Retention time prediction using neural networks increases identifications in crosslinking mass spectrometry

Crosslinking mass spectrometry has developed into a robust technique that is increasingly used to investigate the interactomes of organelles and cells. However, the incomplete and noisy information in the mass spectra of crosslinked peptides limits the numbers of protein–protein interactions that can be confidently identified. Here, we leverage chromatographic retention time information to aid the identification of crosslinked peptides from mass spectra. Our Siamese machine learning model xiRT achieves highly accurate retention time predictions of crosslinked peptides in a multi-dimensional separation of crosslinked E. coli lysate. Importantly, supplementing the search engine score with retention time features leads to a substantial increase in protein–protein interactions without affecting confidence. This approach is not limited to cell lysates and multi-dimensional separation but also improves considerably the analysis of crosslinked multiprotein complexes with a single chromatographic dimension. Retention times are a powerful complement to mass spectrometric information to increase the sensitivity of crosslinking mass spectrometry analyses

Sanat yolunda

Muallim İrfan Emin'in Talebe Defteri'nde tefrika edilen Sanat Yolunda adlı romanıTek sayı görülmüştür. Ancak kaynaklarda tefrikanın tamamlandığı bilgisi mevcuttur

Semiclassical Foundation of Universality in Quantum Chaos

We sketch the semiclassical core of a proof of the so-called Bohigas-Giannoni-Schmit conjecture: A dynamical system with full classical chaos has a quantum energy spectrum with universal fluctuations on the scale of the mean level spacing. We show how in the semiclassical limit all system specific properties fade away, leaving only ergodicity, hyperbolicity, and combinatorics as agents determining the contributions of pairs of classical periodic orbits to the quantum spectral form factor. The small-time form factor is thus reproduced semiclassically. Bridges between classical orbits and (the non-linear sigma model of) quantum field theory are built by revealing the contributing orbit pairs as topologically equivalent to Feynman diagrams.Comment: 4 pages, 2 figures; final version published in PRL, minor change

Evidence for silicate dissolution on Mars from the Nakhla meteorite

Veins containing carbonates, hydrous silicates and sulphates that occur within and between grains of augite and olivine in the Nakhla meteorite are good evidence for the former presence of liquid water in the Martian crust. Aqueous solutions gained access to grain interiors via narrow fractures, and those fractures within olivine whose walls were oriented close to (001) were preferentially widened by etching along [001]. This orientation selective dissolution may have been due to the presence within olivine of shock-formed [001](100) and [001]{110} screw dislocations. The duration of etching is likely to have been brief, possibly less than a year, and the solutions responsible were sufficiently cool and reducing that laihunite is absent and Fe liberated from the olivine was not immediately oxidised. The pores within olivine were mineralised in sequence by siderite, nanocrystalline smectite, a Fe-Mg phyllosilicate, and then gypsum, whereas only the smectite occurs within augite. The nanocrystalline smectite was deposited as sub-micrometre thick layers on etched vein walls, and solution compositions varied substantially between and sometimes during precipitation of each layer. Together with microcrystalline gypsum the Fe-Mg phyllosilicate crystallised as water briefly returned to some of the veins following desiccation fracturing of the smectite. These results show that etching of olivine enhanced the porosity and permeability of the nakhlite parent rock and that dissolution and secondary mineralization took place within the same near-static aqueous system

Arctic in Rapid Transition: Priorities for the future of marine and coastal research in the Arctic.

Understanding and responding to the rapidly occurring environmental changes in the Arctic over the past few decades require new approaches in science. This includes improved collaborations within the scientific community but also enhanced dialogue between scientists and societal stakeholders, especially with Arctic communities. As a contribution to the Third International Conference on Arctic Research Planning (ICARPIII), the Arctic in Rapid Transition (ART) network held an international workshop in France, in October 2014, in order to discuss high-priority requirements for future Arctic marine and coastal research from an early-career scientists (ECS) perspective. The discussion encompassed a variety of research fields, including topics of oceanographic conditions, sea-ice monitoring, marine biodiversity, land-ocean interactions, and geological reconstructions, as well as law and governance issues. Participants of the workshop strongly agreed on the need to enhance interdisciplinarity in order to collect comprehensive knowledge about the modern and past Arctic Ocean's geo-ecological dynamics. Such knowledge enables improved predictions of Arctic developments and provides the basis for elaborate decision-making on future actions under plausible environmental and climate scenarios in the high northern latitudes. Priority research sheets resulting from the workshop's discussions were distributed during the ICARPIII meetings in April 2015 in Japan, and are publicly available online

Near-infrared proper motions and spectroscopy of infrared excess sources at the Galactic Center

There are a number of faint compact infrared excess sources in the central stellar cluster of the Milky Way. Their nature and origin is unclear. In addition to several isolated objects of this kind we find a small but dense cluster of co-moving sources (IRS13N) about 3" west of SgrA* just 0.5" north of the bright IRS13E cluster of WR and O-type stars. Based on their color and brightness, there are two main possibilities: (1) they may be dust embedded stars older than few Myr, or (2) extremely young, dusty stars with ages less than 1Myr. We present fist H- and Ks-band identifications or proper motions of the IRS13N members, the high velocity dusty S-cluster object (DSO), and other infrared excess sources in the central field. We also present results of NIR H- and Ks-band ESO-SINFONI integral field spectroscopy of ISR13N. We show that within the uncertainties, the proper motions of the IRS13N sources in Ks- and L'-band are identical. This indicates that the bright L'-band IRS13N sources are indeed dust enshrouded stars rather than core-less dust clouds. The proper motions show that the IRS13N sources are not strongly gravitationally bound to each other implying that they have been formed recently. We also present a first H- and Ks-band identification as well as proper motions and HKsL'-colors of a fast moving DSO which was recently found in the cluster of high speed S-stars that surround the super-massive black hole Sagittarius A* (SgrA*). Most of the compact L'-band excess emission sources have a compact H- or Ks-band counterpart and therefore are likely stars with dust shells or disks. Our new results and orbital analysis from our previous work favor the hypothesis that the infrared excess IRS13N members and other dusty sources close to SgrA* are very young dusty stars and that star formation at the GC is a continuously ongoing process.Comment: 20 pages, 18 figures, 4 tables plus appendix with 16 figures and 3 tables accepted by A&

Nursing students' trait mindfulness and psychological stress: A correlation and mediation analysis

Background Nursing students face a great amount of psychological stress during their nursing education. Mindfulness-based training has received increased recognition from nurse educators regarding its effect on reducing students' psychological stress. Study evidence has supported that cultivation of trait mindfulness through Mindfulness-based training was the key to this effect. However, there is a lack of research that focuses on intricate relationships between various facets of trait mindfulness and psychological stress. Objective Examining the relationships between various trait mindfulness facets and psychological stress. Design A cross-sectional design was used to collect data on trait mindfulness facets and psychological stress. Participants A convenience sample of 99 undergraduate nursing students from a Bachelor of Nursing program completed this study. Setting This study was conducted in a university in the south-eastern United States. Method Participants completed an online questionnaire, which collected their demographic information, trait mindfulness (the Five Factor Mindfulness Questionnaire), and psychological stress (the Perceived Stress Scale-10). Correlation and mediation analyses were applied. Results Other than the trait mindfulness facet of observing, the remaining three facets (acting with awareness, non-judging, and non-reactivity) were negatively correlated with psychological stress. Observing had little to low correlations with non-judging and acting with awareness, but attained a moderately positive correlation with non-reactivity. Moreover, observing could indirectly predict psychological stress, when non-reactivity served as a mediator. Finally, non-judging partially mediated the relationship between acting with awareness and psychological stress. Conclusions The results of the current study can help nurse educators better understand the intricate relationships between various facets of trait mindfulness and psychological stress. Specifically, facets of acting with awareness, non-judging, and non-reactivity are directly relevant to the reduction of psychological stress. Therefore, regardless of formal or informal practices of mindfulness, nurse educators ought to assist students in cultivating these facets as means toward stress management

Data and 2D scaling relations for galaxies in Abell 1689: a hint of size evolution at z~0.2

{abridged} We present imaging and spectroscopy of Abell 1689 (z=0.183) from GEMINI/GMOS-N and HST/ACS. We measure integrated photometry from the GMOS g' and r' images (for 531 galaxies) and surface photometry from the HST F625W image (for 43 galaxies) as well as velocities and velocity dispersions from the GMOS spectra (for 71 galaxies). We construct the Kormendy relation (KR), Faber-Jackson relation (FJR) and colour-magnitude relation (CMR) for early-type galaxies in Abell 1689 using this data and compare them to those of the Coma cluster. We measure the intrinsic scatter of the CMR in Abell 1689 to be 0.054 \pm 0.004 mag which places degenerate constraints on the ratio of the assembly timescale to the time available (beta) and the age of the population. Making the assumption that galaxies in Abell 1689 will evolve into those of Coma over an interval of 2.26 Gyr breaks this degeneracy and limits beta to be > 0.6 and the age of the red sequence to be > 5.5 Gyr (formed at z > 0.55). Without corrections for size evolution but accounting for magnitude cuts and selection effects, the KR & FJR are inconsistent and disagree at the 2 sigma level regarding the amount of luminosity evolution in the last 2.26 Gyr. However, after correcting for size evolution the KR & FJR show similar changes in luminosity (0.22 \pm 0.11 mag) that are consistent with the passive evolution of the stellar populations from a single burst of star formation 10.2 \pm 3.3 Gyr ago (z = 1.8+inf-0.9). Thus the changes in the KR, FJR & CMR of Abell 1689 relative to Coma all agree and suggest old galaxy populations with little or no synchronisation in the star formation histories. Furthermore, the weak evidence for size evolution in the cluster environment in the last 2.26 Gyr places interesting constraints on the possible mechanisms at work, favouring harassment or secular processes over merger scenarios.Comment: Accepted for publication in MNRA

Quantum phase transitions

In recent years, quantum phase transitions have attracted the interest of both theorists and experimentalists in condensed matter physics. These transitions, which are accessed at zero temperature by variation of a non-thermal control parameter, can influence the behavior of electronic systems over a wide range of the phase diagram. Quantum phase transitions occur as a result of competing ground state phases. The cuprate superconductors which can be tuned from a Mott insulating to a d-wave superconducting phase by carrier doping are a paradigmatic example. This review introduces important concepts of phase transitions and discusses the interplay of quantum and classical fluctuations near criticality. The main part of the article is devoted to bulk quantum phase transitions in condensed matter systems. Several classes of transitions will be briefly reviewed, pointing out, e.g., conceptual differences between ordering transitions in metallic and insulating systems. An interesting separate class of transitions are boundary phase transitions where only degrees of freedom of a subsystem become critical; this will be illustrated in a few examples. The article is aimed on bridging the gap between high-level theoretical presentations and research papers specialized in certain classes of materials. It will give an overview over a variety of different quantum transitions, critically discuss open theoretical questions, and frequently make contact with recent experiments in condensed matter physics.Comment: 50 pages, 7 figs; (v2) final version as publishe

Variability in transport of terrigenous material on the shelves and the deep Arctic Ocean during the Holocene

Arctic coastal zones serve as a sensitive filter for terrigenous matter input onto the shelves via river discharge and coastal erosion. This material is further distributed across the Arctic by ocean currents and sea ice. The coastal regions are particularly vulnerable to changes related to recent climate change. We compiled a pan-Arctic review that looks into the changing Holocene sources, transport processes and sinks of terrigenous sediment in the Arctic Ocean. Existing palaeoceanographic studies demonstrate how climate warming and the disappearance of ice sheets during the early Holocene initiated eustatic sea-level rise that greatly modified the physiography of the Arctic Ocean. Sedimentation rates over the shelves and slopes were much greater during periods of rapid sea-level rise in the early and middle Holocene, as a result of the relative distance to the terrestrial sediment sources. However, estimates of suspended sediment delivery through major Arctic rivers do not indicate enhanced delivery during this time, which suggests enhanced rates of coastal erosion. The increased supply of terrigenous material to the outer shelves and deep Arctic Ocean in the early and middle Holocene might serve as analogous to forecast changes in the future Arctic.Peer reviewe