Predicting protein-ligand binding site using support vector machine with protein properties

Identification of protein-ligand binding site is an important task in structure-based drug design and docking algorithms. In the past two decades, different approaches have been developed to predict the binding site, such as the geometric, energetic, and sequence-based methods. When scores are calculated from these methods, the algorithm for doing classification becomes very important and can affect the prediction results greatly. In this paper, the support vector machine (SVM) is used to cluster the pockets that are most likely to bind ligands with the attributes of geometric characteristics, interaction potential, offset from protein, conservation score, and properties surrounding the pockets. Our approach is compared to LIGSITE, LIGSITEcsc, SURFNET, Fpocket, PocketFinder, Q-SiteFinder, ConCavity, and MetaPocket on the data set LigASite and 198 drug-target protein complexes. The results show that our approach improves the success rate from 60 to 80 percent at AUC measure and from 61 to 66 percent at top 1 prediction. Our method also provides more comprehensive results than the others

A New Differential Evolution with self-terminating ability using fuzzy control and k-nearest neighbors

A new Differential Evolution (DE) that incorporates fuzzy control and k-nearest neighbors algorithm to determine the terminating condition is proposed. A technique called Iteration Windows is introduced to govern the number of iteration in each searching stage. The size of the iteration windows is controlled by a fuzzy controller, which uses the information provided by the k-nearest neighbors system to analyze the population during the searching process. The controller keeps controlling the iteration windows until the end of the searching process. The wavelet based mutation process is embedded in the DE searching process to enhance the searching performance of DE. The F weight of DE is also controlled by the fuzzy controller to further speed up the searching process. A suite of benchmark test functions is employed to evaluate the performance of the proposed method. It is shown empirically that the proposed method can terminate the searching process with a reasonable number of iteration. © 2010 IEEE

Self-managing postoperative pain with the use of a novel, interactive device: a proof of concept study

Background: Pain is commonly experienced following surgical procedures. Suboptimal management is multifactorial. Objectives. The primary objective was to assess whether patients used a device (Navimed) to self-report pain over and above a normal baseline of observations. Secondary outcome measures included comparison of pain scores and patient use of and feedback on the device. Methods: In a prospective randomized controlled trial, elective gynaecological surgery patients received standard postoperative pain care or standard care plus the Navimed, which allowed them to self-report pain and offered interactive self-help options. Results: 52 female patients, 26 in each of device and standard groups, did not differ in the frequency of nurse-documented pain scores or mean pain scores provided to nurses. The device group additionally reported pain on the device (means 18.50 versus 11.90 pain ratings per day, t(32) = 2.75, p < 0.001) that was significantly worse than reported to nurses but retrospectively rated significantly less anxiety. 80% of patients found the device useful. Discussion and Conclusion: This study demonstrates that patients used the Navimed to report pain and to help manage it. Further work is required to investigate the difference in pain scores reported and to develop more sophisticated software

The surged faradic stimulation to the pelvic floor muscles as an adjunct to the medical management in children with rectal prolapse

<p>Abstract</p> <p>Background</p> <p>To assess the role of the surged faradic stimulation to the pelvic floor muscles as an adjunct to the conservative management in the children of idiopathic rectal prolapse</p> <p>Methods</p> <p><it>Study design</it>: Prospective</p> <p><it>Setting</it>: Pediatric Surgery Department, Pt BD Sharma, Post Graduate Institute of Medical Sciences, Rohtak</p> <p><it>Subjects</it>: 47 consecutive children with idiopathic rectal prolapse attending the Pediatric Surgery out patient department from July 2005 to June 2006</p> <p><it>Methodology</it>: The information pertaining to duration and the extent of rectal prolapse, predisposing or associated medical conditions, results of local clinical examination were noted. Surged faradic stimulation using modified intraluminal rectal probe, was given on the alternate days. The conventional conservative medical management was also continued. The extent of relief and the number of the sittings of faradic stimulation required were noted at various stages of follow-ups</p> <p><it>Statistical Methods</it>: Mean values between those completely cured and others; poor responders and others were compared with t-test and proportions were compared with Chi square test. The p-value < 0.05 was considered statistically significant.</p> <p>Results</p> <p>The mean number of sittings in the completely cured group (n = <b>28</b>(64%)) was (12.4 ± 7.8) and was comparable with very poor responder (n = 6(13%). There was higher percentage of relief (76%) at the first follow up (at 15 days) in completely cured Vs other (37%) and also the poor responders showed (20%) Vs other (68%) and was statistically significant.</p> <p>Conclusion</p> <p>With use of faradic stimulation, even the long-standing rectal prolapse can be fully cured. The follow up visit at 2 weeks is very important to gauge the likely success of this modality in treatment of the patients with rectal prolapse. Those showing poor response at this stage may require alternative treatment or take a long time to get cured</p

Plasma treatment of p-GaN/n-ZnO nanorod light-emitting diodes

Conference vol. 8987 entitled: Oxide-based Materials and Devices VZinc oxide (ZnO) is a material of great interest for short-wavelength optoelectronic applications due to its wide band gap (3.37 eV) and high exciton binding energy (60 meV). Due to the difficulty in stable p-type doping of ZnO, other p-type materials such as gallium nitride (GaN) have been used to form heterojunctions with ZnO. p-GaN/n-ZnO heterojunction devices, in particular light-emitting diodes (LED) have been extensively studied. There was a huge variety of electronic properties and emission colors on the reported devices. It is due to the different energy alignment at the interface caused by different properties of the GaN layer and ZnO counterpart in the junction. Attempts have been made on modifying the heterojunction by various methods, such as introducing a dielectric interlayer and post-growth surface treatment, and changing the growth methods of ZnO. In this study, heterojunction LED devices with p-GaN and ZnO nanorods array are demonstrated. The ZnO nanorods were grown by a solution method. The ZnO nanorods were exposed to different kinds of plasma treatments (such as nitrogen and oxygen) after the growth. It was found that the treatment could cause significant change on the optical properties of the ZnO nanorods, as well as the electronic properties and light emissions of the resultant LED devices. © (2014) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE). Downloading of the abstract is permitted for personal use only.Link_to_subscribed_fulltex

Induction of aromatic ring: cleavage dioxygenases in Stenotrophomonas maltophilia strain KB2 in cometabolic systems

Stenotrophomonas maltophilia KB2 is known to produce different enzymes of dioxygenase family. The aim of our studies was to determine activity of these enzymes after induction by benzoic acids in cometabolic systems with nitrophenols. We have shown that under cometabolic conditions KB2 strain degraded 0.25–0.4 mM of nitrophenols after 14 days of incubation. Simultaneously degradation of 3 mM of growth substrate during 1–3 days was observed depending on substrate as well as cometabolite used. From cometabolic systems with nitrophenols as cometabolites and 3,4-dihydroxybenzoate as a growth substrate, dioxygenases with the highest activity of protocatechuate 3,4-dioxygenase were isolated. Activity of catechol 1,2- dioxygenase and protocatechuate 4,5-dioxygenase was not observed. Catechol 2,3-dioxygenase was active only in cultures with 4-nitrophenol. Ability of KB2 strain to induce and synthesize various dioxygenases depending on substrate present in medium makes this strain useful in bioremediation of sites contaminated with different aromatic compounds

Morbidity related to defunctioning ileostomy closure after ileal pouch-anal anastomosis and low colonic anastomosis

Purpose Defunctioning ileostomies are widely performed in order to prevent or treat anastomotic leakage after colorectal surgery. The aim of the present study was to determine morbidity related to stoma closure and to identify predictive factors of a complicated postoperative course. Methods A consecutive series of 138 patients were retrospectively analyzed after stoma reversal. Data collection included general demographics and surgery-related aspects. Morbidity related to stoma closure was retrieved from our prospectively collected registry of complications. Results In 74 of 138 patients, defunctioning ileostomy was performed after restorative proctocolectomy and ileal pouchanal anastomosis (IPAA). The remaining ileostomies (n=64) were constructed after a low colorectal or coloanal anastomosis. A total of 46 complications were recorded in 28 patients resulting in an overall complication rate of 20.3%. Anastomotic leakage rate was 4.3%, and reoperation rate was 8.0%. The number of complications according to the Clavien-Dindo classification was 5 for grade I (10.9%), 26 for grade II (56.5%), 13 for grade III (28.3%), 1 for grade IV (2.2%), and 1 for grade V (2.2%). Multivariate analysis revealed a significantly higher ASA score in the complicated group (P=0.015, odds ratio 2.6, 95% confidence interval 1.2-5.6). Conclusions Closure of a defunctioning ileostomy is associated with 20% morbidity and a reoperation rate of 8%. There is an urgent need for criteria on which a more selective use of a defunctioning ileostomy after low colonic anastomosis or IPAA can be based given its associated morbidit

Ascl1 (Mash1) Defines Cells with Long-Term Neurogenic Potential in Subgranular and Subventricular Zones in Adult Mouse Brain

Ascl1 (Mash1) is a bHLH transcription factor essential for neural differentiation during embryogenesis but its role in adult neurogenesis is less clear. Here we show that in the adult brain Ascl1 is dynamically expressed during neurogenesis in the dentate gyrus subgranular zone (SGZ) and more rostral subventricular zone (SVZ). Specifically, we find Ascl1 levels low in SGZ Type-1 cells and SVZ B cells but increasing as the cells transition to intermediate progenitor stages. In vivo genetic lineage tracing with a tamoxifen (TAM) inducible Ascl1CreERT2 knock-in mouse strain shows that Ascl1 lineage cells continuously generate new neurons over extended periods of time. There is a regionally-specific difference in neuron generation, with mice given TAM at postnatal day 50 showing new dentate gyrus neurons through 30 days post-TAM, but showing new olfactory bulb neurons even 180 days post-TAM. These results show that Ascl1 is not restricted to transit amplifying populations but is also found in a subset of neural stem cells with long-term neurogenic potential in the adult brain

Diagnosis of prostate cancer by detection of minichromosome maintenance 5 protein in urine sediments

Background: The accuracy of prostate-specific antigen (PSA) testing in prostate cancer detection is constrained by low sensitivity and specificity. Dysregulated expression of minichromosome maintenance (Mcm) 2–7 proteins is an early event in epithelial multistep carcinogenesis and thus MCM proteins represent powerful cancer diagnostic markers. In this study we investigate Mcm5 as a urinary biomarker for prostate cancer detection. Methods: Urine was obtained from 88 men with prostate cancer and from two control groups negative for malignancy. A strictly normal cohort included 28 men with complete, normal investigations, no urinary calculi and serum PSA <2 ng ml–1. An expanded control cohort comprised 331 men with a benign final diagnosis, regardless of PSA level. Urine was collected before and after prostate massage in the cancer patient cohort. An immunofluorometric assay was used to measure Mcm5 levels in urine sediments. Results: The Mcm5 test detected prostate cancer with 82% sensitivity (confidence interval (CI)= 72–89%) and with a specificity ranging from 73 (CI=68–78%) to 93% (CI=76–99%). Prostate massage led to increased Mcm5 signals compared with pre-massage samples (median 3440 (interquartile range (IQR) 2280 to 5220) vs 2360 (IQR <1800 to 4360); P=0.009), and was associated with significantly increased diagnostic sensitivity (82 vs 60%; P=0.012). Conclusions: Urinary Mcm5 detection seems to be a simple, accurate and noninvasive method for identifying patients with prostate cancer. Large-scale prospective trials are now required to evaluate this test in diagnosis and screening