In this paper, the authors present three different algorithms for data clustering. These are Self-Organizing Map （SOM）, Neural Gas （NG） and Fuzzy C-Means （FCM） algorithms. SOM and NG algorithms are based on comp...In this paper, the authors present three different algorithms for data clustering. These are Self-Organizing Map （SOM）, Neural Gas （NG） and Fuzzy C-Means （FCM） algorithms. SOM and NG algorithms are based on competitive leaming. An important property of these algorithms is that they preserve the topological structure of data. This means that data that is close in input distribution is mapped to nearby locations in the network. The FCM algorithm is an algorithm based on soft clustering which means that the different clusters are not necessarily distinct, but may overlap. This clustering method may be very useful in many biological problems, for instance in genetics, where a gene may belong to different clusters. The different algorithms are compared in terms of their visualization of the clustering of proteomic data.展开更多
This work demonstrates the so-called PCAC (Protein principal Component Analysis Clustering) method, which clusters large-scale decoy protein structures in protein structure prediction based on principal component anal...This work demonstrates the so-called PCAC (Protein principal Component Analysis Clustering) method, which clusters large-scale decoy protein structures in protein structure prediction based on principal component analysis (PCA), is an ultra-fast and low-memory-requiring clustering method. It can be two orders of magnitude faster than the commonlyused pairwise rmsd-clustering (pRMSD) when enormous of decoys are involved. Instead of N(N – 1)/2 least-square fitting of rmsd calculations and N2 memory units to store the pairwise rmsd values in pRMSD, PCAC only requires N rmsd calculations and N × P memory storage, where N is the number of structures to be clustered and P is the number of preserved eigenvectors. Furthermore, PCAC based on the covariance Cartesian matrix generates essentially the identical result as that from the reference rmsd-clustering (rRMSD). From a test of 41 protein decoy sets, when the eigenvectors that contribute a total of 90% eigenvalues are preserved, PCAC method reproduces the results of near-native selections from rRMSD.展开更多
BACKGROUND Cardiopulmonary bypass(CPB)is a common procedure in cardiac surgery.CPB is a high-risk factor for acute kidney injury(AKI),and diabetes is also such a factor.Diabetes can lead to copper overload.It is curre...BACKGROUND Cardiopulmonary bypass(CPB)is a common procedure in cardiac surgery.CPB is a high-risk factor for acute kidney injury(AKI),and diabetes is also such a factor.Diabetes can lead to copper overload.It is currently unclear whether AKI after CPB in diabetic patients is related to copper overload.AIM To explore whether the occurrence of CPB-AKI in diabetic patients is associated with cuproptosis.METHODS Blood and urine were collected from clinical diabetic and non-diabetic patients before and after CPB.Levels of copper ion,lactate,glucose,heat shock protein-70(HSP-70),and dihydrolipoamide dehydrogenase(DLAT)were determined.A diabetic rat model was established and CPB was performed.The rats were assessed for the development of CPB-AKI,and for the association of AKI with cuproptosis by detecting copper levels,iron-sulfur cluster proteins and observation of mitochondrial structure by electron microscopy.RESULTS CPB resulted in elevations of copper,lactate,HSP-70 and DLAT in blood and urine in both diabetic and nondiabetic patients.CPB was associated with pathologic and mitochondrial damage in the kidneys of diabetic rats.Cuproptosis-related proteins also appeared to be significantly reduced.CONCLUSION CPB-AKI is associated with cuproptosis.Diabetes mellitus is an important factor aggravating CPB-AKI and cuproptosis.展开更多
Clustering is a basic event for the initiation of immune cell responses, and simulation analyses of clustering of membrane proteins have been performed. It was claimed that a cluster is formed by the self-assembly ind...Clustering is a basic event for the initiation of immune cell responses, and simulation analyses of clustering of membrane proteins have been performed. It was claimed that a cluster is formed by the self-assembly induced by protein dimerization with a high binding speed (Woolf and Linderman, Biophys. Chem. 104, 217-227, 2003). We examined the cluster formation with Monte Carlo simulation using two algorithms. The first was that simulation processes were divided into two substeps. All proteins were subjected to movement in the first substep, followed by reaction in the second substep. The second algorithm was that proteins were first selected to react and proteins which did not react were subjected to movement. The self-assembly induced by dimerization was simulated only with the second algorithm. In this algorithm, monomers dissociated from dimers do not move because these monomers are not selected for movement, and a large proportion of such monomers are selected to form dimers in the next step. The self-assembly was again simulated with the first algorithm containing the conditions that monomers dissociated from dimers did not move in the next movement substep. This algorithm seems to be far removed from natural conditions. Thus, it is inferred that the self-assembly induced by dimerization is unlikely in situ, and that some interaction between proteins is required for cluster formation. In contrast to algorithms in previous simulations, our results suggest that it is more appropriate that proteins move to the same direction for a while and reflect when the collision occurs.展开更多
Soymilk is one of the most available beverages, an alternative to dairy milk and is recognized for its nutritional value. The nutritional quality, the presence of anti-nutritional factors, isoflavones and sensory acce...Soymilk is one of the most available beverages, an alternative to dairy milk and is recognized for its nutritional value. The nutritional quality, the presence of anti-nutritional factors, isoflavones and sensory acceptability of soymilk depended on the soybean variety as well as the processing conditions. The soymilks from conventional and specialty Brazilian soybean cultivars were compared regarding the composition and consumer acceptance. There were significant differences on the protein, oil, sugars, isoflavones, presence of anti-nutritional factors (phytate and trypsin inhibitor activity) and NSI (nitrogen solubility index) among cultivars and soymilks and for sensory acceptance of soymilks. The preference mapping and cluster analysis identified three different segments of consumers. The soymilk from the conventional cultivar BRS284 achieved higher and similar acceptance score for the three consumer’s segments while the lipoxygenase free cultivars (BRS213 and BRS257) and specialty cultivar BRS216 showed higher score for two segments of consumers. The sensory evaluation of soymilk from different soybean cultivars could improve consumer uptake.展开更多
文摘In this paper, the authors present three different algorithms for data clustering. These are Self-Organizing Map （SOM）, Neural Gas （NG） and Fuzzy C-Means （FCM） algorithms. SOM and NG algorithms are based on competitive leaming. An important property of these algorithms is that they preserve the topological structure of data. This means that data that is close in input distribution is mapped to nearby locations in the network. The FCM algorithm is an algorithm based on soft clustering which means that the different clusters are not necessarily distinct, but may overlap. This clustering method may be very useful in many biological problems, for instance in genetics, where a gene may belong to different clusters. The different algorithms are compared in terms of their visualization of the clustering of proteomic data.
文摘This work demonstrates the so-called PCAC (Protein principal Component Analysis Clustering) method, which clusters large-scale decoy protein structures in protein structure prediction based on principal component analysis (PCA), is an ultra-fast and low-memory-requiring clustering method. It can be two orders of magnitude faster than the commonlyused pairwise rmsd-clustering (pRMSD) when enormous of decoys are involved. Instead of N(N – 1)/2 least-square fitting of rmsd calculations and N2 memory units to store the pairwise rmsd values in pRMSD, PCAC only requires N rmsd calculations and N × P memory storage, where N is the number of structures to be clustered and P is the number of preserved eigenvectors. Furthermore, PCAC based on the covariance Cartesian matrix generates essentially the identical result as that from the reference rmsd-clustering (rRMSD). From a test of 41 protein decoy sets, when the eigenvectors that contribute a total of 90% eigenvalues are preserved, PCAC method reproduces the results of near-native selections from rRMSD.
基金Supported by the Natural Science Foundation of Heilongjiang Province,No.LH2022H035the First Affiliated Hospital of Harbin Medical University Foundation,No.2024JQ14.
文摘BACKGROUND Cardiopulmonary bypass(CPB)is a common procedure in cardiac surgery.CPB is a high-risk factor for acute kidney injury(AKI),and diabetes is also such a factor.Diabetes can lead to copper overload.It is currently unclear whether AKI after CPB in diabetic patients is related to copper overload.AIM To explore whether the occurrence of CPB-AKI in diabetic patients is associated with cuproptosis.METHODS Blood and urine were collected from clinical diabetic and non-diabetic patients before and after CPB.Levels of copper ion,lactate,glucose,heat shock protein-70(HSP-70),and dihydrolipoamide dehydrogenase(DLAT)were determined.A diabetic rat model was established and CPB was performed.The rats were assessed for the development of CPB-AKI,and for the association of AKI with cuproptosis by detecting copper levels,iron-sulfur cluster proteins and observation of mitochondrial structure by electron microscopy.RESULTS CPB resulted in elevations of copper,lactate,HSP-70 and DLAT in blood and urine in both diabetic and nondiabetic patients.CPB was associated with pathologic and mitochondrial damage in the kidneys of diabetic rats.Cuproptosis-related proteins also appeared to be significantly reduced.CONCLUSION CPB-AKI is associated with cuproptosis.Diabetes mellitus is an important factor aggravating CPB-AKI and cuproptosis.
文摘Clustering is a basic event for the initiation of immune cell responses, and simulation analyses of clustering of membrane proteins have been performed. It was claimed that a cluster is formed by the self-assembly induced by protein dimerization with a high binding speed (Woolf and Linderman, Biophys. Chem. 104, 217-227, 2003). We examined the cluster formation with Monte Carlo simulation using two algorithms. The first was that simulation processes were divided into two substeps. All proteins were subjected to movement in the first substep, followed by reaction in the second substep. The second algorithm was that proteins were first selected to react and proteins which did not react were subjected to movement. The self-assembly induced by dimerization was simulated only with the second algorithm. In this algorithm, monomers dissociated from dimers do not move because these monomers are not selected for movement, and a large proportion of such monomers are selected to form dimers in the next step. The self-assembly was again simulated with the first algorithm containing the conditions that monomers dissociated from dimers did not move in the next movement substep. This algorithm seems to be far removed from natural conditions. Thus, it is inferred that the self-assembly induced by dimerization is unlikely in situ, and that some interaction between proteins is required for cluster formation. In contrast to algorithms in previous simulations, our results suggest that it is more appropriate that proteins move to the same direction for a while and reflect when the collision occurs.
文摘Soymilk is one of the most available beverages, an alternative to dairy milk and is recognized for its nutritional value. The nutritional quality, the presence of anti-nutritional factors, isoflavones and sensory acceptability of soymilk depended on the soybean variety as well as the processing conditions. The soymilks from conventional and specialty Brazilian soybean cultivars were compared regarding the composition and consumer acceptance. There were significant differences on the protein, oil, sugars, isoflavones, presence of anti-nutritional factors (phytate and trypsin inhibitor activity) and NSI (nitrogen solubility index) among cultivars and soymilks and for sensory acceptance of soymilks. The preference mapping and cluster analysis identified three different segments of consumers. The soymilk from the conventional cultivar BRS284 achieved higher and similar acceptance score for the three consumer’s segments while the lipoxygenase free cultivars (BRS213 and BRS257) and specialty cultivar BRS216 showed higher score for two segments of consumers. The sensory evaluation of soymilk from different soybean cultivars could improve consumer uptake.
