Showing papers by "University of Jena published in 2012"

International evidence-based recommendations for point-of-care lung ultrasound.

Abstract: The purpose of this study is to provide evidence-based and expert consensus recommendations for lung ultrasound with focus on emergency and critical care settings. A multidisciplinary panel of 28 experts from eight countries was involved. Literature was reviewed from January 1966 to June 2011. Consensus members searched multiple databases including Pubmed, Medline, OVID, Embase, and others. The process used to develop these evidence-based recommendations involved two phases: determining the level of quality of evidence and developing the recommendation. The quality of evidence is assessed by the grading of recommendation, assessment, development, and evaluation (GRADE) method. However, the GRADE system does not enforce a specific method on how the panel should reach decisions during the consensus process. Our methodology committee decided to utilize the RAND appropriateness method for panel judgment and decisions/consensus. Seventy-three proposed statements were examined and discussed in three conferences held in Bologna, Pisa, and Rome. Each conference included two rounds of face-to-face modified Delphi technique. Anonymous panel voting followed each round. The panel did not reach an agreement and therefore did not adopt any recommendations for six statements. Weak/conditional recommendations were made for 2 statements, and strong recommendations were made for the remaining 65 statements. The statements were then recategorized and grouped to their current format. Internal and external peer-review processes took place before submission of the recommendations. Updates will occur at least every 4 years or whenever significant major changes in evidence appear. This document reflects the overall results of the first consensus conference on “point-of-care” lung ultrasound. Statements were discussed and elaborated by experts who published the vast majority of papers on clinical use of lung ultrasound in the last 20 years. Recommendations were produced to guide implementation, development, and standardization of lung ultrasound in all relevant settings.

Integrative genome analyses identify key somatic driver mutations of small-cell lung cancer

Abstract: Small-cell lung cancer (SCLC) is an aggressive lung tumor subtype with poor prognosis(1-3). We sequenced 29 SCLC exomes, 2 genomes and 15 transcriptomes and found an extremely high mutation rate of 7.4 +/- 1 protein-changing mutations per million base pairs. Therefore, we conducted integrated analyses of the various data sets to identify pathogenetically relevant mutated genes. In all cases, we found evidence for inactivation of TP53 and RB1 and identified recurrent mutations in the CREBBP, EP300 and MLL genes that encode histone modifiers. Furthermore, we observed mutations in PTEN, SLIT2 and EPHA7, as well as focal amplifications of the FGFR1 tyrosine kinase gene. Finally, we detected many of the alterations found in humans in SCLC tumors from Tp53 and Rb1 double knockout mice(4). Our study implicates histone modification as a major feature of SCLC, reveals potentially therapeutically tractable genomic alterations and provides a generalizable framework for the identification of biologically relevant genes in the context of high mutational background.

Genetically Distinct Subsets within ANCA-Associated Vasculitis

Abstract: BACKGROUND Antineutrophil cytoplasmic antibody (ANCA)-associated vasculitis is a severe condition encompassing two major syndromes: granulomatosis with polyangiitis (formerly known as Wegener's granulomatosis) and microscopic polyangiitis. Its cause is unknown, and there is debate about whether it is a single disease entity and what role ANCA plays in its pathogenesis. We investigated its genetic basis. METHODS A genomewide association study was performed in a discovery cohort of 1233 U. K. patients with ANCA-associated vasculitis and 5884 controls and was replicated in 1454 Northern European case patients and 1666 controls. Quality control, population stratification, and statistical analyses were performed according to standard criteria. RESULTS We found both major-histocompatibility-complex (MHC) and non-MHC associations with ANCA-associated vasculitis and also that granulomatosis with polyangiitis and microscopic polyangiitis were genetically distinct. The strongest genetic associations were with the antigenic specificity of ANCA, not with the clinical syndrome. Anti-proteinase 3 ANCA was associated with HLA-DP and the genes encoding alpha(1)-antitrypsin (SERPINA1) and proteinase 3 (PRTN3) (P = 6.2x10(-89), P = 5.6x10(-12), and P = 2.6x10(-7), respectively). Anti-myeloperoxidase ANCA was associated with HLA-DQ (P = 2.1x10(-8)). CONCLUSIONS This study confirms that the pathogenesis of ANCA-associated vasculitis has a genetic component, shows genetic distinctions between granulomatosis with polyangiitis and microscopic polyangiitis that are associated with ANCA specificity, and suggests that the response against the autoantigen proteinase 3 is a central pathogenic feature of proteinase 3 ANCA-associated vasculitis. These data provide preliminary support for the concept that proteinase 3 ANCA-associated vasculitis and myeloperoxidase ANCA-associated vasculitis are distinct autoimmune syndromes. (Funded by the British Heart Foundation and others.)

Surface-enhanced Raman spectroscopy (SERS): progress and trends

Abstract: Surface-enhanced Raman spectroscopy (SERS) combines molecular fingerprint specificity with potential single-molecule sensitivity. Therefore, the SERS technique is an attractive tool for sensing molecules in trace amounts within the field of chemical and biochemical analytics. Since SERS is an ongoing topic, which can be illustrated by the increased annual number of publications within the last few years, this review reflects the progress and trends in SERS research in approximately the last three years. The main reason why the SERS technique has not been established as a routine analytic technique, despite its high specificity and sensitivity, is due to the low reproducibility of the SERS signal. Thus, this review is dominated by the discussion of the various concepts for generating powerful, reproducible, SERS-active surfaces. Furthermore, the limit of sensitivity in SERS is introduced in the context of single-molecule spectroscopy and the calculation of the 'real' enhancement factor. In order to shed more light onto the underlying molecular processes of SERS, the theoretical description of SERS spectra is also a growing research field and will be summarized here. In addition, the recording of SERS spectra is affected by a number of parameters, such as laser power, integration time, and analyte concentration. To benefit from synergies, SERS is combined with other methods, such as scanning probe microscopy and microfluidics, which illustrates the broad applications of this powerful technique.

Functional block copolymers: nanostructured materials with emerging applications.

Abstract: Recent advances in polymer synthesis have significantly enhanced the ability to rationally design block copolymers with tailored functionality. The self-assembly of these macromolecules in the solid state or in solution allows the formation of nanostructured materials with a variety of properties and potential functions. This Review illustrates recent progress in the field of block copolymer materials by highlighting selected emerging applications.

Binary copper oxide semiconductors: From materials towards devices

Abstract: Copper-oxide compound semiconductors provide a unique possibility to tune the optical and electronic properties from insulating to metallic conduction, from bandgap energies of 2.1 eV to the infrared at 1.40 eV, i.e., right into the middle of the efficiency maximum for solar-cell applications. Three distinctly different phases, Cu2O, Cu4O3, and CuO, of this binary semiconductor can be prepared by thin-film deposition techniques, which differ in the oxidation state of copper. Their material properties as far as they are known by experiment or predicted by theory are reviewed. They are supplemented by new experimental results from thin-film growth and characterization, both will be critically discussed and summarized. With respect to devices the focus is on solar-cell performances based on Cu2O. It is demonstrated by photoelectron spectroscopy (XPS) that the heterojunction system p-Cu2O/n-AlGaN is much more promising for the application as efficient solar cells than that of p-Cu2O/n-ZnO heterojunction devices that have been favored up to now.

Catalytic processes monitored at the nanoscale with tip-enhanced Raman spectroscopy

Abstract: Heterogeneous catalysts play a pivotal role in the chemical industry, but acquiring molecular insights into functioning catalysts remains a significant challenge. Recent advances in micro-spectroscopic approaches have allowed spatiotemporal information to be obtained on the dynamics of single active sites and the diffusion of single molecules. However, these methods lack nanometre-scale spatial resolution and/or require the use of fluorescent labels. Here, we show that time-resolved tip-enhanced Raman spectroscopy can monitor photocatalytic reactions at the nanoscale. We use a silver-coated atomic force microscope tip to both enhance the Raman signal and to act as the catalyst. The tip is placed in contact with a self-assembled monolayer of p-nitrothiophenol molecules adsorbed on gold nanoplates. A photocatalytic reduction process is induced at the apex of the tip with green laser light, while red laser light is used to monitor the transformation process during the reaction. This dual-wavelength approach can also be used to observe other molecular effects such as monolayer diffusion.

Precise hierarchical self-assembly of multicompartment micelles

Abstract: Hierarchical self-assembly offers elegant and energy-efficient bottom-up strategies for the structuring of complex materials. For block copolymers, the last decade witnessed great progress in diversifying the structural complexity of solution-based assemblies into multicompartment micelles. However, a general understanding of what governs multicompartment micelle morphologies and polydispersity, and how to manipulate their hierarchical superstructures using straightforward concepts and readily accessible polymers remains unreached. Here we demonstrate how to create homogeneous multicompartment micelles with unprecedented structural control via the intermediate pre-assembly of subunits. This directed self-assembly leads to a step-wise reduction of the degree of conformational freedom and dynamics and avoids undesirable kinetic obstacles during the structure build-up. It yields a general concept for homogeneous populations of well-defined multicompartment micelles with precisely tunable patchiness, while using simple linear ABC triblock terpolymers. We further demonstrate control over the hierarchical step-growth polymerization of multicompartment micelles into micron-scale segmented supracolloidal polymers as an example of programmable mesoscale colloidal hierarchies via well-defined patchy nanoobjects.

Powering up the Future: Radical Polymers for Battery Applications

Abstract: Our society's dependency on portable electric energy, i.e., rechargeable batteries, which permit power consumption at any place and in any time, will eventually culminate in resource wars on limited commodities like lithium, cobalt, and rare earth metals. The substitution of conventional metals as means of electric charge storage by organic and polymeric materials, which may ultimately be derived from renewable resources, appears to be the only feasible way out. In this context, the novel class of organic radical batteries (ORBs) excelling in rate capability (i.e., charging speed) and cycling stability (>1000 cycles) sets new standards in battery research. This review examines stable nitroxide radical bearing polymers, their processing to battery systems, and their promising performance.

A perfect absorber made of a graphene micro-ribbon metamaterial.

Abstract: Metamaterial-based perfect absorbers promise many applications. Perfect absorption is characterized by the complete suppression of transmission and reflection and complete dissipation of the incident energy by the absorptive meta-atoms. A certain absorption spectrum is usually assigned to a bulk medium and serves as a signature of the respective material. Here we show how to use graphene flakes as building blocks for perfect absorbers. Then, an absorbing meta-atom only consists of a molecular monolayer placed at an appropriate distance from a metallic ground plate. We show that the functionality of such device is intuitively and correctly explained by a Fabry-Perot model.

Reactive oxygen species generation and signaling in plants

Abstract: The introduction of molecular oxygen into the atmosphere was accompanied by the generation of reactive oxygen species (ROS) as side products of many biochemical reactions. ROS are permanently generated in plastids, peroxisomes, mitochiondria, the cytosol and the apoplast. Imbalance between ROS generation and safe detoxification generates oxidative stress and the accumulating ROS are harmful for the plants. On the other hand, specific ROS function as signaling molecules and activate signal transduction processes in response to various stresses. Here, we summarize the generation of ROS in the different cellular compartments and the signaling processes which are induced by ROS.

Drug Delivery Strategies for Poorly Water-Soluble Drugs

Abstract: The drug candidates coming from combinatorial chemistry research and/or the drugs selected from biologically based high-throughput screening are quite often very lipophilic, as these drug candidates exert their pharmacological action at or in biological membranes or membrane-associated proteins. This challenges drug delivery institutions in industry or academia to develop carrier systems for the optimal oral and parenteral administration of these drugs. To mention only a few of the challenges for this class of drugs: their oral bioavailability is poor and highly variable, and carrier development for parenteral administration is faced with problems, including the massive use of surface-active excipients for solubilisation. Formulation specialists are confronted with an even higher level of difficulties when these drugs have to be delivered site specifically. This article addresses the emerging formulation designs for delivering of poorly water-soluble drugs.

Scientific objectives of Einstein Telescope

Abstract: The advanced interferometer network will herald a new era in observational astronomy. There is a very strong science case to go beyond the advanced detector network and build detectors that operate in a frequency range from 1 Hz to 10 kHz, with sensitivity a factor 10 better in amplitude. Such detectors will be able to probe a range of topics in nuclear physics, astronomy, cosmology and fundamental physics, providing insights into many unsolved problems in these areas.

New Approaches to Sepsis: Molecular Diagnostics and Biomarkers

Abstract: SUMMARY Sepsis is among the most common causes of death in hospitals. It arises from the host response to infection. Currently, diagnosis relies on nonspecific physiological criteria and culture-based pathogen detection. This results in diagnostic uncertainty, therapeutic delays, the mis- and overuse of antibiotics, and the failure to identify patients who might benefit from immunomodulatory therapies. There is a need for new sepsis biomarkers that can aid in therapeutic decision making and add information about screening, diagnosis, risk stratification, and monitoring of the response to therapy. The host response involves hundreds of mediators and single molecules, many of which have been proposed as biomarkers. It is, however, unlikely that one single biomarker is able to satisfy all the needs and expectations for sepsis research and management. Among biomarkers that are measurable by assays approved for clinical use, procalcitonin (PCT) has shown some usefulness as an infection marker and for antibiotic stewardship. Other possible new approaches consist of molecular strategies to improve pathogen detection and molecular diagnostics and prognostics based on transcriptomic, proteomic, or metabolic profiling. Novel approaches to sepsis promise to transform sepsis from a physiologic syndrome into a group of distinct biochemical disorders and help in the development of better diagnostic tools and effective adjunctive sepsis therapies.

Bayesian localization microscopy reveals nanoscale podosome dynamics

Abstract: We describe a localization microscopy analysis method that is able to extract results in live cells using standard fluorescent proteins and xenon arc lamp illumination. Our Bayesian analysis of the blinking and bleaching (3B analysis) method models the entire dataset simultaneously as being generated by a number of fluorophores that may or may not be emitting light at any given time. The resulting technique allows many overlapping fluorophores in each frame and unifies the analysis of the localization from blinking and bleaching events. By modeling the entire dataset, we were able to use each reappearance of a fluorophore to improve the localization accuracy. The high performance of this technique allowed us to reveal the nanoscale dynamics of podosome formation and dissociation throughout an entire cell with a resolution of 50 nm on a 4-s timescale.

Nilotinib vs imatinib in patients with newly diagnosed Philadelphia chromosome-positive chronic myeloid leukemia in chronic phase: ENESTnd 3-year follow-up

Abstract: Evaluating Nilotinib Efficacy and Safety in Clinical Trials Newly Diagnosed Patients compares nilotinib and imatinib in patients with newly diagnosed chronic myeloid leukemia in chronic phase (CML-CP). With a minimum follow-up of 3 years, major molecular response, molecular response of BCR-ABL≤ 0.01% expressed on the international scale (BCR-ABL(IS); MR(4)) and BCR-ABL(IS)≤ 0.0032% (MR(4.5)) rates were significantly higher with nilotinib compared with imatinib, and differences in the depth of molecular response between nilotinib and imatinib have increased over time. No new progressions occurred on treatment since the 2-year analysis. Nilotinib was associated with a significantly lower probability of progression to accelerated phase/blast crisis vs imatinib (two (0.7%) progressions on nilotinib 300 mg twice daily, three (1.1%) on nilotinib 400 mg twice daily and 12 (4.2%) on imatinib). When considering progressions occurring after study treatment discontinuation, the advantage of nilotinib over imatinib in preventing progression remained significant (nine (3.2%) progressions on nilotinib 300 mg twice daily, six (2.1%) on nilotinib 400 mg twice daily and 19 (6.7%) on imatinib). Both nilotinib and imatinib were well tolerated, with minimal changes in safety over time. Nilotinib continues to demonstrate superior efficacy in all key response and outcome parameters compared with imatinib for the treatment of patients with newly diagnosed CML-CP.

Creation and diagnosis of a solid-density plasma with an X-ray free-electron laser

Abstract: Experimental study of the interactions between intense X-rays and solid matter illustrate the generation of a solid-density plasma governed by electron–ion collisions; these results should inform future high-intensity X-ray experiments involving dense samples, such as X-ray diffractive imaging of biological samples, material science investigations, and the study of matter in extreme conditions. With the advent of free-electron lasers, the high intensities previously only achievable with optical lasers can be produced at X-ray wavelengths. This opens new opportunities for theory and experiment. Here, Vinko et al. report the first detailed study of intense X-ray radiation interacting with solid density matter, carried out on the Linac Coherent Light Source free-electron laser at the SLAC National Accelerator Facility in California. They observe the generation of a solid-density plasma and establish that collisions have a pivotal role. The results should inform future high-intensity X-ray experiments involving dense samples, such as X-ray diffractive imaging of biological samples and materials science investigations. Matter with a high energy density (>105 joules per cm3) is prevalent throughout the Universe, being present in all types of stars1 and towards the centre of the giant planets2,3; it is also relevant for inertial confinement fusion4. Its thermodynamic and transport properties are challenging to measure, requiring the creation of sufficiently long-lived samples at homogeneous temperatures and densities5,6. With the advent of the Linac Coherent Light Source (LCLS) X-ray laser7, high-intensity radiation (>1017 watts per cm2, previously the domain of optical lasers) can be produced at X-ray wavelengths. The interaction of single atoms with such intense X-rays has recently been investigated8. An understanding of the contrasting case of intense X-ray interaction with dense systems is important from a fundamental viewpoint and for applications. Here we report the experimental creation of a solid-density plasma at temperatures in excess of 106 kelvin on inertial-confinement timescales using an X-ray free-electron laser. We discuss the pertinent physics of the intense X-ray–matter interactions, and illustrate the importance of electron–ion collisions. Detailed simulations of the interaction process conducted with a radiative-collisional code show good qualitative agreement with the experimental results. We obtain insights into the evolution of the charge state distribution of the system, the electron density and temperature, and the timescales of collisional processes. Our results should inform future high-intensity X-ray experiments involving dense samples, such as X-ray diffractive imaging of biological systems, material science investigations, and the study of matter in extreme conditions.

Updating the evolutionary history of Carnivora (Mammalia): a new species-level supertree complete with divergence time estimates

Abstract: Although it has proven to be an important foundation for investigations of carnivoran ecology, biology and evolution, the complete species-level supertree for Carnivora of Bininda-Emonds et al. is showing its age. Additional, largely molecular sequence data are now available for many species and the advancement of computer technology means that many of the limitations of the original analysis can now be avoided. We therefore sought to provide an updated estimate of the phylogenetic relationships within all extant Carnivora, again using supertree analysis to be able to analyze as much of the global phylogenetic database for the group as possible. In total, 188 source trees were combined, representing 114 trees from the literature together with 74 newly constructed gene trees derived from nearly 45,000 bp of sequence data from GenBank. The greater availability of sequence data means that the new supertree is almost completely resolved and also better reflects current phylogenetic opinion (for example, supporting a monophyletic Mephitidae, Eupleridae and Prionodontidae; placing Nandinia binotata as sister to the remaining Feliformia). Following an initial rapid radiation, diversification rate analyses indicate a downturn in the net speciation rate within the past three million years as well as a possible increase some 18.0 million years ago; numerous diversification rate shifts within the order were also identified. Together, the two carnivore supertrees remain the only complete phylogenetic estimates for all extant species and the new supertree, like the old one, will form a key tool in helping us to further understand the biology of this charismatic group of carnivores.

Progress and Challenges in the Calculation of Electronic Excited States

Abstract: A detailed understanding of the properties of electronic excited states and the reaction mechanisms that molecules undergo after light irradiation is a fundamental ingredient for following light-driven natural processes and for designing novel photonic materials. The aim of this review is to present an overview of the ab initio quantum chemical and time-dependent density functional theory methods that can be used to model spectroscopy and photochemistry in molecular systems. The applicability and limitations of the different methods as well as the main frontiers are discussed. To illustrate the progress achieved by excited-state chemistry in the recent years as well as the main challenges facing computational chemistry, three main applications that reflect the authors' experience are addressed: the UV/Vis spectroscopy of organic molecules, the assignment of absorption and emission bands of organometallic complexes, and finally, the obtainment of non-adiabatic photoinduced pathways mediated by conical intersections. In the latter case, special emphasis is put on the photochemistry of DNA. These applications show that the description of electronically excited states is a rewarding but challenging area of research.

“Clicking” on/with polymers: a rapidly expanding field for the straightforward preparation of novel macromolecular architectures

Abstract: The combination of controlled polymerization techniques and “click” reactions form an efficient platform for the preparation of polymers in various architectures. In this critical review, an update of our 2007 review in Chem. Soc. Rev., we focus on the “click” reactions that have been used widely in the last four years to create new polymer architectures. Not only block copolymers and star-shaped polymers but also cyclic and dendritic macromolecules could be synthesized using these robust “click” reactions (205 references).

Ionic liquids--promising but challenging solvents for homogeneous derivatization of cellulose.

Abstract: In the past decade, ionic liquids (ILs) have received enormous interest as solvents for cellulose. They have been studied intensively for fractionation and biorefining of lignocellulosic biomass, for dissolution of the polysaccharide, for preparation of cellulosic fibers, and in particular as reaction media for the homogeneous preparation of highly engineered polysaccharide derivatives. ILs show great potential for application on a commercial scale regarding recyclability, high dissolution power, and their broad structural diversity. However, a critical analysis reveals that these promising features are combined with serious drawbacks that need to be addressed in order to utilize ILs for the efficient synthesis of cellulose derivatives. This review presents a comprehensive overview about chemical modification of cellulose in ILs. Difficulties encountered thereby are discussed critically and current as well as future developments in this field of polysaccharide research are outlined.

Candida albicans dimorphism as a therapeutic target

Abstract: The ability to switch between yeast and hyphal growth forms (dimorphism) is one of the most discussed and best investigated virulence attributes of the human pathogenic fungus Candida albicans. Both morphological forms seem to be important for virulence and have distinct functions during the different stages of disease development, including adhesion, invasion, damage, dissemination, immune evasion and host response. In this review, we will provide an overview of the known and potential roles of C. albicans dimorphism and will discuss the potential benefit of drugs that can inhibit the morphological transition.

The deubiquitinase USP9X suppresses pancreatic ductal adenocarcinoma

Abstract: Pancreatic ductal adenocarcinoma (PDA) remains a lethal malignancy despite much progress concerning its molecular characterization. PDA tumours harbour four signature somatic mutations in addition to numerous lower frequency genetic events of uncertain significance. Here we use Sleeping Beauty (SB) transposon-mediated insertional mutagenesis in a mouse model of pancreatic ductal preneoplasia to identify genes that cooperate with oncogenic Kras(G12D) to accelerate tumorigenesis and promote progression. Our screen revealed new candidate genes for PDA and confirmed the importance of many genes and pathways previously implicated in human PDA. The most commonly mutated gene was the X-linked deubiquitinase Usp9x, which was inactivated in over 50% of the tumours. Although previous work had attributed a pro-survival role to USP9X in human neoplasia, we found instead that loss of Usp9x enhances transformation and protects pancreatic cancer cells from anoikis. Clinically, low USP9X protein and messenger RNA expression in PDA correlates with poor survival after surgery, and USP9X levels are inversely associated with metastatic burden in advanced disease. Furthermore, chromatin modulation with trichostatin A or 5-aza-2'-deoxycytidine elevates USP9X expression in human PDA cell lines, indicating a clinical approach for certain patients. The conditional deletion of Usp9x cooperated with Kras(G12D) to accelerate pancreatic tumorigenesis in mice, validating their genetic interaction. We propose that USP9X is a major tumour suppressor gene with prognostic and therapeutic relevance in PDA.