Sequence embedding for fast construction of guide trees for multiple sequence alignment

<p>Abstract</p> <p>Background</p> <p>The most widely used multiple sequence alignment methods require sequences to be clustered as an initial step. Most sequence clustering methods require a full distance matrix to be computed between all pairs of sequences. This requires memory and time proportional to <it>N</it>²for <it>N </it>sequences. When <it>N </it>grows larger than 10,000 or so, this becomes increasingly prohibitive and can form a significant barrier to carrying out very large multiple alignments.</p> <p>Results</p> <p>In this paper, we have tested variations on a class of embedding methods that have been designed for clustering large numbers of complex objects where the individual distance calculations are expensive. These methods involve embedding the sequences in a space where the similarities within a set of sequences can be closely approximated without having to compute all pair-wise distances.</p> <p>Conclusions</p> <p>We show how this approach greatly reduces computation time and memory requirements for clustering large numbers of sequences and demonstrate the quality of the clusterings by benchmarking them as guide trees for multiple alignment. Source code is available for download from <url>http://www.clustal.org/mbed.tgz</url>.</p

An integrated marine data collection for the German Bight – Part 1: Subaqueous geomorphology and surface sedimentology (1996–2016)

Datasets: Themengebiet - Geomorphologie - https://doi.org/10.48437/02.2020.K2.7000.0001Datasets: Themengebiet - Bathymetrie - https://doi.org/10.48437/02.2020.K2.7000.0002Datasets: Themengebiet - Sedimentologie - https://doi.org/10.48437/02.2020.K2.7000.000

Temperature-dependent changes of membrane potentials in cells of thermonastic tepals of Eranthis hyemalis (L.) Salisb

Opisano wpływ temperatury na mierzony wpoprzek błony potencjał bioelektryczny plazmalemmy (PD) komórek płatków rannika (Eranthis hyemalis). Nagłe ogrzanie nie uszkodzonych płatków powodowało niewielki, przejściowy wzrost PD, po którym następowała znaczna i długotrwała depolaryzacja. Efekt ten nazwano reakcją anomalną. Przy nagłym oziębieniu sytuacja była odwrotna: po niewielkiej, przejściowej depolaryzacji następowała znaczna hiperpolaryzacja. To również było traktowane jako reakcja anomalna. Efekty takie były silniej zaznaczone w skórce odosiowej płatka niż w skórce doosiowej. Wskazuje to na elektrofizjologiczną grzbictobrzuszność płatków. Reakcje anomalne były o wiele słabsze w komórkach izolowanych tkanek niż w komórkach nietkniętych płatków. Różnica ta nie wynika jednak ze zranienia lub bezpośredniego kontaktu tkanki z roztworem zewnętrznym, ponieważ w segmentach płatków pozbawionych jedynie odosiowej skórki, PD zmieniało się tak samo jak w nietkniętych płatkach. Zasugerowano, że pojawianie się reakcji anomalnych jest modulowane naprężeniami tkankowymi. Przedyskutowano też znaczenie reakcji anomalnych dla ruchów termonastycznych

Weiterentwicklung des Analyseinstruments Renewbility: Renewbility II - Szenario für einen anspruchsvollen Klimaschutzbeitrag des Verkehrs

Das Projekt Renewbility II hatte zum Ziel den bestehenden Renewbility-Modellverbund weiterzuentwickeln und im Rahmen von Szenariobetrachtungen den möglichen Klimaschutzbeitrag des Verkehrssektors bis zum Jahr 2030 unter Mitwirkung unterschiedlichster gesellschaftlicher Akteure zu quantifizieren. Im Basisszenario werden bestehende Regulierungen im Verkehr berücksichtigt und bestehende Entwicklungen fortgeschrieben. Im Ergebnis können im Basisszenario bei deutlichen Effizienzsteigerungen, dem zunehmenden Einsatz alternativer Kraftstoffe im Verkehr und einer weiter zunehmenden Verkehrsnachfrage die Treibhausgasemissionen bis zum Jahr 2030 um 12 % gegenüber 2005 gesenkt werden. Im Klimaschutzszenario können mit deutlich ambitionierteren Maßnahmen die Treibhausgasemissionen im selben Zeitraum um 37 % reduziert werden bei gleichzeitiger Stärkung der deutschen Wirtschaftskraft und Stabilisierung des Staatshaushaltes. Neben einer weiteren Effizienzsteigerung und dem Einsatz von alternativen Antrieben und Kraftstoffen, trägt insbesondere die Verlagerung, aber auch die Vermeidung von Verkehren zur Emissionsminderung bei

Optical creation and annihilation of skyrmion patches in a bulk chiral magnet

A key challenge for the realization of future skyrmion devices comprises the controlled creation, annihilation and detection of these topologically non-trivial magnetic spin textures. In this study, we report an all-optical approach for writing, deleting, and reading skyrmions in the cubic chiral magnet Fe$_{0.25}$Co$_{0.75}$Si based on thermal quenching. Using focused femtosecond laser pulses, patches of a skyrmion state are created and annihilated locally, demonstrating unprecedented control of thermally metastable skyrmions in a bulk compound. The skyrmion state is read-out by analyzing the microwave spin excitations in time-resolved magneto-optical Kerr effect measurements. Extracting the magnetic field and laser fluence dependence, we find well-separated magnetic field regimes and different laser fluence thresholds for the laser-induced creation and annihilation of metastable skyrmions. The all-optical skyrmion control, as established in this study for a model system, represents a promising and energy-efficient approach for the realization of skyrmions as magnetic bits in future storage devices, reminiscent of magneto-optical storage devices in the past

Outbreak of imported diphtheria with Corynebacterium diphtheriae among migrants arriving in Germany, 2022

From July 2022, cases of imported diphtheria with toxigenic Corynebacterium diphtheriae remarkably increased among migrants arriving in Germany. Up to 30 September 2022, 44 cases have been reported to the national public health institute, all laboratory- confirmed, male, and mainly coming from Syria (n = 21) and Afghanistan (n = 17). Phylogeny and available journey information indicate that most cases (n = 19) were infected along the Balkan route. Active case finding, increased laboratory preparedness and epicentre localisation in countries along this route are important.Peer Reviewe

Laser-Supported CD133+ Cell Therapy in Patients with Ischemic Cardiomyopathy: Initial Results from a Prospective Phase I Multicenter Trial

Objectives: This study evaluates the safety, principal feasibility and restoration potential of laser-supported CD133+ intramyocardial cell transplantation in patients with ischemic cardiomyopathy. Methods: Forty-two patients with severe ischemic cardiomyopathy (left ventricular ejection fraction (LVEF) >15% and 3 myocardial segments) determined in the preoperative MRI was inversely correlated with a LVEF increase after laser-supported cell therapy (p = 0.024). Conclusions: This multicenter trial demonstrates that laser-supported CD133+ cell transplantation is safe and feasible in patients with ischemic cardiomyopathy undergoing CABG, and in most cases, it appears to significantly improve the myocardial function. Importantly, our data show that the beneficial effect was significantly related to the extent of transmural delayed enhancement, suggesting that MRI-guided selection of patients is mandatory to ensure the effectiveness of the therapy. Trial Registration: EudraCT 2005-004051-35) Controlled-Trials.com ISRCTN4999863