cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/tcggv58kjk.1
title: Proteome-wide quantitative RNA interactome capture (qRIC) identifies phosphorylation sites with regulatory potential in RBM20. Vieira-Vieira et al. Figure 5A. S635A RBM20

description: Cellular mRNA-binding proteins (mRBPs) are major regulators of gene expression at the post-transcriptional level. While many posttranslational modification sites in mRBPs have been identified, little is known about how these modifications regulate mRBP function. Here, we developed quantitative RNA-interactome capture (qRIC) to quantify the fraction of cellular mRBPs pulled down with polyadenylated mRNAs. Combining qRIC with phosphoproteomics allowed us to systematically compare pull-down efficiencies of phosphorylated and non-phosphorylated forms of mRBPs. Almost 200 phosphorylation events increased or decreased pull-down efficiency compared to the unmodified mRBPs and thus have regulatory potential. Our data captures known regulatory phosphorylation sites in ELAVL1, SF3B1 and UPF1 and identifies new potentially regulatory sites. Follow-up experiments on the cardiac splicing regulator RBM20 revealed that multiple phosphorylation sites in the C-terminal disordered region affect nucleo-cytoplasmic localization, association with cytoplasmic ribonucleoprotein granules and alternative splicing. Together, we show that qRIC in conjunction with phosphoproteomics is a scalable method to identify functional posttranslational modification sites in mRBPs.
DOI: 10.6084/m9.figshare.19971104
title: Scientific Channeling Answer Dataset

description: Answer dataset for manuscript submission
DOI: 10.6084/m9.figshare.19971104.v1
title: Scientific Channeling Answer Dataset

description: Answer dataset for manuscript submission
DOI: 10.17632/bdx89nn3tp.1
title: Proteome-wide quantitative RNA interactome capture (qRIC) identifies phosphorylation sites with regulatory potential in RBM20. Vieira-Vieira et al. Figure 5A. D10 RBM20

description: Cellular mRNA-binding proteins (mRBPs) are major regulators of gene expression at the post-transcriptional level. While many posttranslational modification sites in mRBPs have been identified, little is known about how these modifications regulate mRBP function. Here, we developed quantitative RNA-interactome capture (qRIC) to quantify the fraction of cellular mRBPs pulled down with polyadenylated mRNAs. Combining qRIC with phosphoproteomics allowed us to systematically compare pull-down efficiencies of phosphorylated and non-phosphorylated forms of mRBPs. Almost 200 phosphorylation events increased or decreased pull-down efficiency compared to the unmodified mRBPs and thus have regulatory potential. Our data captures known regulatory phosphorylation sites in ELAVL1, SF3B1 and UPF1 and identifies new potentially regulatory sites. Follow-up experiments on the cardiac splicing regulator RBM20 revealed that multiple phosphorylation sites in the C-terminal disordered region affect nucleo-cytoplasmic localization, association with cytoplasmic ribonucleoprotein granules and alternative splicing. Together, we show that qRIC in conjunction with phosphoproteomics is a scalable method to identify functional posttranslational modification sites in mRBPs.
DOI: 10.17632/d5h73x6xst.1
title: Proteome-wide quantitative RNA interactome capture (qRIC) identifies phosphorylation sites with regulatory potential in RBM20. Vieira-Vieira et al. Figure 5A. WT RBM20

description: Cellular mRNA-binding proteins (mRBPs) are major regulators of gene expression at the post-transcriptional level. While many posttranslational modification sites in mRBPs have been identified, little is known about how these modifications regulate mRBP function. Here, we developed quantitative RNA-interactome capture (qRIC) to quantify the fraction of cellular mRBPs pulled down with polyadenylated mRNAs. Combining qRIC with phosphoproteomics allowed us to systematically compare pull-down efficiencies of phosphorylated and non-phosphorylated forms of mRBPs. Almost 200 phosphorylation events increased or decreased pull-down efficiency compared to the unmodified mRBPs and thus have regulatory potential. Our data captures known regulatory phosphorylation sites in ELAVL1, SF3B1 and UPF1 and identifies new potentially regulatory sites. Follow-up experiments on the cardiac splicing regulator RBM20 revealed that multiple phosphorylation sites in the C-terminal disordered region affect nucleo-cytoplasmic localization, association with cytoplasmic ribonucleoprotein granules and alternative splicing. Together, we show that qRIC in conjunction with phosphoproteomics is a scalable method to identify functional posttranslational modification sites in mRBPs.
DOI: 10.6084/m9.figshare.19971127
title: BRAZILIAN GASTRIC CANCER ASSOCIATION GUIDELINES (PART 2): UPDATE ON TREATMENT

description: ABSTRACT Background : The II Brazilian Consensus on Gastric Cancer of the Brazilian Gastric Cancer Association BGCA (Part 1) was recently published. On this occasion, countless specialists working in the treatment of this disease expressed their opinion in the face of the statements presented. Aim : To present the BGCA Guidelines (Part 2) regarding indications for surgical treatment, operative techniques, extension of resection and multimodal treatment. Methods: To formulate these guidelines, the authors carried out an extensive and current review regarding each declaration present in the II Consensus, using the Medline/PubMed, Cochrane Library and SciELO databases initially with the following descriptors: gastric cancer, gastrectomy, lymphadenectomy, multimodal treatment. In addition, each statement was classified according to the level of evidence and degree of recommendation. Results : Of the 43 statements present in this study, 11 (25,6%) were classified with level of evidence A, 20 (46,5%) B and 12 (27,9%) C. Regarding the degree of recommendation, 18 (41,9%) statements obtained grade of recommendation 1, 14 (32,6%) 2a, 10 (23,3%) 2b e one (2,3%) 3. Conclusion : The guidelines complement of the guidelines presented here allows surgeons and oncologists who work to combat gastric cancer to offer the best possible treatment, according to the local conditions available.
DOI: 10.6084/m9.figshare.19971127.v1
title: BRAZILIAN GASTRIC CANCER ASSOCIATION GUIDELINES (PART 2): UPDATE ON TREATMENT

description: ABSTRACT Background : The II Brazilian Consensus on Gastric Cancer of the Brazilian Gastric Cancer Association BGCA (Part 1) was recently published. On this occasion, countless specialists working in the treatment of this disease expressed their opinion in the face of the statements presented. Aim : To present the BGCA Guidelines (Part 2) regarding indications for surgical treatment, operative techniques, extension of resection and multimodal treatment. Methods: To formulate these guidelines, the authors carried out an extensive and current review regarding each declaration present in the II Consensus, using the Medline/PubMed, Cochrane Library and SciELO databases initially with the following descriptors: gastric cancer, gastrectomy, lymphadenectomy, multimodal treatment. In addition, each statement was classified according to the level of evidence and degree of recommendation. Results : Of the 43 statements present in this study, 11 (25,6%) were classified with level of evidence A, 20 (46,5%) B and 12 (27,9%) C. Regarding the degree of recommendation, 18 (41,9%) statements obtained grade of recommendation 1, 14 (32,6%) 2a, 10 (23,3%) 2b e one (2,3%) 3. Conclusion : The guidelines complement of the guidelines presented here allows surgeons and oncologists who work to combat gastric cancer to offer the best possible treatment, according to the local conditions available.
DOI: 10.6084/m9.figshare.19971130
title: WIRELESS PH MONITORING AND CONVENTIONAL ESOPHAGEAL PH MONITORING: COMPARATIVE STUDY OF DISCOMFORT, LIMITATIONS IN DAILY ACTIVITIES AND COMPLICATIONS

description: ABSTRACT Background: The catheter of the esophageal pH monitoring is associated with nasal and throat discomfort, and different behave in patients. The capsule of the wireless pH monitoring may cause chest pain and complications. Aim: To compare the wireless and conventional pH monitoring concerning the degree of discomfort and limitations in daily activities, complications, ability to diagnose pathological reflux, and costs. Methods: Twenty-five patients with symptoms of gastroesophageal reflux were prospectively submitted, in a simultaneous initial period, to 24-hour catheter esophageal pH monitoring and 48-hour wireless system. After removing each system, patients underwent a specific clinical questionnaire. Results: Fifteen patients (60%) pointed a higher discomfort in the introduction of the capsule (p=0.327). Discomfort and limitations in daily activities were lower on 2nd day (p&lt;0.05); however, continued to be expressive (32% to 44%). Chest pain occurred in 13 (52%) patients. The diagnostic gain of pathological reflux was 12% with the wireless system (p=0.355). Conclusions: 1) There is no significant difference between the discomfort mentioned in the introduction of the capsule and the catheter; 2) during reflux monitoring, the wireless system provides significant less discomfort and limitations in daily activities; 3) there is no significant difference between the two methods in the ability to diagnose pathological reflux; 4) wireless pH monitoring has higher cost.
DOI: 10.6084/m9.figshare.19971130.v1
title: WIRELESS PH MONITORING AND CONVENTIONAL ESOPHAGEAL PH MONITORING: COMPARATIVE STUDY OF DISCOMFORT, LIMITATIONS IN DAILY ACTIVITIES AND COMPLICATIONS

description: ABSTRACT Background: The catheter of the esophageal pH monitoring is associated with nasal and throat discomfort, and different behave in patients. The capsule of the wireless pH monitoring may cause chest pain and complications. Aim: To compare the wireless and conventional pH monitoring concerning the degree of discomfort and limitations in daily activities, complications, ability to diagnose pathological reflux, and costs. Methods: Twenty-five patients with symptoms of gastroesophageal reflux were prospectively submitted, in a simultaneous initial period, to 24-hour catheter esophageal pH monitoring and 48-hour wireless system. After removing each system, patients underwent a specific clinical questionnaire. Results: Fifteen patients (60%) pointed a higher discomfort in the introduction of the capsule (p=0.327). Discomfort and limitations in daily activities were lower on 2nd day (p&lt;0.05); however, continued to be expressive (32% to 44%). Chest pain occurred in 13 (52%) patients. The diagnostic gain of pathological reflux was 12% with the wireless system (p=0.355). Conclusions: 1) There is no significant difference between the discomfort mentioned in the introduction of the capsule and the catheter; 2) during reflux monitoring, the wireless system provides significant less discomfort and limitations in daily activities; 3) there is no significant difference between the two methods in the ability to diagnose pathological reflux; 4) wireless pH monitoring has higher cost.
DOI: 10.17632/jmg3nrvj9d.1
title: HardwareX - CultureLED

description: STL and INO files for CultureLED system
DOI: 10.17632/sp3xdygfxj.1
title: Proteome-wide quantitative RNA interactome capture (qRIC) identifies phosphorylation sites with regulatory potential in RBM20. Vieira-Vieira et al. Figure 5A. A10 RBM20

description: Cellular mRNA-binding proteins (mRBPs) are major regulators of gene expression at the post-transcriptional level. While many posttranslational modification sites in mRBPs have been identified, little is known about how these modifications regulate mRBP function. Here, we developed quantitative RNA-interactome capture (qRIC) to quantify the fraction of cellular mRBPs pulled down with polyadenylated mRNAs. Combining qRIC with phosphoproteomics allowed us to systematically compare pull-down efficiencies of phosphorylated and non-phosphorylated forms of mRBPs. Almost 200 phosphorylation events increased or decreased pull-down efficiency compared to the unmodified mRBPs and thus have regulatory potential. Our data captures known regulatory phosphorylation sites in ELAVL1, SF3B1 and UPF1 and identifies new potentially regulatory sites. Follow-up experiments on the cardiac splicing regulator RBM20 revealed that multiple phosphorylation sites in the C-terminal disordered region affect nucleo-cytoplasmic localization, association with cytoplasmic ribonucleoprotein granules and alternative splicing. Together, we show that qRIC in conjunction with phosphoproteomics is a scalable method to identify functional posttranslational modification sites in mRBPs.
DOI: 10.17632/n938bchmv2.1
title: Proteome-wide quantitative RNA interactome capture (qRIC) identifies phosphorylation sites with regulatory potential in RBM20. Vieira-Vieira et al. Figure S5C

description: Cellular mRNA-binding proteins (mRBPs) are major regulators of gene expression at the post-transcriptional level. While many posttranslational modification sites in mRBPs have been identified, little is known about how these modifications regulate mRBP function. Here, we developed quantitative RNA-interactome capture (qRIC) to quantify the fraction of cellular mRBPs pulled down with polyadenylated mRNAs. Combining qRIC with phosphoproteomics allowed us to systematically compare pull-down efficiencies of phosphorylated and non-phosphorylated forms of mRBPs. Almost 200 phosphorylation events increased or decreased pull-down efficiency compared to the unmodified mRBPs and thus have regulatory potential. Our data captures known regulatory phosphorylation sites in ELAVL1, SF3B1 and UPF1 and identifies new potentially regulatory sites. Follow-up experiments on the cardiac splicing regulator RBM20 revealed that multiple phosphorylation sites in the C-terminal disordered region affect nucleo-cytoplasmic localization, association with cytoplasmic ribonucleoprotein granules and alternative splicing. Together, we show that qRIC in conjunction with phosphoproteomics is a scalable method to identify functional posttranslational modification sites in mRBPs.
DOI: 10.6084/m9.figshare.19971199
title: PRIMARY TUMOR LYMPHOVASCULAR INVASION NEGATIVELY AFFECTS SURVIVAL AFTER COLORECTAL LIVER METASTASIS RESECTION?

description: ABSTRACT Background: About 50% of the patients with colorectal adenocarcinoma will present with liver metastasis and 20% are synchronic. Liver resection is associated with improvement in survival in comparison to chemotherapy alone. Aim: To analyze the overall survival in patients submitted to liver resection of colorectal cancer metastasis and prognostic factors related to the primary and secondary tumors. Methods: A retrospective analysis of a prospectively maintained database regarding demographic, primary tumor and liver metastasis characteristics. Results: There were 84 liver resections due to colorectal cancer metastasis in the period. The 5-year disease-free and overall survivals were 27.5% and 48.8% respectively. The statistically significant factors for survival were tumor grade (p=0.050), lymphovascular invasion (p=0.021), synchronous metastasis (p=0.020), as well as number (p=0.004), bilobar distribution (p=0.019) and diameter of the liver metastasis over 50 mm (p=0.027). Remained as independent negative predictive factors: lymphovascular invasion (HR=2.7; CI 95% 1.106-6.768; p=0.029), synchronous metastasis (HR=2.8; CI 95% 1.069-7.365; p=0.036) and four or more liver metastasis (HR=1.7; CI 95% 1.046-2.967; p=0.033). Conclusion: The resection of liver metastasis of colorectal adenocarcinoma leads to good survival rates. Lymphovascular invasion was the single prognostic factor related to the primary tumor. Synchronous disease and four or more metastasis were the most significant factors related to the secondary tumor.
DOI: 10.6084/m9.figshare.19971199.v1
title: PRIMARY TUMOR LYMPHOVASCULAR INVASION NEGATIVELY AFFECTS SURVIVAL AFTER COLORECTAL LIVER METASTASIS RESECTION?

description: ABSTRACT Background: About 50% of the patients with colorectal adenocarcinoma will present with liver metastasis and 20% are synchronic. Liver resection is associated with improvement in survival in comparison to chemotherapy alone. Aim: To analyze the overall survival in patients submitted to liver resection of colorectal cancer metastasis and prognostic factors related to the primary and secondary tumors. Methods: A retrospective analysis of a prospectively maintained database regarding demographic, primary tumor and liver metastasis characteristics. Results: There were 84 liver resections due to colorectal cancer metastasis in the period. The 5-year disease-free and overall survivals were 27.5% and 48.8% respectively. The statistically significant factors for survival were tumor grade (p=0.050), lymphovascular invasion (p=0.021), synchronous metastasis (p=0.020), as well as number (p=0.004), bilobar distribution (p=0.019) and diameter of the liver metastasis over 50 mm (p=0.027). Remained as independent negative predictive factors: lymphovascular invasion (HR=2.7; CI 95% 1.106-6.768; p=0.029), synchronous metastasis (HR=2.8; CI 95% 1.069-7.365; p=0.036) and four or more liver metastasis (HR=1.7; CI 95% 1.046-2.967; p=0.033). Conclusion: The resection of liver metastasis of colorectal adenocarcinoma leads to good survival rates. Lymphovascular invasion was the single prognostic factor related to the primary tumor. Synchronous disease and four or more metastasis were the most significant factors related to the secondary tumor.
DOI: 10.6084/m9.figshare.19971201.v1
title: LACTATE CAN BE A MARKER OF METABOLIC SYNDROME IN SEVERE OBESITY?

description: ABSTRACT Background: In the last decades, numerous studies have confirmed the importance of lactate - by-product to the nutrient signal of the intracellular redox state - to regulatory functions in energy metabolism. Aim: To evaluate changes in blood lactate in patients with severe obesity and its correlation with body composition and metabolic profile. Methods: Twenty-four people with severe obesity (BMI=40 kg/m2) were evaluated in a prospective case-control study before and six months after Roux-in-Y gastric bypass. The blood lactate, total cholesterol, and fractions, C-reactive protein and HOMA-IR were analyzed after 12 h fasting. Body mass composition was evaluated by bioelectrical impedance and respiratory quotient was measured by indirect calorimetry. Results: The initial lactate level was 2.5±1.1 mmol/l and returned to normal level (1.9±3.6 mmol/l, p=0.0018) after surgery. This reduction was positively correlated with a decrease in BMI (p=0.0001), % free fat mass (p=0,001), % fat mass (p=0.001) and HOMA-IR (p=0.01). There was normalization of lactatemia in 70% of patients. There was no correlation between lactatemia and C-reactive protein. Conclusions: There was a significant improvement of metabolic parameters, normalization of blood lactate, fat mass loss, although these individuals remained with a high BMI.
DOI: 10.6084/m9.figshare.19971201
title: LACTATE CAN BE A MARKER OF METABOLIC SYNDROME IN SEVERE OBESITY?

description: ABSTRACT Background: In the last decades, numerous studies have confirmed the importance of lactate - by-product to the nutrient signal of the intracellular redox state - to regulatory functions in energy metabolism. Aim: To evaluate changes in blood lactate in patients with severe obesity and its correlation with body composition and metabolic profile. Methods: Twenty-four people with severe obesity (BMI=40 kg/m2) were evaluated in a prospective case-control study before and six months after Roux-in-Y gastric bypass. The blood lactate, total cholesterol, and fractions, C-reactive protein and HOMA-IR were analyzed after 12 h fasting. Body mass composition was evaluated by bioelectrical impedance and respiratory quotient was measured by indirect calorimetry. Results: The initial lactate level was 2.5±1.1 mmol/l and returned to normal level (1.9±3.6 mmol/l, p=0.0018) after surgery. This reduction was positively correlated with a decrease in BMI (p=0.0001), % free fat mass (p=0,001), % fat mass (p=0.001) and HOMA-IR (p=0.01). There was normalization of lactatemia in 70% of patients. There was no correlation between lactatemia and C-reactive protein. Conclusions: There was a significant improvement of metabolic parameters, normalization of blood lactate, fat mass loss, although these individuals remained with a high BMI.
DOI: 10.6084/m9.figshare.19971238
title: THERE ARE NO ADVANTAGES BETWEEN LAPAROSCOPIC AND OPEN LIVER RESECTIONS WITHIN AN ENHANCED RECOVERY PROGRAM (ERAS)

description: ABSTRACT Background: The use of a successful Enhanced Recovery After Surgery (ERAS) in colorectal surgery favored its application in other organs, and hepatic resections were not excluded from this tendency. Some authors suggest that the laparoscopic approach is a central element to obtain better results. Aim: To compare the laparoscopic vs. open hepatic resections within an ERAS to evaluate if there are any differences between them. Methods: In a descriptive study 80 hepatic resections that were divided into two groups, regarding to whether they were submitted to laparoscopy or open surgery. Demographic data, those referring to the hepatectomy and the ERAS was analyzed. Results: Forty-seven resections were carried out in open surgery and the rest laparoscopically; in the first group there was only one conversion to open surgery. Of the total, 17 resections were major hepatectomies and in 18 simultaneous resections. There were no differences between procedures regarding hospital stay and number of complications. There was a greater adherence to the ERAS (p=0.046) and a faster ambulation (p=0.001) in the open surgery. Conclusion: The procedure, whether open or laparoscopically done in hepatic resections, does not seem to show differences in an ERAS evaluation.
DOI: 10.6084/m9.figshare.19971238.v1
title: THERE ARE NO ADVANTAGES BETWEEN LAPAROSCOPIC AND OPEN LIVER RESECTIONS WITHIN AN ENHANCED RECOVERY PROGRAM (ERAS)

description: ABSTRACT Background: The use of a successful Enhanced Recovery After Surgery (ERAS) in colorectal surgery favored its application in other organs, and hepatic resections were not excluded from this tendency. Some authors suggest that the laparoscopic approach is a central element to obtain better results. Aim: To compare the laparoscopic vs. open hepatic resections within an ERAS to evaluate if there are any differences between them. Methods: In a descriptive study 80 hepatic resections that were divided into two groups, regarding to whether they were submitted to laparoscopy or open surgery. Demographic data, those referring to the hepatectomy and the ERAS was analyzed. Results: Forty-seven resections were carried out in open surgery and the rest laparoscopically; in the first group there was only one conversion to open surgery. Of the total, 17 resections were major hepatectomies and in 18 simultaneous resections. There were no differences between procedures regarding hospital stay and number of complications. There was a greater adherence to the ERAS (p=0.046) and a faster ambulation (p=0.001) in the open surgery. Conclusion: The procedure, whether open or laparoscopically done in hepatic resections, does not seem to show differences in an ERAS evaluation.