Towards chemically accurate QM/MM simulations on GPUs.

Computational chemistry simulations are extensively used to model natural phenomena. To maintain performance similar to molecular mechanics, but achieve comparable accuracy to quantum mechanical calculations, many researchers are using hybrid QM/MM methods. In this article we evaluate our GPU-accelerated ONIOM implementation by measurements on the crambin and HIV integrase proteins with different size QM model systems. We demonstrate that by using a larger QM region, a better energy accuracy can be achieved at the expense of simulation time. This trade-off is important to consider for the researcher running QM/MM calculations. Furthermore, we show that the ONIOM energy monotonically approaches the pure quantum mechanical energy of the whole system. The experiments are made feasible by utilizing the cutting-edge BrianQC quantum chemistry module for Hartree-Fock level SCF and our GPU-accelerated MMFF94 force field implementation for molecular mechanics calculations.

[The idopathic granulomatous mastitis. A rare entity in our departments practice]. / Az idiopátiás granulomatózus mastitis. Egy ritka kórkép elofordulása osztályunkon.

Introduction: Two cases of idiopathic granolomatous mastitis were diagnosed by histological examination in our Surgical Department in 2017. The idiopathic granulomatous mastitis is a rare, benign inflammatory laesion of the breast which can mimic malignancy in it's clinical appearance. We would like to draw attention to this differential diagnostic problem based on the cases of our Surgery Department.

Calculation of Quantum Chemical Two-Electron Integrals by Applying Compiler Technology on GPU.

In this article, we present an effective approach to calculate quantum chemical two-electron integrals over basis sets consisting of Gaussian-type basis functions on graphical processing unit (GPU). Our framework generates several different variants called routes to the same integral problem with different integral algorithms (McMurchie-Davidson, Head-Gordon-Pople, and Rys) and precision. Each route is benchmarked on more GPU architectures, and with this data, a model is fitted to select the best available route for an integral task given a GPU architecture. Moreover, this approach supports the computation of high angular momentum orbitals up to g effectively on GPU, tested up to cc-pVQZ-sized basis sets. Rigorous analysis is shown regarding the effectiveness of our method. Molecule simulations with several basis sets are measured using NVIDIA GTX 1080 Ti, NVIDIA P100, and NVIDIA V100 cards.

[Our experiences with the use of 3-dimensional meshes to prevent and to repair parastomal hernias]. / Parastomalis sérvek megelozése és megoldása: a háromdimenziós hálókkal szerzett eddigi tapasztalataink.

INTRODUCTION: Albeit there is decreasing tendency nowadays for stoma construction, if it still happens, parastomal herniation might occur in up to 50% of cases afterwards. One third of the cases requires surgical correction, not rarely as an emergency. The different methods of repair can be quite demanding and the complication rates are high. From 2003 we have started to use specially designed 3-dimensional meshes for the prevention and repair of parastomal hernias. METHODS: From 1st of January 2012 to 1st of June 2016 we have used these devices within the framework of a prospective, controlled, randomized study enrolling the patients in preventive and repair arms. Until now mesh was implanted for prevention at the time of the index operation in 38 cases, (control group: 46 cases), and for repair in 14 cases (control group: 18 cases). Recruitment of the patients will end in 2017. The operations were performed by laparoscopic approach in 22 cases and by open approach in 62 cases in the preventive arm, and 6/26 cases in the repair arm respectively. Mean follow up period is 19.2 months in the mesh group and 22.6 months in the non mesh group in the preventive arm, and 25.9/20.4 months in the repair arm respectively. RESULTS: No statistical analysis was used to interpret these interim results in this paper, we intend to analyze our results at the end of the study. At this stage apparently there is no difference between the group of patients in terms of complications in both arms. Parastomal herniation was found in 18 cases (39.1%) in the non mesh group and in 3 cases (7.8%) in the mesh group in the preventive arm. Recurrency was noted in 8 cases (44%) in the non mesh group, and in 1 case (7.1%) in the mesh group in the repair arm. CONCLUSIONS: Our results correlate with other studies where mesh insertion was used to prevent and/or repair parastomal hernias. We attribute these results mainly to the special, 3-dimensional design of the meshes used by us. This construction was developed based on understanding the patomechanism of parastomal hernia formation.

[Proctocolectomy with J pouch. Ileo-anal anastomosis performed with PPH stapler. Our experiences after 88 cases]. / J-pouchcsal rekonstruált proctocolectomia során PPH-géppel készített ileoanalis anastomosis. Tapasztalataink 88 eset kapcsán.

AIM: Ulcerative colitis (CU) or Familiar Polyposis (FAP) can be the indication for proctocolectomy reconstructed with J pouch. The complete removal of the colon mucosa is essential regarding the late complications and at the same time the atraumatic surgical technique is very important concerning on the long term functional results. Both aspects seems to be answered by the stapled ileo-anal anastomosis using a "procedure for prolaps and haemorrhoids (PPH)" stapler applied by us since 2000. PATIENTS AND METHODS: 117 proctocolectomies reconstructed with J pouch and ileo-anal anastomosis were performed in our department between March 1990 and September 2016 indicated by CU or by FAP. In the first time period the ileo-anal anastomosis was sutured by hand (29 cases) and since 2000 the PPH stapler was applied as a routine (88 patients). Deviating ileostomy was performed in most cases of us. The data of the 117 patients were collected from the database of our hospital, 45 of them were interviewed personally and another 31 patients were contacted by phone, so 76 patients (65%) were eligible for follow-up. Frequency of stool, use of loperamid, level of incontinence (Wexner score) and perianal dermatitis were detected. The mean follow-up time was 18.6 years in the hand-sewn anastomosis group and 7.6 years in the PPH group. RESULTS: In the hand-sewn anastomosis group in 4/29 cases (13.8%) the removal of the pouch with definite ileostomy were necessary (2 pouchitis, 1 pouch necrosis, 1 recidiv rectum cancer); the mean stool frequency was 4.3 per day; the Wexner incontinence score was 8.5 and 2/15 patients (13.3%) live with ileostomy caused by incontinence. In the PPH stapled ileo-anal anastomosis group in 4/88 cases (4.5%) were the pouch removed (caused by pouchitis), the mean stool frequency was 4.0 per day; the Wexner score was 7.6 and 4/61 patients (6.6%) live with ileostomy caused by incontinence. CONCLUSIONS: Based on our experience the ileo-anal anastomosis performed by PPH stapler is technically feasible, seems to be effective concerning on the complete removal of the rectal mucosa and we observed better functional results compared with the hand-sewn anastomosis. Our data should be confirmed because of the low patients' volume.

[Our metabolic surgical activity, 2010-2016]. / Metabolikus sebészeti tevékenységünk, 2010­2016.

INTRODUCTION: The prevalence of morbid obesity and its co-morbidities - first of all diabetes type 2 - increased dramatically in the last decades. As the conservative ways of treatment (diet, training, etc.) in most cases does not lead to effective and long term weight loss, there is an increasing need for the metabolic surgical interventions. METHOD: During the last 6 and half years 514 laparoscopic RouxY gastric bypass (LRYGB) and 54 laparoscopic gastric sleeve resection (LGSR) were performed in our department. The data of random selected 40 patients after primary LRYGB and 15 patients after sleeve resection were collected. The applied criteria of the indication for surgery, the routine examinations and treatments before and after the intervention, the results and the type and the rate of the complications will be presented. RESULTS: According to our experience both procedures are long term effective for weight loss and for the resolution of co-morbidities, and can be performed with low risk of complications. After LRYGB more effective weight loss (extra weight loss 88% vs. 68%) and higher rate of resolution of diabetes type 2, hypertension and gastro-esophageal reflux were found compared to sleeve resection. CONCLUSION: Based on our results we prefer LRYGB. Gastric sleeve resection is indicated by us, when there is no way - or only with high risk - to perform gastric bypass, taking into consideration of course the individual requirements of the patients.

[Minimal invasive esophageal resection with anastomosis on the neck [McKeown]. Our experiences after 20 cases]. / Minimálisan invazív oesophagusreszekció nyaki anastomosissal (McKeown-mutét). Tapasztalataink 20 eset kapcsán.

OBJECTIVE: Esophageal resection is a traumatic intervention usually performed on patients with poor condition, resulting high mortality and morbidity. To improve the high incidence of complications, minimal invasive interventions were introduced. The results of the thoracoscopically and laparoscopically performed esophageal resection (McKeown) was investigated after 20 cases and the technical details of the surgical intervention are presented. PATIENTS AND METHOD: 20 thoracoscopic esophageal resection with laparoscopic gastric tube formation (sec. Akiyama) preparing the esophago-gastric anastomosis on the neck were performed in our department in the last four years. 1 patient with stricture and the other 19 patients with esophageal cancer were operated on, among them11 had T4 stage. 17 patient received neoadjuvant chemo-radiotherapy because of advanced disease. Regular follow up examinations were performed in the oncological outpatient department. RESULTS: 8 patients are alive after a mean follow up period of 25 months, 2 of them are treated oncologically because of recurrent disease. 19 patients were extubated within 12 hours after the intervention and the time spent in the intensive care unit were reduced to 1 or 2 days. The mean duration of the intervention was 320 minutes. Thoracoscopic dissection was performed in 8 patients without ventilation of the right lung using double lumen tracheal tube, among them 3 patients developed pneumonia in the postoperative period. The remaining 12 patients were operated with ventilated right lung, among them one patient developed pneumonia. One patient was converted because of injury of the thoracic aorta, after urgent thoracotomy we managed to suture the aortic wall. 1 patient died in 30 days after the operation, caused by leakage of the anastomosis, resulting mediastinitis and esophago-tracheal fistula. In two patients re-thoracoscopy and ligation of the thoracic duct was performed because of chylothorax refractory for conservative treatment. CONCLUSIONS: According to our observation the minimal invasive esophageal resection resulted in comparable oncological results with relevant reduction of mortality and morbidity compared to the open procedure. After procedures performed with ventilated lung further reduction of pulmonary complication was found. In case of tumors infiltrating the tracheal or the aortic wall, thoracotomy should be considered to explore the thoracic cavity and to carry out the dissection, if it is possible. Our results should be reinforced because of low number of patients.

Quality of life, weight loss and improvement of co-morbidities after primary and revisional laparoscopic roux Y gastric bypass procedure-comparative match pair study.

BACKGROUND: The prevalence of morbid obesity and its co-morbidities is dramatically increasing, as is the extent of weight loss surgery. A large number of patients after various bariatric procedures need revisional intervention for various reasons. We investigated the efficacy and the safety of revisional laparoscopic Roux Y gastric bypass (LRYGB) among our patients, who were revised as a consequence of inadequate weight loss or weight regain after previous bariatric interventions. METHODS: A comparative, double-centre, match pair study was performed comparing the data of 44 patients after revisional surgery with 44 patients after primary gastric bypasses, focusing on weight loss, life quality and improvement of co-morbidities. Matching criteria were age, gender, preoperative BMI and follow-up period. Previous procedures consisted of 23 gastric bandings, 13 sleeve resections, 4 LRYGB and 4 vertical banded gastroplasties. RESULTS: Extra weight loss (EWL) was significantly reduced after revisional gastric bypasses compared to primary intervention (EWL 66 vs. 91 %, p<0.05). Life quality scores were also decreased in the revisional group compared to the control group without statistical significance (SF 36 score 635 vs. 698.5, p=0.22; Moorehead-Aldert II score 1.4 vs. 2.0, p=0.10). The resolution rate of co-morbidities (T2DM, hypertension, gastro-oesophageal reflux (GER), osteoarthrosis, sleep apnoea) was also higher after primary gastric bypasses. CONCLUSIONS: Revisional LRYGB is an effective and safe method for patients with inadequate weight loss after previous bariatric surgery concerning weight reduction, life quality and improvement of co-morbidities. Our results indicate lower efficacy of revisional compared to primary LRYGB reaching statistical significance in regard to weight loss.

Fast DRR generation for 2D to 3D registration on GPUs.

PURPOSE: The generation of digitally reconstructed radiographs (DRRs) is the most time consuming step on the CPU in intensity based two-dimensional x-ray to three-dimensional (CT or 3D rotational x-ray) medical image registration, which has application in several image guided interventions. This work presents optimized DRR rendering on graphical processor units (GPUs) and compares performance achievable on four commercially available devices. METHODS: A ray-cast based DRR rendering was implemented for a 512 × 512 × 72 CT volume. The block size parameter was optimized for four different GPUs for a region of interest (ROI) of 400 × 225 pixels with different sampling ratios (1.1%-9.1% and 100%). Performance was statistically evaluated and compared for the four GPUs. The method and the block size dependence were validated on the latest GPU for several parameter settings with a public gold standard dataset (512 × 512 × 825 CT) for registration purposes. RESULTS: Depending on the GPU, the full ROI is rendered in 2.7-5.2 ms. If sampling ratio of 1.1%-9.1% is applied, execution time is in the range of 0.3-7.3 ms. On all GPUs, the mean of the execution time increased linearly with respect to the number of pixels if sampling was used. CONCLUSIONS: The presented results outperform other results from the literature. This indicates that automatic 2D to 3D registration, which typically requires a couple of hundred DRR renderings to converge, can be performed quasi on-line, in less than a second or depending on the application and hardware in less than a couple of seconds. Accordingly, a whole new field of applications is opened for image guided interventions, where the registration is continuously performed to match the real-time x-ray.