One-dimensional Si chains embedded in Pt(111)and protected by a hexagonal boron-nitride monolayer

Using scanning tunneling microscopy, we show that Si deposition on Pt(111) at 300K leads to a network of one-dimensional Si chains. On the bare Pt(111) surface, the chains, embedded into the Pt surface, are orientated along the -direction. They disappear within a few hours in ultrahigh vacuum due to the presence of residual gas. Exposing the chains to different gases deliberately reveals that CO is largely responsible for the disappearance of the chains. The chains can be stabilized by a monolayer of hexagonal boron nitride, which is deposited prior to the Si deposition. The resulting Si chains are rotated by 30{\deg} with respect to the chains on the bare Pt(111) surface and survive even an exposure to air for 10 minutes.Comment: 8 pages, 4 Figure

New journal: Algorithms for Molecular Biology

This editorial announces Algorithms for Molecular Biology, a new online open access journal published by BioMed Central. By launching the first open access journal on algorithmic bioinformatics, we provide a forum for fast publication of high-quality research articles in this rapidly evolving field. Our journal will publish thoroughly peer-reviewed papers without length limitations covering all aspects of algorithmic data analysis in computatioal biology. Publications in Algorithms for Molecular Biology are easy to find, highly visible and tracked by organisations such as PubMed. An established online submission system makes a fast reviewing procedure possible and enables us to publish accepted papers without delay. All articles published in our journal are permanently archived by PubMed Central and other scientific archives. We are looking forward to receiving your contributions

Oligo kernels for datamining on biological sequences: a case study on prokaryotic translation initiation sites

BACKGROUND: Kernel-based learning algorithms are among the most advanced machine learning methods and have been successfully applied to a variety of sequence classification tasks within the field of bioinformatics. Conventional kernels utilized so far do not provide an easy interpretation of the learnt representations in terms of positional and compositional variability of the underlying biological signals. RESULTS: We propose a kernel-based approach to datamining on biological sequences. With our method it is possible to model and analyze positional variability of oligomers of any length in a natural way. On one hand this is achieved by mapping the sequences to an intuitive but high-dimensional feature space, well-suited for interpretation of the learnt models. On the other hand, by means of the kernel trick we can provide a general learning algorithm for that high-dimensional representation because all required statistics can be computed without performing an explicit feature space mapping of the sequences. By introducing a kernel parameter that controls the degree of position-dependency, our feature space representation can be tailored to the characteristics of the biological problem at hand. A regularized learning scheme enables application even to biological problems for which only small sets of example sequences are available. Our approach includes a visualization method for transparent representation of characteristic sequence features. Thereby importance of features can be measured in terms of discriminative strength with respect to classification of the underlying sequences. To demonstrate and validate our concept on a biochemically well-defined case, we analyze E. coli translation initiation sites in order to show that we can find biologically relevant signals. For that case, our results clearly show that the Shine-Dalgarno sequence is the most important signal upstream a start codon. The variability in position and composition we found for that signal is in accordance with previous biological knowledge. We also find evidence for signals downstream of the start codon, previously introduced as transcriptional enhancers. These signals are mainly characterized by occurrences of adenine in a region of about 4 nucleotides next to the start codon. CONCLUSIONS: We showed that the oligo kernel can provide a valuable tool for the analysis of relevant signals in biological sequences. In the case of translation initiation sites we could clearly deduce the most discriminative motifs and their positional variation from example sequences. Attractive features of our approach are its flexibility with respect to oligomer length and position conservation. By means of these two parameters oligo kernels can easily be adapted to different biological problems

Genetische und exogene Risikofaktoren in der Entstehung von Hodentumoren

Hintergrund: Hodentumoren gehören zu den am besten behandelbaren Tumoren. Dennoch ist eine frühzeitige Diagnose entscheidend für die Therapie. Es wurden verschiedene genetische und exogene Faktoren untersucht, inwieweit sie ein Risiko für die Entstehung von Hodentumoren darstellen. Untersucht wurde die Vererbbarkeit der Tumore, der Einfluss frühkindlicher Ernährung sowie die Bedeutung eines ländlichen Wohnorts als Risikofaktor für die Entstehung dieser Neoplasien.Material und Methoden: In einer retrospektiven Studie wurden 128 Akten von Patienten mit einem einseitigen Hodentumor auf Ihre Körpergröße und ihr Gewicht zum Operationszeitpunkt hin sowie 128 Kontrollfälle untersucht. Die Patienten waren zwischen 1965 und 1980 geboren. Körpergröße ist mit frühkindlichen Ernährung assoziiert und dient demnach als Parameter zur Erfassung der Hochwertigkeit dieser Ernährung und einem damit verbundenen Östrogenüberschuss. Zur Auswertung wurde eine uni- und multivariante statistische Analyse möglicher Risikofaktoren durchgeführt. Auch wurden die Wohnorte der Fälle und Kontrollen auf ihre ländliche Lage untersucht und verglichen. Zur Erfassung familiärer Vererbbarkeit wurden Patienten mit bilateralen Hodentumoren, für die eine Vererbbarkeit angenommen wird, mit einem Fragebogen auf weitere Hodentumorfälle unter Blutsverwandten befragt.18 bilaterale Fälle wurden einer Kontrollgruppe von 38 unilateraler Patienten gegenübergestellt.Ergebnisse: Es konnte eine statistisch signifikante Assoziation zwischen dem Auftreten von Hodentumoren und großer Körpergröße nachgewiesen werden. Es fanden sich weniger kleine Menschen zwischen 170 und 174 cm (im Vergleich zur Durchschnittsgröße von 175 bis 179 cm) unter den Tumorpatienten als in der Kontrollgruppe (OR 0,32 KI 0,12;0,83). Ein Zusammenhang zwischen dem Gewicht und dem Auftreten von Hodentumoren war statistisch nur schwach signifikant. Dahingegen zeigte sich deutlich eine Assoziation eines niedrigen BMI und dem Auftreten von Hodentumoren. So fanden sich in der Gruppe eines BMI von 25-29 kg/m² weniger Patienten mit einer Hodentumorerkrankung (OR 0,25 KI 0,27;0,84). Auch die Multivariante Analyse bestätigt dieses Ergebnis (p=0,0005). Die Verteilung der Patienten auf die Stadtgröße gibt Hinweise auf ein gehäuftes Auftreten von Hodentumoren bei Wohnorten in Land- und Kleinstädten gegenüber der Kontrolle. Bezüglich der Vererbbarkeit und familiären Häufung konnten unter 18 Fälle von bilateralen Hodentumoren drei mal Hodentumore in der Verwandtschaft identifiziert werden, wohingegen unter 38 Kontrollfällen keine weiteren Fälle unter Verwandten auftraten.Diskussion: Sowohl die Körpergröße als auch ein niedriger BMI sind signifikant mit Hodentumoren assoziiert. Da frühkindliche Ernährung über "Insulin like growth-factors" sowohl auf die Körpergröße als auch auf die Spermiogenese Einfluss nimmt wäre dies eine mögliche Erklärung für die Assoziation. Die Assoziation eines ländlichen Wohnortes mit Hodentumoren lässt sich mit den in der Landwirtschaft eingesetzten und als Risikofaktor für Hodentumore bekannten Düngemitteln erklären. Die Untersuchung der bilateralen Hodentumore zeigt, dass es in dieser Gruppe familiäre Häufung und damit wahrscheinlich eine Untergruppe mit zugrunde liegender genetischer Disposition gibt

Electrostatically confined monolayer graphene quantum dots with orbital and valley splittings

The electrostatic confinement of massless charge carriers is hampered by Klein tunneling. Circumventing this problem in graphene mainly relies on carving out nanostructures or applying electric displacement fields to open a band gap in bilayer graphene. So far, these approaches suffer from edge disorder or insufficiently controlled localization of electrons. Here we realize an alternative strategy in monolayer graphene, by combining a homogeneous magnetic field and electrostatic confinement. Using the tip of a scanning tunneling microscope, we induce a confining potential in the Landau gaps of bulk graphene without the need for physical edges. Gating the localized states towards the Fermi energy leads to regular charging sequences with more than 40 Coulomb peaks exhibiting typical addition energies of 7-20 meV. Orbital splittings of 4-10 meV and a valley splitting of about 3 meV for the first orbital state can be deduced. These experimental observations are quantitatively reproduced by tight binding calculations, which include the interactions of the graphene with the aligned hexagonal boron nitride substrate. The demonstrated confinement approach appears suitable to create quantum dots with well-defined wave function properties beyond the reach of traditional techniques

Continuous Synthesis of Artemisinin-Derived Medicines

Described is a continuous, divergent synthesis system which is coupled to continuous purification and is capable of producing four anti-malarial APIs. The system is comprised of three linked reaction modules for photooxidation/cyclization, reduction, and derivatization. A fourth module couples the crude reaction stream with continuous purification to yield pure API

Corrigendum to ‘‘Alumino-mesostructured Ni catalysts for the direct conversion of ethene to propene” [J. Catal. 305 (2013) 154–168]

Ni/MCM-41 and Ni/AlMCM-41 were synthesized at different Si/Al ratios and tested in the direct conversion of ethene to propene (ETP-reaction). It was intended to evaluate the effect of modifying the catalyst acidity on the ETP-reaction rather than optimizing its performance. All catalysts were characterized by powder XRD, N2-physisorption, 29Si and 27Al MAS NMR, TEM, NH3-TPD, pyridine-DRITFS, H2-TPR, and TPO. Ni/MCM-41 showed low catalytic activity due to its low acidity. Ni/AlMCM-41 catalyst with a Si/Al ratio of 60 had high catalytic activity. Characterization results revealed that the catalyst structure does not have effect on the catalytic activity. Al could be incorporated into the MCM-41 framework up to Si/Al ratio of 16. Two different Ni-composites on the surface of the MCM-41 and AlMCM-41 were observed. Deeper characterization is required to know the Ni state. Important deactivation was observed at 450 °C. The nature of the carbonaceous species and reaction mechanism require deeper characterization

Solar Forcing Recorded by Aerosol Concentrations in Coastal Antarctic Glacier Ice, McMurdo Dry Valleys

Ice-core chemistry data from Victoria Lower Glacier, Antarctica, suggest, at least for the last 50 years, a direct influence of solar activity variations on the McMurdo Dry Valleys (MDV) climate system via controls on air-mass input from two competing environments: the East Antarctic ice sheet and the Ross Sea. During periods of increased solar activity, when total solar irradiance is relatively high, the MDV climate system appears to be dominated by air masses originating from the Ross Sea, leading to higher aerosol deposition. During reduced solar activity, the Antarctic interior seems to be the dominant air-mass source, leading to lower aerosol concentration in the ice-core record. We propose that the sensitivity of the MDV to variations in solar irradiance is caused by strong albedo differences between the ice-free MDV and the ice sheet

Alumino-mesostructured Ni catalysts for the direct conversion of ethene to propene

Ni/MCM-41 and Ni/AlMCM-41 were synthesized at different Si/Al ratios and tested in the direct conversion of ethene to propene (ETP-reaction). It was intended to evaluate the effect of modifying the catalyst acidity on the ETP-reaction rather than optimizing its performance. All catalysts were characterized by powder XRD, N2-physisorption, 29Si and 27Al MAS NMR, TEM, NH3-TPD, pyridine-DRITFS, H2-TPR, and TPO. Ni/MCM-41 showed low catalytic activity due to its low acidity. Ni/AlMCM-41 catalyst with a Si/ Al ratio of 60 had high catalytic activity. Characterization results revealed that the catalyst structure does not have effect on the catalytic activity. Al could be incorporated into the MCM-41 framework up to Si/Al ratio of 16. Two different Ni-composites on the surface of the MCM-41 and AlMCM-41 were observed. Deeper characterization is required to know the Ni state. Important deactivation was observed at 450 !C. The nature of the carbonaceous species and reaction mechanism require deeper characterization