Pub Date : 2014-09-15DOI: 10.14293/S2199-1006.1.SOR-MATSCI.AKA0J6.V2
Patrick Drawe, N. Lüttschwager, M. Suhm
We report vibrational Raman spectra of small extended perfluoro- n -alkanes (C n F 2 n +2 with n = 6, 8 – 10, 12 – 14) isolated in supersonic jet expansions and use wavenumbers of longitudinal acoustic vibrations to extrapolate the elastic modulus of cold, isolated polytetrafluoroethylene filaments. The derived value E = 209(10) GPa defines an upper limit for the elastic modulus of the perfectly crystalline, noninteracting polymer at low temperatures and serves as a benchmark for quantum chemical predictions.
我们报道了在超音速射流膨胀中孤立的小扩展的全氟- n -烷烃(C n F 2 n +2, n = 6,8 - 10,12 - 14)的振动拉曼光谱，并使用纵向声学振动的波数来推断冷的、孤立的聚四氟乙烯细丝的弹性模量。推导值E = 209(10) GPa定义了低温下完美结晶、无相互作用聚合物弹性模量的上限，并作为量子化学预测的基准。
{"title":"The elastic modulus of isolated polytetrafluoroethylene filaments","authors":"Patrick Drawe, N. Lüttschwager, M. Suhm","doi":"10.14293/S2199-1006.1.SOR-MATSCI.AKA0J6.V2","DOIUrl":"https://doi.org/10.14293/S2199-1006.1.SOR-MATSCI.AKA0J6.V2","url":null,"abstract":"We report vibrational Raman spectra of small extended perfluoro- n -alkanes (C n F 2 n +2 with n = 6, 8 – 10, 12 – 14) isolated in supersonic jet expansions and use wavenumbers of longitudinal acoustic vibrations to extrapolate the elastic modulus of cold, isolated polytetrafluoroethylene filaments. The derived value E = 209(10) GPa defines an upper limit for the elastic modulus of the perfectly crystalline, noninteracting polymer at low temperatures and serves as a benchmark for quantum chemical predictions.","PeriodicalId":91169,"journal":{"name":"ScienceOpen research","volume":"268 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2014-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76599671","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2014-09-05DOI: 10.14293/S2199-1006.1.SOR-CHEM.AKS7SX.V1
T. Sørensen, A. Madsen, Peter, A. Madsen, Martin, K. Bechgaard
Two new model systems for use within the rapidly develop- ing ultrafast time resolved x-ray scattering techniques have been prepared. Their photoisomerisation from norbornadiene to quadricyclane was found to be a suitable reaction to fol- low. Simulations of scattering patterns (not included in this report) showed that if heavy atoms are included in these molecular structures, then the transformation can be followed by transient X-ray scattering techniques. Two new bromosub- stituted norbornadienes were synthesised and characterised. Absorption spectroscopy showed that the norbornadienes are converted quantitatively to quadricyclanes under ultra- violet irradiation. Nuclear magnetic resonance (NMR) studies showed that the process was fully reversible and that the norbornadienes could be completely recovered even without addition of catalysts. Furthermore, it was shown that the formation of quadricyclane from norbornadiene was unaf- fected by triplet sensitisers. The two new model systems synthesised thus are strong candidates for use in time- resolved X-ray scattering studies in both gas and condensed phases.
{"title":"Bromosubstituted Norbornadienes and Their Reversible Photolytic Transformation to Quadricyclanes","authors":"T. Sørensen, A. Madsen, Peter, A. Madsen, Martin, K. Bechgaard","doi":"10.14293/S2199-1006.1.SOR-CHEM.AKS7SX.V1","DOIUrl":"https://doi.org/10.14293/S2199-1006.1.SOR-CHEM.AKS7SX.V1","url":null,"abstract":"Two new model systems for use within the rapidly develop- ing ultrafast time resolved x-ray scattering techniques have been prepared. Their photoisomerisation from norbornadiene to quadricyclane was found to be a suitable reaction to fol- low. Simulations of scattering patterns (not included in this report) showed that if heavy atoms are included in these molecular structures, then the transformation can be followed by transient X-ray scattering techniques. Two new bromosub- stituted norbornadienes were synthesised and characterised. Absorption spectroscopy showed that the norbornadienes are converted quantitatively to quadricyclanes under ultra- violet irradiation. Nuclear magnetic resonance (NMR) studies showed that the process was fully reversible and that the norbornadienes could be completely recovered even without addition of catalysts. Furthermore, it was shown that the formation of quadricyclane from norbornadiene was unaf- fected by triplet sensitisers. The two new model systems synthesised thus are strong candidates for use in time- resolved X-ray scattering studies in both gas and condensed phases.","PeriodicalId":91169,"journal":{"name":"ScienceOpen research","volume":"3 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2014-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82484718","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2014-07-11DOI: 10.14293/S2199-1006.1.SOR-MED.A4QF5Y.V2
S. Wilkinson, T. Chiavegatti, B. Nauche, Given Names Deactivated Family Name Deactivated, N. Pai
Timely detection, staging, and treatment initiation are pertinent to controlling HIV infection. CD4+ cell-based point-of-care (POC) devices offer the potential to rapidly stage patients, and decide on initiating treatment, but a comparative evaluation of their performance has not yet been performed. With this in mind, we conducted a systematic review and metaanalyses. For the period January 2000 to April 2014, 19 databases were systematically searched, 6619 citations retrieved, and 25 articles selected. Diagnostic performance was compared across devices (i.e., PIMA, CyFlow, miniPOC, MBioCD4 System) and across specimens (i.e., capillary blood vs. venous blood). A Bayesian approach was used to meta-analyze the data. The primary outcome, the Bland–Altman (BA) mean bias (which represents agreement between cell counts from POC device and flow cytometry), was analyzed with a Bayesian hierarchical normal model. We performed a headto-head comparison of two POC devices such as PIMA and PointCareNOW CD4. PIMA appears to perform better vs. PointCareNOW with venous samples (BA mean bias: –9.5 cells/μL; 95% CrI: –37.71 to 18.27, vs. 139.3 cells/μL; 95% CrI: –0.85 to 267.4, mean difference = 148.8, 95% CrI: 11.8, 285.8); however, PIMA’s best performed when used with capillary samples (BA mean bias: 2.2 cells/μL; 95% CrI: – 19.32 to 23.6). Sufficient data were available to allow pooling of sensitivity and specificity data only at the 350 cells/μL cutoff. For PIMA device sensitivity 91.6 (84.7–95.5) and specificity was 94.8 (90.1–97.3), respectively. There were not sufficient data to allow comparisons between any other devices. PIMA device was comparable to flow cytometry. The estimated differences between the CD4+ cell counts of the device and the reference was small and best estimated in capillary blood specimens. As the evidence stands, the PointCareNOW device will need to improve prior to widespread use and more data on MBio and MiniPOC are needed. Findings inform implementation of PIMA and improvements in other CD4 POC device prior to recommending widespread use. INTRODUCTION Universal access to antiretroviral therapy (ART) and increased levels of HIV testing have created hope that HIV infection can be controlled globally. Approximately 9.7 mil‐ lion people now receive ART in lowand middle-income countries, representing a 32-fold increase over the last decade [1]. Effective ART reduces viral load (VL) to undetectable levels and dramatically reduces associated mortality and morbidity [2–4]. As a public health intervention, ART is at the core of a treatment-as-prevention strategy, as reducing community viral load reduces HIV transmissions [4]. CD4+ cells counts and measures of VL are surrogate biomarkers of disease progression that help to stage, initiate and monitor treatment. CD4+ cell counts provide an immunological measure of HIV progression; these counts are utilized in the care of HIV+ patients for staging infections and in assessing patients for ART el
{"title":"Head to head comparisons in performance of CD4 point-of-care assays: a Bayesian meta-analysis (2000–2013)","authors":"S. Wilkinson, T. Chiavegatti, B. Nauche, Given Names Deactivated Family Name Deactivated, N. Pai","doi":"10.14293/S2199-1006.1.SOR-MED.A4QF5Y.V2","DOIUrl":"https://doi.org/10.14293/S2199-1006.1.SOR-MED.A4QF5Y.V2","url":null,"abstract":"Timely detection, staging, and treatment initiation are pertinent to controlling HIV infection. CD4+ cell-based point-of-care (POC) devices offer the potential to rapidly stage patients, and decide on initiating treatment, but a comparative evaluation of their performance has not yet been performed. With this in mind, we conducted a systematic review and metaanalyses. For the period January 2000 to April 2014, 19 databases were systematically searched, 6619 citations retrieved, and 25 articles selected. Diagnostic performance was compared across devices (i.e., PIMA, CyFlow, miniPOC, MBioCD4 System) and across specimens (i.e., capillary blood vs. venous blood). A Bayesian approach was used to meta-analyze the data. The primary outcome, the Bland–Altman (BA) mean bias (which represents agreement between cell counts from POC device and flow cytometry), was analyzed with a Bayesian hierarchical normal model. We performed a headto-head comparison of two POC devices such as PIMA and PointCareNOW CD4. PIMA appears to perform better vs. PointCareNOW with venous samples (BA mean bias: –9.5 cells/μL; 95% CrI: –37.71 to 18.27, vs. 139.3 cells/μL; 95% CrI: –0.85 to 267.4, mean difference = 148.8, 95% CrI: 11.8, 285.8); however, PIMA’s best performed when used with capillary samples (BA mean bias: 2.2 cells/μL; 95% CrI: – 19.32 to 23.6). Sufficient data were available to allow pooling of sensitivity and specificity data only at the 350 cells/μL cutoff. For PIMA device sensitivity 91.6 (84.7–95.5) and specificity was 94.8 (90.1–97.3), respectively. There were not sufficient data to allow comparisons between any other devices. PIMA device was comparable to flow cytometry. The estimated differences between the CD4+ cell counts of the device and the reference was small and best estimated in capillary blood specimens. As the evidence stands, the PointCareNOW device will need to improve prior to widespread use and more data on MBio and MiniPOC are needed. Findings inform implementation of PIMA and improvements in other CD4 POC device prior to recommending widespread use. INTRODUCTION Universal access to antiretroviral therapy (ART) and increased levels of HIV testing have created hope that HIV infection can be controlled globally. Approximately 9.7 mil‐ lion people now receive ART in lowand middle-income countries, representing a 32-fold increase over the last decade [1]. Effective ART reduces viral load (VL) to undetectable levels and dramatically reduces associated mortality and morbidity [2–4]. As a public health intervention, ART is at the core of a treatment-as-prevention strategy, as reducing community viral load reduces HIV transmissions [4]. CD4+ cells counts and measures of VL are surrogate biomarkers of disease progression that help to stage, initiate and monitor treatment. CD4+ cell counts provide an immunological measure of HIV progression; these counts are utilized in the care of HIV+ patients for staging infections and in assessing patients for ART el","PeriodicalId":91169,"journal":{"name":"ScienceOpen research","volume":"18 1","pages":"1-13"},"PeriodicalIF":0.0,"publicationDate":"2014-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75208269","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2014-06-12DOI: 10.14293/A2199-1006.01.SOR-MED.YXBIK.V1
T. Lisman
{"title":"The anti-coagulants ASIS or APC do not protect against renal ischemia/ reperfusion injury","authors":"T. Lisman","doi":"10.14293/A2199-1006.01.SOR-MED.YXBIK.V1","DOIUrl":"https://doi.org/10.14293/A2199-1006.01.SOR-MED.YXBIK.V1","url":null,"abstract":"","PeriodicalId":91169,"journal":{"name":"ScienceOpen research","volume":"35 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2014-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77207652","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2014-06-12DOI: 10.14293/S2199-1006.1.SOR-MED.AYXBIK.V1
S. Loubele, Arnold Spek, P. Leenders, R. Matthijsen, W. Buurman, C. Peutz-Kootstra, H. Cate, H. Spronk
{"title":"The anti-coagulants ASIS or APC do not protect against renal ischemia/ reperfusion injury","authors":"S. Loubele, Arnold Spek, P. Leenders, R. Matthijsen, W. Buurman, C. Peutz-Kootstra, H. Cate, H. Spronk","doi":"10.14293/S2199-1006.1.SOR-MED.AYXBIK.V1","DOIUrl":"https://doi.org/10.14293/S2199-1006.1.SOR-MED.AYXBIK.V1","url":null,"abstract":"","PeriodicalId":91169,"journal":{"name":"ScienceOpen research","volume":"16 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2014-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73430119","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2014-05-16DOI: 10.14293/S2199-1006.1.SOR-MED.ABG1R6.V1
V. Shumaster, O. Jawitz, D. Yuh, P. Bonde
Extracorporeal membrane oxygenation (ECMO) has been used infrequently as a bridge to lung transplantation due to lack of consensus and data regarding the benefits of such a strategy. We present data from the United Network of Organ Sharing (UNOS) database on the outcomes of patients bridged to lung transplantation with ECMO. We used the UNOS database to analyze data between January 1, 2000 and December 31, 2011. During this time 14,263 lung transplants were performed, of which 143 (1.0%) were bridged using ECMO. Patients on ECMO as a bridge to lung transplantation were compared to those transplanted without prior ECMO support. Demographics, survival rates, complications, and rejection episodes were compared between the two groups. The 30-day, 6-month, 1-year, 3-year, and 5-year survival rates were 69%, 56%, 48%, 26%, and 11%, respectively, for the ECMO bridge group and 95%, 88%, 81%, 58%, and 38% respectively, for the control group (p ≤ 0.01). The ECMO group incurred higher rate of postoperative complications, including airway dehiscence (4% vs. 1%, p ≤ 0.01), stroke (3% vs. 2%, p ≤ 0.01), infection (56% vs. 42%, p ≤ 0.01), and pulmonary embolism (10% vs. 0.6%, p ≤ 0.01). The length of hospital stay was longer for the ECMO group (41 vs. 25 days, p ≤ 0.01), and they were treated for rejection more often (49% vs. 36%, p = 0.02). The use of ECMO as a bridge to lung transplantation is associated with significantly worse survival and more frequent postoperative complications. Therefore, we advocate very careful patient selection and cautious use of ECMO.
由于缺乏共识和数据，体外膜氧合(ECMO)很少被用作肺移植的桥梁。我们提供了来自联合器官共享网络(UNOS)数据库的数据，关于经ECMO桥接肺移植患者的结果。我们使用UNOS数据库分析2000年1月1日至2011年12月31日之间的数据。在此期间进行了14,263例肺移植，其中143例(1.0%)采用ECMO桥接。将ECMO作为肺移植的桥梁的患者与没有ECMO支持的移植患者进行比较。比较两组患者的人口统计学、生存率、并发症和排斥反应。ECMO桥接组的30天、6个月、1年、3年和5年生存率分别为69%、56%、48%、26%和11%，对照组的生存率分别为95%、88%、81%、58%和38% (p≤0.01)。ECMO组术后并发症发生率较高，分别为气道破裂(4%比1%，p≤0.01)、脑卒中(3%比2%，p≤0.01)、感染(56%比42%，p≤0.01)、肺栓塞(10%比0.6%，p≤0.01)。ECMO组住院时间更长(41天vs. 25天，p≤0.01)，排斥反应发生率更高(49% vs. 36%， p = 0.02)。使用ECMO作为肺移植的桥梁与明显较差的生存率和更频繁的术后并发症相关。因此，我们提倡慎重选择患者，谨慎使用ECMO。
{"title":"Lessons learned from extracorporeal membrane oxygenation as a bridge to lung transplantation","authors":"V. Shumaster, O. Jawitz, D. Yuh, P. Bonde","doi":"10.14293/S2199-1006.1.SOR-MED.ABG1R6.V1","DOIUrl":"https://doi.org/10.14293/S2199-1006.1.SOR-MED.ABG1R6.V1","url":null,"abstract":"Extracorporeal membrane oxygenation (ECMO) has been used infrequently as a bridge to lung transplantation due to lack of consensus and data regarding the benefits of such a strategy. We present data from the United Network of Organ Sharing (UNOS) database on the outcomes of patients bridged to lung transplantation with ECMO. We used the UNOS database to analyze data between January 1, 2000 and December 31, 2011. During this time 14,263 lung transplants were performed, of which 143 (1.0%) were bridged using ECMO. Patients on ECMO as a bridge to lung transplantation were compared to those transplanted without prior ECMO support. Demographics, survival rates, complications, and rejection episodes were compared between the two groups. The 30-day, 6-month, 1-year, 3-year, and 5-year survival rates were 69%, 56%, 48%, 26%, and 11%, respectively, for the ECMO bridge group and 95%, 88%, 81%, 58%, and 38% respectively, for the control group (p ≤ 0.01). The ECMO group incurred higher rate of postoperative complications, including airway dehiscence (4% vs. 1%, p ≤ 0.01), stroke (3% vs. 2%, p ≤ 0.01), infection (56% vs. 42%, p ≤ 0.01), and pulmonary embolism (10% vs. 0.6%, p ≤ 0.01). The length of hospital stay was longer for the ECMO group (41 vs. 25 days, p ≤ 0.01), and they were treated for rejection more often (49% vs. 36%, p = 0.02). The use of ECMO as a bridge to lung transplantation is associated with significantly worse survival and more frequent postoperative complications. Therefore, we advocate very careful patient selection and cautious use of ECMO.","PeriodicalId":91169,"journal":{"name":"ScienceOpen research","volume":"27 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2014-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75454243","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2014-05-16DOI: 10.14293/A2199-1006.01.SOR-MED.BG1R6.V1
Zhongjun J. Wu
{"title":"Lessons learned from extracorporeal membrane oxygenation as a bridge to lung transplantation","authors":"Zhongjun J. Wu","doi":"10.14293/A2199-1006.01.SOR-MED.BG1R6.V1","DOIUrl":"https://doi.org/10.14293/A2199-1006.01.SOR-MED.BG1R6.V1","url":null,"abstract":"","PeriodicalId":91169,"journal":{"name":"ScienceOpen research","volume":"72 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2014-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74138961","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2014-05-14DOI: 10.14293/S2199-1006.1.SOR-LIFE.AAC0E6.V2
Maria-Ioanna Ellina, P. Bouris, D. Kletsas, A. Aletras, Nikos Karamanos
Colon cancer is the third most common type of cancer worldwide. Epidermal growth factor receptor (EGFR) plays a crucial role in the (patho)physiology of the disease. EGFR controls vital cellular processes, while this action is associated with poor prognosis. In addition, K-Ras mutations are associated with the promotion of the disease and the anti-EGFR resistance. The ubiquitin-proteasome system plays also a very important role in cancer, modulating cell cycle and other cellular processes such as the growth and the survival of cancer cells. Proteasome inhibition affects, in several cases, the action and the protein levels of EGFR. Nevertheless, little is known whether the reversed option is possible. In this study, we, therefore, investigated the impact of epidermal growth factor (EGF)/EGFR signaling axis on gene expression and the proteolytic activity of the proteasome subunits, as well as whether Nrf2, an activator of proteasome expression, plays a role in this process. Moreover, we evaluated whether EGF regulates the expression of its own receptor and the proliferation rate of DLD-1 (K-Ras mutated) colon cancer cells. The obtained data showed that, although EGF has no significant effect on the proliferation of DLD-1 colon cancer cells, it significantly upregulates the expression of EGFR as well as the expression and the activity of the proteasome, suggesting that the EGF-mediated proteasome activation could possibly lead to enhanced EGFR degradation leading to autoregulation of EGF–EGFR pathway. Nrf2 activation did not induce proteasome gene expression in DLD-1 colon cancer cells.
{"title":"EGF/EGFR signaling axis is a significant regulator of the proteasome expression and activity in colon cancer cells","authors":"Maria-Ioanna Ellina, P. Bouris, D. Kletsas, A. Aletras, Nikos Karamanos","doi":"10.14293/S2199-1006.1.SOR-LIFE.AAC0E6.V2","DOIUrl":"https://doi.org/10.14293/S2199-1006.1.SOR-LIFE.AAC0E6.V2","url":null,"abstract":"Colon cancer is the third most common type of cancer worldwide. Epidermal growth factor receptor (EGFR) plays a crucial role in the (patho)physiology of the disease. EGFR controls vital cellular processes, while this action is associated with poor prognosis. In addition, K-Ras mutations are associated with the promotion of the disease and the anti-EGFR resistance. The ubiquitin-proteasome system plays also a very important role in cancer, modulating cell cycle and other cellular processes such as the growth and the survival of cancer cells. Proteasome inhibition affects, in several cases, the action and the protein levels of EGFR. Nevertheless, little is known whether the reversed option is possible. In this study, we, therefore, investigated the impact of epidermal growth factor (EGF)/EGFR signaling axis on gene expression and the proteolytic activity of the proteasome subunits, as well as whether Nrf2, an activator of proteasome expression, plays a role in this process. Moreover, we evaluated whether EGF regulates the expression of its own receptor and the proliferation rate of DLD-1 (K-Ras mutated) colon cancer cells. The obtained data showed that, although EGF has no significant effect on the proliferation of DLD-1 colon cancer cells, it significantly upregulates the expression of EGFR as well as the expression and the activity of the proteasome, suggesting that the EGF-mediated proteasome activation could possibly lead to enhanced EGFR degradation leading to autoregulation of EGF–EGFR pathway. Nrf2 activation did not induce proteasome gene expression in DLD-1 colon cancer cells.","PeriodicalId":91169,"journal":{"name":"ScienceOpen research","volume":"37 8","pages":""},"PeriodicalIF":0.0,"publicationDate":"2014-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72484421","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2014-05-14DOI: 10.14293/A2199-1006.01.SOR-LIFE.AC0E6.V1
S. Tanida
{"title":"EGF/EGFR signaling axis is a significant regulator of the proteasome expression and activity in colon cancer cells","authors":"S. Tanida","doi":"10.14293/A2199-1006.01.SOR-LIFE.AC0E6.V1","DOIUrl":"https://doi.org/10.14293/A2199-1006.01.SOR-LIFE.AC0E6.V1","url":null,"abstract":"","PeriodicalId":91169,"journal":{"name":"ScienceOpen research","volume":"83 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2014-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73103966","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2014-04-29DOI: 10.14293/S2199-1006.1.SOR-LIFE.A67837.V2
M. Andrade, Caroline Louis-Jeune, C. Perez-Iratxeta
Abstract The ever increasing number of sequences in protein databases usually turns out large numbers of homologs in sequence similarity searches. While information from homology can be very useful for functional prediction based on amino acid conservation, many of these homologs usually have high levels of identity among themselves, which hinders multiple sequence alignment computation and, especially, visualization. More generally, high redundancy reduces the usability of a protein set in machine learning applications and biases statistical analyses. We developed an algorithm to identify redundant sequence homologs that can be culled producing a streamlined FASTA file. As a difference from other automatic approaches that only aggregate sequences with high identity, our method clusters near-full length homologs allowing for lower sequence identity thresholds. Our method was fully tested and implemented in a web application called FASTA Herder, publicly available at http://fh.ogic.ca/.
{"title":"FASTA Herder: a web application to trim protein sequence sets","authors":"M. Andrade, Caroline Louis-Jeune, C. Perez-Iratxeta","doi":"10.14293/S2199-1006.1.SOR-LIFE.A67837.V2","DOIUrl":"https://doi.org/10.14293/S2199-1006.1.SOR-LIFE.A67837.V2","url":null,"abstract":"Abstract\u0000The ever increasing number of sequences in protein databases usually turns out large numbers of homologs in sequence similarity searches. While information from homology can be very useful for functional prediction based on amino acid conservation, many of these homologs usually have high levels of identity among themselves, which hinders multiple sequence alignment computation and, especially, visualization. More generally, high redundancy reduces the usability of a protein set in machine learning applications and biases statistical analyses. We developed an algorithm to identify redundant sequence homologs that can be culled producing a streamlined FASTA file. As a difference from other automatic approaches that only aggregate sequences with high identity, our method clusters near-full length homologs allowing for lower sequence identity thresholds. Our method was fully tested and implemented in a web application called FASTA Herder, publicly available at http://fh.ogic.ca/.","PeriodicalId":91169,"journal":{"name":"ScienceOpen research","volume":"138 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2014-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88723664","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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