Publications by authors named "Stefan Richter"

92 Publications

Self-Assembly of Stimuli-Responsive [2]Rotaxanes by Amidinium Exchange.

J Am Chem Soc 2021 Oct 24;143(40):16448-16457. Epub 2021 Sep 24.

Institute of Organic Chemistry, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany.

Advances in supramolecular chemistry are often underpinned by the development of fundamental building blocks and methods enabling their interconversion. In this work, we report the use of an underexplored dynamic covalent reaction for the synthesis of stimuli-responsive [2]rotaxanes. The formamidinium moiety lies at the heart of these mechanically interlocked architectures, because it enables both dynamic covalent exchange and the binding of simple crown ethers. We demonstrated that the rotaxane self-assembly follows a unique reaction pathway and that the complex interplay between crown ether and thread can be controlled in a transient fashion by addition of base and fuel acid. Dynamic combinatorial libraries, when exposed to diverse nucleophiles, revealed a profound stabilizing effect of the mechanical bond as well as intriguing reactivity differences between seemingly similar [2]rotaxanes.
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http://dx.doi.org/10.1021/jacs.1c05230DOI Listing
October 2021

Imaging Trapped Ion Structures via Fluorescence Cross-Correlation Detection.

Phys Rev Lett 2021 Apr;126(17):173602

QUANTUM, Institut für Physik, Johannes Gutenberg-Universität Mainz, Staudingerweg 7, 55128 Mainz, Germany.

Cross-correlation signals are recorded from fluorescence photons scattered in free space off a trapped ion structure. The analysis of the signal allows for unambiguously revealing the spatial frequency, thus the distance, as well as the spatial alignment of the ions. For the case of two ions we obtain from the cross-correlations a spatial frequency f_{spatial}=1490±2_{stat}±8_{syst}  rad^{-1}, where the statistical uncertainty improves with the integrated number of correlation events as N^{-0.51±0.06}. We independently determine the spatial frequency to be 1494±11  rad^{-1}, proving excellent agreement. Expanding our method to the case of three ions, we demonstrate its functionality for two-dimensional arrays of emitters of indistinguishable photons, serving as a model system to yield structural information where direct imaging techniques fail.
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http://dx.doi.org/10.1103/PhysRevLett.126.173602DOI Listing
April 2021

Locomotion in Anaspides (Anaspidacea, Malacostraca) - insights from a morpho-functional study of thoracopods with some observations on swimming and walking.

Zoology (Jena) 2021 02 9;144:125883. Epub 2020 Dec 9.

Allgemeine & Spezielle Zoologie, Institut für Biowissenschaften, Universität Rostock, Rostock, Germany.

Anaspidacea is probably the most enigmatic higher taxon within the Malacostraca. Representatives of the genus Anaspides are often considered "living fossils" due to their strong resemblance to their Triassic relatives. In comparison to other extant Malacostraca, they possess a high number of plesiomorphic characters. Anaspidacea are often combined with another freshwater taxon, Bathynellacea, into the Syncarida, but actual evidence for monophyletic Syncarida is weak. Other potential sister groups are Eucarida, Euphausiacea, or Euphausiacea + Peracarida. Like Euphausiacea, Mysidacea and "natant" decapods, Anaspidacea show what has been called a "caridoid facies". In malacostracan crustaceans, a prominent mode of locomotion is swimming, as it almost certainly was for the malacostracans' common ancestor. However, when considered in detail, swimming is found to take quite different forms in the various taxa. To obtain a better understanding of the evolution of swimming, we analyzed locomotion in several species of Anaspides endemic to Tasmania. The morphology of the protopodal and exopodal musculature as well as the exo- and endoskeletal structures of the thoracopods were examined using 3D reconstruction of CLSM- and μCT data. Various aspects of locomotion were documented and described using recording techniques including in-habitat underwater filming and macro high-speed recording. Our analysis shows the high level of complexity of the muscular arrangement and skeletal construction in the thoracopods of these - in many regards plesiomorphic - malacostracans, and demonstrates the presence of epipodal musculature. Our recordings provide insight into various aspects of locomotion of Anaspides, including the congruence of locomotive kinematics in swimming and walking. Our morphological findings and observations on locomotion in Anaspides are compared to findings in other malacostracan shrimps and discussed in a phylogenetic context, with our analysis providing further support for Xenommacarida (sensuRichter, 1999: Anaspidacea + Euphausiacea + Peracarida). Further, a new hypothesis for the origin of the ventral brood pouch, the marsupium, of Peracarida is discussed. On the basis of a comparison of their morphology and biology, the oostegites which form the marsupium are suggested to be derived thoracopodal endites as present in female Anaspides. Finally, an evolutionary scenario is presented and mapped on a cladogram in which the evolution of malacostracan swimming from a common caridoid ancestor up to the different taxa present today is discussed.
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http://dx.doi.org/10.1016/j.zool.2020.125883DOI Listing
February 2021

Phylogeny and Biogeography of Spinicaudata (Crustacea: Branchiopoda).

Zool Stud 2020 5;59:e44. Epub 2020 Aug 5.

Kansas Biological Survey, and The Biodiversity Institute, The University of Kansas, Higuchi Hall, 2101 Constant Avenue, Lawrence, KS 66047-3759, USA. E-mail: (Rogers).

Spinicaudata (spiny clam shrimp) is a taxon of Branchiopoda occurring since the Devonian and today it occurs nearly globally in temporary water bodies. We present the most species-rich phylogenetic analyses of this taxon based on four molecular loci: , , and . Our results support previous findings that Cyzicidae is paraphyletic. To render Cyzicidae monophyletic we establish a fourth extant spinicaudatan family to accommodate . Within Cyzicidae, none of the genera , or are monophyletic, and the morphological characters used to define these genera (condyle length and rostrum shape) are not associated with well-delimited clades within Cyzicidae. There is insufficient resolution to elucidate the relationships within Leptestheriidae. However, there is sufficient evidence to show that the leptestheriid genera and are non-monophyletic, and there is no support for the genus . Molecular clock analyses suggest that the wide geographic distribution of many spinicaudatan taxa across multiple continents is largely based on vicariance associated with the break-up of Pangea and Gondwana. Trans-oceanic dispersal has occurred in some taxa (, and within Leptestheriidae) but has been relatively rare. Our results highlight the need to revise the taxonomy of Cyzicidae and Leptestheriidae and provide evidence that the global spinicaudatan diversity may be underestimated due to the presence of numerous cryptic species. We establish Eocyzicidae fam. nov. to accommodate the genus . Consequently, Cyzicidae comprises only two genera - and . occurs also in Africa and Asia and new comb. is assigned to this genus.
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http://dx.doi.org/10.6620/ZS.2020.59-44DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7746975PMC
August 2020

Kinematics and morphology: A comparison of 3D-patterns in the fifth pereiopod of swimming and non-swimming crab species (Malacostraca, Decapoda, Brachyura).

J Morphol 2020 12 27;281(12):1547-1566. Epub 2020 Oct 27.

Allgemeine und Spezielle Zoologie, Institut für Biowissenschaften, Universität Rostock, Rostock, Germany.

Swimming crabs of the taxon Portunoidea show specialized, paddle-shaped fifth pereiopods (P5), which play a role in these crabs' ability to swim. In this study, the morphology of the fifth pereiopod in swimming and non-swimming crabs was studied in detail and the mobility in the articulations between podomeres was calculated from reconstructed three-dimensional (3D)-models. This way, we aimed to provide new estimates of kinematic parameters, and to answer the question on a possible homology of the P5 within several portunoid clades. We measured and compared podomere length ratios, orientations of the joint axes, and modeled single range of motion (sROM) of each joint as well as the total range of motion (tROM) of all joints of the P5 as a whole. Seven Portunoidea species, four of them belonging to the P5-swimming crab morphotype (Liocarcinus depurator, Polybius henslowii, Callinectes sapidus, Portunus pelagicus) and three not belonging to this morphotype (Carcinus aestuarii, Portumnus latipes, and with uncertain status Carupa tenuipes) were compared with the non-portunoids Sternodromia monodi, Ranina ranina, Raninoides bouvieri, Eriocheir sinensis, Varuna litterata, Ashtoret lunaris, and Cancer pagurus. The study was carried out using a combination of microcomputer tomography (μCT)-techniques and 3D-reconstructions. The μCT-data were used to create surface models of the P5 in Amira, which were then 3D-animated and manipulated in Maya to qualitatively compare modeled kinematic parameters. Results show that the merus and carpus in swimming crabs are shorter than in non-swimming crabs, while sROM angles are generally larger. The tROM of all joints expressed as Euclidean distances is generally higher in the portunoids (except for Carcinus). Our comparison of the complete trajectory of the dactylus tip regarding all maximum joint positions of the studied species suggests that the P5-swimming leg might have evolved once in the Portunoidea and got lost afterward in certain clades.
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http://dx.doi.org/10.1002/jmor.21268DOI Listing
December 2020

Why "swimming crabs" are able to swim - The importance of the axial skeleton: A comparison between the "swimming crab" Liocarcinus depurator and two other brachyuran crabs (Cancer pagurus, Carcinus maenas) using μCT and 3D-reconstruction.

Arthropod Struct Dev 2020 Nov 9;59:100972. Epub 2020 Oct 9.

Allgemeine & Spezielle Zoologie, Institut für Biowissenschaften, Universität Rostock, Universitätsplatz 2, 18055, Rostock, Germany.

Most brachyuran crabs use their pereiopods as walking legs, but there are also a number of species, in which the last (5) pair of pereiopods (P5) are specialized to permit a unique mode of swimming. One of these P5-swimming crabs is Liocarcinus depurator, commonly found on European shores. We present 3-dimensional μCT-based reconstructions of the axial skeletons and 5 pereiopods (P5), including the intrinsic and extrinsic musculature of the P5, of L. depurator and of two other non-swimming brachyuran crabs, Cancer pagurus and Carcinus maenas. In Liocarcinus, we also present a reconstruction of the 4 pereiopod (P4) together with its intrinsic musculature. We further use 3-dimensional prints of the reconstructed P5 coxa and basi-ischium of L. depurator as well as thoracal parts near the thoracal-coxal arthrodial cavity to build a model which can simulate the effects of muscular activity based on muscle insertions in our 3D reconstruction and under various simulated tensile vectors. This enables us to test muscular functions that had previously been speculated upon. Reconstructed morphological structures are compared to find differences that may explain why of the three species, only L. depurator is able to swim. Significant differences between Liocarcinus and the non-swimmers Cancer and Carcinus were found in the shape of the axial skeleton, external P5 morphology and the dimensions and origin sites of the extrinsic P5 musculature, but not in the intrinsic musculature of the P5. Inclination angle measurements of P1 thoracal-coxal articulation axes against P5 axes showed that in Cancer and Carcinus, angles in the longitudinal plane were smaller than in the lateral one, whereas in Liocarcinus, they were greater. Inclination angles in the longitudinal plane were also much greater in Liocarcinus than in Cancer and Carcinus. 3D print muscular activity simulation showed that muscles inserting at the basi-ischium, which are often referred to as "levator" or "depressor" muscles, may actually also function as promotors or remotors, depending on the tensile vector within which the muscle is acting.
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http://dx.doi.org/10.1016/j.asd.2020.100972DOI Listing
November 2020

A workflow for exploring ligand dissociation from a macromolecule: Efficient random acceleration molecular dynamics simulation and interaction fingerprint analysis of ligand trajectories.

J Chem Phys 2020 Sep;153(12):125102

Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.

The dissociation of ligands from proteins and other biomacromolecules occurs over a wide range of timescales. For most pharmaceutically relevant inhibitors, these timescales are far beyond those that are accessible by conventional molecular dynamics (MD) simulation. Consequently, to explore ligand egress mechanisms and compute dissociation rates, it is necessary to enhance the sampling of ligand unbinding. Random Acceleration MD (RAMD) is a simple method to enhance ligand egress from a macromolecular binding site, which enables the exploration of ligand egress routes without prior knowledge of the reaction coordinates. Furthermore, the τRAMD procedure can be used to compute the relative residence times of ligands. When combined with a machine-learning analysis of protein-ligand interaction fingerprints (IFPs), molecular features that affect ligand unbinding kinetics can be identified. Here, we describe the implementation of RAMD in GROMACS 2020, which provides significantly improved computational performance, with scaling to large molecular systems. For the automated analysis of RAMD results, we developed MD-IFP, a set of tools for the generation of IFPs along unbinding trajectories and for their use in the exploration of ligand dynamics. We demonstrate that the analysis of ligand dissociation trajectories by mapping them onto the IFP space enables the characterization of ligand dissociation routes and metastable states. The combined implementation of RAMD and MD-IFP provides a computationally efficient and freely available workflow that can be applied to hundreds of compounds in a reasonable computational time and will facilitate the use of τRAMD in drug design.
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http://dx.doi.org/10.1063/5.0019088DOI Listing
September 2020

Optical and hidden transport properties of BaFeNiAsfilm.

J Phys Condens Matter 2020 Sep 28. Epub 2020 Sep 28.

Institut fur Metallische Werkstoffe, Leibniz-Institut fur Festkorper- und Werkstoffforschung Dresden eV, Helmholtzstrasse 20, 01069 Dresden, Dresden, 01069, GERMANY.

Optical spectroscopy was used to study the electrodynamics and hidden transport properties of a BaFeNiAsthin superconducting film. We analyzed the normal state data using a Drude-Lorentz model with two Drude components: one narrow (D) and another broad one (D). In the superconducting state, two gaps with 2Δ/kT= 1.9-2.0 and 2Δ/kT= 4.0-4.3 are formed from the narrow component Dwhile the broad component Dremains ungapped. The calculated total DC resistivity of the film and the low-temperature scattering rate for the narrow Drude component show a hidden Fermi-liquid behavior. The change of total electron-boson coupling (λ) and representative energy (Ω) in the normal state with respect to the superconducting state is typical of other iron-based materials as well as high-temperature superconducting (HTSC) cuprates.
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http://dx.doi.org/10.1088/1361-648X/abbc33DOI Listing
September 2020

Light of Two Atoms in Free Space: Bunching or Antibunching?

Phys Rev Lett 2020 Feb;124(6):063603

QUANTUM, Institut für Physik, Johannes Gutenberg-Universität Mainz, Staudingerweg 7, 55128 Mainz, Germany.

Photon statistics divides light sources into three different categories, characterized by bunched, antibunched, or uncorrelated photon arrival times. Single atoms, ions, molecules, or solid state emitters display antibunching of photons, while classical thermal sources exhibit photon bunching. Here we demonstrate a light source in free space, where the photon statistics depends on the direction of observation, undergoing a continuous crossover between photon bunching and antibunching. We employ two trapped ions, observe their fluorescence under continuous laser light excitation, and record spatially resolved the autocorrelation function g^{(2)}(τ) with a movable Hanbury Brown and Twiss detector. Varying the detector position we find a minimum value for antibunching, g^{(2)}(0)=0.60(5) and a maximum of g^{(2)}(0)=1.46(8) for bunching, demonstrating that this source radiates fundamentally different types of light alike. The observed variation of the autocorrelation function is understood in the Dicke model from which the observed maximum and minimum values can be modeled, taking independently measured experimental parameters into account.
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http://dx.doi.org/10.1103/PhysRevLett.124.063603DOI Listing
February 2020

Druggability Assessment in TRAPP Using Machine Learning Approaches.

J Chem Inf Model 2020 03 11;60(3):1685-1699. Epub 2020 Mar 11.

Molecular and Cellular Modeling Group, Heidelberg Institute of Theoretical Studies (HITS), 69118 Heidelberg, Germany.

Accurate protein druggability predictions are important for the selection of drug targets in the early stages of drug discovery. Because of the flexible nature of proteins, the druggability of a binding pocket may vary due to conformational changes. We have therefore developed two statistical models, a logistic regression model (TRAPP-LR) and a convolutional neural network model (TRAPP-CNN), for predicting druggability and how it varies with changes in the spatial and physicochemical properties of a binding pocket. These models are integrated into TRAnsient Pockets in Proteins (TRAPP), a tool for the analysis of binding pocket variations along a protein motion trajectory. The models, which were trained on publicly available and self-augmented datasets, show equivalent or superior performance to existing methods on test sets of protein crystal structures and have sufficient sensitivity to identify potentially druggable protein conformations in trajectories from molecular dynamics simulations. Visualization of the evidence for the decisions of the models in TRAPP facilitates identification of the factors affecting the druggability of protein binding pockets.
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http://dx.doi.org/10.1021/acs.jcim.9b01185DOI Listing
March 2020

Analysis of Electronic Properties from Magnetotransport Measurements on Ba(FexNi)As Thin Films.

Materials (Basel) 2020 Jan 31;13(3). Epub 2020 Jan 31.

V.L. Ginzburg Center for High-Temperature Superconductivity and Quantum Materials, P.N. Lebedev Physical Institute of the Russian Academy of Sciences, Moscow 119991, Russia.

We performed a detailed structural, magnetotransport, and superconducting analysis of thin epitaxial Ba(FeNi)As films with Ni doping of = 0.05 and 0.08, as prepared by pulsed laser deposition. X-ray diffraction studies demonstrate the high crystalline perfection of the films, which have a similar quality to single crystals. Furthermore, magnetotransport measurements of the films were performed in magnetic fields up to 9 T. The results we used to estimate the density of electronic states at the Fermi level, the coefficient of electronic heat capacity, and other electronic parameters for this compound, in their dependence on the dopant concentration within the framework of the Ginzburg-Landau-Abrikosov-Gorkov theory. The comparison of the determined parameters with measurement data on comparable Ba(FeNi)As single crystals shows good agreement, which confirms the high quality of the obtained films.
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http://dx.doi.org/10.3390/ma13030630DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7040726PMC
January 2020

The brain and the corresponding sense organs in calanoid copepods - Evidence of vestiges of compound eyes.

Arthropod Struct Dev 2020 Jan 25;54:100902. Epub 2020 Jan 25.

Allgemeine & Spezielle Zoologie, Institut für Biowissenschaften, Universität Rostock, 18055, Rostock, Germany.

Copepoda is one of the crustacean taxa with still unresolved phylogenetic relationships within Tetraconata. Recent phylogenomic studies place them close to Malacostraca and Cirripedia. Little is known about the morphological details of the copepod nervous system, and the available data are sometimes contradictory. We investigated several representatives of the subgroup Calanoida using immunohistochemical labeling against alpha-tubulin and various neuroactive substances, combining this with confocal laser scanning analysis and 3D reconstruction. Our results show that the studied copepods exhibit only a single anterior protocerebral neuropil which is connected to the nerves of two protocerebral sense organs: the frontal filament organ and a photoreceptor known as the Gicklhorn's organ. We suggest, on the basis of its position and the innervation it provides, that Gicklhorn's organ is homologous to the compound eye in arthropods. With regard to the frontal filament organ, we reveal detailed innervation to the lateral protocerebrum and the appearance of spherical bodies that stain intensely against alpha tubulin. A potential homology of these bodies to the onion bodies in malacostacan crustaceans and in Mystacocarida is suggested. The nauplius eye in all the examined calanoids shows the same basic pattern of innervation with the middle cup sending its neurites into the median nerve, while the axons of the lateral cups proceed into both the median and the lateral nerves. The early development of the axonal scaffold of the nauplius eye neuropil from the proximal parts of the nauplius eye nerves follows the same pattern as in other crustaceans. In our view, this specific innervation pattern is a further feature supporting the homology of the nauplius eye in crustaceans.
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http://dx.doi.org/10.1016/j.asd.2019.100902DOI Listing
January 2020

Risk factors for development of aminoglycoside resistance among gram-negative rods.

Am J Health Syst Pharm 2019 10;76(22):1838-1847

Infectious Disease Clinical Outcome Research Unit Los Angeles Biomedical Research Institute at Harbor-UCLA, Los Angeles, CA.

Purpose: Development of scoring systems to predict the risk of aminoglycoside resistance and to guide therapy is described.

Methods: Infections due to aminoglycoside-resistant gram-negative rods (AR-GNRs) are increasingly common and associated with adverse outcomes; selection of effective initial antibiotic therapy is necessary to reduce adverse consequences and shorten length of stay. To determine risk factors for AR-GNR recovery from culture, cases of GNR infection among patients admitted to 2 institutions in a major academic hospital system during the period 2011-2016 were retrospectively analyzed. Gentamicin and tobramycin resistance (GTR-GNR) and amikacin resistance (AmR-GNR) patterns were analyzed separately. A total of 26,154 GNR isolates from 12,516 patients were analyzed, 6,699 of which were GTR, and 2,467 of which were AmR.

Results: In multivariate analysis, risk factors for GTR-GNR were presence of weight loss, admission from another medical or long-term care facility, a hemoglobin level of <11 g/dL, receipt of any carbapenem in the prior 30 days, and receipt of any fluoroquinolone in the prior 30 days (C statistic, 0.63). Risk factors for AmR-GNR were diagnosis of cystic fibrosis, male gender, admission from another medical or long-term care facility, ventilation at any point prior to culture during the index hospitalization, receipt of any carbapenem in the prior 30 days, and receipt of any anti-MRSA agent in the prior 30 days (C statistic, 0.74). Multinomial and ordinal models demonstrated that the risk factors for the 2 resistance patterns differed significantly.

Conclusion: A scoring system derived from the developed risk prediction models can be applied by providers to guide empirical antimicrobial therapy for treatment of GNR infections.
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http://dx.doi.org/10.1093/ajhp/zxz201DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7170722PMC
October 2019

Bare metal or drug-eluting stent versus drug-coated balloon in non-ST-elevation myocardial infarction: the randomised PEPCAD NSTEMI trial.

EuroIntervention 2020 Apr;15(17):1527-1533

Universitätsklinikum des Saarlandes, Homburg/Saar, Germany.

Aims: Drug-coated balloons (DCB) may avoid stent-associated long-term complications. This trial compared the clinical outcomes of patients with non-ST-elevation myocardial infarction (NSTEMI) treated with either DCB or stents.

Methods And Results: A total of 210 patients with NSTEMI were enrolled in a randomised, controlled, non-inferiority multicentre trial comparing a paclitaxel iopromide-coated DCB with primary stent treatment. The main inclusion criterion was an identifiable culprit lesion without angiographic evidence of large thrombus. The primary endpoint was target lesion failure (TLF; combined clinical endpoint consisting of cardiac or unknown death, reinfarction, and target lesion revascularisation) after nine months. Secondary endpoints included total major adverse cardiovascular events (MACE) and individual clinical endpoints. Mean age was 67±12 years, 67% were male, 62% had multivessel disease, and 31% were diabetics. One hundred and four patients were randomised to DCB, 106 to stent treatment. In the stent group, 56% of patients were treated with BMS, 44% with current-generation DES. In the DCB group, 85% of patients were treated with DCB only whereas 15% underwent additional stent implantation. During a follow-up of 9.2±0.7 months, DCB treatment was non-inferior to stent treatment with a TLF rate of 3.8% versus 6.6% (intention-to-treat, p=0.53). There was no significant difference between BMS and current-generation DES. The total MACE rate was 6.7% for DCB versus 14.2% for stent treatment (p=0.11), and 5.9% versus 14.4% in the per protocol analysis (p=0.056), respectively.

Conclusions: In patients with NSTEMI, treatment of coronary de novo lesions with DCB was non-inferior to stenting with BMS or DES. These data warrant further investigation of DCB in this setting, in larger trials with DES as comparator (ClinicalTrials.gov Identifier: NCT01489449).
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http://dx.doi.org/10.4244/EIJ-D-19-00723DOI Listing
April 2020

KBbox: A Toolbox of Computational Methods for Studying the Kinetics of Molecular Binding.

J Chem Inf Model 2019 09 20;59(9):3630-3634. Epub 2019 Aug 20.

Heidelberg Institute for Theoretical Studies , Schloss-Wolfsbrunnenweg 35 , 69118 Heidelberg , Germany.

The past few years have seen increasing recognition of the importance of understanding molecular binding kinetics. This has led to the development of myriad computational methods for studying the kinetics of binding processes and predicting their associated rate constants that show varying ranges of application, degrees of accuracy, and computational requirements. In order to help researchers decide which method might be suitable for their projects, we have developed KBbox, a web server that guides users in choosing the methods they should consider on the basis of the information they wish to obtain, the data they currently have available, and the computational resources to which they have access. KBbox provides information on the toolbox of available methods, their associated software tools, an expanding list of curated examples of published applications, and tutorials explaining how to apply some of the methods. It has been designed to allow the easy addition of new methods, tools, and examples as they are developed and published. KBbox is available at https://kbbox.h-its.org/ .
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http://dx.doi.org/10.1021/acs.jcim.9b00485DOI Listing
September 2019

Invasive Validation of Antares, a New Algorithm to Calculate Central Blood Pressure from Oscillometric Upper Arm Pulse Waves.

J Clin Med 2019 Jul 22;8(7). Epub 2019 Jul 22.

EPC-European Prevention Center, Luise-Rainer-Straße 6-10, D-40235 Düsseldorf, Germany.

Antares is an algorithm for pulse wave analysis (PWA) by oscillometric blood pressure (BP) monitors in order to estimate central (aortic) blood pressure (cBP). Antares aims to enable brachial cuff-based BP monitors to be type II-devices, determining absolute cBP values independently of potential peripheral BP inaccuracies. The present study is an invasive validation of the Antares algorithm in the custo screen 400. We followed entirely the 2017 ARTERY protocol for validation of non-invasive cBP devices, the 2013 American National Standards Institute, Inc./Association for the Advancement of Medical Instrumentation/International Organization for Standardization (ANSI/AAMI/ISO) 81060-2 and 2018 AAMI/European Society of Hypertension (ESH)/ISO validation standard protocols. In total, 191 patients undergoing cardiac catheterization were included, of which 145 patients entered analysis. Invasive cBP recordings were compared to simultaneous non-invasive cBP estimations using the Antares algorithm, integrated into an oscillometric BP monitor. Mean difference between invasive and non-invasively estimated systolic cBP was 0.71 mmHg with standard deviation of 5.95 mmHg, fulfilling highest validation criteria. Antares is the first algorithm for estimation of cBP that entirely fulfills the 2017 ARTERY and AAMI/ESH/ISO validation protocols. The Antares algorithm turns the custo screen 400 BP monitor into a type II-device. Integration of Antares into commercially available BP monitors could make it possible to measure PWA parameters in virtually every practice in future.
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http://dx.doi.org/10.3390/jcm8071073DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6678985PMC
July 2019

Risk Factors for Development of Carbapenem Resistance Among Gram-Negative Rods.

Open Forum Infect Dis 2019 Mar 23;6(3):ofz027. Epub 2019 Jan 23.

Infectious Disease Clinical Outcome Research Unit, Los Angeles Biomedical Research Institute at Harbor-UCLA, University of California, Los Angeles, Los Angeles, California.

Background: Infections due to carbapenem-resistant Gram-negative rods (CR-GNR) are increasing in frequency and result in high morbidity and mortality. Appropriate initial antibiotic therapy is necessary to reduce adverse consequences and shorten length of stay.

Methods: To determine risk factors for recovery on culture of CR-GNR, cases were retrospectively analyzed at a major academic hospital system from 2011 to 2016. Ertapenem resistance (ER-GNR) and antipseudomonal (nonertapenem) carbapenem resistance (ACR-GNR) patterns were analyzed separately. A total of 30951 GNR isolates from 12370 patients were analyzed, 563 of which were ER and 1307 of which were ACR.

Results: In multivariate analysis, risk factors for ER-GNR were renal disease, admission from another health care facility, ventilation at any point before culture during the index hospitalization, receipt of any carbapenem in the prior 30 days, and receipt of any anti-methicillin-resistant (anti-MRSA) agent in the prior 30 days (c-statistic, 0.74). Risk factors for ACR-GNR were male sex, admission from another health care facility, ventilation at any point before culture during the index hospitalization, receipt of any carbapenem in the prior 30 days, and receipt of any anti-MRSA agent in the prior 30 days (c-statistic, 0.76).

Conclusions: A straightforward scoring system derived from these models can be applied by providers to guide empiric antimicrobial therapy; it outperformed use of a standard hospital antibiogram in predicting infections with ER-GNR and ACR-GNR.
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http://dx.doi.org/10.1093/ofid/ofz027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6405936PMC
March 2019

Multimaterial 3D laser microprinting using an integrated microfluidic system.

Sci Adv 2019 Feb 8;5(2):eaau9160. Epub 2019 Feb 8.

Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), 76128 Karlsruhe, Germany.

Three-dimensional (3D) laser micro- and nanoprinting has become a versatile, reliable, and commercially available technology for the preparation of complex 3D architectures for diverse applications. However, the vast majority of structures published so far have been composed of only a single constituent material. Here, we present a system based on a microfluidic chamber integrated into a state-of-the-art laser lithography apparatus. This system is scalable in terms of the number of materials and eliminates the need to go back and forth between the lithography instrument and the chemistry room numerous times, with tedious realignment steps in between. As an application, we present 3D deterministic microstructured security features requiring seven different liquids: a nonfluorescent photoresist as backbone, two photoresists containing different fluorescent quantum dots, two photoresists with different fluorescent dyes, and two developers. Our integrated microfluidic 3D printing system opens the door to truly multimaterial 3D additive manufacturing on the micro- and nanoscale.
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http://dx.doi.org/10.1126/sciadv.aau9160DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6368435PMC
February 2019

Drug-coated balloons for small coronary artery disease (BASKET-SMALL 2): an open-label randomised non-inferiority trial.

Lancet 2018 09 28;392(10150):849-856. Epub 2018 Aug 28.

University Hospital Saarland, Homburg, Germany.

Background: Drug-coated balloons (DCB) are a novel therapeutic strategy for small native coronary artery disease. However, their safety and efficacy is poorly defined in comparison with drug-eluting stents (DES).

Methods: BASKET-SMALL 2 was a multicentre, open-label, randomised non-inferiority trial. 758 patients with de-novo lesions (<3 mm in diameter) in coronary vessels and an indication for percutaneous coronary intervention were randomly allocated (1:1) to receive angioplasty with DCB versus implantation of a second-generation DES after successful predilatation via an interactive internet-based response system. Dual antiplatelet therapy was given according to current guidelines. The primary objective was to show non-inferiority of DCB versus DES regarding major adverse cardiac events (MACE; ie, cardiac death, non-fatal myocardial infarction, and target-vessel revascularisation) after 12 months. The non-inferiority margin was an absolute difference of 4% in MACE. This trial is registered with ClinicalTrials.gov, number NCT01574534.

Findings: Between April 10, 2012, and February 1, 2017, 382 patients were randomly assigned to the DCB group and 376 to DES group. Non-inferiority of DCB versus DES was shown because the 95% CI of the absolute difference in MACE in the per-protocol population was below the predefined margin (-3·83 to 3·93%, p=0·0217). After 12 months, the proportions of MACE were similar in both groups of the full-analysis population (MACE was 7·5% for the DCB group vs 7·3% for the DES group; hazard ratio [HR] 0·97 [95% CI 0·58-1·64], p=0·9180). There were five (1·3%) cardiac-related deaths in the DES group and 12 (3·1%) in the DCB group (full analysis population). Probable or definite stent thrombosis (three [0·8%] in the DCB group vs four [1·1%] in the DES group; HR 0·73 [0·16-3·26]) and major bleeding (four [1·1%] in the DCB group vs nine [2·4%] in the DES group; HR 0·45 [0·14-1·46]) were the most common adverse events.

Interpretation: In small native coronary artery disease, DCB was non-inferior to DES regarding MACE up to 12 months, with similar event rates for both treatment groups.

Funding: Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung, Basel Cardiovascular Research Foundation, and B Braun Medical AG.
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http://dx.doi.org/10.1016/S0140-6736(18)31719-7DOI Listing
September 2018

Tetraconatan phylogeny with special focus on Malacostraca and Branchiopoda: highlighting the strength of taxon-specific matrices in phylogenomics.

Proc Biol Sci 2018 08 22;285(1885). Epub 2018 Aug 22.

Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA.

Understanding the evolution of Tetraconata or Pancrustacea-the clade that includes crustaceans and insects-requires a well-resolved hypothesis regarding the relationships within and among its constituent taxa. Here, we assembled a taxon-rich phylogenomic dataset focusing on crustacean lineages based solely on genomes and new-generation Illumina-generated transcriptomes, including 89 representatives of Tetraconata. This constitutes, to our knowledge, the first phylogenomic study specifically addressing internal relationships of Malacostraca (with 26 species included) and Branchiopoda (36 species). Seven matrices comprising 81-684 orthogroups and 17 690-242 530 amino acid positions were assembled and analysed under five different analytical approaches. To maximize gene occupancy and to improve resolution, taxon-specific matrices were designed for Malacostraca and Branchiopoda. Key tetraconatan taxa (i.e. Oligostraca, Multicrustacea, Branchiopoda, Malacostraca, Thecostraca, Copepoda and Hexapoda) were monophyletic and well supported. Within Branchiopoda, Phyllopoda, Diplostraca, Cladoceromorpha and Cladocera were monophyletic. Within Malacostraca, the clades Eumalacostraca, Decapoda and Reptantia were well supported. Recovery of Caridoida or Peracarida was highly dependent on the analysis for the complete matrix, but it was consistently monophyletic in the malacostracan-specific matrices. From such examples, we demonstrate that taxon-specific matrices and particular evolutionary models and analytical methods, namely CAT-GTR and Dayhoff recoding, outperform other approaches in resolving certain recalcitrant nodes in phylogenomic analyses.
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http://dx.doi.org/10.1098/rspb.2018.1524DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6125901PMC
August 2018

Risk Factors for Colistin Resistance among Gram-Negative Rods and Klebsiella pneumoniae Isolates.

J Clin Microbiol 2018 09 27;56(9). Epub 2018 Aug 27.

Infectious Disease Clinical Outcome Research Unit, Los Angeles Biomedical Research Institute at Harbor-UCLA, Los Angeles, California, USA.

Infections due to colistin-resistant (Col) Gram-negative rods (GNRs) and colistin-resistant isolates in particular result in high associated mortality and poor treatment options. To determine the risk factors for recovery on culture of Col GNRs and Col, analyses were chosen to aid decisions at two separate time points: the first when only Gram stain results are available without any bacterial species information (corresponding to the Col GNR model) and the second when organism identification is performed but prior to reporting of antimicrobial susceptibility testing results (corresponding to the Col model). Cases were retrospectively analyzed at a major academic hospital system from 2011 to 2016. After excluding bacteria that were intrinsically resistant to colistin, a total of 28,512 GNR isolates (4,557 isolates) were analyzed, 128 of which were Col (i.e., MIC > 2 μg/ml), including 68 of which that were Col In multivariate analysis, risk factors for Col GNRs were neurologic disease, residence in a skilled nursing facility prior to admission, receipt of carbapenems in the last 90 days, prior infection with a carbapenem-resistant organism, and receipt of ventilatory support (-statistic = 0.81). Risk factors for Col specifically were neurologic disease, residence in a skilled nursing facility prior to admission, receipt of carbapenems in the last 90 days, receipt of an anti-methicillin-resistant antimicrobial in the last 90 days, and prior infection with a carbapenem-resistant organism (-statistic = 0.89). A scoring system derived from these models can be applied by providers to guide empirical antimicrobial therapy in patients with infections with suspected Col GNR and Col isolates.
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http://dx.doi.org/10.1128/JCM.00149-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6113453PMC
September 2018

The chewing lice (Phthiraptera: Ischnocera, Amblycera) of the great cormorant (Phalacrocorax carbo).

Parasitol Int 2018 Aug 5;67(4):528-532. Epub 2018 May 5.

University of Rostock, Institut für Biowissenschaften, Allgemeine und Spezielle Zoologie, Universitätsplatz 2, Rostock 18055, Germany.

The Great Cormorant is a widespread bird species with almost worldwide distribution. Accordingly, its general biology has been investigated thoroughly. Less well known, however, are the chewing lice that live inside the plumage of this diving bird. We examined the two known species of Great Cormorant chewing lice, Eidmanniella pellucida (Rudow, 1869) (Amblycera: Menoponidae) and Pectinopygus gyricornis (Denny, 1842) (Ischnocera: Philopteridae). Taking advantage of the autofluorescence of the cuticle, confocal laser scanning microscopy (CLSM) was used to explore the external morphology of all developmental stages of P. gyricornis. Morphometric analyses revealed a standard increase in body size from first larval instar to the adult. In addition, all instars exhibited increasing body segment differentiation, especially in the abdomen and the head. A total of 277 individuals of Pectinopygus gyricornis and 2 individuals of Eidmanniella pellucida were collected from eleven Great Cormorants from Mecklenburg-Western Pomerania, Germany, in 2015.
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http://dx.doi.org/10.1016/j.parint.2018.05.003DOI Listing
August 2018

Constant morphological patterns in the hemolymph vascular system of crayfish (Crustacea, Decapoda).

Arthropod Struct Dev 2018 May 16;47(3):248-267. Epub 2018 Apr 16.

Universität Rostock, Institut für Biowissenschaften, Allgemeine und Spezielle Zoologie, Universitätsplatz 2, 18055, Rostock, Germany.

We present a study of the hemolymph vascular system of the marbled crayfish, Procambarus fallax f. virginalis, the only crayfish species known to be parthenogenetic. To identify potential evolutionary patterns, we compared data from a total of 48 specimens of P. fallax with 22 specimens of Orconectes limosus. Visualizations (2D and 3D) were carried out using a combination of classical and modern morphological techniques. Our data were compared to the existing literature. Like all Decapoda, both P. fallax and O. limosus have a hemolymph vascular system, consisting of a globular heart with seven off-branching arteries. We were able to visualize in detail the heart of crayfish for the first time, i.e., the myocard with its clusters of muscles running through the lumen of the heart, the valves and flaps of ostia and arteries. Furthermore, the branching patterns of the seven artery systems were analyzed. Anatomical structures identified to be consistent in all specimens of both species were combined as ground pattern of hemolymph vascular system features for Astacida.
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http://dx.doi.org/10.1016/j.asd.2017.12.005DOI Listing
May 2018

Unexpected UBX expression in the maxilliped of the mystacocarid crustacean Derocheilocharis remanei-evidence for a different way of making a maxilliped?

Dev Genes Evol 2017 07 18;227(4):289-296. Epub 2017 Jul 18.

Universität Rostock, Allgemeine und Spezielle Zoologie, Institut für Biowissenschaften, Universitätsplatz 2, 18055, Rostock, Germany.

In terms of morphology, crustacean maxillipeds are hybrid appendages. They arise in anterior thoracic segments and display characteristics of both locomotory (thoracic) and feeding (gnathal) appendages. Maxillipeds are functionally integrated with the anterior gnathal appendages. Hox gene expression patterns and immunolabeling with the FP6.87 antibody, which detects conserved epitopes of UBX and ABD-A proteins, reveal that maxillipeds are consistently associated with a shift in the expression of the homeotic gene Ubx. Ubx transcription products or proteins only appear in thoracic segments with a typical locomotory thoracopod and are consistently absent in the maxilliped. This pattern is found in various crustaceans: the copepod Mesocyclops, the mysid Mysidium, the decapods Homarus and Periclimenes, the isopod Porcellio, and the amphipod Parhyale. In Parhyale, which possesses maxillipeds on the first thoracic segment, gene manipulation experiments have shown that a leg-like thoracic appendage can be recovered by mis-expressing Ubx in that segment and walking legs can be transformed into maxillipeds by Ubx-knockdown. This survey focuses on the expression of UBX/ABD-A proteins, studied using the FP6.87 antibody, in the larval stages of the mystacocarid crustacean Derocheilocaris remanei. Mystacocarids inhabit the intertidal meiofauna zone of sandy beaches and possess one pair of maxillipeds on the first thoracic segment. Strong UBX/ABD-A expression in the developing maxilliped makes Derocheilocaris unique among crustaceans. Our data might also show that the transformation from locomotory thoracopod to maxilliped cannot be accounted for by the mere presence or absence of UBX, because in mystacocarids, UBX is present in both kinds of limbs. The role of the other Hox gene known to be involved in this transformation, Sex combs reduced (Scr), is unclear. The results presented here may document a new example of a shift in Hox gene function in arthropods. The difference in UBX/ABD-A expression between D. remanei and the copepod maxillipeds is of particular interest because correspondences between the feeding apparatus-including the maxilliped-in mystacocarids and copepods have been suggested as being of phylogenetic significance.
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http://dx.doi.org/10.1007/s00427-017-0586-3DOI Listing
July 2017

TRAPP webserver: predicting protein binding site flexibility and detecting transient binding pockets.

Nucleic Acids Res 2017 07;45(W1):W325-W330

Molecular and Cellular Modeling group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Baden-Württemberg 69118, Germany.

The TRAnsient Pockets in Proteins (TRAPP) webserver provides an automated workflow that allows users to explore the dynamics of a protein binding site and to detect pockets or sub-pockets that may transiently open due to protein internal motion. These transient or cryptic sub-pockets may be of interest in the design and optimization of small molecular inhibitors for a protein target of interest. The TRAPP workflow consists of the following three modules: (i) TRAPP structure- generation of an ensemble of structures using one or more of four possible molecular simulation methods; (ii) TRAPP analysis-superposition and clustering of the binding site conformations either in an ensemble of structures generated in step (i) or in PDB structures or trajectories uploaded by the user; and (iii) TRAPP pocket-detection, analysis, and visualization of the binding pocket dynamics and characteristics, such as volume, solvent-exposed area or properties of surrounding residues. A standard sequence conservation score per residue or a differential score per residue, for comparing on- and off-targets, can be calculated and displayed on the binding pocket for an uploaded multiple sequence alignment file, and known protein sequence annotations can be displayed simultaneously. The TRAPP webserver is freely available at http://trapp.h-its.org.
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http://dx.doi.org/10.1093/nar/gkx277DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5570179PMC
July 2017

The First Organ-Based Ontology for Arthropods (Ontology of Arthropod Circulatory Systems - OArCS) and its Integration into a Novel Formalization Scheme for Morphological Descriptions.

Syst Biol 2017 Sep;66(5):754-768

Allgemeine & Spezielle Zoologie, Institut fuer Biowissenschaften, Universitaet Rostock, 18055 Rostock, Germany.

Morphology, the oldest discipline in the biosciences, is currently experiencing a renaissance in the field of comparative phenomics. However, morphological/phenotypic research still suffers on various levels from a lack of standards. This shortcoming, first highlighted as the "linguistic problem of morphology", concerns the usage of terminology and also the need for formalization of morphological descriptions themselves, something of paramount importance not only to the field of morphology but also when it comes to the use of phenotypic data in systematics and evolutionary biology. We therefore argue, that for morphological descriptions, the basis of all systematic and evolutionary interpretations, ontologies need to be utilized which are based exclusively on structural qualities/properties and which in no case include statements about homology and/or function. Statements about homology and function constitute interpretations on a different or higher level. Based on these "anatomy ontologies", further ontological dimensions (e.g., referring to functional properties or homology) may be exerted for a broad use in evolutionary phenomics. To this end we present the first organ-based ontology for the most species-rich animal group, the Arthropoda. Our Ontology of Arthropod Circulatory Systems (OArCS) contains a comprehensive collection of 383 terms (i.e., labels) tied to 296 concepts (i.e., definitions) collected from the literature on phenotypic aspects of circulatory organ features in arthropods. All of the concepts used in OArCS are based exclusively on structural features, and in the context of the ontology are independent of homology and functional assumptions. We cannot rule out that in some cases, terms are used which in traditional usage and previous accounts might have implied homology and/or function (e.g. heart, sternal artery). Concepts are composed of descriptive elements that are used to classify observed instances into the organizational framework of the ontology. That is, descriptions in ontologies are only descriptions of individuals if they are necessary/and or sufficient representations of attributes (independently) observed and recorded for an individual. In addition, we here present for the first time an entirely new approach to formalizing phenotypic research, a semantic model for the description of a complex organ system in a highly disparate taxon, the arthropods. We demonstrate this with a formalized morphological description of the hemolymph vascular system in one specimen of the European garden spider Araneus diadematus. Our description targets five categories of descriptive statement: "position", "spatial relationships", "shape", "constituents", and "connections", as the corresponding formalizations constitute exemplary patterns useful not only when talking about the circulatory system, but also in descriptions in general. The downstream applications of computer-parsable morphological descriptions are widespread, with their core utility being the fact that they make it possible to compare collective description sets in computational time, that is, very quickly. Among other things, this facilitates the identification of phenotypic plasticity and variation when single individuals are compared, the identification of those traits which correlate between and within taxa, and the identification of links between morphological traits and genetic (using GO, Gene Ontology) or environmental (using ENVO, Environmental Ontology) factors. [Arthropoda; concept; function; hemolymph vascular system; homology; terminology.].
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http://dx.doi.org/10.1093/sysbio/syw108DOI Listing
September 2017

Comparative Case-Control analysis of a dedicated self-expanding Biolimus A9-eluting Bifurcation stent versus provisional or mandatory side branch intervention strategies in the treatment of coronary bifurcation lesions.

Catheter Cardiovasc Interv 2017 Jul 21;90(1):39-47. Epub 2016 Sep 21.

Department of Cardiology, Zentralklinik, Bad Berka, Germany.

Background: In a number of coronary bifurcation lesions, both the main vessel and the side branch (SB) need stent coverage.

Objectives: To analyze the procedural performance and the impact on radiation times (RT) and contrast medium consumption (CMC) of the Axxess™ stent system (Biosensors, Switzerland) treating de novo bifurcation lesions (DBL).

Methods: One hundred and ten consecutive prospectively enrolled cases (Axxess Group) and 110 age, sex, and lesion location matched controls undergoing mandatory (Group A, n = 56) or provisional (Group B, n = 54) SB intervention were analyzed.

Results: Although more pre-dilatation was performed in the Axxess Group (92.7% vs. 46.4% [Group A] vs. 24.1% [Group B]), and more stents were used (2.4 vs. 1.2 vs. 1.05), RT and CMC were significantly lower in the Axxess Group [7.9 min/129 ml vs. 14.2 min/209 ml vs. 7.8 min/152 ml; P < 0.001]. Final Thrombolysis In Myocardial Infarction three flow in both branches was significantly more frequent in the Axxess Group (98.2% vs. 94.6% vs. 88.9%; P = 0.02), and post-interventional troponin T elevations were the lowest in the Axxess Group. Eighty one percent of the Axxess-stents could be implanted without technical difficulties. Difficult implantations procedures were mainly related to coronary anatomy. There was no safety concerns (cardiac death, stent-thrombosis) compared to controls. Cumulative 6-months MACE rates were 11% versus 23% versus 25%. TLR rates at 6-months were 5%, 18%, and 15%, respectively.

Conclusions: Axxess bifurcation stent system procedures were associated with significantly less RT and CMC compared to conventional DBL therapy strategies. Difficult coronary anatomy may hinder successful implantation and a learning curve has to be considered. © 2016 Wiley Periodicals, Inc.
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http://dx.doi.org/10.1002/ccd.26799DOI Listing
July 2017

Nervous system development in the fairy shrimp Branchinella sp. (Crustacea: Branchiopoda: Anostraca): Insights into the development and evolution of the branchiopod brain and its sensory organs.

J Morphol 2016 11 5;277(11):1423-1446. Epub 2016 Aug 5.

Universität Rostock, Institut für Biowissensschaften, Allgemeine und Spezielle Zoologie, Universitätsplatz 2, D-18055 Rostock, Germany.

Using immunohistochemical labeling against acetylated a-tubulin and serotonin in combination with confocal laser scanning microscopy and 3D-reconstruction, we investigated the temporary freshwater pond inhabitant Branchinella sp. (Crustacea: Branchiopoda: Anostraca) for the first time to provide detailed data on the development of the anostracan nervous system. Protocerebral sense organs such as the nauplius eye and frontal filament organs are present as early as the hatching stage L0. In the postnaupliar region, two terminal pioneer neurons grow from posterior to anterior to connect the mandibular neuromeres. The first protocerebral neuropil to emerge is not part of the central complex but represents the median neuropil, and begins to develop from L0+ onwards. In stage L3, the first evidence of developing compound eyes is visible. This is followed by the formation of the visual neuropils and the neuropils of the central complex in the protocerebrum. From the deutocerebral lobes, the projecting neuron tract proceeds to both sides of the lateral protocerebrum, forming a chiasma just behind the central body. In the postnaupliar region, the peripheral nervous system, commissures and connectives develop along an anterior-posterior gradient after the fasciculation of the terminal pioneer neurons with the mandibular neuromere. The peripheral nervous system in the thoracic segments consists of two longitudinal neurite bundles on each side which connect the intersegmental nerves, together with the ventral nervous system forming an orthogon-like network. Here, we discuss, among other things, the evidence of a fourth nauplius eye nerve and decussating projecting neuron tract found in Branchinella sp., and provide arguments to support our view that the crustacean frontal filament (organ) and onychophoran primary antenna are homologous. J. Morphol. 277:1423-1446, 2016. © 2016 Wiley Periodicals, Inc.
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http://dx.doi.org/10.1002/jmor.20585DOI Listing
November 2016

ProSAT+: visualizing sequence annotations on 3D structure.

Protein Eng Des Sel 2016 08 9;29(8):281-4. Epub 2016 Jun 9.

Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, Heidelberg 69118, Germany Center for Molecular Biology at Heidelberg University (ZMBH), DKFZ-ZMBH Alliance and Interdisciplinary Center for Scientific Computing (IWR), Im Neuenheimer Feld 282, Heidelberg 69120, Germany

PRO: tein S: tructure A: nnotation T: ool-plus (ProSAT(+)) is a new web server for mapping protein sequence annotations onto a protein structure and visualizing them simultaneously with the structure. ProSAT(+) incorporates many of the features of the preceding ProSAT and ProSAT2 tools but also provides new options for the visualization and sharing of protein annotations. Data are extracted from the UniProt KnowledgeBase, the RCSB PDB and the PDBe SIFTS resource, and visualization is performed using JSmol. User-defined sequence annotations can be added directly to the URL, thus enabling visualization and easy data sharing. ProSAT(+) is available at http://prosat.h-its.org.
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http://dx.doi.org/10.1093/protein/gzw021DOI Listing
August 2016

Antiproliferative activity of ruthenium(ii) arene complexes with mono- and bidentate pyridine-based ligands.

Dalton Trans 2016 Aug;45(33):13114-25

Universität Leipzig, Institut für Anorganische Chemie, Johannisallee 29, 04103 Leipzig, Germany.

A series of Ru(II) arene complexes of mono- and bidentate N-donor ligands with carboxyl or ester groups and chlorido ancillary ligands were synthesised and structurally characterised. The complexes have a distorted tetrahedral piano-stool geometry. The binding interaction was studied with calf thymus DNA (CT-DNA) by absorption titration, viscosity measurement, thermal melting, circular dichroism, ethidium bromide displacement assay and DNA cleavage of plasmid DNA (pBR322), investigated by gel electrophoresis. The dichlorido complexes bind covalently to DNA in the dark, similar to cisplatin, while the monochlorido complexes bind covalently on irradiation, similar to cisplatin analogues. The compounds are selectively cytotoxic against several tumour cell lines and show specific nonlinear correlation between dose and activity. This phenomenon is closely related to their potential to act preferentially as inhibitors of cell division.
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http://dx.doi.org/10.1039/c6dt01782gDOI Listing
August 2016
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