The role of symmetric vibrational modes in the dehoherence of correlation-driven charge migration

Due to the electron correlation, a fast removal of an electron from a molecule may create a coherent superposition of cationic states and in this way initiate pure electronic dynamics in which the hole-charge left by ionization migrates throughout the system on an ultrashort time scale. The coupling to the nuclear motion introduces a decoherence that eventually traps the charge and a crucial question in the field of attochemistry is how long the electronic coherence lasts and which nuclear degrees of freedom are mostly responsible for the decoherence. Here, we report full-dimensional quantum calculations of the concerted electron-nuclear dynamics following outer-valence ionization of propynamide, which reveal that the pure electronic coherences last only 2-3 fs before being destroyed by the nuclear motion. Our analysis shows that the normal modes that are mostly responsible for the fast electronic decoherence are the symmetric in-plane modes. All other modes have little or no effect on the charge migration. This information can be useful to guide the development of reduced dimensionality models for larger systems or the search of molecules with long coherence times

Enzymatic incorporation of LNA nucleotides

The present invention relates to oligonucleotides comprising LNA units and enzymatic methods of synthesizing such oligonucleotides. Oligonucleotide comprising LNA units have various characteristics, e.g. improved biostability and increased > affinity for complementary oligonucleotides. The methods may be part of detection reactions, polymerase chain reaction, RNA transcription or in vitro evolution processes such as SELEX

Enzymatic incorporation of LNA nucleotides

The present invention relates to oligonucleotides comprising LNA units and enzymatic methods of synthesizing such oligonucleotides. Oligonucleotide comprising LNA units have various characteristics, e.g. improved biostability and increased > affinity for complementary oligonucleotides. The methods may be part of detection reactions, polymerase chain reaction, RNA transcription or in vitro evolution processes such as SELEX

GOAL-DTU: Development of Distributed Intelligence for the Multi-Agent Programming Contest

We provide a brief description of the GOAL-DTU system for the agent contest, including the overall strategy and how the system is designed to apply this strategy. Our agents are implemented using the GOAL programming language. We evaluate the performance of our agents for the contest, and finally also discuss how to improve the system based on analysis of its strengths and weaknesses.Comment: 28 pages, 45 figure

Genomic and exoproteomic analyses of cold- and alkaline-adapted bacteria reveal an abundance of secreted subtilisin-like proteases

Proteases active at low temperature or high pH are used in many commercial applications, including the detergent, food and feed industries, and bacteria specifically adapted to these conditions are a potential source of novel proteases. Environments combining these two extremes are very rare, but offer the promise of proteases ideally suited to work at both high pH and low temperature. In this report, bacteria from two cold and alkaline environments, the ikaite columns in Greenland and alkaline ponds in the McMurdo Dry Valley region, Antarctica, were screened for extracellular protease activity. Two isolates, Arsukibacterium ikkense from Greenland and a related strain, Arsukibacterium sp. MJ3, from Antarctica, were further characterized with respect to protease production. Genome sequencing identified a range of potential extracellular proteases including a number of putative secreted subtilisins. An extensive liquid chromatography–tandem mass spectrometry analysis of proteins secreted by A. ikkense identified six subtilisin‐like proteases as abundant components of the exoproteome in addition to other peptidases potentially involved in complete degradation of extracellular protein. Screening of Arsukibacterium genome libraries in Escherichia coli identified two orthologous secreted subtilisins active at pH 10 and 20°C, which were also present in the A. ikkense exoproteome. Recombinant production of both proteases confirmed the observed activity

Probing the O-glycoproteome of gastric cancer cell lines for biomarker discovery

Circulating O-glycoproteins shed from cancer cells represent important serum biomarkers for diagnostic and prognostic purposes. We have recently shown that selective detection of cancer-associated aberrant glycoforms of circulating O-glycoprotein biomarkers can increase specificity of cancer biomarker assays. However, the current knowledge of secreted and circulating O-glycoproteins is limited. Here, we used the COSMC KO "Simple- Cell" (SC) strategy to characterize the O-glycoproteome of two gastric cancer SimpleCell lines (AGS, MKN45) as well as a gastric cell line (KATO III) which naturally expresses at least partially truncated O-glycans. Overall, we identified 499 O-glycoproteins and 1236 O-glycosites in gastric cancer SimpleCells, and a total 47 O-glycoproteins and 73 O-glycosites in the KATO III cell line. We next modified the glycoproteomic strategy to apply it to pools of sera from gastric cancer and healthy individuals to identify circulating O-glycoproteins with the STn glycoform. We identified 37 O-glycoproteins in the pool of cancer sera, and only nine of these were also found in sera from healthy individuals. Two identified candidate O-glycoprotein biomarkers (CD44 and GalNAc-T5) circulating with the STn glycoform were further validated as being expressed in gastric cancer tissue. A proximity ligation assay was used to show that CD44 was expressed with the STn glycoform in gastric cancer tissues. The study provides a discovery strategy for aberrantly glycosylated O-glycoproteins and a set of O-glycoprotein candidates with biomarker potential in gastric cancer.This work was supported by The Danish Research Councils, The Mizutani Foundation, The Danish National Research Foundation (DNRF107) and Fundacão para a Ciência e a Tecnologia (FCT) and COMPETE (Programa Operacional Temático Factores de Competitividade, comparticipado pelo fundo comunitário europeu FEDER) in the framework of the projects: PTDC/BBB-EBI/0786/2012; EXPL/CTM-BIO/0762/2013. Grants were received from FCT (SFRH/BD/73717/2010 to DC), (SFRH/BPD/75871/2011 to AM), (SFRH/BPD/96510/2013 to CG) and (SFRH/BPD/66288/2009 to JAF). IPATIMUP is an Associate Laboratory of the Portuguese Ministry of Science, Technology and Higher Education, and is partially supported by FCT

Cyclosporine-A-induced nephrotoxicity in children with minimal-change nephrotic syndrome: long-term treatment up to 10 years

The impact of cyclosporine A (CsA) therapy in patients with steroid-dependent nephrotic-syndrome (SDNS) on long-term renal function is controversial. Data beyond 5 years are rare. Long-term renal function was evaluated in children with SDNS with and without CsA therapy, especially beyond 5 years. Twenty children were treated with CsA (study group) for a mean of 5.4 ± 2.2 years (ten patients for 5–11 years). Glomerular filtration rate (GFR) was calculated before and after 3 and 12 months and at latest follow-up of therapy. Fifteen children with cyclophosphamide-treated SDNS without CsA served as controls. In the study group, GFR decreased within 12 months from 136 ± 19 to 120 ± 31, to 114 ± 14 ml/min per 1.73 m2 at latest follow-up (p < 0.0001). Patients with CsA > 5 years had a GFR of 111 ± 14 ml/min per 1.73 m2 at latest follow-up without a GFR below 90 ml/min per 1.73 m2. No CsA toxicity was found in biopsies. In the control group, GFR dropped within 3 months, from 137 ± 27 to 130 ± 24, to 126 ± 19 ml/min per 1.73 m2 at latest follow-up (p = 0.1). Patients with and without nephrotoxic CsA therapy showed a drop in GFR. In CsA-treated patients, GFR was about 12% lower at latest follow-up compared with patients without nephrotoxic therapy but always remained within normal range. CsA seems to be safe, even in long-term treatment for more than 5 years

Evidence for discrimination between feeding sounds of familiar fish and unfamiliar mammal-eating killer whale ecotypes by long-finned pilot whales

Research funding was provided by the US Office of Naval Research, the DGA/TN (France), the UK Natural Environmental Research Council, and the Ministries of Defence of Norway and The Netherlands. PLT acknowledges funding received from the MASTS pooling initiative (The Marine Alliance for Science and Technology for Scotland). MASTS is funded by the Scottish Funding Council (Grant reference HR09011) and contributing institutions. CC acknowledges statistical support provided by the Multi-study OCean acoustics Human effects Analysis (MOCHA) project funded by the United States Office of Naval Research (Grant N00014-12-1-0204).Killer whales (KW) may be predators or competitors of other cetaceans. Since their foraging behavior and acoustics differ among populations ('ecotypes'), we hypothesized that other cetaceans can eavesdrop on KW sounds and adjust their behavior according to the KW ecotype. We performed playback experiments on long-finned pilot whales (Globicephala melas) in Norway using familiar fish-eating KW sounds (fKW) simulating a sympatric population that might compete for foraging areas, unfamiliar mammal-eating KW sounds (mKW) simulating a potential predator threat, and two control sounds. We assessed behavioral responses using animal-borne multi-sensor tags and surface visual observations. Pilot whales barely changed behavior to a broadband noise (CTRL-), whereas they were attracted and exhibited spyhops to fKW, mKW, and to a repeated-tonal upsweep signal (CTRL+). Whales never stopped nor started feeding in response to fKW, whereas they reduced or stopped foraging to mKW and CTRL+. Moreover, pilot whales joined other subgroups in response to fKW and CTRL+, whereas they tightened individual spacing within group and reduced time at surface in response to mKW. Typical active intimidation behavior displayed to fKW might be an antipredator strategy to a known low-risk ecotype or alternatively a way of securing the habitat exploited by a heterospecific sympatric population. Cessation of feeding and more cohesive approach to mKW playbacks might reflect an antipredator behavior towards an unknown KW ecotype of potentially higher risk. We conclude that pilot whales are able to acoustically discriminate between familiar and unfamiliar KW ecotypes, enabling them to adjust their behavior according to the perceived disturbance type.PostprintPeer reviewe