Utility of CD123 immunohistochemistry in differentiating lupus erythematosus from cutaneous T cell lymphoma

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/149293/1/his13817_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/149293/2/his13817.pd

Structure of the hDmc1-ssDNA filament reveals the principles of its architecture

In eukaryotes, meiotic recombination is a major source of genetic diversity, but its defects in humans lead to abnormalities such as Down's, Klinefelter's and other syndromes. Human Dmc1 (hDmc1), a RecA/Rad51 homologue, is a recombinase that plays a crucial role in faithful chromosome segregation during meiosis. The initial step of homologous recombination occurs when hDmc1 forms a filament on single-stranded (ss) DNA. However the structure of this presynaptic complex filament for hDmc1 remains unknown. To compare hDmc1-ssDNA complexes to those known for the RecA/Rad51 family we have obtained electron microscopy (EM) structures of hDmc1-ssDNA nucleoprotein filaments using single particle approach. The EM maps were analysed by docking crystal structures of Dmc1, Rad51, RadA, RecA and DNA. To fully characterise hDmc1-DNA complexes we have analysed their organisation in the presence of Ca2+, Mg2+, ATP, AMP-PNP, ssDNA and dsDNA. The 3D EM structures of the hDmc1-ssDNA filaments allowed us to elucidate the principles of their internal architecture. Similar to the RecA/Rad51 family, hDmc1 forms helical filaments on ssDNA in two states: extended (active) and compressed (inactive). However, in contrast to the RecA/Rad51 family, and the recently reported structure of hDmc1-double stranded (ds) DNA nucleoprotein filaments, the extended (active) state of the hDmc1 filament formed on ssDNA has nine protomers per helical turn, instead of the conventional six, resulting in one protomer covering two nucleotides instead of three. The control reconstruction of the hDmc1-dsDNA filament revealed 6.4 protein subunits per helical turn indicating that the filament organisation varies depending on the DNA templates. Our structural analysis has also revealed that the N-terminal domain of hDmc1 accomplishes its important role in complex formation through domain swapping between adjacent protomers, thus providing a mechanistic basis for coordinated action of hDmc1 protomers during meiotic recombination

Cosmology of codimension-two braneworlds

We present a comprehensive study of the cosmological solutions of 6D braneworld models with azimuthal symmetry in the extra dimensions, moduli stabilization by flux or a bulk scalar field, and which contain at least one 3-brane that could be identified with our world. We emphasize an unusual property of these models: their expansion rate depends on the 3-brane tension either not at all, or in a nonstandard way, at odds with the naive expected dimensional reduction of these systems to 4D general relativity at low energies. Unlike other braneworld attempts to find a self-tuning solution to the cosmological constant problem, the apparent failure of decoupling in these models is not associated with the presence of unstabilized moduli; rather it is due to automatic cancellation of the brane tension by the curvature induced by the brane. This provides some corroboration for the hope that these models provide a distinctive step toward understanding the smallness of the observed cosmological constant. However, we point out some challenges for obtaining realistic cosmology within this framework.Comment: 30 pages, 4 figures; generalized result for nonconventional Friedmann equation, added referenc

Electrochemistry at nanoscale electrodes : individual single-walled carbon nanotubes (SWNTs) and SWNT-templated metal nanowires

Individual nanowires (NWs) and native single-walled carbon nanotubes (SWNTs) can be readily used as well-defined nanoscale electrodes (NSEs) for voltammetric analysis. Here, the simple photolithography-free fabrication of submillimeter long Au, Pt, and Pd NWs, with sub-100 nm heights, by templated electrodeposition onto ultralong flow-aligned SWNTs is demonstrated. Both individual Au NWs and SWNTs are employed as NSEs for electron-transfer (ET) kinetic quantification, using cyclic voltammetry (CV), in conjunction with a microcapillary-based electrochemical method. A small capillary with internal diameter in the range 30–70 μm, filled with solution containing a redox-active mediator (FcTMA+ ((trimethylammonium)methylferrocene), Fe(CN)64–, or hydrazine) is positioned above the NSE, so that the solution meniscus completes an electrochemical cell. A 3D finite-element model, faithfully reproducing the experimental geometry, is used to both analyze the experimental CVs and derive the rate of heterogeneous ET, using Butler–Volmer kinetics. For a 70 nm height Au NW, intrinsic rate constants, k0, up to ca. 1 cm s–1 can be resolved. Using the same experimental configuration the electrochemistry of individual SWNTs can also be accessed. For FcTMA+/2+ electrolysis the simulated ET kinetic parameters yield very fast ET kinetics (k0 > 2 ± 1 cm s–1). Some deviation between the experimental voltammetry and the idealized model is noted, suggesting that double-layer effects may influence ET at the nanoscale

SimRank*: effective and scalable pairwise similarity search based on graph topology

Given a graph, how can we quantify similarity between two nodes in an effective and scalable way? SimRank is an attractive measure of pairwise similarity based on graph topologies. Its underpinning philosophy that “two nodes are similar if they are pointed to (have incoming edges) from similar nodes” can be regarded as an aggregation of similarities based on incoming paths. Despite its popularity in various applications (e.g., web search and social networks), SimRank has an undesirable trait, i.e., “zero-similarity”: it accommodates only the paths of equal length from a common “center” node, whereas a large portion of other paths are fully ignored. In this paper, we propose an effective and scalable similarity model, SimRank*, to remedy this problem. (1) We first provide a sufficient and necessary condition of the “zero-similarity” problem that exists in Jeh and Widom’s SimRank model, Li et al. ’s SimRank model, Random Walk with Restart (RWR), and ASCOS++. (2) We next present our treatment, SimRank*, which can resolve this issue while inheriting the merit of the simple SimRank philosophy. (3) We reduce the series form of SimRank* to a closed form, which looks simpler than SimRank but which enriches semantics without suffering from increased computational overhead. This leads to an iterative form of SimRank*, which requires O(Knm) time and O(n2) memory for computing all (n2) pairs of similarities on a graph of n nodes and m edges for K iterations. (4) To improve the computational time of SimRank* further, we leverage a novel clustering strategy via edge concentration. Due to its NP-hardness, we devise an efficient heuristic to speed up all-pairs SimRank* computation to O(Knm~) time, where m~ is generally much smaller than m. (5) To scale SimRank* on billion-edge graphs, we propose two memory-efficient single-source algorithms, i.e., ss-gSR* for geometric SimRank*, and ss-eSR* for exponential SimRank*, which can retrieve similarities between all n nodes and a given query on an as-needed basis. This significantly reduces the O(n2) memory of all-pairs search to either O(Kn+m~) for geometric SimRank*, or O(n+m~) for exponential SimRank*, without any loss of accuracy, where m~≪n2 . (6) We also compare SimRank* with another remedy of SimRank that adds self-loops on each node and demonstrate that SimRank* is more effective. (7) Using real and synthetic datasets, we empirically verify the richer semantics of SimRank*, and validate its high computational efficiency and scalability on large graphs with billions of edges

High resolution fluorescence bio-imaging upconversion nanoparticles in insects

Imaging fluorescent markers with brightness, photostability, and continuous emission with auto fluorescence background suppression in biological samples has always been challenging due to limitations of available and economical techniques. Here we report a new approach, to achieve high contrast imaging inside small and difficult biological systems with special geometry such as fire ants, an important agricultural pest, using a homemade cost-effective optical system. Unlike the commonly used rare-earth doped fluoride nanoparticles, we utilized nanoparticles with a high upconversion efficiency in water. Specifically Y_2O_3:Er^(+3),Yb^(+3) nanoparticles (40-50 nm diameter) were fed to fire ants as food and then a simple illuminating experiment was conducted at 980 nm wavelength at relatively low pump intensity 8 kW.cm^(−2). The locations were further confirmed by X-ray tomography, where most particles aggregated inside the ant’s mouth. High resolution, fast, and economical optical imaging system opens the door for studying more complex biological system

Field-Grown Transgenic Switchgrass (Panicum virgatum L.) with Altered Lignin Does Not Affect Soil Chemistry, Microbiology, and Carbon Storage Potential

Cell wall recalcitrance poses a major challenge on cellulosic biofuel production from feedstocks such as switchgrass (Panicum virgatum L.). As lignin is a known contributor of recalcitrance, transgenic switchgrass plants with altered lignin have been produced by downregulation of caffeic acid O-methyltransferase (COMT). Field trials of COMT-downregulated plants previously demonstrated improved ethanol conversion with no adverse agronomic effects. However, the rhizosphere impacts of altering lignin in plants are unknown. We hypothesized that changing plant lignin composition may affect residue degradation in soils, ultimately altering soil processes. The objective of this study was to evaluate effects of two independent lines of COMT-downregulated switchgrass plants on soils in terms of chemistry, microbiology, and carbon cycling when grown in the field. Over the first two years of establishment, we observed no significant differences between transgenic and control plants in terms of soil pH or the total concentrations of 19 elements. An analysis of soil bacterial communities via high-throughput 16S rRNA gene amplicon sequencing revealed no effects of transgenic plants on bacterial diversity, richness, or community composition. We also did not observe a change in the capacity for soil carbon storage: There was no significant effect on soil respiration or soil organic matter. After five years of establishment, δ13C of plant roots, leaves, and soils was measured and an isotopic mixing model used to estimate that 11.2 to 14.5% of soil carbon originated from switchgrass. Switchgrass-contributed carbon was not significantly different between transgenic and control plants. Overall, our results indicate that over the short term (two and five years), lignin modification in switchgrass through manipulation of COMT expression does not have an adverse effect on soils in terms of total elemental composition, bacterial community structure and diversity, and capacity for carbon storage

A syndrome of altered cardiovascular, craniofacial, neurocognitive and skeletal development caused by mutations in TGFBR1 or TGFBR2

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Management of Chlamydia Cases in Australia (MoCCA): protocol for a non-randomised implementation and feasibility trial

INTRODUCTION: The sexually transmitted infection chlamydia can cause significant complications, particularly among people with female reproductive organs. Optimal management includes timely and appropriate treatment, notifying and treating sexual partners, timely retesting for reinfection and detecting complications including pelvic inflammatory disease (PID). In Australia, mainstream primary care (general practice) is where most chlamydia infections are diagnosed, making it a key setting for optimising chlamydia management. High reinfection and low retesting rates suggest partner notification and retesting are not uniformly provided. The Management of Chlamydia Cases in Australia (MoCCA) study seeks to address gaps in chlamydia management in Australian general practice through implementing interventions shown to improve chlamydia management in specialist services. MoCCA will focus on improving retesting, partner management (including patient-delivered partner therapy) and PID diagnosis. METHODS AND ANALYSIS: MoCCA is a non-randomised implementation and feasibility trial aiming to determine how best to implement interventions to support general practice in delivering best practice chlamydia management. Our method is guided by the Consolidated Framework for Implementation Research and the Normalisation Process Theory. MoCCA interventions include a website, flow charts, fact sheets, mailed specimen kits and autofills to streamline chlamydia consultation documentation. We aim to recruit 20 general practices across three Australian states (Victoria, New South Wales, Queensland) through which we will implement the interventions over 12–18 months. Mixed methods involving qualitative and quantitative data collection and analyses (observation, interviews, surveys) from staff and patients will be undertaken to explore our intervention implementation, acceptability and uptake. Deidentified general practice and laboratory data will be used to measure pre-post chlamydia testing, retesting, reinfection and PID rates, and to estimate MoCCA intervention costs. Our findings will guide scale-up plans for Australian general practice. ETHICS AND DISSEMINATION: Ethics approval was obtained from The University of Melbourne Human Research Ethics Committee (Ethics ID: 22665). Findings will be disseminated via conference presentations, peer-reviewed publications and study reports