Dynamic computer simulations of electrophoresis: a versatile research and teaching tool

Software is available, which simulates all basic electrophoretic systems, including moving boundary electrophoresis, zone electrophoresis, ITP, IEF and EKC, and their combinations under almost exactly the same conditions used in the laboratory. These dynamic models are based upon equations derived from the transport concepts such as electromigration, diffusion, electroosmosis and imposed hydrodynamic buffer flow that are applied to user-specified initial distributions of analytes and electrolytes. They are able to predict the evolution of electrolyte systems together with associated properties such as pH and conductivity profiles and are as such the most versatile tool to explore the fundamentals of electrokinetic separations and analyses. In addition to revealing the detailed mechanisms of fundamental phenomena that occur in electrophoretic separations, dynamic simulations are useful for educational purposes. This review includes a list of current high-resolution simulators, information on how a simulation is performed, simulation examples for zone electrophoresis, ITP, IEF and EKC and a comprehensive discussion of the applications and achievements.

Precision of fit of implant-supported screw-retained 10-unit computer-aided-designed and computer-aided-manufactured frameworks made from zirconium dioxide and titanium: an in vitro study

OBJECTIVE To analyze the precision of fit of implant-supported screw-retained computer-aided-designed and computer-aided-manufactured (CAD/CAM) zirconium dioxide (ZrO) frameworks. MATERIALS AND METHODS Computer-aided-designed and computer-aided-manufactured ZrO frameworks (NobelProcera) for a screw-retained 10-unit implant-supported reconstruction on six implants (FDI positions 15, 13, 11, 21, 23, 25) were fabricated using a laser (ZrO-L, N = 6) and a mechanical scanner (ZrO-M, N = 5) for digitizing the implant platform and the cuspid-supporting framework resin pattern. Laser-scanned CAD/CAM titanium (TIT-L, N = 6) and cast CoCrW-alloy frameworks (Cast, N = 5) fabricated on the same model and designed similar to the ZrO frameworks were the control. The one-screw test (implant 25 screw-retained) was applied to assess the vertical microgap between implant and framework platform with a scanning electron microscope. The mean microgap was calculated from approximal and buccal values. Statistical comparison was performed with non-parametric tests. RESULTS No statistically significant pairwise difference was observed between the relative effects of vertical microgap between ZrO-L (median 14 μm; 95% CI 10-26 μm), ZrO-M (18 μm; 12-27 μm) and TIT-L (15 μm; 6-18 μm), whereas the values of Cast (236 μm; 181-301 μm) were significantly higher (P < 0.001) than the three CAD/CAM groups. A monotonous trend of increasing values from implant 23 to 15 was observed in all groups (ZrO-L, ZrO-M and Cast P < 0.001, TIT-L P = 0.044). CONCLUSIONS Optical and tactile scanners with CAD/CAM technology allow for the fabrication of highly accurate long-span screw-retained ZrO implant-reconstructions. Titanium frameworks showed the most consistent precision. Fit of the cast alloy frameworks was clinically inacceptable.

Genetic diversity of EBV-encoded LMP1 in the Swiss HIV Cohort Study and implication for NF-Κb activation

Epstein-Barr virus (EBV) is associated with several types of cancers including Hodgkin's lymphoma (HL) and nasopharyngeal carcinoma (NPC). EBV-encoded latent membrane protein 1 (LMP1), a multifunctional oncoprotein, is a powerful activator of the transcription factor NF-κB, a property that is essential for EBV-transformed lymphoblastoid cell survival. Previous studies reported LMP1 sequence variations and induction of higher NF-κB activation levels compared to the prototype B95-8 LMP1 by some variants. Here we used biopsies of EBV-associated cancers and blood of individuals included in the Swiss HIV Cohort Study (SHCS) to analyze LMP1 genetic diversity and impact of sequence variations on LMP1-mediated NF-κB activation potential. We found that a number of variants mediate higher NF-κB activation levels when compared to B95-8 LMP1 and mapped three single polymorphisms responsible for this phenotype: F106Y, I124V and F144I. F106Y was present in all LMP1 isolated in this study and its effect was variant dependent, suggesting that it was modulated by other polymorphisms. The two polymorphisms I124V and F144I were present in distinct phylogenetic groups and were linked with other specific polymorphisms nearby, I152L and D150A/L151I, respectively. The two sets of polymorphisms, I124V/I152L and F144I/D150A/L151I, which were markers of increased NF-κB activation in vitro, were not associated with EBV-associated HL in the SHCS. Taken together these results highlighted the importance of single polymorphisms for the modulation of LMP1 signaling activity and demonstrated that several groups of LMP1 variants, through distinct mutational paths, mediated enhanced NF-κB activation levels compared to B95-8 LMP1.

Regulatory mechanism of the light-activable allosteric switch LOV-TAP for the control of DNA binding: a computer simulation study

The spatio-temporal control of gene expression is fundamental to elucidate cell proliferation and deregulation phenomena in living systems. Novel approaches based on light-sensitive multiprotein complexes have recently been devised, showing promising perspectives for the noninvasive and reversible modulation of the DNA-transcriptional activity in vivo. This has lately been demonstrated in a striking way through the generation of the artificial protein construct light-oxygen-voltage (LOV)-tryptophan-activated protein (TAP), in which the LOV-2-Jα photoswitch of phototropin1 from Avena sativa (AsLOV2-Jα) has been ligated to the tryptophan-repressor (TrpR) protein from Escherichia coli. Although tremendous progress has been achieved on the generation of such protein constructs, a detailed understanding of their functioning as opto-genetical tools is still in its infancy. Here, we elucidate the early stages of the light-induced regulatory mechanism of LOV-TAP at the molecular level, using the noninvasive molecular dynamics simulation technique. More specifically, we find that Cys450-FMN-adduct formation in the AsLOV2-Jα-binding pocket after photoexcitation induces the cleavage of the peripheral Jα-helix from the LOV core, causing a change of its polarity and electrostatic attraction of the photoswitch onto the DNA surface. This goes along with the flexibilization through unfolding of a hairpin-like helix-loop-helix region interlinking the AsLOV2-Jα- and TrpR-domains, ultimately enabling the condensation of LOV-TAP onto the DNA surface. By contrast, in the dark state the AsLOV2-Jα photoswitch remains inactive and exerts a repulsive electrostatic force on the DNA surface. This leads to a distortion of the hairpin region, which finally relieves its tension by causing the disruption of LOV-TAP from the DNA.

In vitro precision of fit of computer-aided design and computer-aided manufacturing titanium and zirconium dioxide bars

OBJECTIVES Optical scanners combined with computer-aided design and computer-aided manufacturing (CAD/CAM) technology provide high accuracy in the fabrication of titanium (TIT) and zirconium dioxide (ZrO) bars. The aim of this study was to compare the precision of fit of CAD/CAM TIT bars produced with a photogrammetric and a laser scanner. METHODS Twenty rigid CAD/CAM bars were fabricated on one single edentulous master cast with 6 implants in the positions of the second premolars, canines and central incisors. A photogrammetric scanner (P) provided digitized data for TIT-P (n=5) while a laser scanner (L) was used for TIT-L (n=5). The control groups consisted of soldered gold bars (gold, n=5) and ZrO-P with similar bar design. Median vertical distance between implant and bar platforms from non-tightened implants (one-screw test) was calculated from mesial, buccal and distal scanning electron microscope measurements. RESULTS Vertical microgaps were not significantly different between TIT-P (median 16μm; 95% CI 10-27μm) and TIT-L (25μm; 13-32μm). Gold (49μm; 12-69μm) had higher values than TIT-P (p=0.001) and TIT-L (p=0.008), while ZrO-P (35μm; 17-55μm) exhibited higher values than TIT-P (p=0.023). Misfit values increased in all groups from implant position 23 (3 units) to 15 (10 units), while in gold and TIT-P values decreased from implant 11 toward the most distal implant 15. SIGNIFICANCE CAD/CAM titanium bars showed high precision of fit using photogrammetric and laser scanners. In comparison, the misfit of ZrO bars (CAM/CAM, photogrammetric scanner) and soldered gold bars was statistically higher but values were clinically acceptable.

Productive Diversification and Sustainable Use of Complex Social-Ecological Systems: A Comparative Study of Indigenous and Settler Communities in the Bolivian Amazon

Agricultural and forest productive diversification depends on multiple socioeconomic drivers—like knowledge, migration, productive capacity, and market—that shape productive strategies and influence their ecological impacts. Our comparison of indigenous and settlers allows a better understanding of how societies develop different diversification strategies in similar ecological contexts and how the related socioeconomic aspects of diversification are associated with land cover change. Our results suggest that although indigenous people cause less deforestation and diversify more, diversification is not a direct driver of deforestation reduction. A multidimensional approach linking sociocognitive, economic, and ecological patterns of diversification helps explain this contradiction.

A comparison of initial antiretroviral therapy in the Swiss HIV Cohort Study and the recommendations of the International AIDS Society-USA

In order to facilitate and improve the use of antiretroviral therapy (ART), international recommendations are released and updated regularly. We aimed to study if adherence to the recommendations is associated with better treatment outcomes in the Swiss HIV Cohort Study (SHCS).

Uncovering the dynamics of cardiac systems using stochastic pacing and frequency domain analyses

Alternans of cardiac action potential duration (APD) is a well-known arrhythmogenic mechanism which results from dynamical instabilities. The propensity to alternans is classically investigated by examining APD restitution and by deriving APD restitution slopes as predictive markers. However, experiments have shown that such markers are not always accurate for the prediction of alternans. Using a mathematical ventricular cell model known to exhibit unstable dynamics of both membrane potential and Ca2+ cycling, we demonstrate that an accurate marker can be obtained by pacing at cycle lengths (CLs) varying randomly around a basic CL (BCL) and by evaluating the transfer function between the time series of CLs and APDs using an autoregressive-moving-average (ARMA) model. The first pole of this transfer function corresponds to the eigenvalue (λalt) of the dominant eigenmode of the cardiac system, which predicts that alternans occurs when λalt≤−1. For different BCLs, control values of λalt were obtained using eigenmode analysis and compared to the first pole of the transfer function estimated using ARMA model fitting in simulations of random pacing protocols. In all versions of the cell model, this pole provided an accurate estimation of λalt. Furthermore, during slow ramp decreases of BCL or simulated drug application, this approach predicted the onset of alternans by extrapolating the time course of the estimated λalt. In conclusion, stochastic pacing and ARMA model identification represents a novel approach to predict alternans without making any assumptions about its ionic mechanisms. It should therefore be applicable experimentally for any type of myocardial cell.

Is clipping the preferable technique to perform sympathicotomy? A retrospective study and review of the literature

PURPOSE Thoracoscopic sympathetic surgery is nowadays a broadly accepted technique in the treatment of primary hyperhidrosis as well as facial blushing. The objective of this study was to compare the two currently most commonly used methods for thoracic sympathicotomy: transection (ETS) and clipping (ETC.). METHODS This is a retrospective study on a total of 63 patients, who underwent rib-oriented sympathicotomy, either by transection (n = 36, 57 %) or by clipping (n = 27, 43 %). Moreover, the up-to-date international literature is reviewed concerning which level(s) of the sympathetic trunk should be addressed, depending on the patients underlying condition. Furthermore, the highly controversial topic of reversibility of sympathetic clipping is debated. RESULTS Our results confirm that clipping is at least as effective as transection of the sympathetic chain in the treatment of hyperhidrosis and facial blushing. Furthermore, the analysis of all larger studies on unclipping in humans shows a surprisingly high reported reversal rate between 48 and 77 %. CONCLUSIONS Depending on the symptoms of the patient, different levels of the sympathetic chain should be addressed. When a higher rib level such as R2 is approached, which more likely will result in moderate to severe compensatory sweating, clipping should be preferred as it seems that this technique has indeed a potential for reversibility. As demonstrated, this method is at least as effective as an irreversible transection of the sympathetic chain.

Are We Sims? How Computer Simulations Represent and What this Means for the Simulation Argument

N. Bostrom’s simulation argument and two additional assumptions imply that we are likely to live in a computer simulation. The argument is based upon the following assumption about the workings of realistic brain simulations: The hardware of a computer on which a brain simulation is run bears a close analogy to the brain itself. To inquire whether this is so, I analyze how computer simulations trace processes in their targets. I describe simulations as fictional, mathematical, pictorial, and material models. Even though the computer hardware does provide a material model of the target, this does not suffice to underwrite the simulation argument because the ways in which parts of the computer hardware interact during simulations do not resemble the ways in which neurons interact in the brain. Further, there are computer simulations of all kinds of systems, and it would be unreasonable to infer that some computers display consciousness just because they simulate brains rather than, say, galaxies.

Computer assisted planning and navigation of periacetabular osteotomy with range of motion optimization

Femoroacetabular impingement (FAI) before or after Periacetabular Osteotomy (PAO) is surprisingly frequent and surgeons need to be aware of the risk preoperatively and be able to avoid it intraoperatively. In this paper we present a novel computer assisted planning and navigation system for PAO with impingement analysis and range of motion (ROM) optimization. Our system starts with a fully automatic detection of the acetabular rim, which allows for quantifying the acetabular morphology with parameters such as acetabular version, inclination and femoral head coverage ratio for a computer assisted diagnosis and planning. The planned situation was optimized with impingement simulation by balancing acetabuar coverage with ROM. Intra-operatively navigation was conducted until the optimized planning situation was achieved. Our experimental results demonstrated: 1) The fully automated acetabular rim detection was validated with accuracy 1.1 ± 0.7mm; 2) The optimized PAO planning improved ROM significantly compared to that without ROM optimization; 3) By comparing the pre-operatively planned situation and the intra-operatively achieved situation, sub-degree accuracy was achieved for all directions.

The relationship between competencies acquired through Swiss academic sports science courses and the job requirements

In view of the changes in and growing variety of sports-related occupations, it is highly relevant for educational institutions 10 to know how well the educational contents of their sport science courses meet the professional requirements. This study analyses the relationship between the competencies acquired through academic sports science courses and the requirements of the relevant jobs in Switzerland. The data for this empirical analysis were drawn from a sample of n = 1054 graduates of different academic sport science programmes at all eight Swiss universities. The results show that academic sport science courses primarily communicate sports-specific expertise and practical sports skills. On the other hand, most graduates consider that the acquisition of interdisciplinary competencies plays a comparatively minor role in sport science education, even though these competencies are felt to be an important requirement in a variety of work-related environments and challenges.