[DeRAS I-German situation of robotic-assisted surgery-an online survey]. / DeRAS I ­ deutsche Situation der robotisch assistierten Chirurgie ­ eine Online-Survey-Studie.

BACKGROUND: Robotic assistance has become established in surgery but is not yet a standard procedure. The current status of clinical dissemination in Germany remains unclear. Industry independent sources are scarce. AIM OF THE WORK: The aim of this survey was to investigate the current status of robotic-assisted surgery (RAS) across specialties in Germany from 2014 to 2018. MATERIAL AND METHODS: An internet search was used to identify hospitals and departments (DP) with access to RAS. The DPs were asked to share their data from 2014-2018. In addition to clinical data, data on utilization, implementation, training, and funding were requested. RESULTS: As of 31 December 2018 RAS was offered at 121 hospitals in Germany, 383 DPs with access to RAS were identified and 26% (n = 98) of DPs responded. On average each DP had two consultant surgeons, 10% of DPs had more than one RAS system and 100% of the RAS systems recorded were from Intuitive Surgical Inc., CA, USA. RAS was implemented in 65% in urology and in 12% in visceral surgery (VS). 21% of programs were interdisciplinary and 4% multidisciplinary (> 3). 83% of systems were purchased and 17% otherwise funded. For additional operating room costs, 74% of hospitals reported paying for them themselves. 14% chose pay as you go. Since 2014, procedures increased by a factor of 4 to approximately 8000. The proportion of VS increased by a factor of 5 since 2016. CONCLUSION: RAS in Germany experienced strong growth through 2018. The range of procedures is similar to that of laparoscopy. With a current lack of reimbursement for the additional technical effort, RAS is predominantly used in the medium and high complexity range. The online survey is a good method to collect independent data without high administrative effort.

Structure-Altering Mutations of the SARS-CoV-2 Frame Shifting RNA Element.

With the rapid rate of Covid-19 infections and deaths, treatments and cures besides hand washing, social distancing, masks, isolation, and quarantines are urgently needed. The treatments and vaccines rely on the basic biophysics of the complex viral apparatus. While proteins are serving as main drug and vaccine targets, therapeutic approaches targeting the 30,000 nucleotide RNA viral genome form important complementary approaches. Indeed, the high conservation of the viral genome, its close evolutionary relationship to other viruses, and the rise of gene editing and RNA-based vaccines all argue for a focus on the RNA agent itself. One of the key steps in the viral replication cycle inside host cells is the ribosomal frameshifting required for translation of overlapping open reading frames. The frameshifting element (FSE), one of three highly conserved regions of coronaviruses, includes an RNA pseudoknot considered essential for this ribosomal switching. In this work, we apply our graph-theory-based framework for representing RNA secondary structures, "RAG" (RNA-As Graphs), to alter key structural features of the FSE of the SARS-CoV-2 virus. Specifically, using RAG machinery of genetic algorithms for inverse folding adapted for RNA structures with pseudoknots, we computationally predict minimal mutations that destroy a structurally-important stem and/or the pseudoknot of the FSE, potentially dismantling the virus against translation of the polyproteins. Additionally, our microsecond molecular dynamics simulations of mutant structures indicate relatively stable secondary structures. These findings not only advance our computational design of RNAs containing pseudoknots; they pinpoint to key residues of the SARS-CoV-2 virus as targets for anti-viral drugs and gene editing approaches.

Dynamic simulations of 13 TATA variants refine kinetic hypotheses of sequence/activity relationships.

The fundamental relationship between DNA sequence/deformability and biological function has attracted numerous experimental and theoretical studies. A classic prototype system used for such studies in eukaryotes is the complex between the TATA element transcriptional regulator and the TATA-box binding protein (TBP). The recent crystallographic study by Burley and co-workers demonstrated the remarkable structural similarity contrasted to different transcriptional activity of 11 TBP/DNA complexes in which the DNAs differed by single base-pairs. By simulating these TATA variants and two other single base-pair variants that were not crystallizable, we uncover sequence-dependent structural, energetic, and flexibility properties that tailor TATA elements to TBP interactions, complementing many previous studies by refining kinetic hypotheses on sequence/activity correlations. The factors that combine to produce favorable elements for TBP activity include overall flexibility; minor groove widening, as well as roll, rise, and shift increases at the ends of the TATA element; untwisting within the TATA element accompanied by large roll at the TATA element ends; and relatively low maximal water densities around the DNA. These features accompany the severe deformation induced by the minor-groove binding protein, which kinks the TATA element at the ends and displaces local water molecules to form stabilizing hydrophobic contacts. Interestingly, the preferred bending direction itself is not a significant predictor of activity disposition, although certain variants (such as wild-type AdMLP, 5'-TATA4G-3', and inactive A29, 5'-TA6G-3') exhibit large preferred bends in directions consistent with their activity or inactivity (major groove and minor groove bends, respectively). These structural, flexibility, and hydration preferences, identified here and connected to a new crystallographic study of a larger group of DNA variants than reported to date, highlight the profound influence of single base-pair DNA variations on DNA motion. Our refined kinetic hypothesis suggests the functional implications of these motions in a kinetic model of TATA/TBP recognition, inviting further theoretical and experimental research.

Computational modeling predicts the structure and dynamics of chromatin fiber.

BACKGROUND: The compact form of the chromatin fiber is a critical regulator of fundamental processes such as transcription and replication. These reactions can occur only when the fiber is unraveled and the DNA strands contained within are exposed to interact with nuclear proteins. While progress on identifying the biochemical mechanisms that control localized folding and hence govern access to genetic information continues, the internal structure of the chromatin fiber, let alone the structural pathways for folding and unfolding, remain unknown. RESULTS: To offer structural insights into how this nucleoprotein complex might be organized, we present a macroscopic computer model describing the mechanics of the chromatin fiber on the polymer level. We treat the core particles as electrostatically charged disks linked via charged elastic DNA segments and surrounded by a microionic hydrodynamic solution. Each nucleosome unit is represented by several hundred charges optimized so that the effective Debye-Hückel electrostatic field matches the field predicted by the nonlinear Poisson-Boltzmann equation. On the basis of Brownian dynamics simulations, we show that oligonucleosomes condense and unfold in a salt-dependent manner analogous to the chromatin fiber. CONCLUSIONS: Our predicted chromatin model shows good agreement with experimental diffusion coefficients and small-angle X-ray scattering data. A fiber of width 30 nm, organized in a compact helical zigzag pattern with about 4 nucleosomes per 10 nm, naturally emerges from a repeating nucleosome folding motif. This fiber has a cross-sectional radius of gyration of R(c) = 8.66 nm, in close agreement with corresponding values for rat thymus and chicken erythrocyte chromatin (8.82 and 8.5 nm, respectively).

Lattice protein folding with two and four-body statistical potentials.

The cooperative folding of proteins implies a description by multibody potentials. Such multibody potentials can be generalized from common two-body statistical potentials through a relation to probability distributions of residue clusters via the Boltzmann condition. In this exploratory study, we compare a four-body statistical potential, defined by the Delaunay tessellation of protein structures, to the Miyazawa-Jernigan (MJ) potential for protein structure prediction, using a lattice chain growth algorithm. We use the four-body potential as a discriminatory function for conformational ensembles generated with the MJ potential and examine performance on a set of 22 proteins of 30-76 residues in length. We find that the four-body potential yields comparable results to the two-body MJ potential, namely, an average coordinate root-mean-square deviation (cRMSD) value of 8 A for the lowest energy configurations of all-alpha proteins, and somewhat poorer cRMSD values for other protein classes. For both two and four-body potentials, superpositions of some predicted and native structures show a rough overall agreement. Formulating the four-body potential using larger data sets and direct, but costly, generation of conformational ensembles with multibody potentials may offer further improvements. Proteins 2001;43:161-174.

Dynamics of site juxtaposition in supercoiled DNA.

Juxtaposition kinetics between specific sites in supercoiled DNA is investigated at close to physiological ionic conditions by Brownian dynamics simulations. At such conditions, supercoiled DNA is interwound, and the probability of spatial site juxtaposition is much higher than in relaxed DNA. We find, however, that supercoiling does not correspondingly increase the rate of juxtaposition at these physiological conditions. An explanation to this unexpected finding emerges on analysis of the juxtaposition dynamics. We note that although a particular site i(1) in supercoiled DNA is often in close proximity (juxtaposed) to another site i(2), the change of i(2) occurs very slowly and depends largely on internal slithering of opposite segments of the DNA superhelix. Such slithering results in long correlations between successive values of i(2); these correlations increase the average time of juxtaposition between two DNA sites. Random collisions between sites located on different superhelix branches-although increasing in importance with DNA size-contribute less substantially to site juxtaposition at high salt than slithering for DNA up to 6 kb in length.

Modeling salt-mediated electrostatics of macromolecules: the discrete surface charge optimization algorithm and its application to the nucleosome.

Much progress has been achieved on quantitative assessment of electrostatic interactions on the all-atom level by molecular mechanics and dynamics, as well as on the macroscopic level by models of continuum solvation. Bridging of the two representations-an area of active research-is necessary for studying integrated functions of large systems of biological importance. Following perspectives of both discrete (N-body) interaction and continuum solvation, we present a new algorithm, DiSCO (Discrete Surface Charge Optimization), for economically describing the electrostatic field predicted by Poisson-Boltzmann theory using a discrete set of Debye-Hückel charges distributed on a virtual surface enclosing the macromolecule. The procedure in DiSCO relies on the linear behavior of the Poisson-Boltzmann equation in the far zone; thus contributions from a number of molecules may be superimposed, and the electrostatic potential, or equivalently the electrostatic field, may be quickly and efficiently approximated by the summation of contributions from the set of charges. The desired accuracy of this approximation is achieved by minimizing the difference between the Poisson-Boltzmann electrostatic field and that produced by the linearized Debye-Hückel approximation using our truncated Newton optimization package. DiSCO is applied here to describe the salt-dependent electrostatic environment of the nucleosome core particle in terms of several hundred surface charges. This representation forms the basis for modeling-by dynamic simulations (or Monte Carlo)-the folding of chromatin. DiSCO can be applied more generally to many macromolecular systems whose size and complexity warrant a model resolution between the all-atom and macroscopic levels.

A-Tract bending: insights into experimental structures by computational models.

While solution structures of adenine tract (A-tract) oligomers have indicated a unique bend direction equivalent to negative global roll (commonly termed "minor-groove bending"), crystallographic data have not unambiguously characterized the bend direction; nevertheless, many features are shared by all A-tract crystal and solution structures (e.g. propeller twisting, narrow minor grooves, and localized water spines). To examine the origin of bending and to relate findings to the crystallographic and solution data, we analyze molecular dynamics trajectories of two solvated A-tract dodecamers: 1D89, d(CGCGA(6)CG), and 1D98, d(CGCA(6)GCG), using a new general global bending framework for analyzing bent DNA and DNA/protein complexes. It is significant that the crystallographically-based initial structures are converted from dissimilar to similar bend directions equivalent to negative global roll, with the average helical-axis bend ranging from 10.5 degrees to 14.1 degrees. The largest bend occurs as positive roll of 12 degrees on the 5' side of the A-tracts (supporting a junction model) and is reinforced by gradual curvature at each A-tract base-pair (bp) step (supporting a wedge model). The precise magnitude of the bend is subtly sequence dependent (consistent with a curved general sequence model). The conversion to negative global roll only requires small local changes at each bp, accumulated over flexible moieties both outside and inside the A-tract. In contrast, the control sequence 1BNA, d(CGCGA(2)TTCGCG), bends marginally (only 6.9 degrees ) with no preferred direction. The molecular features that stabilize the bend direction in the A-tract dodecamers include propeller twisting of AT base-pairs, puckering differences between A and T deoxyriboses, a narrow minor groove, and a stable water spine (that extends slightly beyond the A-tract, with lifetimes approaching 0.2 ns). The sugar conformations, in particular, are proposed as important factors that support bent DNA. It is significant that all these curvature-stabilizing features are also observed in the crystallographic structures, but yield overall different bending paths, largely due to the effects of sequences outside the A-tract. These results merge structural details reported for A-tract structures by experiment and theory and lead to structural and dynamic insights into sequence-dependent DNA flexibility, as highlighted by the effect of an A-tract variant of a TATA-box element on bending and flexibility required for TBP binding.

An efficient projection protocol for chemical databases: singular value decomposition combined with truncated-newton minimization.

A rapid algorithm for visualizing large chemical databases in a low-dimensional space (2D or 3D) is presented as a first step in database analysis and design applications. The projection mapping of the compound database (described as vectors in the high-dimensional space of chemical descriptors) is based on the singular value decomposition (SVD) combined with a minimization procedure implemented with the efficient truncated-Newton program package (TNPACK). Numerical experiments on four chemical datasets with real-valued descriptors (ranging from 58 to 27 255 compounds) show that the SVD/TNPACK projection duo achieves a reasonable accuracy in 2D, varying from 30% to about 100% of pairwise distance segments that lie within 10% of the original distances. The lowest percentages, corresponding to scaled datasets, can be made close to 100% with projections onto a 10-dimensional space. We also show that the SVD/TNPACK duo is efficient for minimizing the distance error objective function (especially for scaled datasets), and that TNPACK is much more efficient than a current popular approach of steepest descent minimization in this application context. Applications of our projection technique to similarity and diversity sampling in drug design can be envisioned.

Carcinoma of the hypopharynx and the cervical oesophagus: a surgical challenge.

OBJECTIVE: To report our results after reconstruction of the upper digestive tract for locally advanced carcinoma of the hypopharynx and cervical oesophagus. DESIGN: Open study. SETTING: Teaching University hospital, Germany. SUBJECTS: Of the 517 patients who presented with carcinoma of the oesophagus between September 1985 and March 1997, 16 had a locally advanced tumour of the hypopharynx and 25 of the cervical oesophagus. INTERVENTIONS: Free jejunal grafts were used after circular resection in all patients with carcinoma of the hypopharynx, and for the 3 with oesophageal carcinoma in whom we obtained adequate resection margins. In the remainder stomach was used in 21 and colon in 1. MAIN OUTCOME MEASURES: Morbidity and mortality. RESULTS: After jejunal grafting 1 patient died within 30 days and 2 died in hospital. After gastric or colonic reconstruction 2 patients died within 30 days and 4 in hospital. There was 1 anastomotic leak, 1 transplant became necrotic and had to be replaced, in 2 patients the recurrent nerve was damaged, 1 patient developed a wound infection and 1 a cardiac infarction. After gastric or colonic replacement 7 patients had paralysed recurrent laryngeal nerves, there was 6 anastomotic leaks, 1 chylous leak, 1 haemorrhage, and in 1 the transplant necrosed. CONCLUSION: Despite the fact that we compared tumours in different sites, these results suggest that the jejunal graft is safer for upper oesophageal and hypopharyngeal reconstruction.

The examiner's learning effect and its influence on the quality of endoscopic ultrasonography in carcinoma of the esophagus and gastric cardia.

BACKGROUND: The preoperative diagnosis of tumors of the esophagus and the gastric cardia is an important element in their stage-oriented therapy. The goal of the present study was to evaluate the accuracy of endosonographic ultrasound (EUS) and to test its usefulness in tumor staging and the assessment of operability. METHODS: A total of 139 tumors were scanned via EUS by one examiner 75 examinations have been done. EUS is a valuable tool in tumor staging when it is performed by an experienced examiner or under the direct supervision of such a person.

[Pulmonary complications following esophageal surgery. Significance of aspiration]. / Pulmonale Komplikationen nach Osophagusresektion. Die Bedeutung der Aspiration.

Objective of this study was to show the different causes and the importance of pulmonary complications after esophageal surgery and their management by general and intensive care measures. In the University Hospital for General and Abdominal Surgery of Mainz 222 patients were treated for esophageal cancer from 9/1985 to 5/1997. Data of 214 patients were available for this investigation. In 65 cases a transhiatal dissection (blunt dissection) and in 149 patients a abdomino-thoracic dissection were performed. 54 (25.2%) patients had to be reintubated. 30-day lethality was 7.9% (n = 17) and hospital lethality was 13.1% (n = 28). 82 (38.3%) patients developed pulmonal dysfunction (pneumonia) which was aggravated by a following ARDS in 16 patients (19.5%). 21 (25.6%) of these patients died. In only 24 (29.3%) patients an isolated pneumonia occurred without evidence of general or surgical complications. In 65 of 82 patients further microbiologically examinations were documented. In 39 (60%) cases gastrointestinal bacteria were found. Therefore aspiration or microaspiration respectively are considered to co-cause pulmonary complications. Postoperative psychosyndrome, recurrent nerve palsy and ASA-risk stratification were accompanied by elevated rates of pneumonia. Careful selection of patients for esophageal resection, atraumatic surgical technique and reduction of general and surgical complications and intensive care measures can help to avoid postoperative pulmonary complications. Reduction of mediators activated by surgical trauma is not feasible so in the moment prevention of aspiration seems to be the most effective therapy in the postoperative course.

Internal motion of supercoiled DNA: brownian dynamics simulations of site juxtaposition.

Thermal motions in supercoiled DNA are studied by Brownian dynamics (BD) simulations with a focus on the site juxtaposition process. It had been shown in the last decade that the BD approach is capable of describing actual times of large-scale DNA motion. The bead model of DNA used here accounts for bending and torsional elasticity as well as the electrostatic repulsion among DNA segments. The hydrodynamic interaction among the beads of the model chain and the aqueous solution is incorporated through the Rotne-Prager tensor. All simulations were performed for the sodium ion concentration of 0.01 M. We first showed, to test our BD procedure, that the same distributions of equilibrium conformational properties are obtained as by Monte Carlo simulations for the corresponding DNA model. The BD simulations also predict with accuracy published experimental values of the diffusion coefficients of supercoiled DNA. To describe the rate of conformational changes, we also calculated the autocorrelation functions for the writhe and radius of gyration for the supercoiled molecules. The rate of site juxtaposition was then studied for DNA molecules up to 3000 bp in length. We find that site juxtaposition is a very slow process: although accelerated by a factor of more than 100 by DNA supercoiling, the times of juxtaposition are in the range of ms even for highly supercoiled DNA, about two orders of magnitude higher than the relaxation times of writhe and the radius of gyration for the same molecules. By inspecting successive simulated conformations of supercoiled DNA, we conclude that slithering of opposing segments of the interwound superhelix is not an efficient mechanism to accomplish site juxtaposition, at least for conditions of low salt concentration. Instead, transient distortions of the interwound superhelix, followed by continuous reshaping of the molecule, contribute more significantly to site juxtaposition kinetics.

The loop opening/closing motion of the enzyme triosephosphate isomerase.

To explore the origin of the large-scale motion of triosephosphate isomerase's flexible loop (residues 166 to 176) at the active site, several simulation protocols are employed both for the free enzyme in vacuo and for the free enzyme with some solvent modeling: high-temperature Langevin dynamics simulations, sampling by a "dynamics driver" approach, and potential-energy surface calculations. Our focus is on obtaining the energy barrier to the enzyme's motion and establishing the nature of the loop movement. Previous calculations did not determine this energy barrier and the effect of solvent on the barrier. High-temperature molecular dynamics simulations and crystallographic studies have suggested a rigid-body motion with two hinges located at both ends of the loop; Brownian dynamics simulations at room temperature pointed to a very flexible behavior. The present simulations and analyses reveal that although solute/solvent hydrogen bonds play a crucial role in lowering the energy along the pathway, there still remains a high activation barrier. This finding clearly indicates that, if the loop opens and closes in the absence of a substrate at standard conditions (e.g., room temperature, appropriate concentration of isomerase), the time scale for transition is not in the nanosecond but rather the microsecond range. Our results also indicate that in the context of spontaneous opening in the free enzyme, the motion is of rigid-body type and that the specific interaction between residues Ala176 and Tyr208 plays a crucial role in the loop opening/closing mechanism.

[Abrikossoff granular cell tumor: a rare tumor of the esophagus]. / Abrikossoff-Granulosazelltumor: Ein seltener Tumor des Oesophagus.

In the present case of a granular cell tumor an abdomino-thoracal resection of the esophagus was performed in a 41-year-old patient after preoperative diagnosis had suggested esophageal cancer. Granular cell tumors (Abrikossoff's tumor) of the esophagus are rather rare tumors of neuroectodermal benign histogenesis. Diagnosis can be obtained by endoscopic and histological study and immunohistochemical forceps biopsy. Because of the peculiar histological feature of the tumor, it can be mistaken for an squamous cell carcinoma.

Configurational transitions in Fourier series-represented DNA supercoils.

A new Fourier series representation of supercoiled DNA is employed in Langevin dynamics simulations to study large-scale configurational motions of intermediate-length chains. The polymer is modeled as an ideal elastic rod subject to long-range van der Waals' interactions. The van der Waals' term prevents the self-contact of distant chain segments and also mimics attractive forces thought to stabilize the association of closely spaced charged rods. The finite Fourier series-derived polymer formulation is an alternative to the piecewise B-spline curves used in past work to describe the motion of smoothly deformed supercoiled DNA in terms of a limited number of independent variables. This study focuses on two large-scale configurational events: the interconversion between circular and figure-8 forms at a relatively low level of supercoiling, and the transformation between branched and interwound structures at a higher superhelical density.

Biomolecular dynamics at long timesteps: bridging the timescale gap between simulation and experimentation.

Innovative algorithms have been developed during the past decade for simulating Newtonian physics for macromolecules. A major goal is alleviation of the severe requirement that the integration timestep be small enough to resolve the fastest components of the motion and thus guarantee numerical stability. This timestep problem is challenging if strictly faster methods with the same all-atom resolution at small timesteps are sought. Mathematical techniques that have worked well in other multiple-timescale contexts--where the fast motions are rapidly decaying or largely decoupled from others--have not been as successful for biomolecules, where vibrational coupling is strong. This review examines general issues that limit the timestep and describes available methods (constrained, reduced-variable, implicit, symplectic, multiple-timestep, and normal-mode-based schemes). A section compares results of selected integrators for a model dipeptide, assessing physical and numerical performance. Included is our dual timestep method LN, which relies on an approximate linearization of the equations of motion every delta t interval (5 fs or less), the solution of which is obtained by explicit integration at the inner timestep delta tau (e.g., 0.5 fs). LN is computationally competitive, providing 4-5 speedup factors, and results are in good agreement, in comparison to 0.5 fs trajectories. These collective algorithmic efforts help fill the gap between the time range that can be simulated and the timespans of major biological interest (milliseconds and longer). Still, only a hierarchy of models and methods, along with experimentational improvements, will ultimately give theoretical modeling the status of partner with experiment.

Buckling transitions in superhelical DNA: dependence on the elastic constants and DNA size.

Buckling transitions in superhelical DNA are sudden changes in shape that accompany a smooth variation in a key parameter, such as superhelical density. Here we explore the dependence of these transitions on the elastic constants for bending and twisting. A and C, important characteristics of DNA's bending and twisting persistence lengths. The large range we explore extends to other elastic materials with self-contact interactions, modeled here by a Debye-Hückel electrostatic potential. Our collective description of DNA shapes and energies over a wide range of p = A/C reveals a dramatic dependence of DNA shape and associated configurational transitions on p: transitions are sharp for large p but masked for small p. In particular, at small p, a nonplanar circular family emerges, in agreement with Jülicher's recent analytical predictions: a continuum of forms (and associated writhing numbers) is also observed. The relevance of these buckling transitions to DNA in solution is examined through studies of size dependence and thermal effects. Buckling transitions smooth considerably as size increases, and this can be explained in part by the lower curvature in larger plasmids. This trend suggests that buckling transitions should not be detectable for isolated (i.e., unbound) DNA plasmids of biological interest, except possibly for very large p. Buckling phenomena would nonetheless be relevant for small DNA loops, particularly for higher values of p, and might have a role in regulatory mechanisms: a small change in superhelical stress could lead to a large configurational change. Writhe distributions as a function of p, generated by Langevin dynamics simulations, reveal the importance of thermal fluctuations. Each distribution range (and multipeaked shape) can be interpreted by our buckling profiles. Significantly, the distributions for moderate to high superhelical densities are most sensitive to p, isolating different distribution patterns. If this effect could be captured experimentally for small plasmids by currently available imaging techniques, such results suggest a slightly different experimental procedure for estimating the torsional stiffness of supercoiled DNA than considered to date.