post-infarction）, a mixed edema was observed. After reperfusion, there was a mild improvement in cell edema, while the angioedema became more serious. A high DWI signal and a low apparent diffusion coefficient signal were observed, and some rats showed high T2WI and T2FLAIR signals. For the late cerebral infarction phase （4-6 hours post-infarction）, significant angioedema was visible in the infarction site. After reperfusion, there was a significant increase in angioedema, while there was evidence of hemorrhage and necrosis. A mixed signal was observed on DWI, while a high apparent diffusion coefficient signal, a high T2WI signal, and a high T2FLAIR signal were also observed. All 86 cerebral infarction patients were subjected to T2WI, T2FLAIR, and DWI. MRI results of clinic data similar to the early infarction phase of animal experiments were found in 51 patients, for which 10 patients （10/51） had an onset time greater than 6 hours. A total of 35 patients had MRI results similar to the middle and late infarction phase of animal experiments, of which eight patients （8/35） had an onset time less than 6 hours. These data suggest that defining the ＂therapeutic time window＂ as 展开更多
基金funded by the National Basic Research Program of China (973 Program) to JY (Grant No.2006CB910404)
文摘We present an integrated stand-alone software package named KaKs_Calculator 2.0 as an updated version. It incorporates 17 methods for the calculation of nonsynonymous and synonymous substitution rates; among them, we added our modified versions of several widely used methods as the gamma series including y-NG, y-LWL, ）,-MLWL, y-LPB, y-MLPB, y-YN and y-MYN, which have been demonstrated to perform better under certain conditions than their original forms and are not implemented in the previous version. The package is readily used for the identification of positively selected sites based on a sliding window across the sequences of interests in 5＇ to 3＇ direction of protein-coding sequences, and have improved the overall performance on sequence analysis for evolution studies. A toolbox, including C＋＋ and Java source code and executable files on both Windows and Linux platforms together with a user instruction, is downloadable from the website for academic purpose at https：//sourceforge.net/projects/kakscalculator2/.
文摘Objective: To explore cell death and apoptosis in rat hippocampal neurons at different time points after ischemia, hypoxia and reperfusion injury and to elucidate time window characteristics in ischemia neuronal injury. Methods: Hippocampal neurons were obtained from rat embryo and were cultured in vitro. The ischemia and reperfusion of cultured rat hippocampal neurons were simulated by oxygen-glucose deprivation (OGD) and recovery. OGD at different time points ((0.25) h to (3.0) h) and then the same recovery (24 h) were prepared. Annexin (V-PI) staining and flow cytometry examined neuron death and apoptosis at different time after injury. Results: After OGD and recovery, both necrosis and apoptosis were observed. At different times after OGD, there were statistically significant differences in neuron necrosis rate (P<(0.05)), but not in apoptosis rate (P>(0.05)). At recovery, survival rate of hippocampal neurons further decreased while apoptosis rate increased. Furthermore, apoptosis rates of different time differed greatly (P<(0.05)). Apoptosis rate gradually increased with significant difference among those of different time points (P<(0.05)). However, 2 h after ischemia, apoptosis rate decreased markedly. Conclusions: Apoptosis is an important pathway of delayed neuron death. The therapeutic time window should be within 2 h after cerebral ischemia and hypoxia.
基金Supported by China Geological Survey (Grant No. 1212010610611) the Ministry of Land and Resources (Grant No. 200811015)
文摘We report here geochemical data, U-Pb zircon ages, and Hf isotopes for the high-Mg diorites (HMDs), Nb-enriched basaltic porphyrys (NEBPs) and plagiogranites (PLAGs) in the Pingshui segment of the Jiangshan-Shaoxing suture zone. The HMDs are characterized by high Mg# (>60), high Na and LREE contents, depletion of HREE and HFSE, and pronounced positive εNd(t) values of 7.0 to 7.7, similar to some adakitic high-Mg andesites. The NEBPs are relatively Na-rich (Na2O/K2O>6) and display high abundances of P2O5 (～1.00%), TiO2 (～3.08%) and HFSE (e.g., Nb=9.53–10.27 ppm). Their Nd isotopic compositions (εNd(t)=6.8–8.0) are comparable to those of the HMDs. The PLAGs are metaluminous (A/CNK=0.84–0.89) and sodic (Na2O/K2O>10). Their depletion in HFSE (e.g., Nb, Ta) is consistent with “SSZ-type” plagiogranite. Zircon LA-ICP-MS U-Pb dating yields an age of 932±7 Ma for the HMD, 916±6 Ma for the NEBP, and 902±5 Ma for the PLAG, respectively, indicating that they were products of early Neoproterozoic magmatism. The PLAGs exhibit relatively high zircon Hf isotopes and positive εHf(t) values of 11.0 to 16.2, consistent with their Nd isotopic data (εNd(t)=7.5–8.4). Such features are similar to those of oceanic plagiogranites in ophiolites and distinct from those of crust-derived granites. The PLAGs were most likely derived from partial melting of subducted oceanic crust in an active continental margin. Considering these results in the context of the regional geology, we suggest that a slab window in the subducting oceanic crust between the Yangtze Block and Cathaysia Block was possibly the principal cause for the unique arc magmatism in the area. The upwelling asthenosphere below the slab window may have provided significant thermodynamic conditions.
文摘Objective To estimate the feasibility and the efficacy of early extubation and sequential non-invasive mechanical ventilation (MV) in chronic obstructive pulmonary disease (COPD) with exacerbated hypercapnic respiratory failure.Methods Twenty-two intubated COPD patients with severe hypercapnic respiratory failure due to pulmonary infection (pneumonia or purulent bronchitis) were involved in the study. At the time of pulmonary infection control window (PIC window) appeared, when pulmonary infection had been significantly controlled (resolution of fever and decrease in purulent sputum, radiographic infiltrations, and leukocytosis) after the antibiotic and the comprehensive therapy, the early extubation was conducted and followed by non-invasive MV via facial mask immediately in 11 cases (study group). Other 11 COPD cases with similar clinical characteristics who continuously received invasive MV after PIC window were recruited as control group.Results All patients had similar clinical characteristics and gas exchange before treatment, as well as the initiating time and all indices at the time of the PIC window. For study group and control group, the duration of invasive MV was (7.1±2.9) vs (23.0±14.0) days, respectively, P<0.01. The total duration of ventilatory support was (13±7) vs (23±14) days, respectively, P<0.05. The incidence of ventilator associated pneumonia (VAP) were 0/11 vs 6/11, respectively, P<0.01. The duration of intensive care unit (ICU) stay was (13±7) vs (26±14) days, respectively, P<0.05. Conclusions In COPD patients requiring intubation and MV for pulmonary infection and hypercapnic respiratory failure, early extubation followed by non-invasive MV initiated at the point of PIC window significantly decreases the invasive and total durations of ventilatory support, the risk of VAP, and the duration of ICU stay.
基金国家自然科学基金( the National Natural Science Foundation of China under Grant No60673153) 山东省自然科学基金( the NaturalScience Foundation of Shandong Province of China under Grant NoY2005G09)
基金supported by the National Natural Science Foundation of China,No.30960399,and No.81160181
文摘In this study, we established a Wistar rat model of right middle cerebral artery occlusion and observed pathological imaging changes （T2-weighted imaging [T2WI], T2FLAIR, and diffusion-weighted imaging [DWI]） following cerebral infarction. The pathological changes were divided into three phases： early cerebral infarction, middle cerebral infarction, and late cerebral infarction. In the early cerebral infarction phase （less than 2 hours post-infarction）, there was evidence of intracellular edema, which improved after reperfusion. This improvement was defined as the ischemic penumbra. In this phase, a high DWI signal and a low apparent diffusion coefficient were observed in the right basal ganglia region. By contrast, there were no abnormal T2WI and T2FLAIR signals. For the middle cerebral infarction phase （2-4 hours post-infarction）, a mixed edema was observed. After reperfusion, there was a mild improvement in cell edema, while the angioedema became more serious. A high DWI signal and a low apparent diffusion coefficient signal were observed, and some rats showed high T2WI and T2FLAIR signals. For the late cerebral infarction phase （4-6 hours post-infarction）, significant angioedema was visible in the infarction site. After reperfusion, there was a significant increase in angioedema, while there was evidence of hemorrhage and necrosis. A mixed signal was observed on DWI, while a high apparent diffusion coefficient signal, a high T2WI signal, and a high T2FLAIR signal were also observed. All 86 cerebral infarction patients were subjected to T2WI, T2FLAIR, and DWI. MRI results of clinic data similar to the early infarction phase of animal experiments were found in 51 patients, for which 10 patients （10/51） had an onset time greater than 6 hours. A total of 35 patients had MRI results similar to the middle and late infarction phase of animal experiments, of which eight patients （8/35） had an onset time less than 6 hours. These data suggest that defining the ＂therapeutic time window＂ as
