Two C++ libraries for counting trees on a phylogenetic terrace.

Motivation: The presence of terraces in phylogenetic tree space, i.e. a potentially large number of distinct tree topologies that have exactly the same analytical likelihood score, was first described by Sanderson et al. However, popular software tools for maximum likelihood and Bayesian phylogenetic inference do not yet routinely report, if inferred phylogenies reside on a terrace, or not. We believe, this is due to the lack of an efficient library to (i) determine if a tree resides on a terrace, (ii) calculate how many trees reside on a terrace and (iii) enumerate all trees on a terrace. Results: In our bioinformatics practical that is set up as a programming contest we developed two efficient and independent C++ implementations of the SUPERB algorithm by Constantinescu and Sankoff (1995) for counting and enumerating trees on a terrace. Both implementations yield exactly the same results, are more than one order of magnitude faster, and require one order of magnitude less memory than a previous thirrd party python implementation. Availability and implementation: The source codes are available under GNU GPL at https://github.com/terraphast. Supplementary information: Supplementary data are available at Bioinformatics online.

Recovery of High-Energy Photoelectron Circular Dichroism through Fano Interference.

It is commonly accepted that the magnitude of a photoelectron circular dichroism (PECD) is governed by the ability of an outgoing photoelectron wave packet to probe the chiral asymmetry of a molecule. To be able to accumulate this characteristic asymmetry while escaping the chiral ion, photoelectrons need to have relatively small kinetic energies of up to a few tens of electron volts. Here, we demonstrate a substantial PECD for very fast photoelectrons above 500 eV kinetic energy released from methyloxirane by a participator resonant Auger decay of its lowermost O 1s excitation. This effect emerges as a result of the Fano interference between the direct and resonant photoionization pathways, notwithstanding that their individual effects are negligibly small. The resulting dichroic parameter has an anomalous dispersion: It changes its sign across the resonance, which can be considered as an analogue of the Cotton effect in the x-ray regime.

Piscirickettsia salmonis infection in cultured lumpfish (Cyclopterus lumpus L.).

A Piscirickettsia salmonis infection was diagnosed in lumpfish (Cyclopterus lumpus L.) juveniles held in a marine research facility on the west coast of Ireland. The main clinical signs and pathology included marked ascites, severe multifocal liver necrosis and severe diffuse inflammation and necrosis of the exocrine pancreas and peri-pancreatic adipose tissue. Numerous Piscirickettsia-like organisms were observed by histopathology in the affected organs, and the bacterial species was characterized by molecular analysis. Sequencing of the partial 16S rDNA gene and internal transcribed spacer region showed the lumpfish sequences to be closely related to previously identified Atlantic salmon (Salmo salar L.) sequences from Ireland. To the authors' knowledge, this is the first detection of P. salmonis in lumpfish worldwide. The infection is considered potentially significant in terms of lumpfish health and biosecurity.

First record of Tetramicra brevifilum in lumpfish (Cyclopterus lumpus, L.).

A microsporidian species with 98.3-98.4% nucleotide identity to Tetramicra brevifilum (Journal of Fish Diseases, 3, 1980, 495) was diagnosed in lumpfish (Cyclopterus lumpus, L.) broodstock held at a breeding and rearing facility in western Ireland. The fish were wild-caught from the west coast of Ireland, and the first case was diagnosed one year after capture. Clinical signs included severe bloating, lethargy, exophthalmos, anorexia, white patches on the cornea and externally visible parasitic cysts on skin and fins. Necropsy revealed severe ascites, white nodules and vacuoles in all the internal organs and partial liquefaction of the skeletal muscle. On histological examination, microsporidian xenomas were observed in all internal organs, the skin, skeletal muscle, gills and the eyes. The microsporidian species was identified by molecular analysis and transmission electron microscopy. This is the first record of T. brevifilum infecting lumpfish, and the disease is considered to be of potential significance to the rising aquaculture industry of this species.

Cold atmospheric pressure plasma for treatment of chronic wounds: drug or medical device?

OBJECTIVE: The use of cold atmospheric pressure plasma (CAPP) as a new therapeutic option to aid the healing of chronic wounds appears promising. Currently, uncertainty exists regarding their classification as medical device or medical drug. Because the classification of CAPP has medical, legal, and economic consequences as well as implications for the level of preclinical and clinical testing, the correct classification is not an academic exercise, but an ethical need. METHOD: A multidisciplinary team of physicians, surgeons, pharmacists, physicists and lawyers has analysed the physical and technical characteristics as well as legal conditions of the biological action of CAPP. RESULTS: It was concluded that the mode of action of the locally generated CAPP, with its main active components being different radicals, is pharmacological and not physical in nature. CONCLUSION: Depending on the intended use, CAPP should be classified as a drug, which is generated by use of a medical device directly at the point of therapeutic application.

[Heart involvement in Friedreich's ataxia]. / Herzbeteiligung bei Friedreich-Ataxie.

Friedreich's ataxia is a rare hereditary disease and although the gene defect has already been identified as a deficiency of the mitochondrial protein frataxin, the pathophysiology is still unknown. Although a multisystem disorder organ involvement is predominantly neurological. Besides the characteristic features of spinocerebellar ataxia the heart is frequently also affected. Cardiac involvement typically manifests as hypertrophic cardiomyopathy, which can progress to heart failure and death. So far most research has focused on the neurological aspects and cardiac involvement in Friedreich's ataxia has not been systematically investigated. Thus, a better understanding of the progression of the cardiomyopathy, cardiac complications and long-term cardiac outcome is warranted. Although no specific treatment is available general cardiac therapeutic options for cardiomyopathy should be considered. The current review focuses on clinical and diagnostic features of cardiomyopathy and discusses potential therapeutic developments for Friedreich's ataxia.

Angular momentum sensitive two-center interference.

In quantum mechanics the Young-type double-slit experiment can be performed with electrons either traveling through a double slit or being coherently emitted from two inversion symmetric molecular sites. In the latter one the valence photoionization cross sections of homonuclear diatomic molecules were predicted to oscillate over kinetic energy almost 50 years ago. Beyond the direct proof of the oscillatory behavior of these photoionization cross sections σ, we show that the angular distribution of the emitted electrons reveals hitherto unexplored information on the relative phase shift between the corresponding partial waves through two-center interference patterns.

Perigastric appendagitis: CT and clinical features in eight patients.

AIM: To describe perigastric appendagitis (PA) on CT as a new and distinct clinical entity to enable recognition and prevent additional unnecessary investigation or intervention. MATERIALS AND METHODS: Institutional review board approval was obtained and informed consent was waived. Retrospective review of the clinical data and CT findings in eight patients with PA encountered over 10 years at one institution was performed. The English literature was reviewed and summarized. Two experienced abdominal radiologists reviewed the CT images by consensus. RESULTS: Seven of eight patients had moderate to severe epigastric pain for 1­7 days. All eight patients (four men, four women; mean age 44 years, range 33­81 years) had no fever or leukocytosis. All underwent abdominal CT which showed ovoid fat inflammation along the course of the perigastric ligaments (gastrohepatic, gastrosplenic, and falciform). Two had gastric wall thickening. Although the inflammation was correctly described, the specific diagnosis was not made on initial interpretation in five patients. Subsequently, they underwent further diagnostic testing [an upper gastrointestinal examination and hepatobiliary iminodiacetic acid (HIDA) cholescintigraphy, an upper endoscopy and MRI examination, HIDA cholescintigraphy, another CT, and an MRI examination, respectively]. The HIDA cholescintigraphy, upper GI examination, and upper endoscopy examinations were normal. No repeated examination was performed on the other three patients. Pain resolved spontaneously in all within two days. CONCLUSION: Perigastric appendagitis can present with an acute abdomen, which is safely managed conservatively if diagnosed correctly. Radiologists should be aware of the entity to avoid unnecessary intervention, and recognize the CT findings of ovoid fat inflammation in the distribution of the perigastric ligaments.

[Otitis media with effusion : frequency, diagnosis, and therapy in early childhood]. / Seromukotympanon : Häufigkeit, Diagnose und Therapie im frühen Kindesalter.

BACKGROUND: Otitis media with effusion (OME) as the most common cause of hearing loss in childhood plays an important role in the follow-up after failed newborn hearing screening (NHS). The introduction of the NHS allows OME to be diagnosed and treated in the first months of life. MATERIAL AND METHODS: In 715 children referred to the Department of Phoniatrics and Pedaudiology of the Ear, Nose, Throat University Hospital of Magdeburg during the period 2006-2010, the prevalence and therapy process of OME during follow-up could be determined. RESULTS: OME was diagnosed in 16 % of the patients. Spontaneous resolution was observed in 37 % of the cases, while 46 % of the children were treated surgically. A substantially increased risk for persistent OME was observed in children with craniofacial dysmorphia or cleft palate. CONCLUSION: Using NHS, OME can be diagnosed and treated early, thus, preventing potential problems in the linguistic, social and intellectual development of children.

[EYECUBE as 3D multimedia imaging in macular diagnostics]. / Der EYECUBE als 3-D-Multimedia-Imaging der Makuladiagnostik.

BACKGROUND: In the new generation of EYECUBE devices, the angiography image and the OCT are included in a 3D illustration as an integration. Other diagnostic procedures such as autofluorescence and ICG can also be correlated to the OCT. The aim was to precisely classify various two-dimensional findings in relation to each other. METHOD: The new generation of OCT devices enables imaging with a low incidence of motion artefacts with very good fundus image quality - and with that, permits a largely automatic classification. The feature enabling the integration of the EYECUBE was further developed with new software, so that not only the topographic image (red-free, autofluorescence) can be correlated to the Cirrus OCT, but also all other findings gathered within the same time frame can be correlated to each other. These were brightened and projected onto the cube surface in a defined interval. The imaging procedures can be selected in a menu toolbar. Topographic volumetry OCT images can be overlayed. The practical application of the new method was tested on patients with macular disorders. RESULTS: By lightening up the results from various diagnostic procedures, it is possible of late to directly compare pathologies to each other and to the OCT results. In all patients (n = 45 eyes) with good single-image quality, the automated integration into the EYECUBE was possible (to a great extent). The application is not dependent on a certain type of device used in the procedures performed. CONCLUSIONS: The increasing level of precision in imaging procedures and the handling of large data volumes has led to the possibility of examining each macular diagnostics procedure from the comparative perspective: imaging (photo) with perfusion (FLA, ICG) and morphology (OCT). The exclusion of motion artefacts and the reliable scan position in the course of the imaging process increases the informative value of OCT.

[Clinical relevance of a new digital integration method (DIM) for the precise integration of OCT and fluorescein angiography (FLA)]. / Die Bedeutung der digitalen Integrationsmethode (DIM) von OCT und FLA für die klinische Anwendung.

BACKGROUND: We describe the establishment of a new digital integration method (DIM) for the anatomically precise and objective correlation of OCT and FLA. The aim of the study was to evaluate the clinical impact of DIM and deduce possible new knowledge in unclear angiographic findings. PATIENTS AND METHOD: DIM uses a newly developed software for the integration of OCT and FLA images of the same date. Corresponding vascular bifurcations and OCT scan position are marked in OCT and FLA images. Pathological areas in OCT or FLA can be marked and compared. A fundus enhancement system (FES) was developed for a better fundus image quality in OCT. Using a retinal tracking system (RTS) eye movements can be compensated. DIM was evaluated in 225 patients with macular diseases. RESULTS: Using FES, the DIM was successful in 95 % of the patients in contrast to 25 % without FES. Using the video system of RTS eye movement artefacts could be compensated in all patients. Cases with clear angiographic findings showed a high correspondence (66 %) with the OCT findings. A discrepancy between FLA and OCT findings was found in 33 %, especially in leakages of unknown origin. DIM was of high value in age-related macular degeneration (AMD), detecting a heterogeneous morphology of serous, solid RPE detachments, retinal cystoid formation and choroidal neovascularisation (CNV) and differentiating it in a precise topography. The lesion size of classic CNV with a hypofluorescent halo was in OCT always larger than in FLA. CONCLUSION: Through the correction of the eye movement artefacts by DIM and FES, a fundamental weak point in the previous OCT pictures is counterbalanced. Using DIM the OCT scan position for the follow-up can now be assessed in a safe and reliable manner which is mandatory for the evidence of OCT studies. The detection of precise morphology (serous RPE detachments) in angiographically unclear phenomena can lead to treatment consequences, e. g., avoiding contraindicated areas in photodynamic therapy. Using the new morphological information new knowledge is obtained on uncertain angiographic phenomena by this integration method (DIM).

Walter Krösche (1882-1957) and the Mannich reaction.

Walter Krösche was the Ph.D. student of Carl Mannich, with whom the latter published the school forming paper where the first 'Mannich reaction' has been described. For the first time biographic details and photos of Krösche are published here in a short biographic sketch.

Note: Soft X-ray transmission polarizer based on ferromagnetic thin films.

A transmission polarizer for producing elliptically polarized soft X-ray radiation from linearly polarized light is presented. The setup is intended for use at synchrotron and free-electron laser beamlines that do not directly offer circularly polarized light for, e.g., X-ray magnetic circular dichroism (XMCD) measurements or holographic imaging. Here, we investigate the degree of ellipticity upon transmission of linearly polarized radiation through a cobalt thin film. The experiment was performed at a photon energy resonant to the Co L3-edge, i.e., 778 eV, and the polarization of the transmitted radiation was determined using a polarization analyzer that measures the directional dependence of photo electrons emitted from a gas target. Elliptically polarized radiation can be created at any absorption edge showing the XMCD effect by using the respective magnetic element.

Symmetry breakdown of electron emission in extreme ultraviolet photoionization of argon.

Short wavelength free-electron lasers (FELs), providing pulses of ultrahigh photon intensity, have revolutionized spectroscopy on ionic targets. Their exceptional photon flux enables multiple photon absorptions within a single femtosecond pulse, which in turn allows for deep insights into the photoionization process itself as well as into evolving ionic states of a target. Here we employ ultraintense pulses from the FEL FERMI to spectroscopically investigate the sequential emission of electrons from gaseous, atomic argon in the neutral as well as the ionic ground state. A pronounced forward-backward symmetry breaking of the angularly resolved emission patterns with respect to the light propagation direction is experimentally observed and theoretically explained for the region of the Cooper minimum, where the asymmetry of electron emission is strongly enhanced. These findings aim to originate a better understanding of the fundamentals of photon momentum transfer in ionic matter.

[OCT in epiretinal gliosis]. / OCT bei epiretinaler Gliose.

Biomorphometric studies using optical coherence tomography (OCT) in patients with epiretinal membranes reveal a highly reflective membrane, a significant foveal thickening, loss of the foveal depression, and the presence of intraretinal cysts. Epiretinal membranes are more frequently totally adherent than separated with focal points of adherence. Visual acuity correlates with foveal thickness prior to and 6 months after vitrectomy and surgical removal of epiretinal membranes. Foveal thickening regresses postoperatively, but normal values are seldom reached. Marked foveal thickening, nonexistent foveal depression, and extensive cyst formation are supposed to correlate with a rather poor visual outcome. OCT plays a pivotal role in the differential diagnosis of pseudomacular hole in epiretinal membranes and of full-thickness macular hole. In addition to biomicroscopy and fluorescein angiography, OCT images provide valuable information for a structural assessment of the macula, especially in evaluating the postoperative course of macular surgery.

Electrochemical Deposition and Dissolution of Thallium from Sulfate Solutions.

The electrochemical behavior of thallium was studied on glassy carbon electrodes in sulfate solutions. Cyclic voltammetry was used to study the kinetics of the electrode processes and to determine the nature of the limiting step of the cathodic reduction of thallium ions. According to the dependence of current on stirring rate and scan rate, this process is diffusion limited. Chronocoulometry showed that the electrodeposition can be performed with a current efficiency of up to 96% in the absence of oxygen.

Expression and regulation of phospholipase D in the human keratinocyte cell line HaCaT.

The generation of lipid second messengers via phosphatidylcholine (PC)-specific phospholipase D (PLD) has emerged as an important step leading to transduction of extracellular signals. In the present investigation the expression of human cytosolic PLD isoenzymes in the immortalized human keratinocyte cell line HaCat was determined. At the mRNA level we found the expression of hPLD1b and for the first time in human cells also the expression of hPLD2. For further analysis of enzyme expression at the protein level, hPLD1 peptide fragments were synthesized and specific antibodies were generated (rabbit) to be used for detection of hPLD1 in Western blot experiments. Furthermore, small G-proteins were found to be involved in the regulation of PLD activity in HaCaT cells using the guanine nucleotide analogue GTPgammaS.

Digital subtraction angiography.

Digital subtraction angiography is a new imaging technique that uses a computer to subtract background distractions and to enhance contrast and density. The intravenous administration of contrast material permits safe outpatient screening for arterial disease. The exact role of intravenous digital subtraction angiography in cerebrovascular disease is still in evolution and remains the subject of debate. The value of intravenous digital subtraction angiography in screening for renovascular hypertension is less controversial, but selection of patients remains a subject for further study. Intra-arterial digital subtraction angiography has become a standard imaging technique that offers both the inherent safety produced by reduction of the volume of contrast material and the added safety afforded by reduction of both the size of the catheter and the time required to perform complex arterial interventional procedures. With the evolution of more sophisticated computed technology and radiographic equipment, the impact of both intravenous and arterial digital subtraction angiography will become even more dramatic.

Ischemic bowel disease.

The pathophysiologic events occurring in the ischemic process are described so that radiologic findings are understood rather than memorized. Depending on the underlying disease, the ischemic process can lead almost instantly to infarction or may be so indolent that years or even decades of low-grade ischemia may occur. The spectrum is discussed and illustrated.