Mycoplasma penetrans bacteremia in an immunocompromised patient detected by metagenomic sequencing: a case report.

Background Mycoplasma sp. are well recognized as etiological agents of respiratory and sexually transmitted disease. Mycoplasma penetrans, a species of Mycoplasma sp., has been frequently detected in HIV-positive patients and associated with the progression of HIV-associated disease. To date, there is only a single case report describing M. penetrans as the causative agent of a severe respiratory tract infection in a HIV-negative patient. Case presentation In this report, we describe the case of M. penetrans bacteremia in a HIV-negative, 38-year-old, female, immunocompromised, solid organ transplant patient (combined kidney and pancreas transplantation in 2016), who was admitted to our hospital with anemic uterine bleeding and fever of 38.3 °C. Several hours before her admission at our university hospital, a latex bladder catheter was inserted into her uterus and she complained about fatigue, dizziness and ongoing vaginal bleeding. Laboratory examination showed severe anemia, but microbiological examination was inconspicuous (culture negative vaginal and cervical smears, negative urine culture). Bacterial blood cultures showed a growth signal after 4 h, but microscopic examination with Gram staining and subcultures on different agar media did not identify bacterial pathogens. To identify the bacterial cause of malignancy in the patient, metagenomic sequencing of the blood culture was performed that identified M. penetrans. Conclusion Metagenomic sequencing identified M. penetrans in an immunosuppressed patient with culture-negative bacteremia. Clinicians should be aware of the opportunistic potential of M. penetrans that may cause severe infections in certain vulnerable patient populations and the limitations of culture and Gram staining for confirming the presence of fastidious bacterial pathogens like Mycoplasma spp

BALL-SNP: combining genetic and structural information to identify candidate non-synonymous single nucleotide polymorphisms

Background: High-throughput genetic testing is increasingly applied in clinics. Next-Generation Sequencing (NGS) data analysis however still remains a great challenge. The interpretation of pathogenicity of single variants or combinations of variants is crucial to provide accurate diagnostic information or guide therapies. Methods: To facilitate the interpretation of variants and the selection of candidate non-synonymous polymorphisms (nsSNPs) for further clinical studies, we developed BALL-SNP. Starting from genetic variants in variant call format (VCF) files or tabular input, our tool, first, visualizes the three-dimensional (3D) structure of the respective proteins from the Protein Data Bank (PDB) and highlights mutated residues, automatically. Second, a hierarchical bottom up clustering on the nsSNPs within the 3D structure is performed to identify nsSNPs, which are close to each other. The modular and flexible implementation allows for straightforward integration of different databases for pathogenic and benign variants, but also enables the integration of pathogenicity prediction tools. The collected background information of all variants is presented below the 3D structure in an easily interpretable table format. Results: First, we integrated different data resources into BALL-SNP, including databases containing information on genetic variants such as ClinVar or HUMSAVAR; third party tools that predict stability or pathogenicity in silico such as I-Mutant2.0; and additional information derived from the 3D structure such as a prediction of binding pockets. We then explored the applicability of BALL-SNP on the example of patients suffering from cardiomyopathies. Here, the analysis highlighted accumulation of variations in the genes JUP, VCL, and SMYD2. Conclusion: Software solutions for analyzing high-throughput genomics data are important to support diagnosis and therapy selection. Our tool BALL-SNP, which is freely available at http://www.ccb.uni-saarland.de/BALL-SNP , combines genetic information with an easily interpretable and interactive, graphical representation of amino acid changes in proteins. Thereby relevant information from databases and computational tools is presented. Beyond this, proximity to functional sites or accumulations of mutations with a potential collective effect can be discovered

Varying whole body vibration amplitude differentially affects tendon and ligament structural and material properties

Whole Body Vibration (WBV) is becoming increasingly popular for helping to maintain bone mass and strengthening muscle. Vibration regimens optimized for bone maintenance often operate at hypogravity levels (1 G) vibrations. The effect of vibratory loads on tendon and ligament properties is unclear though excessive vibrations may be injurious. Our objective was to evaluate how tendon gene expression and the mechanical/histological properties of tendon and ligament were affected in response to WBV in the following groups: no vibration, low vibration (0.3 G peak-to-peak), and high vibration (2 G peak-to-peak). Rats were vibrated for 20 min a day, 5 days a week, for 5 weeks. Upon sacrifice, the medial collateral ligament (MCL), patellar tendon (PT), and the Achilles Tendon (AT) were isolated with insertion sites intact. All tissues were tensile tested to determine structural and material properties or used for histology. Patellar tendon was also subjected to quantitative RT-PCR to evaluate expression of anabolic and catabolic genes. No differences in biomechanical data between the control and the low vibration groups were found. There was evidence of significant weakness in the MCL with high vibration, but no significant effect on the PT or AT. Histology of the MCL and PT showed a hypercellular tissue response and some fiber disorganization with high vibration. High vibration caused an increase in collagen expression and a trend for an increase in IGF-1 expression suggesting a potential anabolic response to prevent tendon overuse injury

Rapid-scan nonlinear time-resolved spectroscopy over arbitrary delay intervals

Femtosecond dual-comb lasers have revolutionized linear Fourier-domain spectroscopy by offering a rapid motion-free, precise and accurate measurement mode with easy registration of the combs beat note in the RF domain. Extensions of this technique found already application for nonlinear time-resolved spectroscopy within the energy limit available from sources operating at the full oscillator repetition rate. Here, we present a technique based on time filtering of femtosecond frequency combs by pulse gating in a laser amplifier. This gives the required boost to the pulse energy and provides the flexibility to engineer pairs of arbitrarily delayed wavelength-tunable pulses for pump-probe techniques. Using a dual-channel millijoule amplifier, we demonstrate programmable generation of both extremely short, fs, and extremely long (>ns) interpulse delays. A predetermined arbitrarily chosen interpulse delay can be directly realized in each successive amplifier shot, eliminating the massive waiting time required to alter the delay setting by means of an optomechanical line or an asynchronous scan of two free-running oscillators. We confirm the versatility of this delay generation method by measuring chi^(2) cross-correlation and chi^(3) multicomponent population recovery kinetics

Magic Numbers and Optical Absorption Spectrum in Vertically Coupled Quantum Dots in the Fractional Quantum Hall Regime

Exact diagonalization is used to study the quantum states of vertically coupled quantum dots in strong magnetic fields. We find a new sequence of angular momentum magic numbers which are a consequence of the electron correlation in the double dot. The new sequence occurs at low angular momenta and changes into the single dot sequence at a critical angular momentum determined by the strength of the inter-dot electron tunneling. We also propose that the magic numbers can be investigated experimentally in vertically coupled dots. Because of the generalized Kohn theorem, the far-infrared optical absorption spectrum of a single dot is unaffected by correlation but the theorem does not hold for two vertically coupled dots which have different confining potentials. We show that the absorption energy of the double dot should exhibit discontinuities at the magnetic fields where the total angular momentum changes from one magic number to another.Comment: 4 pages, 3 Postscript figures, RevTeX. (to appear in Phys.Rev.B

Random attractors for degenerate stochastic partial differential equations

We prove the existence of random attractors for a large class of degenerate stochastic partial differential equations (SPDE) perturbed by joint additive Wiener noise and real, linear multiplicative Brownian noise, assuming only the standard assumptions of the variational approach to SPDE with compact embeddings in the associated Gelfand triple. This allows spatially much rougher noise than in known results. The approach is based on a construction of strictly stationary solutions to related strongly monotone SPDE. Applications include stochastic generalized porous media equations, stochastic generalized degenerate p-Laplace equations and stochastic reaction diffusion equations. For perturbed, degenerate p-Laplace equations we prove that the deterministic, infinite dimensional attractor collapses to a single random point if enough noise is added.Comment: 34 pages; The final publication is available at http://link.springer.com/article/10.1007%2Fs10884-013-9294-

Water waves generated by a moving bottom

Tsunamis are often generated by a moving sea bottom. This paper deals with the case where the tsunami source is an earthquake. The linearized water-wave equations are solved analytically for various sea bottom motions. Numerical results based on the analytical solutions are shown for the free-surface profiles, the horizontal and vertical velocities as well as the bottom pressure.Comment: 41 pages, 13 figures. Accepted for publication in a book: "Tsunami and Nonlinear Waves", Kundu, Anjan (Editor), Springer 2007, Approx. 325 p., 170 illus., Hardcover, ISBN: 978-3-540-71255-8, available: May 200

Evolutionary distances in the twilight zone -- a rational kernel approach

Phylogenetic tree reconstruction is traditionally based on multiple sequence alignments (MSAs) and heavily depends on the validity of this information bottleneck. With increasing sequence divergence, the quality of MSAs decays quickly. Alignment-free methods, on the other hand, are based on abstract string comparisons and avoid potential alignment problems. However, in general they are not biologically motivated and ignore our knowledge about the evolution of sequences. Thus, it is still a major open question how to define an evolutionary distance metric between divergent sequences that makes use of indel information and known substitution models without the need for a multiple alignment. Here we propose a new evolutionary distance metric to close this gap. It uses finite-state transducers to create a biologically motivated similarity score which models substitutions and indels, and does not depend on a multiple sequence alignment. The sequence similarity score is defined in analogy to pairwise alignments and additionally has the positive semi-definite property. We describe its derivation and show in simulation studies and real-world examples that it is more accurate in reconstructing phylogenies than competing methods. The result is a new and accurate way of determining evolutionary distances in and beyond the twilight zone of sequence alignments that is suitable for large datasets.Comment: to appear in PLoS ON

Open Science principles for accelerating trait-based science across the Tree of Life.

Synthesizing trait observations and knowledge across the Tree of Life remains a grand challenge for biodiversity science. Species traits are widely used in ecological and evolutionary science, and new data and methods have proliferated rapidly. Yet accessing and integrating disparate data sources remains a considerable challenge, slowing progress toward a global synthesis to integrate trait data across organisms. Trait science needs a vision for achieving global integration across all organisms. Here, we outline how the adoption of key Open Science principles-open data, open source and open methods-is transforming trait science, increasing transparency, democratizing access and accelerating global synthesis. To enhance widespread adoption of these principles, we introduce the Open Traits Network (OTN), a global, decentralized community welcoming all researchers and institutions pursuing the collaborative goal of standardizing and integrating trait data across organisms. We demonstrate how adherence to Open Science principles is key to the OTN community and outline five activities that can accelerate the synthesis of trait data across the Tree of Life, thereby facilitating rapid advances to address scientific inquiries and environmental issues. Lessons learned along the path to a global synthesis of trait data will provide a framework for addressing similarly complex data science and informatics challenges