ESLpred2: improved method for predicting subcellular localization of eukaryotic proteins

<p>Abstract</p> <p>Background</p> <p>The expansion of raw protein sequence databases in the post genomic era and availability of fresh annotated sequences for major localizations particularly motivated us to introduce a new improved version of our previously forged eukaryotic subcellular localizations prediction method namely "ESLpred". Since, subcellular localization of a protein offers essential clues about its functioning, hence, availability of localization predictor would definitely aid and expedite the protein deciphering studies. However, robustness of a predictor is highly dependent on the superiority of dataset and extracted protein attributes; hence, it becomes imperative to improve the performance of presently available method using latest dataset and crucial input features.</p> <p>Results</p> <p>Here, we describe augmentation in the prediction performance obtained for our most popular ESLpred method using new crucial features as an input to Support Vector Machine (SVM). In addition, recently available, highly non-redundant dataset encompassing three kingdoms specific protein sequence sets; 1198 fungi sequences, 2597 from animal and 491 plant sequences were also included in the present study. First, using the evolutionary information in the form of profile composition along with whole and N-terminal sequence composition as an input feature vector of 440 dimensions, overall accuracies of 72.7, 75.8 and 74.5% were achieved respectively after five-fold cross-validation. Further, enhancement in performance was observed when similarity search based results were coupled with whole and N-terminal sequence composition along with profile composition by yielding overall accuracies of 75.9, 80.8, 76.6% respectively; best accuracies reported till date on the same datasets.</p> <p>Conclusion</p> <p>These results provide confidence about the reliability and accurate prediction of SVM modules generated in the present study using sequence and profile compositions along with similarity search based results. The presently developed modules are implemented as web server "ESLpred2" available at <url>http://www.imtech.res.in/raghava/eslpred2/</url>.</p

Causes, Timing, and Impact of Dual Antiplatelet Therapy Interruption for Surgery (From the PARIS Registry)

Temporary interruption of dual antiplatelet therapy (DAPT) is not infrequently required in patients undergoing percutaneous coronary intervention (PCI). We sought to describe the procedures and outcomes associated with DAPT interruption in patients treated with DAPT following successful PCI from the Patterns of non-adherence to anti-platelet regimens in stented patients registry (n = 5018). DAPT interruption was prespecified as physician recommended cessation forcohort, 490 patients (9.8%) experienced 594 DAPT interruptions over 2 years following PCI. Only 1 antiplatelet agent was interrupted in 57.2% cases and interruption was frequently recommended by noncardiologists (51.3%). Where type of surgery was reported, majority of DAPT interruptions occurred for minor surgery (68.4% vs 31.6%) and a similar cessation pattern of single versus dual antiplatelet cessation was observed regardless of minor or major surgery. Subsequent to DAPT interruption, 12 patients (2.4%) experienced 1 thrombotic event each, of which 5 (1.0%) occurred during the interruption period. All events occurred in patients who either stopped both agents (8 of 12) or clopidogrel-only (4 of 12), with no events occurring due to aspirin cessation alone. In conclusion, in the Patterns of Non-adherence to Anti-platelet Regiments in Stented Patients registry, 1 in 10 patients were recommended DAPT interruption for surgery within 2 years of PCI. Interruption was more common for a single agent rather than both antiplatelet agents regardless of severity of surgery, and was frequently recommended by noncardiologists. Only 1% of patients with DAPT interruption experienced a subsequent thrombotic event during the interruption period, which mainly occurred in patients stopping both antiplatelet agents

Support vector machine-based method for subcellular localization of human proteins using amino acid compositions, their order, and similarity search

Here we report a systematic approach for predicting subcellular localization (cytoplasm, mitochondrial, nuclear, and plasma membrane) of human proteins. First, support vector machine (SVM)-based modules for predicting subcellular localization using traditional amino acid and dipeptide (i � 1) composition achieved overall accuracy of 76.6 and 77.8%, respectively. PSI-BLAST, when carried out using a similarity-based search against a nonredundant data base of experimentally annotated proteins, yielded 73.3 % accuracy. To gain further insight, a hybrid module (hybrid1) was developed based on amino acid composition, dipeptide composition, and similarity information and attained better accuracy of 84.9%. In addition, SVM modules based on a different higher order dipeptide i.e. i � 2, i � 3, and i

Clinico-Radiographic research evaluating crestal bone level and bone density surrounding dental implants

Aim: Planning the surgical operation, choosing the type of implant, and the effectiveness of the implant all heavily rely on the quantity and quality of the accessible bone. This study's goal was to determine how promptly inserted dental implants affected postoperative changes in bone density and crestal bone level by Cone bean computed tomography (CBCT) gray-scale value during a follow-up of three to six months. Method: A prospective clinical-radiographic investigation was conducted. Twenty participants with a partly edentulous arch who were also systemically healthy were chosen from the OPD of the Department of Periodontics and Oral Implantology. Each patient's oral hygiene status was noted, and a preoperative CBCT was performed to assess bone density. The following clinical parameters were noted before surgical procedures: plaque index (PI) (Silness and Loe, 1964), gingival index (GI) (Loe and Sillness, 1964), probing pocket depth (PPD), and primary stability. Result: A weak connection between Hounsfield unit (HU) in three months and six months was found. Moreover, a slender positive connection between baseline primary stability and three months was found. PI was shown to have a statistically significant difference between the means at several follow-ups (P value of 0.0001). PI and probing depth were not statistically different between baseline and six months (P values = 0.0001) or between three months and six months (P values = 0.050), respectively. Conclusion: The main outcome of this study shows that insertion torque is directly proportional to bone density and crestal bone level