We have developed a web-server for predicting the folding rate of a protein based on its amino acid sequence information alone. The web- server is called Pred-PFR (Predicting Protein Folding Rate). Pred-PFR is feature...We have developed a web-server for predicting the folding rate of a protein based on its amino acid sequence information alone. The web- server is called Pred-PFR (Predicting Protein Folding Rate). Pred-PFR is featured by fusing multiple individual predictors, each of which is established based on one special feature derived from the protein sequence. The ensemble pre-dictor thus formed is superior to the individual ones, as demonstrated by achieving higher correlation coefficient and lower root mean square deviation between the predicted and observed results when examined by the jack-knife cross-validation on a benchmark dataset constructed recently. As a user-friendly web- server, Pred-PFR is freely accessible to the public at www.csbio.sjtu.edu.cn/bioinf/Folding Rate/.展开更多
Background: ESR and CRP measurements reflect different aspects of systemic inflammation. Generally, they are either elevated or depressed at the same time. This study was aimed at evaluating the clinical ability of th...Background: ESR and CRP measurements reflect different aspects of systemic inflammation. Generally, they are either elevated or depressed at the same time. This study was aimed at evaluating the clinical ability of these markers in the early diagnosis of pulmonary tuberculosis. Materials and Methods: A total of 50 (male 39, female 21) patients who tested positive to Acid Alcohol Fast Bacilli (AAFB) were studied. ESR and CRP values were estimated using standard procedures. Results: The mean ESR value among the AAFB positive patients was 53.16 ± 4.92 mm/hr while the CRP value was 0.273 ± 0.035 mg/L. Gender and age were not found to have any influence on the ESR and CRP values. No relationship was found to exist between ESR and CRP (r = 0.17;p = 0.235) and age (r = 0.125;p = 0.388). Conclusion: A moderately elevated ESR and low CRP values exist at the early diagnosis of tuberculosis. There is no correlation between ESR and CRP at the onset of tuberculosis;hence CRP cannot be used as a screening tool for early diagnosis of tuberculosis.展开更多
Chronic kidney disease (CKD) is a common health problem worldwide. CKD staging or classification, together with patients’ prognosis and treatment plan depend on the patients’ kidney function which is assessed by mea...Chronic kidney disease (CKD) is a common health problem worldwide. CKD staging or classification, together with patients’ prognosis and treatment plan depend on the patients’ kidney function which is assessed by measurement of glomerular filtration rate (GFR). Estimated GFR can be obtained using serum or plasma creatinine as a main variable in equations or formulae such as Cockcroft-Gault equation, MDRD equation (Modification of Diet in Renal Disease), the Schwartz and Counahan-Barratt formulae. These equations, though widely accepted, still have to be adjusted or validated among different groups of patients according to the variation in some factors such as race, diet, and genetic heterogenicity. Diet, especially the high protein load, can affect GFR representing the renal functional reserve. A high protein diet can cause an increase in GFR that lasts for many hours. Long-term consumption of vegetarian diet which is low in protein and contains only protein from plant sources can cause a low baseline GFR while the renal functional reserve is still preserved. This paper aims to remind of the role of protein diet effect on GFR measurement especially when assessing the renal function in vegetarians or individuals on long-term low-protein intake.展开更多
The DNA sequences of an organism play an important influence on its transcription and translation process, thus affecting its protein production and growth rate. Due to the com-plexity of DNA, it was extremely difficu...The DNA sequences of an organism play an important influence on its transcription and translation process, thus affecting its protein production and growth rate. Due to the com-plexity of DNA, it was extremely difficult to predict the macroscopic characteristics of or-ganisms. However, with the rapid development of machine learning in recent years, it be-comes possible to use powerful machine learning algorithms to process and analyze biolog-ical data. Based on the synthetic DNA sequences of a specific microbe, <em>E. coli</em>, I designed a process to predict its protein production and growth rate. By observing the properties of a data set constructed by previous work, I chose to use supervised learning regressors with encoded DNA sequences as input features to perform the predictions. After comparing different encoders and algorithms, I selected three encoders to encode the DNA sequences as inputs and trained seven different regressors to predict the outputs. The hy-per-parameters are optimized for three regressors which have the best potential prediction performance. Finally, I successfully predicted the protein production and growth rates, with the best <em>R</em><sup><em>2</em></sup> score 0.55 and 0.77, respectively, by using encoders to catch the potential fea-tures from the DNA sequences.展开更多
It is a challenging task to investigate the different in- fluence of long-range and short-range interactions on two-state and three-state folding kinetics of protein. The networks of the 30 two-state proteins and 15 t...It is a challenging task to investigate the different in- fluence of long-range and short-range interactions on two-state and three-state folding kinetics of protein. The networks of the 30 two-state proteins and 15 three-state proteins were constructed by complex networks analysis at three length scales: Protein Contact Networks, Long-range Interaction Networks and Short-range Interaction Networks. To uncover the relationship between structural properties and folding kinetics of the proteins, the correlations of protein network parameters with protein folding rate and topology parameters contact order were analyzed. The results show that Protein Contact Networks and Short-range Interaction Networks (for both two-state and three-state proteins) exhibit the “small-world” property and Long-range Interaction networks indicate “scale-free” behavior. Our results further indicate that all Protein Contact Networks and Short- range Interaction networks are assortative type. While some of Long-range Interaction Networks are of assortative type, the others are of disassortative type. For two-state proteins, the clustering coefficients of Short-range Interaction Networks show prominent correlation with folding rate and contact order. The assortativity coefficients of Short-range Interaction Networks also show remarkable correlation with folding rate and contact order. Similar correlations exist in Protein Contact Networks of three-state proteins. For two-state proteins, the correlation between contact order and folding rate is determined by the numbers of local contacts. Short- range interactions play a key role in determining the connecting trend among amino acids and they impact the folding rate of two-state proteins directly. For three-state proteins, the folding rate is determined by short-range and long-range interactions among residues together.展开更多
文摘We have developed a web-server for predicting the folding rate of a protein based on its amino acid sequence information alone. The web- server is called Pred-PFR (Predicting Protein Folding Rate). Pred-PFR is featured by fusing multiple individual predictors, each of which is established based on one special feature derived from the protein sequence. The ensemble pre-dictor thus formed is superior to the individual ones, as demonstrated by achieving higher correlation coefficient and lower root mean square deviation between the predicted and observed results when examined by the jack-knife cross-validation on a benchmark dataset constructed recently. As a user-friendly web- server, Pred-PFR is freely accessible to the public at www.csbio.sjtu.edu.cn/bioinf/Folding Rate/.
文摘Background: ESR and CRP measurements reflect different aspects of systemic inflammation. Generally, they are either elevated or depressed at the same time. This study was aimed at evaluating the clinical ability of these markers in the early diagnosis of pulmonary tuberculosis. Materials and Methods: A total of 50 (male 39, female 21) patients who tested positive to Acid Alcohol Fast Bacilli (AAFB) were studied. ESR and CRP values were estimated using standard procedures. Results: The mean ESR value among the AAFB positive patients was 53.16 ± 4.92 mm/hr while the CRP value was 0.273 ± 0.035 mg/L. Gender and age were not found to have any influence on the ESR and CRP values. No relationship was found to exist between ESR and CRP (r = 0.17;p = 0.235) and age (r = 0.125;p = 0.388). Conclusion: A moderately elevated ESR and low CRP values exist at the early diagnosis of tuberculosis. There is no correlation between ESR and CRP at the onset of tuberculosis;hence CRP cannot be used as a screening tool for early diagnosis of tuberculosis.
文摘Chronic kidney disease (CKD) is a common health problem worldwide. CKD staging or classification, together with patients’ prognosis and treatment plan depend on the patients’ kidney function which is assessed by measurement of glomerular filtration rate (GFR). Estimated GFR can be obtained using serum or plasma creatinine as a main variable in equations or formulae such as Cockcroft-Gault equation, MDRD equation (Modification of Diet in Renal Disease), the Schwartz and Counahan-Barratt formulae. These equations, though widely accepted, still have to be adjusted or validated among different groups of patients according to the variation in some factors such as race, diet, and genetic heterogenicity. Diet, especially the high protein load, can affect GFR representing the renal functional reserve. A high protein diet can cause an increase in GFR that lasts for many hours. Long-term consumption of vegetarian diet which is low in protein and contains only protein from plant sources can cause a low baseline GFR while the renal functional reserve is still preserved. This paper aims to remind of the role of protein diet effect on GFR measurement especially when assessing the renal function in vegetarians or individuals on long-term low-protein intake.
文摘The DNA sequences of an organism play an important influence on its transcription and translation process, thus affecting its protein production and growth rate. Due to the com-plexity of DNA, it was extremely difficult to predict the macroscopic characteristics of or-ganisms. However, with the rapid development of machine learning in recent years, it be-comes possible to use powerful machine learning algorithms to process and analyze biolog-ical data. Based on the synthetic DNA sequences of a specific microbe, <em>E. coli</em>, I designed a process to predict its protein production and growth rate. By observing the properties of a data set constructed by previous work, I chose to use supervised learning regressors with encoded DNA sequences as input features to perform the predictions. After comparing different encoders and algorithms, I selected three encoders to encode the DNA sequences as inputs and trained seven different regressors to predict the outputs. The hy-per-parameters are optimized for three regressors which have the best potential prediction performance. Finally, I successfully predicted the protein production and growth rates, with the best <em>R</em><sup><em>2</em></sup> score 0.55 and 0.77, respectively, by using encoders to catch the potential fea-tures from the DNA sequences.
文摘It is a challenging task to investigate the different in- fluence of long-range and short-range interactions on two-state and three-state folding kinetics of protein. The networks of the 30 two-state proteins and 15 three-state proteins were constructed by complex networks analysis at three length scales: Protein Contact Networks, Long-range Interaction Networks and Short-range Interaction Networks. To uncover the relationship between structural properties and folding kinetics of the proteins, the correlations of protein network parameters with protein folding rate and topology parameters contact order were analyzed. The results show that Protein Contact Networks and Short-range Interaction Networks (for both two-state and three-state proteins) exhibit the “small-world” property and Long-range Interaction networks indicate “scale-free” behavior. Our results further indicate that all Protein Contact Networks and Short- range Interaction networks are assortative type. While some of Long-range Interaction Networks are of assortative type, the others are of disassortative type. For two-state proteins, the clustering coefficients of Short-range Interaction Networks show prominent correlation with folding rate and contact order. The assortativity coefficients of Short-range Interaction Networks also show remarkable correlation with folding rate and contact order. Similar correlations exist in Protein Contact Networks of three-state proteins. For two-state proteins, the correlation between contact order and folding rate is determined by the numbers of local contacts. Short- range interactions play a key role in determining the connecting trend among amino acids and they impact the folding rate of two-state proteins directly. For three-state proteins, the folding rate is determined by short-range and long-range interactions among residues together.
