P-Match: transcription factor binding site search by combining patterns and weight matrices

P-Match is a new tool for identifying transcription factor (TF) binding sites in DNA sequences. It combines pattern matching and weight matrix approaches thus providing higher accuracy of recognition than each of the methods alone. P-Match is closely interconnected with the TRANSFAC(®) database. In particular, P-Match uses the matrix library as well as sets of aligned known TF-binding sites collected in TRANSFAC(®) and therefore provides the possibility to search for a large variety of different TF binding sites. Using results of extensive tests of recognition accuracy, we selected three sets of optimized cut-off values that minimize either false negatives or false positives, or the sum of both errors. Comparison with the weight matrix approaches such as Match™ tool shows that P-Match generally provides superior recognition accuracy in the area of low false negative errors (high sensitivity). As familiar to the user of Match™, P-Match also allows to save user-specific profiles that include selected subsets of matrices with corresponding TF-binding sites or user-defined cut-off values. Furthermore, a number of tissue-specific profiles are provided that were compiled by the TRANSFAC(®) team. A public version of the P-Match tool is available at

Tree-based solvers for adaptive mesh refinement code FLASH -- III: a novel scheme for radiation pressure on dust and gas and radiative transfer from diffuse sources

Radiation is an important contributor to the energetics of the interstellar medium, yet its transport is difficult to solve numerically. We present a novel approach towards solving radiative transfer of diffuse sources via backwards ray tracing. Here we focus on the radiative transfer of infrared radiation and the radiation pressure on dust. The new module, \textsc{TreeRay/RadPressure}, is an extension to the novel radiative transfer method \textsc{TreeRay} implemented in the grid-based MHD code {\sc Flash}. In \textsc{TreeRay/RadPressure}, every cell and every star particle is a source of infrared radiation. We also describe how gas, dust and radiation are coupled via a chemical network. This allows us to compute the local dust temperature in thermal equilibrium, leading to a significantly improvement over the classical grey approximation. In several tests, we demonstrate that the scheme produces the correct radiative intensities as well as the correct momentum input by radiation pressure. Subsequently, we apply our new scheme to model massive star formation from a collapsing, turbulent core of 150 ${\rm M}_\odot$. We trace the effects of both, ionizing and infrared radiation on the dynamics of the core. We find that the newborn massive star(s) prevent fragmentation in their proximity through radiative heating. Over time, dust and radiation temperature equalize, while the gas temperature can be either warmer due to shock heating or colder due to insufficient dust-gas coupling. Compared to gravity, the effects of radiation pressure become significant on the core scale only at an evolved stage.Comment: 25 pages, 19 figures, submitted to MNRA

Monitoring Active Sites for Hydrogen Evolution Reaction at Model Carbon Surfaces

Carbon is ubiquitous as an electrode material in electrochemical energy conversion devices. If used as support material, the evolution of H2 is undesired on carbon. However, recently carbon-based materials are of high interest as economic and eco-conscious alternative to noble metal catalysts. The targeted design of improved carbon electrode materials requires atomic scale insight into the structure of the sites that catalyse H2 evolution. This work demonstrates that electrochemical scanning tunnelling microscopy under reaction conditions (n-EC-STM) can monitor active sites of highly oriented pyrolytic graphite for the hydrogen evolution reaction. With down to atomic resolution, the most active sites in acidic medium are pinpointed near edge sites and defects, whereas the basal planes remain inactive. Density functional theory calculations support these findings and reveal that only specific defects on graphite are active. Motivated by these results, the extensive usage of n-EC-STM on doped carbon-based materials is encouraged to locate their active sites and guide the synthesis of enhanced electrocatalysts.The authors thank Prof. Plamen Atanassov (University of California, Irvine, USA) and Dr. Jun Maruyama (Osaka Research Institute of Industrial Science and Technology, Japan) for fruitful discussion regarding some experimental results. RMK, RWH and ASB acknowledge the financial support from the German Research Foundation (DFG), in the framework of the projects BA 5795/4-1 and BA 5795/3-1, and under Germany's Excellence Strategy–EXC 2089/1–390776260, cluster of excellence ‘e-conversion’. ASB acknowledges the funding from the European Union's Horizon 2020 research and innovation programme under grant agreement HERMES No. 952184. FCV acknowledges financial support from Spanish MICIUN through RTI2018-095460-B-I00 and María de Maeztu (MDM-2017-0767) grants and a Ramón y Cajal research contract (RYC-2015-18996), and also from Generalitat de Catalunya (grants 2017SGR13 and XRQTC). The use of supercomputing facilities at SURFsara was sponsored by NWO Physical Sciences, with financial support from NWO

Modelling the supernova-driven ISM in different environments

We use hydrodynamical simulations in a (256 pc)3 periodic box to model the impact of supernova (SN) explosions on the multiphase interstellar medium (ISM) for initial densities n=0.5-30cm−3 and SN rates 1-720Myr−1. We include radiative cooling, diffuse heating, and the formation of molecular gas using a chemical network. The SNe explode either at random positions, at density peaks, or both. We further present a model combining thermal energy for resolved and momentum input for unresolved SNe. Random driving at high SN rates results in hot gas (T≳106K) filling >90 per cent of the volume. This gas reaches high pressures (10450 per cent), residing in small, dense clumps. Such a model might resemble the dense ISM in high-redshift galaxies. Peak driving results in huge radiative losses, producing a filamentary ISM with virtually no hot gas, and a small molecular hydrogen mass fraction (≪1 per cent). Varying the ratio of peak to random SNe yields ISM properties in between the two extremes, with a sharp transition for equal contributions. The velocity dispersion in H i remains≲10 km s−1 in all cases. For peak driving, the velocity dispersion in Hα can be as high as 70 km s−1 due to the contribution from young, embedded SN remnant

Modelling the supernova-driven ISM in different environments

We use hydrodynamical simulations in a $(256\;{\rm pc})^3$ periodic box to model the impact of supernova (SN) explosions on the multi-phase interstellar medium (ISM) for initial densities $n = 0.5-30$ cm$^{-3}$ and SN rates $1-720$ Myr$^{-1}$. We include radiative cooling, diffuse heating, and the formation of molecular gas using a chemical network. The SNe explode either at random positions, at density peaks, or both. We further present a model combining thermal energy for resolved and momentum input for unresolved SNe. Random driving at high SN rates results in hot gas ($T\gtrsim 10^6$ K) filling $> 90$% of the volume. This gas reaches high pressures ($10^4 < P/k_\mathrm{B} < 10^7$ K cm$^{-3}$) due to the combination of SN explosions in the hot, low density medium and confinement in the periodic box. These pressures move the gas from a two-phase equilibrium to the single-phase, cold branch of the cooling curve. The molecular hydrogen dominates the mass ($>50$%), residing in small, dense clumps. Such a model might resemble the dense ISM in high-redshift galaxies. Peak driving results in huge radiative losses, producing a filamentary ISM with virtually no hot gas, and a small molecular hydrogen mass fraction ($\ll 1$%). Varying the ratio of peak to random SNe yields ISM properties in between the two extremes, with a sharp transition for equal contributions. The velocity dispersion in HI remains $\lesssim 10$ km s$^{-1}$ in all cases. For peak driving the velocity dispersion in H$_\alpha$ can be as high as $70$ km s$^{-1}$ due to the contribution from young, embedded SN remnants.Comment: 19 pages, 12 figures, 2 tables. Accepted for publication in MNRAS. Minor revisions to match published versio

October 1966

Massachusetts Turf and Lawn Grass CouncilBetter Turf Through Research and Educatio

The use of oral recombinant feline interferon omega in two cats with type II diabetes mellitus and concurrent feline chronic gingivostomatitis syndrome

Articles in International JournalsFeline Chronic Gingivostomatitis Syndrome (FCGS) is a common disease in clinical practice. Among the therapeutic options available, long-acting corticosteroids are frequently used due to their anti-inflammatory and immunosuppressive properties. Although they may improve the clinical symptoms, they can lead to a progressive form of the disease that becomes refractory to treatment. Furthermore, their direct relationship with type II diabetes mellitus (DM) is well known. Consequently, these drugs are controversial and not recommended for routine management of FCGS. Recombinant feline interferon-omega (rFeIFN-ω) is an immunomodulatory compound. Recently, its daily oral administration has been shown to be successful in treating refractory cases of FCGS. This case study describes two clinical cases of type II DM complicated by FCGS. Both animals were calicivirus positive and they had been previously treated with long-acting corticosteroids, which may have been the major cause of DM. The two cats were treated with glargine insulin (Lantus, starting dose 1 IU/cat twice daily (BID)), achieving remission 10 and 18 weeks later respectively. Considering the difficulty with control of FCGS in these animals, an oral daily dose of rFeIFN-ω was started as an alternative to long-acting corticosteroids. In both cats oral clinical signs gradually improved and 60 days after the start of therapy the owners reported a significant relief of pain during mastication. According to the authors’ knowledge, this is the first case report that describes the successful use of rFeIFN-ω in the management of FCGS in type II diabetic cats, in which long-acting corticosteroids are contraindicated

Spinal involvement in mucopolysaccharidosis IVA (Morquio-Brailsford or Morquio A syndrome): presentation, diagnosis and management.

Mucopolysaccharidosis IVA (MPS IVA), also known as Morquio-Brailsford or Morquio A syndrome, is a lysosomal storage disorder caused by a deficiency of the enzyme N-acetyl-galactosamine-6-sulphate sulphatase (GALNS). MPS IVA is multisystemic but manifests primarily as a progressive skeletal dysplasia. Spinal involvement is a major cause of morbidity and mortality in MPS IVA. Early diagnosis and timely treatment of problems involving the spine are critical in preventing or arresting neurological deterioration and loss of function. This review details the spinal manifestations of MPS IVA and describes the tools used to diagnose and monitor spinal involvement. The relative utility of radiography, computed tomography (CT) and magnetic resonance imaging (MRI) for the evaluation of cervical spine instability, stenosis, and cord compression is discussed. Surgical interventions, anaesthetic considerations, and the use of neurophysiological monitoring during procedures performed under general anaesthesia are reviewed. Recommendations for regular radiological imaging and neurologic assessments are presented, and the need for a more standardized approach for evaluating and managing spinal involvement in MPS IVA is addressed