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.

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.

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.

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.

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.