This paper investigates particle transportation using a numerical model application approach to understand the final fate of suspended sediment particle masses due to a dredging operation in a navigational harbor inle...This paper investigates particle transportation using a numerical model application approach to understand the final fate of suspended sediment particle masses due to a dredging operation in a navigational harbor inlet using PTM (Particle Tracking Model). The investigation applied PTM and simulated particle transportation at a navigational harbor called St Jerome Creek Inlet in Chesapeake Bay in Maryland. The United States Army Corps of Engineers (USACE), Maryland District, designed jetties for the inlet, which, when constructed, would minimize dredging requirements from once in a two-year period to once in a ten-year period. In the meantime, due to the frequent dredging requirements of the inlet, there exists a need to understand the fate of the suspended sediments from the dredging operations to assess the environmental impact on the aquatic environment and the coastal community. This study used PTM to simulate the transportation of sediments in a 30-day period during a dredging operation. Ten sediment source locations were selected as possible sites from which dredged materials could be introduced into the flow system. The model output was analyzed to draw conclusions. Results showed that most suspended sediment particle masses moved from their initial site locations and settled along the shoreline, whilst the sediments that found their way out of the inlet system towards the ocean migrated southward and settled approximately 6 miles at the tip of the mainland. The objective of the study is to track sediment particles from a dredging operation. This would be significant in tracking possible contaminants in an aquatic environment for future environmental management decisions.展开更多
Post-translational modification (PTM) increases the functional diversity of proteins by introducing new functional groups to the side chain of amino acid of a protein. Among all amino acid residues, the side chain of ...Post-translational modification (PTM) increases the functional diversity of proteins by introducing new functional groups to the side chain of amino acid of a protein. Among all amino acid residues, the side chain of lysine (K) can undergo many types of PTM, called K-PTM, such as “acetylation”, “crotonylation”, “methylation” and “succinylation” and also responsible for occurring multiple PTM in the same lysine of a protein which leads to the requirement of multi-label PTM site identification. However, most of the existing computational methods have been established to predict various single-label PTM sites and a very few have been developed to solve multi-label issue which needs further improvement. Here, we have developed a computational tool termed mLysPTMpred to predict multi-label lysine PTM sites by 1) incorporating the sequence-coupled information into the general pseudo amino acid composition, 2) balancing the effect of skewed training dataset by Different Error Cost method, and 3) constructing a multi-label predictor using a combination of support vector machine (SVM). This predictor achieved 83.73% accuracy in predicting the multi-label PTM site of K-PTM types. Moreover, all the experimental results along with accuracy outperformed than the existing predictor iPTM-mLys. A user-friendly web server of mLysPTMpred is available at http://research.ru.ac.bd/mLysPTMpred/.展开更多
目的:探讨并分析超声造影时间-强度曲线参数达峰时间(TTP)与平均渡越时间(MTT)的乘积(Product of TTP and MTT,PTM)和剪切波弹性成像速度(VTQ)测定在鉴别诊断肝血管瘤与肝细胞癌(HCC)中的应用价值。方法:将2014年12月至2019年2月期间川...目的:探讨并分析超声造影时间-强度曲线参数达峰时间(TTP)与平均渡越时间(MTT)的乘积(Product of TTP and MTT,PTM)和剪切波弹性成像速度(VTQ)测定在鉴别诊断肝血管瘤与肝细胞癌(HCC)中的应用价值。方法:将2014年12月至2019年2月期间川北医学院收治的20例HCC患者(其病情均经病理检查得到确诊)、20例肝血管瘤患者(其病情均经影像学检查得到确诊)和20例进行体检的健康人作为研究对象。将其中20例HCC患者设为HCC组,将其中20例肝血管瘤患者设为肝血管瘤组,将其中20例健康人设为对照组。对这三组研究对象均进行超声造影检查和超声剪切波弹性成像检查,然后测定并比较其PTM与VTQ。结果:HCC组患者的PTM小于肝血管瘤组患者与对照组健康人,差异有统计学意义,P<0.017。对照组健康人的PTM小于肝血管瘤组患者,差异有统计学意义,P<0.017。HCC组患者的VTQ大于肝血管瘤组患者与对照组健康人,差异有统计学意义,P<0.017。肝血管瘤组患者的VTQ大于对照组健康人,差异有统计学意义,P<0.017。结论:HCC患者与肝血管瘤患者的PTM与VTQ存在较大的差异,通过测定和比较PTM与VTQ可为临床上鉴别诊断肝血管瘤与HCC提供一定的依据。展开更多
CART(Constituent-oriented age and residence time theory) and PTM(Particle-tracking method) are two widely used numerical methods to calculate water age. These two methods are essentially equivalent in theory but their...CART(Constituent-oriented age and residence time theory) and PTM(Particle-tracking method) are two widely used numerical methods to calculate water age. These two methods are essentially equivalent in theory but their results may be different in practice. The difference of the two methods was evaluated by applying them to calculate water age in an idealized one-dimensional domain. The model results by the two methods are consistent with each other in the case with either spatially uniform flow field or spatially uniform diffusion coefficient. If we allow the spatial variation in horizontal diffusion, a term called pseudo displacement arising from the spatial variation of diffusion coefficient likely plays an important role for the PTM to obtain accurate water age. In particular, if the water particle is released at a place where the diffusion is not the weakest, the water age calculated by the PTM without pseudo displacement is much larger than that by the CART. This suggests that the pseudo displacement cannot be neglected in the PTM to calculate water age in a realistic ocean. As an example, we present its potential importance in the Bohai Sea where the diffusion coefficient varies spatially and greatly.展开更多
文摘This paper investigates particle transportation using a numerical model application approach to understand the final fate of suspended sediment particle masses due to a dredging operation in a navigational harbor inlet using PTM (Particle Tracking Model). The investigation applied PTM and simulated particle transportation at a navigational harbor called St Jerome Creek Inlet in Chesapeake Bay in Maryland. The United States Army Corps of Engineers (USACE), Maryland District, designed jetties for the inlet, which, when constructed, would minimize dredging requirements from once in a two-year period to once in a ten-year period. In the meantime, due to the frequent dredging requirements of the inlet, there exists a need to understand the fate of the suspended sediments from the dredging operations to assess the environmental impact on the aquatic environment and the coastal community. This study used PTM to simulate the transportation of sediments in a 30-day period during a dredging operation. Ten sediment source locations were selected as possible sites from which dredged materials could be introduced into the flow system. The model output was analyzed to draw conclusions. Results showed that most suspended sediment particle masses moved from their initial site locations and settled along the shoreline, whilst the sediments that found their way out of the inlet system towards the ocean migrated southward and settled approximately 6 miles at the tip of the mainland. The objective of the study is to track sediment particles from a dredging operation. This would be significant in tracking possible contaminants in an aquatic environment for future environmental management decisions.
文摘Post-translational modification (PTM) increases the functional diversity of proteins by introducing new functional groups to the side chain of amino acid of a protein. Among all amino acid residues, the side chain of lysine (K) can undergo many types of PTM, called K-PTM, such as “acetylation”, “crotonylation”, “methylation” and “succinylation” and also responsible for occurring multiple PTM in the same lysine of a protein which leads to the requirement of multi-label PTM site identification. However, most of the existing computational methods have been established to predict various single-label PTM sites and a very few have been developed to solve multi-label issue which needs further improvement. Here, we have developed a computational tool termed mLysPTMpred to predict multi-label lysine PTM sites by 1) incorporating the sequence-coupled information into the general pseudo amino acid composition, 2) balancing the effect of skewed training dataset by Different Error Cost method, and 3) constructing a multi-label predictor using a combination of support vector machine (SVM). This predictor achieved 83.73% accuracy in predicting the multi-label PTM site of K-PTM types. Moreover, all the experimental results along with accuracy outperformed than the existing predictor iPTM-mLys. A user-friendly web server of mLysPTMpred is available at http://research.ru.ac.bd/mLysPTMpred/.
文摘目的:探讨并分析超声造影时间-强度曲线参数达峰时间(TTP)与平均渡越时间(MTT)的乘积(Product of TTP and MTT,PTM)和剪切波弹性成像速度(VTQ)测定在鉴别诊断肝血管瘤与肝细胞癌(HCC)中的应用价值。方法:将2014年12月至2019年2月期间川北医学院收治的20例HCC患者(其病情均经病理检查得到确诊)、20例肝血管瘤患者(其病情均经影像学检查得到确诊)和20例进行体检的健康人作为研究对象。将其中20例HCC患者设为HCC组,将其中20例肝血管瘤患者设为肝血管瘤组,将其中20例健康人设为对照组。对这三组研究对象均进行超声造影检查和超声剪切波弹性成像检查,然后测定并比较其PTM与VTQ。结果:HCC组患者的PTM小于肝血管瘤组患者与对照组健康人,差异有统计学意义,P<0.017。对照组健康人的PTM小于肝血管瘤组患者,差异有统计学意义,P<0.017。HCC组患者的VTQ大于肝血管瘤组患者与对照组健康人,差异有统计学意义,P<0.017。肝血管瘤组患者的VTQ大于对照组健康人,差异有统计学意义,P<0.017。结论:HCC患者与肝血管瘤患者的PTM与VTQ存在较大的差异,通过测定和比较PTM与VTQ可为临床上鉴别诊断肝血管瘤与HCC提供一定的依据。
基金funded by the National Natural Science Foundation of China (Nos. 41176007 and 40706007)
文摘CART(Constituent-oriented age and residence time theory) and PTM(Particle-tracking method) are two widely used numerical methods to calculate water age. These two methods are essentially equivalent in theory but their results may be different in practice. The difference of the two methods was evaluated by applying them to calculate water age in an idealized one-dimensional domain. The model results by the two methods are consistent with each other in the case with either spatially uniform flow field or spatially uniform diffusion coefficient. If we allow the spatial variation in horizontal diffusion, a term called pseudo displacement arising from the spatial variation of diffusion coefficient likely plays an important role for the PTM to obtain accurate water age. In particular, if the water particle is released at a place where the diffusion is not the weakest, the water age calculated by the PTM without pseudo displacement is much larger than that by the CART. This suggests that the pseudo displacement cannot be neglected in the PTM to calculate water age in a realistic ocean. As an example, we present its potential importance in the Bohai Sea where the diffusion coefficient varies spatially and greatly.
