dbPTM: an information repository of protein post-translational modification

dbPTM is a database that compiles information on protein post-translational modifications (PTMs), such as the catalytic sites, solvent accessibility of amino acid residues, protein secondary and tertiary structures, protein domains and protein variations. The database includes all of the experimentally validated PTM sites from Swiss-Prot, PhosphoELM and O-GLYCBASE. Only a small fraction of Swiss-Prot proteins are annotated with experimentally verified PTM. Although the Swiss-Prot provides rich information about the PTM, other structural properties and functional information of proteins are also essential for elucidating protein mechanisms. The dbPTM systematically identifies three major types of protein PTM (phosphorylation, glycosylation and sulfation) sites against Swiss-Prot proteins by refining our previously developed prediction tool, KinasePhos (). Solvent accessibility and secondary structure of residues are also computationally predicted and are mapped to the PTM sites. The resource is now freely available at

Clinical Experience of Percutaneous Endoscopic Gastrostomy in Taiwanese Patients - 310 Cases in 8 Years

Although percutaneous endoscopic gastrostorny (PEG) has become a popular method for long-term tube feeding worldwide , there are only a few reports about its application in Taiwan. From May 1997 to May 2005, we performed 302 PEG insertions successfully in 310 attempts (97.4% success rate) using modified Ponsky's pull method with 24-Fr feeding tubes. All the patients received PEG for tube feeding except for two patients with cancerous peritonitis for decompression. The underlying diseases in these 308 patients who received PEG for tube feeding were 161 cerebrovascular accidents (52.3%), 62 head and neck cancers (20.1%), 21 cases of Parkinsonism (6.8%), and others. There were 11 major complications (3.6%) and 57 minor complications (18.9% ). Ten patients (3.3%) died within 30 days after PEG insertion. However, no procedure-related mortality occurred . In conclusion, PEG is an effective method for tube feeding and drainage with a high success rate. PEG insertion was often indicated for patients with dysphagia caused by cerebrovascular accident, head and neck cancer, and Parkinsonism in Taiwan. It is a relatively safe procedure, with a 3.6% rate of major complications and 18.9% rate of minor complications

Low Frequency of Bacteremia after Endoscopic Mucosal Resection

BACKGROUND: Endoscopic mucosal resection has become a popular alternative for the treatment of early-stage neoplasia of the gastrointestinal tract. However, there are still no data on the frequency of bacteremia associated with this form of treatment. METHODS: We conducted a prospective study of 21 men and 17 women undergoing endoscopic mucosal resection with a cap-fitted panendoscope for upper gastrointestinal lesions. Blood cultures were performed before, 10 minutes after, and 4 hours after the procedure for both aerobic and anaerobic bacteria. RESULTS : Blood culture at baseline was negative in all the patients. Two of 38 patients (5.3 %) had positive blood culture at 10 minutes after the procedure. The isolated microorganisms were Streptococcus salivarius and Corynebacterium species. All patients had negative blood cultures 4 hours later. None of these 38 patients had any symptoms or signs associated with infection. CONCLUSIONS: Bacteremia associated with endoscopic mucosal resection is infrequent and transient

Clinical Manifestations and Management of Buried Bumper Syndrome in Patients with Percutaneous Endoscopic Gastrostomy

BACKGROUND: Buried bumper syndrome has been regarded as an uncommon and late complication after percutaneous endoscopic gastrostomy (PEG) tube insertion. A variety of techniques have been reported to treat this problem, but only a few published cases exist. OBJECTIVE: Our purpose was to present the clinical manifestations and our management of a series of 19 patients with buried bumper syndrome. DESIGN: Case series study. SETTING: Referral medical centers. PATIENTS: Within 5 years, 31 episodes of buried bumper syndrome occurred in 10 men and 9 women. The estimated prevalence was 8.8% (19 in 216 PEG procedures during this period). INTERVENTION: All the buried tubes were removed smoothly by external traction and replaced with a new pull-type feeding tube by the pull method or a button or balloon replacement tube after dilation of the old tract. MAIN OUTCOME MEASUREMENTS: Success rate, complication rate. RESULTS: The duration between occurrence of buried bumper syndrome and PEG placement ranged from 1 to 50 months, with a median of 18 months. All the episodes were treated successfully except for one, in which reinsertion failed and a new PEG tube was inserted 1 week later. No significant complications occurred. LIMITATION: Small sample size. CONCLUSIONS: Buried bumper syndrome is not that uncommon and can occur soon after insertion of a PEG tube. The buried tube can be safely removed by external traction and in most cases can then be replaced with a pull-type or balloon replacement tube

Changes in Gastroesophageal Reflux in Patients With Nasogastric Tube Followed by Percutaneous Endoscopic Gastrostomy

Background/PurposeDespite frequent use of percutaneous endoscopic gastrostomy (PEG) for enteral feeding, the relationship between it and gastroesophageal reflux (GER) remains an incompletely answered question. We conducted this study to compare the GER between the same patients fed with a nasogastric (NG) tube and later with a PEG tube.MethodsWe enrolled 15 patients who had received NG tube feeding for > 6 months and were about to receive PEG tube insertion. We used Ponsky's pull method with 24 Fr feeding tubes. They received two GER scans, one just before PEG tube insertion and another 1 week after insertion. We drew regions of interest of radioactivity in the esophagus and stomach manually. The ratios of radioactivity of the region of interest in the esophagus over the stomach (GER ratio) were calculated to evaluate the severity of GER and compared.ResultsThe GER ratios of these patients were all small and <3% except one that was 4.7% in one patient before PEG tube insertion. There was a small but substantial decrease (65% risk reduction) in GER ratio after PEG tube insertion. After arcsine transformation, the difference in the transformed data between patients fed with an NG tube and after PEG tube insertion was significant (t= 2.46, p = 0.028), and was lower after PEG tube insertion.ConclusionOur study demonstrates by scintigraphy a small but significant reduction of GER after shifting from NG to PEG tube feeding

Comparison of the efficacy of esomeprazole and famotidine against stress ulcers in a neurosurgical intensive care unit

To compare the efficacy of esomeprazole and famotidine against stress ulcers and the association of these prophylactic agents with ventilator-associated pneumonia in patients admitted to neurosurgical intensive care unit (ICU). Sixty patients were randomly allocated into two groups (the esomeprazole and famotidine groups, n = 30 each) to receive prophylaxis medication for 7 days within 24 hours of admission in a neurosurgical ICU. Patients in the esomeprazole group received esomeprazole (40 mg) dissolved in water once a day through a nasogastric tube, whereas patients in the famotidine group received an intravenous infusion of famotidine (20 mg) every 12 hours. We then compared the occurrence of overt upper gastrointestinal bleeding and ventilator-associated pneumonia between these two groups. One patient in the famotidine group had overt upper gastrointestinal bleeding (3.3%), whereas the bleeding was not observed in patients in the esomeprazole group. Ventilator-associated pneumonia occurred in one patient (3.3%) from each group. One patient died within 30 days (3.3%) in the esomeprazole group and three patients (10%) died in the famotidine group. There was no difference in the occurrence of overt upper gastrointestinal bleeding (p = 1.000), ventilator-associated pneumonia (p = 1.000), and 30-day mortality (p = 0.612) between these two groups. In this small-scale study, the effect of administration of esomeprazole through a nasogastric tube on stress ulcer was similar to that of intravenous famotidine infusion in neurosurgical ICU patients. In addition, the association between prevalence of ventilator-associated pneumonia and administration of esomeprazole was also similar to that observed with famotidine infusion

Clinical Experience of Percutaneous Endoscopic Gastrostomy in Taiwanese Patients—310 Cases in 8 Years

Although percutaneous endoscopic gastrostomy (PEG) has become a popular method for long-term tube feeding worldwide, there are only a few reports about its application in Taiwan. From May 1997 to May 2005, we performed 302 PEG insertions successfully in 310 attempts (97.4% success rate) using modified Ponsky's pull method with 24-Fr feeding tubes. All the patients received PEG for tube feeding except for two patients with cancerous peritonitis for decompression. The underlying diseases in these 308 patients who received PEG for tube feeding were 161 cerebrovascular accidents (52.3%), 62 head and neck cancers (20.1%), 21 cases of Parkinsonism (6.8%), and others. There were 11 major complications (3.6%) and 57 minor complications (18.9%). Ten patients (3.3%) died within 30 days after PEG insertion. However, no procedure-related mortality occurred. In conclusion, PEG is an effective method for tube feeding and drainage with a high success rate. PEG insertion was often indicated for patients with dysphagia caused by cerebrovascular accident, head and neck cancer, and Parkinsonism in Taiwan. It is a relatively safe procedure, with a 3.6% rate of major complications and 18.9% rate of minor complications

Comparison of the efficacy of esomeprazole and famotidine against stress ulcers in a neurosurgical intensive care unit

Background: To compare the efficacy of esomeprazole and famotidine against stress ulcers and the association of these prophylactic agents with ventilator-associated pneumonia in patients admitted to neurosurgical intensive care unit (ICU). Patients and Methods: Sixty patients were randomly allocated into two groups (the esomeprazole and famotidine groups; n = 30 each) to receive prophylaxis medication for 7 days within 24 hours of admission in a neurosurgical ICU. Patients in the esomeprazole group received esomeprazole (40 mg) dissolved in water once a day through a nasogastric tube, whereas patients in the famotidine group received an intravenous infusion of famotidine (20 mg) every 12 hours. We then compared the occurrence of overt upper gastrointestinal bleeding and ventilator-associated pneumonia between these two groups. Results: One patient in the famotidine group had overt upper gastrointestinal bleeding (3.3%), whereas the bleeding was not observed in patients in the esomeprazole group. Ventilator-associated pneumonia occurred in one patient (3.3%) from each group. One patient died within 30 days (3.3%) in the esomeprazole group and three patients (10%) died in the famotidine group. There was no difference in the occurrence of overt upper gastrointestinal bleeding (p = 1.000), ventilator-associated pneumonia (p = 1.000), and 30-day mortality (p = 0.612) between these two groups. Conclusion: In this small-scale study, the effect of administration of esomeprazole through a nasogastric tube on stress ulcer was similar to that of intravenous famotidine infusion in neurosurgical ICU patients. In addition, the association between prevalence of ventilator-associated pneumonia and administration of esomeprazole was also similar to that observed with famotidine infusion