How the Choice of Force-Field Affects the Stability and Self-Assembly Process of Supramolecular CTA Fibers.

In recent years, computational methods have become an essential element of studies focusing on the self-assembly process. Although they provide unique insights, they face challenges, from which two are the most often mentioned in the literature: the temporal and spatial scale of the self-assembly. A less often mentioned issue, but not less important, is the choice of the force-field. The repetitive nature of the supramolecular structure results in many similar interactions. Consequently, even a small deviation in these interactions can lead to significant energy differences in the whole structure. However, studies comparing different force-fields for self-assembling systems are scarce. In this article, we compare molecular dynamics simulations for trifold hydrogen-bonded fibers performed with different force-fields, namely GROMOS, CHARMM General Force Field (CGenFF), CHARMM Drude, General Amber Force-Field (GAFF), Martini, and polarized Martini. Briefly, we tested the force-fields by simulating: (i) spontaneous self-assembly (none form a fiber within 500 ns), (ii) stability of the fiber (observed for CHARMM Drude, GAFF, MartiniP), (iii) dimerization (observed for GROMOS, GAFF, and MartiniP), and (iv) oligomerization (observed for CHARMM Drude and MartiniP). This system shows that knowledge of the force-field behavior regarding interactions in oligomer and larger self-assembled structures is crucial for designing efficient simulation protocols for self-assembling systems.

High level of patient satisfaction and comfort during diagnostic urological procedures performed by urologists and residents.

OBJECTIVE: The aim of this study was to investigate how patients experience diagnostic urological procedures performed by urologists, junior residents and senior residents, and to assess the influence of procedure-related factors on patient experiences. METHODS: Data were collected during 222 procedures: 84 transrectal ultrasound-guided prostate biopsies (TRUSP; urologists n = 39, residents n = 45) and 138 urethrocystoscopies (UCS; urologists n = 44, residents n = 94) in six hospitals. Patient experiences were assessed using a questionnaire focusing on pain, comfort and satisfaction (visual analogue scale, 0-10) and communication aspects on a four-point Likert scale. Clinical observations were made to identify influencing factors. RESULTS: Median values for patient experiences across procedures were 10 (range 5-10) for patient satisfaction, 2 (0-9) for pain and 8 (0-10) for comfort. Generalized estimating equations revealed no significant differences between urologists, senior residents and junior residents in terms of experienced patient comfort, satisfaction or pain. Procedural time was longer for residents, but this did not correlate significantly with patient-experienced comfort (p = 0.3). In UCS, patient comfort and satisfaction were higher in the supine position for male and female patients, respectively (p < 0.01). In TRUSP, local anaesthesia resulted in a significant decrease in pain (p = 0.002) and an increase in comfort (p = 0.03). Finally, older patients experienced less pain and gave higher comfort and satisfaction responses than younger patients. CONCLUSIONS: Patients expressed high levels of satisfaction and comfort during diagnostic urological procedures. Experiences were not affected by the level of training, suggesting highly developed interpersonal and communication skills for residents in an early stage of residency training. Patients demonstrated significant preferences for local anaesthesia in TRUSP and performance of UCS in the supine position over the lithotomy position.

Benchmark of Schemes for Multiscale Molecular Dynamics Simulations.

In multiscale molecular dynamics simulations the accuracy of detailed models is combined with the efficiency of a reduced representation. For several applications - namely those of sampling enhancement - it is desirable to combine fine-grained (FG) and coarse-grained (CG) approaches into a single hybrid approach with an adjustable mixing parameter. We present a benchmark of three algorithms that use a mixing of the two representation layers using a Lagrangian formalism. The three algorithms use three different approaches for keeping the particles at the FG level of representation together: 1) addition of forces, 2) mass scaling, and 3) temperature scaling. The benchmark is applied to liquid hexadecane and includes an evaluation of the average configurational entropy of the FG and CG subsystems. The temperature-scaling scheme achieved a 3-fold sampling speedup with little deviation of FG properties. The addition-of-forces scheme kept FG properties the best but provided little sampling speedup. The mass-scaling scheme yielded a 5-fold speedup but deviated the most from FG properties.

Training robotic surgery in urology: experience and opinions of robot urologists.

BACKGROUND: To answer the research questions: (a) what were the training pathways followed by the first generation of robot urologists; and (b) what are their opinions on the ideal training for the future generation? METHODS: Data were gathered with a questionnaire and semi-structured interviews in a mixed-method research design. RESULTS: The results show that training approaches differed from hardly any formal training to complete self-initiated training programmes, with all available learning resources. The median number of supervised procedures at the start of robot-assisted laparoscopy was five (range 0-100). Before patient-related console time, respondents indicated that the minimum training of robot trainees should consist of: live observations (94% indicated this as essential), video observations (90%), knowledge (88%), table assisting (87%) and basic skills (70%). CONCLUSION: The first generation of robot urologists used different training approaches to start robotic surgery. There is a need for a structured and compulsory training programme for robotic surgery. Copyright © 2014 John Wiley & Sons, Ltd.

Experimental and molecular dynamics characterization of dense microemulsion systems: morphology, conductivity and SAXS.

Microemulsions are exciting systems that are promising as tuneable self-assembling templating reaction vessels at the nanoscale. Determination of the nano-structure of microemulsions is, however, not trivial, and there are fundamental questions regarding their design. We were able to reproduce experimental data for an important microemulsion system, sodium-AOT-n-heptane-water, using coarse-grained simulations involving relatively limited computational costs. The simulation allows visualization and deeper investigation of controversial phenomena such as bicontinuity and ion mobility. Simulations were performed using the Martini coarse-grained force field. AOT bonded parameters were fine-tuned by matching the geometry obtained from atomistic simulations. We investigated several compositions with a constant ratio of surfactant to oil while the water content was varied from 10 to 60% in weight. From mean square displacement calculation of all species, it was possible to quantify caging effects and ion mobility. Average diffusion coefficients were calculated for all charged species and trends in the diffusion coefficients were used to rationalize experimental conductivity data. Especially, the diffusion coefficient of charged species qualitatively matched the variation in conductivity as a function of water content. The scattering function was calculated for the hydrophilic species and up to 40% water content quantitatively matched the experimental data obtained from small angle X-ray scattering measurements. For higher water contents, discrepancies were observed and attributed to a nearby phase separation. In particular, bicontinuity of water and oil was computationally visualized by plotting the coordinates of hydrophilic beads. Equilibrated coarse-grained simulations were reversed to atomistic models in order both to compare ion mobility and to catch finer simulation details. Especially, it was possible to capture the intimate ion pair interaction between the sodium ion and the surfactant head group.

[Complications due to lack of knowledge of the urinary sphincter prosthesis]. / Complicaties door gebrekkige kennis van urinaire sfincterprothese.

BACKGROUND: The placement of an artificial urinary sphincter prosthesis is a recognised treatment for men with urinary incontinence that is caused by insufficient sphincter action, although it is rarely used. Physicians from specialties other than urology know little about the components and mechanism of action of this prosthesis, which can lead to severe complications. CASE DESCRIPTION: A 67-year-old patient with a history of radical prostatectomy came to the emergency department with abdominal pain after a colonoscopy. A few years prior, he had received an artificial urinary sphincter prosthesis because of urinary incontinence. An abdominal CT scan showed a cystic lesion, which was punctured under ultrasonic guidance. The patient was completely incontinent after the intervention. It appeared to have been the pressure balloon of the urinary sphincter prosthesis that was punctured. The pressure balloon was operatively replaced several weeks later. During this procedure, the pressure balloon was placed intravesically instead of in the retropubic space and a reoperation was necessary. CONCLUSION: To prevent complications, all physicians should know how medical implants function, including the ones that are rarely used. In addition, patients need to be well informed of their use.

Efficient Algorithms for Langevin and DPD Dynamics.

In this article, we present several algorithms for stochastic dynamics, including Langevin dynamics and different variants of Dissipative Particle Dynamics (DPD), applicable to systems with or without constraints. The algorithms are based on the impulsive application of friction and noise, thus avoiding the computational complexity of algorithms that apply continuous friction and noise. Simulation results on thermostat strength and diffusion properties for ideal gas, coarse-grained (MARTINI) water, and constrained atomic (SPC/E) water systems are discussed. We show that the measured thermal relaxation rates agree well with theoretical predictions. The influence of various parameters on the diffusion coefficient is discussed.

Minimizing light exposure with the programmable array microscope.

The exposure of fluorophores to intense illumination in a microscope often results in photobleaching and phototoxicity, thus constituting a major limiting factor in time lapse live cell or single molecule imaging. Laser scanning confocal microscopes are particularly prone to this problem, inasmuch as they require high irradiances to compensate for the inherently low duty cycle of point scanning systems. In the attempt to maintain adequate speed and signal-to-noise ratios, the fluorophores are often driven into saturation, thereby generating a nonlinear response. One approach for reducing photodegradation in the laser scanning confocal microscope is represented by controlled light exposure microscopy, introduced by Manders and colleagues. The strategy is to reduce the illumination intensity in both background areas (devoid of information) as well as in bright foreground regions, for which an adequate signal-to-noise ratio can be achieved with lower excitation levels than those required for the less intense foreground pixels/voxels. Such a variable illumination scheme can also be exploited in widefield microscopes that employ lower irradiance but higher illumination duty cycles. We report here on the adaptation of the controlled light exposure microscopy principle to the programmable array microscope, which achieves optical sectioning by use of a spatial light modulator (SLM) in an image plane as a programmable mask for illumination and conjugate (and nonconjugate) detection. By incorporating the basic controlled light exposure microscopy concept for minimizing exposure, we have obtained a reduction in the rate of photobleaching of up to ~5-fold, while maintaining an image quality comparable to regular imaging with the programmable array microscope.

CT colonography with minimal bowel preparation: evaluation of tagging quality, patient acceptance and diagnostic accuracy in two iodine-based preparation schemes.

PURPOSE: The aim of this study was to compare a 1-day with a 2-day iodine bowel preparation for CT colonography in a positive faecal occult blood test (FOBT) screening population. MATERIALS AND METHODS: One hundred consecutive patients underwent CT colonography and colonoscopy with segmental unblinding. The first 50 patients (group 1) ingested 7 50 ml iodinated contrast starting 2 days before CT colonography. The latter 50 patients (group 2) ingested 4 50 ml iodinated contrast starting 1 day before CT colonography. Per colonic segment measurements of residual stool attenuation and homogeneity were performed, and a subjective evaluation of tagging quality (grade 1-5) was done. Independently, two reviewers performed polyp and carcinoma detection. RESULTS: The tagging density was 638 and 618 HU (p = 0.458) and homogeneity 91 and 86 HU for groups 1 and 2, respectively (p = 0.145). The tagging quality was graded 5 (excellent) in 90% of all segments in group 1 and 91% in group 2 (p = 0.749). Mean per-polyp sensitivity for lesions >or=10 mm was 86% in group 1 and 97% in group 2 (p = 0.355). Patient burden from diarrhoea significantly decreased for patients in group 2. CONCLUSIONS: One-day preparation with meglumine ioxithalamate results in an improved patient acceptability compared with 2-day preparation and has a comparable, excellent image quality and good diagnostic performance.

Using CT colonography as a triage technique after a positive faecal occult blood test in colorectal cancer screening.

OBJECTIVE: The purpose of this study was to evaluate the effectiveness of CT colonography (CTC) as a triage technique in faecal occult blood test (FOBT)-positive screening participants. METHODS: Consecutive guaiac (G-FOBT) and immunochemical (I-FOBT) FOBT-positive patients scheduled for colonoscopy underwent CTC with iodine tagging bowel preparation. Each CTC was read independently by two experienced observers. Per patient sensitivity, specificity and positive and negative predictive values (PPV and NPV) were calculated based on double reading with different CTC cut-off lesion sizes using segmental unblinded colonoscopy as the reference standard. The acceptability of the technique to patients was evaluated with questionnaires. RESULTS: 302 FOBT-positive patients were included (54 G-FOBT and 248 I-FOBT). 22 FOBT-positive patients (7%) had a colorectal carcinoma and 211 (70%) had a lesion >or=6 mm. Participants considered colonoscopy more burdensome than CTC (p<0.05). Using a 6 mm CTC size cut-off, per patient sensitivity for CTC was 91% (95% CI 85% to 91%) and specificity was 69% (95% CI 60% to 89%) for the detection of colonoscopy lesions >or=6 mm. The PPV of CTC was 87% (95% CI 80% to 93%) and NPV 77% (95% CI 69% to 85%). Using CTC as a triage technique in 100 FOBT-positive patients would mean that colonoscopy could be prevented in 28 patients while missing >or=10 mm lesions in 2 patients. CONCLUSION: CTC with limited bowel preparation has reasonable predictive values in an FOBT-positive population and a higher acceptability to patients than colonoscopy. However, due to the high prevalence of clinically relevant lesions in FOBT-positive patients, CTC is unlikely to be an efficient triage technique in a first round FOBT population screening programme.

Protrusion method for automated estimation of polyp size on CT colonography.

OBJECTIVE: The purpose of this study was to assess the accuracy and measurement variability of automated lesion measurement on CT colonography in comparison with manual 2D and 3D techniques under varying scanning conditions. MATERIALS AND METHODS: The study included phantoms (23 phantom objects) and patients (16 polyps). Measurement with sliding calipers served as the reference for the phantom data. The mean of two independent colonoscopic measurements was the reference for the polyps. The automated measurement was developed for a computer-aided detection scheme, and the size of any detected object was obtained from measurement of its largest diameter. The automated measurement was compared with manual 2D and 3D measurements by two experienced observers. RESULTS: For phantom data, the measurement variability of the automated method was significantly less than that of the two observers (p < 0.05), except for the 3D measurement by observer 1, as follows: automated, 0.86 mm; observer 1, 1.76 mm (2D), 0.96 (3D); observer 2, 1.34 mm (2D), 1.45 mm (3D). The variability of the automated method did not differ significantly from that of manual methods in measurement with patient data. The automated method had a systematic error for phantom data (1.9 mm). CONCLUSION: For phantoms, the automated method has less measurement variability than manual 2D and 3D techniques. For true polyps, the measurement variability of the automated method is comparable with that of manual methods. The automated method does not suffer from intraobserver variability. Because systematic error can be calibrated, automated size measurement may contribute to a practical evaluation strategy.

Perceptive errors in CT colonography.

Published results to date have indicated a good per patient sensitivity of computed tomographic colonography (CTC) for colorectal cancer and for polyps measuring 10 mm or more together with a very good specificity. Sensitivity and specificity for polyps in the range of 6-10 mm are moderate. These results, however, can be achieved only with meticulous attention to technique including adequate colonic distention, and acquisition of supine and prone thin-section computed tomographic (CT) images. Moreover, there is a significant learning curve involved in the interpretation of CTC studies, with performance statistics improving with operator experience. Radiologists must be comfortable in reporting directly from workstation monitors and have access to and be familiar with software for multiplanar and endoluminal reconstructions. In addition to maximize polyp detection and minimize false positive results, reporting radiologists must have a working knowledge of normal colorectal anatomy and pathology on CTC and be familiar with potential pitfalls in interpretation. Besides the description of several possible causes for perceptive errors, also a literature search of perceptive errors in CTC is included in this paper.

Feasibility of automated matching of supine and prone CT-colonography examinations.

Matching of prone and supine positions in CT colonography may improve accuracy of polyp detection. The purpose of this study was to investigate the feasibility of automatic prone-supine matching in CT-colonography using proven polyps as fixed points of reference. The method is based on similarities in the direction of centre-lines and allows for compression and extraction of the centre-lines in both positions. To illustrate the impact of the match error of the new method in practice, the visibility of the matched polyps in a primary three-dimensional unfolded cube setting was determined as well. The method was compared with a method that relies on the normalized distance along the centre-line (NDAC method). The median absolute match error was 14 mm (range 0-59 mm, average 20 mm) either proximal or distal from the actual polyp in prone position. In the observer study, 70% (26/37) of the polyps were directly visible in prone view. The overall difference in median absolute match error between both methods was small (2 mm), although half way along the centre-line there were polyps with substantial differences in match error (larger with NDAC). We concluded that automated prone-supine matching of CT-colonography studies is feasible and has a low match error. The difference with the NDAC method was small and not significant, although half way along the centre-line some differences were seen.

Theoretical characterization of the ground and optically excited states of alpha'-NaV2O5.

The character of the ground and optically excited states was investigated by quantum chemical calculations. We propose a rung ground state with V 3d(1)(xy)-O 2p(1)(y)-V 3d(1)(xy) character, instead of the conventional picture of one unpaired electron shared by 2 V ions. The unpaired electron on O is low-spin coupled to the V d electrons and spin density is predicted to be localized on vanadium. The absorption peak at 0.9 eV is assigned to a state with similar orbital occupations but a different spin coupling scheme, resulting in spin density localized on the bridging oxygen.

Dried sera for confirming blood-borne virus infections (HCV, HTLV-I, HIV & HBsAg).

For safe blood transfusion, developing countries face considerable problems including serological screening and confirmation of blood-borne virus infections (HCV, HTLV-I, HIV and HBsAg). Confirmation tests are not only costly but also require sophisticated techniques and expertise. In order to provide this support we have attempted to perform a virus antibody confirmation test on samples dried on blotting paper (BP). Forty-nine sera derived from selected patients and donors from Bombay, and nine donors' sera from Bellarussia were transported on BP. In control experiments, dilutions of antibody-positive sera (HIV, HTLV-I & HCV) and 'blinded' HTLV-I antibody-positive and antibody-negative donors were applied on BP. Eluates from snipped BP were tested initially by screening tests, and the reactives were subjected to confirmatory tests for three types of virus antibody tests (HCV, HTLV-I & HIV) by blotting methods and neutralisation tests for HBsAg. There was considerable reduction of titres in dry sera but all BP-derived dry specimens gave excellent qualitative concordance with their liquid-equivalent sera, and the HTLV-I-positive donor was identified and reconfirmed correctly. Presence of only HCV antibody was confirmed in all the nine selected Bellarussian donors. Blood donors in Bombay had 3% HIV antibody, 6% HBsAg and none had HCV antibody, while selected patients showed substantially higher levels of these markers: HIV-antibody 64%, HBsAg 57% and HCV-antibody 17% confirmed positive. The cause of this high level remains to be established. Dry samples received by post seem to be an economical approach to a first step in providing some levels of independent confirmation of reactives in developing countries.