AIM： To investigate the association between the configurational and compositional changes of nuclear matrix and the differentiation of carcinoma cells. METHODS： Cells cultured with or without 5 × 10^-3 mmol/L o...AIM： To investigate the association between the configurational and compositional changes of nuclear matrix and the differentiation of carcinoma cells. METHODS： Cells cultured with or without 5 × 10^-3 mmol/L of hexamethylene bisacetamide （HMBA） on Nickel grids were treated by selective extraction and prepared for whole mount observation under electron microscopy. The samples were examined under transmission electron microscope. Nuclear matrix proteins were selectively extracted and subjected to subcellular proteomics study. The protein expression patterns were analyzed by PDQuest software. Spots of differentially expressed nuclear matrix proteins were excised and subjected to in situ digestion with trypsin. The peptides were analyzed by matrix-assisted laser- desorption/ionization time of flight mass spectrometry （MALDI-TOF-MS）. Data were submitted for database searching using Mascot tool （www.matrixscience.com）. RESULTS： The nuclear matrix （NM） and intermediate filament （IF） in SMMC-7721 hepatocarcinoma cells were found relatively sparse and arranged irregularly. The nuclear lamina was non-uniform, and two kinds of filaments were not tightly connected. After induction for differentiation by HMBA, the NM-IF filaments were concentrated and distributed uniformly. The heterogeneous population of filaments, including highly branched utrathin filaments could also be seen in the regular meshwork. The connection between the two kinds of filaments and the relatively thin, condensed and sharply demarcated lamina composed of intermediate- sized filaments was relatively fastened. Meanwhile, 21 NM proteins changed remarkably during SMMC-7721 cell differentiation. Four proteins, i.e. mutant Pystl, hypothetical protein, nucleophosminl, and LBP were downregulated, whereas four other proteins, eIF6, p44 subunit, 13-tubulin, and SIN3B were upregulated with the last one, SR2/ASF found only in the differentiated SMMC-7721 cells. CONCLUSION： The induced differentiation of SMMC-7721 cells by HMBA is accompanied by the configurational changes of nuclear matrix-intermediate filament （NM-IF） system and the compositional changes of nuclear matrix protein expression. These changes may be important morphological or functional indications of the cancer cell reversion.展开更多
Communication and coordination between OSS developers who do not work physically in the same location have always been the challenging issues.The pull-based development model,as the state-of-art collaborative developm...Communication and coordination between OSS developers who do not work physically in the same location have always been the challenging issues.The pull-based development model,as the state-of-art collaborative development mechanism,provides high openness and transparency to improve the visibility of contributors'work.However,duplicate contributions may still be submitted by more than one contributors to solve the same problem due to the parallel and uncoordinated nature of this model.If not detected in time,duplicate pull-requests can cause contributors and reviewers to waste time and energy on redundant work.In this paper,we propose an approach combining textual and change similarities to automatically detect duplicate contributions in pull-based model at submission time.For a new-arriving contribution,we first compute textual similarity and change similarity between it and other existing contributions.And then our method returns a list of candidate duplicate contributions that are most similar with the new contribution in terms of the combined textual and change similarity.The evaluation shows that 83.4%of the duplicates can be found in average when we use the combined textual and change similarity compared to 54.8%using only textual similarity and 78.2%using only change similarity.展开更多
Human osteosarcoma MG-63 cells were induced into differentiation by 5 mmol/L hexamethylene bisacetamide （HMBA）. Their nuclear matrix proteins （NMPs） were selectively extracted and subjected to two-dimensional gel ...Human osteosarcoma MG-63 cells were induced into differentiation by 5 mmol/L hexamethylene bisacetamide （HMBA）. Their nuclear matrix proteins （NMPs） were selectively extracted and subjected to two-dimensional gel electrophoresis analysis. The results of protein patterns were analyzed by Melanie software. The spots of differentially expressed NMPs were excised and subjected to in situ digestion with trypsin. The maps of peptide mass fingerprinting were obtained by MALDI-TOF-MS analysis, and were submitted for NCBI database searches by Mascot tool. There were twelve spots changed remarkably during the differentiation induced by HMBA, nine of which were identified. The roles of the regulated proteins during the MG-63 differentiation were analyzed. This study suggests that the induced differentiation of cancer cells is accompanied by the changes of NMPs, and confirms the presence of some specific NMPs related to the cancer cell proliferation and differentiation. The changed NMPs are potential markers for cancer diagnosis or targets for cancer therapy.展开更多
Code reviews in pull-based model are open to community users on GitHub. Various participants are taking part in the review discussions and the review topics are not only about the improvement of code contributions but...Code reviews in pull-based model are open to community users on GitHub. Various participants are taking part in the review discussions and the review topics are not only about the improvement of code contributions but also about project evolution and social interaction. A comprehensive understanding of the review topics in pull-based model would be useful to better organize the code review process and optimize review tasks such as reviewer recommendation and pull-request prioritization. In this paper, we first conduct a qualitative study on three popular open-source software projects hosted on GitHub and construct a fine-grained two-level taxonomy covering four level-1 categories （code correctness, pull- request decision-making, project management, and social interaction） and 11 level-2 subcategories （e.g., defect detecting, reviewer assigning, contribution encouraging）. Second, we conduct preliminary quantitative analysis on a large set of review comments that were labeled by TSHC （a two-stage hybrid classification algorithm）, which is able to automatically classify review comments by combining rule-based and machine-learning techniques. Through the quantitative study, we explore the typical review patterns. We find that the three projects present similar comments distribution on each subeategory. Pull-requests submitted by inexperienced contributors tend to contain potential issues even though they have passed the tests. Furthermore, external contributors are more likely to break project conventions in their early contributions.展开更多
基金Supported by the National Natural Science Foundation of China, No. 30470877
文摘AIM： To investigate the association between the configurational and compositional changes of nuclear matrix and the differentiation of carcinoma cells. METHODS： Cells cultured with or without 5 × 10^-3 mmol/L of hexamethylene bisacetamide （HMBA） on Nickel grids were treated by selective extraction and prepared for whole mount observation under electron microscopy. The samples were examined under transmission electron microscope. Nuclear matrix proteins were selectively extracted and subjected to subcellular proteomics study. The protein expression patterns were analyzed by PDQuest software. Spots of differentially expressed nuclear matrix proteins were excised and subjected to in situ digestion with trypsin. The peptides were analyzed by matrix-assisted laser- desorption/ionization time of flight mass spectrometry （MALDI-TOF-MS）. Data were submitted for database searching using Mascot tool （www.matrixscience.com）. RESULTS： The nuclear matrix （NM） and intermediate filament （IF） in SMMC-7721 hepatocarcinoma cells were found relatively sparse and arranged irregularly. The nuclear lamina was non-uniform, and two kinds of filaments were not tightly connected. After induction for differentiation by HMBA, the NM-IF filaments were concentrated and distributed uniformly. The heterogeneous population of filaments, including highly branched utrathin filaments could also be seen in the regular meshwork. The connection between the two kinds of filaments and the relatively thin, condensed and sharply demarcated lamina composed of intermediate- sized filaments was relatively fastened. Meanwhile, 21 NM proteins changed remarkably during SMMC-7721 cell differentiation. Four proteins, i.e. mutant Pystl, hypothetical protein, nucleophosminl, and LBP were downregulated, whereas four other proteins, eIF6, p44 subunit, 13-tubulin, and SIN3B were upregulated with the last one, SR2/ASF found only in the differentiated SMMC-7721 cells. CONCLUSION： The induced differentiation of SMMC-7721 cells by HMBA is accompanied by the configurational changes of nuclear matrix-intermediate filament （NM-IF） system and the compositional changes of nuclear matrix protein expression. These changes may be important morphological or functional indications of the cancer cell reversion.
基金This work was supported by the National Key Research and Development Program of China under Grant No. 2018YFB1004202the National Natural Science Foundation of China under Grant No. 61702534.
文摘Communication and coordination between OSS developers who do not work physically in the same location have always been the challenging issues.The pull-based development model,as the state-of-art collaborative development mechanism,provides high openness and transparency to improve the visibility of contributors'work.However,duplicate contributions may still be submitted by more than one contributors to solve the same problem due to the parallel and uncoordinated nature of this model.If not detected in time,duplicate pull-requests can cause contributors and reviewers to waste time and energy on redundant work.In this paper,we propose an approach combining textual and change similarities to automatically detect duplicate contributions in pull-based model at submission time.For a new-arriving contribution,we first compute textual similarity and change similarity between it and other existing contributions.And then our method returns a list of candidate duplicate contributions that are most similar with the new contribution in terms of the combined textual and change similarity.The evaluation shows that 83.4%of the duplicates can be found in average when we use the combined textual and change similarity compared to 54.8%using only textual similarity and 78.2%using only change similarity.
文摘Human osteosarcoma MG-63 cells were induced into differentiation by 5 mmol/L hexamethylene bisacetamide （HMBA）. Their nuclear matrix proteins （NMPs） were selectively extracted and subjected to two-dimensional gel electrophoresis analysis. The results of protein patterns were analyzed by Melanie software. The spots of differentially expressed NMPs were excised and subjected to in situ digestion with trypsin. The maps of peptide mass fingerprinting were obtained by MALDI-TOF-MS analysis, and were submitted for NCBI database searches by Mascot tool. There were twelve spots changed remarkably during the differentiation induced by HMBA, nine of which were identified. The roles of the regulated proteins during the MG-63 differentiation were analyzed. This study suggests that the induced differentiation of cancer cells is accompanied by the changes of NMPs, and confirms the presence of some specific NMPs related to the cancer cell proliferation and differentiation. The changed NMPs are potential markers for cancer diagnosis or targets for cancer therapy.
基金This work was supported by the National Key Research and Development Program of China under Grant No. 2016YFB1000805 and the National Natural Science Foundation of China under Grant Nos. 61432020, 61303064, 61472430 and 61502512.
文摘Code reviews in pull-based model are open to community users on GitHub. Various participants are taking part in the review discussions and the review topics are not only about the improvement of code contributions but also about project evolution and social interaction. A comprehensive understanding of the review topics in pull-based model would be useful to better organize the code review process and optimize review tasks such as reviewer recommendation and pull-request prioritization. In this paper, we first conduct a qualitative study on three popular open-source software projects hosted on GitHub and construct a fine-grained two-level taxonomy covering four level-1 categories （code correctness, pull- request decision-making, project management, and social interaction） and 11 level-2 subcategories （e.g., defect detecting, reviewer assigning, contribution encouraging）. Second, we conduct preliminary quantitative analysis on a large set of review comments that were labeled by TSHC （a two-stage hybrid classification algorithm）, which is able to automatically classify review comments by combining rule-based and machine-learning techniques. Through the quantitative study, we explore the typical review patterns. We find that the three projects present similar comments distribution on each subeategory. Pull-requests submitted by inexperienced contributors tend to contain potential issues even though they have passed the tests. Furthermore, external contributors are more likely to break project conventions in their early contributions.
