Ultrafast electron dynamics in excited states of conjugated thiophene-fluorene organic polymer (pF8T2) thin films.

The electronic states of poly(9,9-dioctylfluorenyl-alt-bithiophene) pF8T2 on H/Si(100) substrates, prototypical for organic photovoltaics, were investigated by ultrafast photoelectron spectroscopy and by time-resolved fluorescence studies. Occupied and unoccupied electronic states were analysed by ultraviolet photoelectron spectroscopy (UPS), static and dynamic femtosecond two-photon photoemission (2PPE), and time-correlated single photon counting (TCSPC). Time-resolved measurements allow assessment of population lifetimes of intermediate states. The combination of time-resolved photoelectron spectroscopy and fluorescence excitation allows following the electronic dynamics in excited states from the femtosecond to the nanosecond time scale. For this prototypical material the electron kinetic energy resolved lifetimes range from about a few tens of femtoseconds up to hundreds of picoseconds. After annealing these types of organic thin films the efficiency of organic solar cells usually increases. We show that annealing does not influence the initial ultrafast charge generation processes, but the long-lived states. However, the nanosecond scale fluorescence lifetimes measured by TCSPC are prolonged after annealing, which therefore is identified as the cause of a greater exciton diffusion range and thus is beneficial for charge carrier extraction.

BITES: balanced individual treatment effect for survival data.

MOTIVATION: Estimating the effects of interventions on patient outcome is one of the key aspects of personalized medicine. Their inference is often challenged by the fact that the training data comprises only the outcome for the administered treatment, and not for alternative treatments (the so-called counterfactual outcomes). Several methods were suggested for this scenario based on observational data, i.e. data where the intervention was not applied randomly, for both continuous and binary outcome variables. However, patient outcome is often recorded in terms of time-to-event data, comprising right-censored event times if an event does not occur within the observation period. Albeit their enormous importance, time-to-event data are rarely used for treatment optimization. We suggest an approach named BITES (Balanced Individual Treatment Effect for Survival data), which combines a treatment-specific semi-parametric Cox loss with a treatment-balanced deep neural network; i.e. we regularize differences between treated and non-treated patients using Integral Probability Metrics (IPM). RESULTS: We show in simulation studies that this approach outperforms the state of the art. Furthermore, we demonstrate in an application to a cohort of breast cancer patients that hormone treatment can be optimized based on six routine parameters. We successfully validated this finding in an independent cohort. AVAILABILITY AND IMPLEMENTATION: We provide BITES as an easy-to-use python implementation including scheduled hyper-parameter optimization (https://github.com/sschrod/BITES). The data underlying this article are available in the CRAN repository at https://rdrr.io/cran/survival/man/gbsg.html and https://rdrr.io/cran/survival/man/rotterdam.html. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Impact of real mirror profiles inside a split-and-delay unit on the spatial intensity profile in pump/probe experiments at the European XFEL.

For the High-Energy-Density (HED) beamline at the SASE2 undulator of the European XFEL, a hard X-ray split-and-delay unit (SDU) has been built enabling time-resolved pump/probe experiments with photon energies between 5 keV and 24 keV. The optical layout of the SDU is based on geometrical wavefront splitting and multilayer Bragg mirrors. Maximum delays between Δτ = ±1 ps at 24 keV and Δτ = ±23 ps at 5 keV will be possible. Time-dependent wavefront propagation simulations were performed by means of the Synchrotron Radiation Workshop (SRW) software in order to investigate the impact of the optical layout, including diffraction on the beam splitter and recombiner edges and the three-dimensional topography of all eight mirrors, on the spatio-temporal properties of the XFEL pulses. The radiation is generated from noise by the code FAST which simulates the self-amplified spontaneous emission (SASE) process. A fast Fourier transformation evaluation of the disturbed interference pattern yields for ideal mirror surfaces a coherence time of τc = 0.23 fs and deduces one of τc = 0.21 fs for the real mirrors, thus with an error of Δτ = 0.02 fs which is smaller than the deviation resulting from shot-to-shot fluctuations of SASE2 pulses. The wavefronts are focused by means of compound refractive lenses in order to achieve fluences of a few hundred mJ mm-2 within a spot width of 20 µm (FWHM) diameter. Coherence effects and optics imperfections increase the peak intensity between 200 and 400% for pulse delays within the coherence time. Additionally, the influence of two off-set mirrors in the HED beamline are discussed. Further, we show the fluence distribution for Δz = ±3 mm around the focal spot along the optical axis. The simulations show that the topographies of the mirrors of the SDU are good enough to support X-ray pump/X-ray probe experiments.

Time-Resolved XUV Opacity Measurements of Warm Dense Aluminum.

The free-free opacity in plasmas is fundamental to our understanding of energy transport in stellar interiors and for inertial confinement fusion research. However, theoretical predictions in the challenging dense plasma regime are conflicting and there is a dearth of accurate experimental data to allow for direct model validation. Here we present time-resolved transmission measurements in solid-density Al heated by an XUV free-electron laser. We use a novel functional optimization approach to extract the temperature-dependent absorption coefficient directly from an oversampled pool of single-shot measurements, and find a pronounced enhancement of the opacity as the plasma is heated to temperatures of order of the Fermi energy. Plasma heating and opacity enhancement are observed on ultrafast timescales, within the duration of the femtosecond XUV pulse. We attribute further rises in the opacity on ps timescales to melt and the formation of warm dense matter.

Draft Genome Sequence of Rhizobium tropici SARCC-755, a Free-Living Rhizobium That Nodulated and Promoted Growth in Pigeonpea [Cajanus cajan (L.) Millsp.].

Rhizobium tropici SARCC-755 is a free-living soil bacterium that formed nodules on pigeonpea roots in the present study. However, the draft genome sequence reveals that this Rhizobium species contains the nolR gene but lacks the common nodulation (nodABC) genes and probably uses other pathways to induce nodules on the legume plant.

Probing the non-equilibrium transient state in magnetite by a jitter-free two-color X-ray pump and X-ray probe experiment.

We present a general experimental concept for jitter-free pump and probe experiments at free electron lasers. By generating pump and probe pulse from one and the same X-ray pulse using an optical split-and-delay unit, we obtain a temporal resolution that is limited only by the X-ray pulse lengths. In a two-color X-ray pump and X-ray probe experiment with sub 70 fs temporal resolution, we selectively probe the response of orbital and charge degree of freedom in the prototypical functional oxide magnetite after photoexcitation. We find electronic order to be quenched on a time scale of (30 ± 30) fs and hence most likely faster than what is to be expected for any lattice dynamics. Our experimental result hints to the formation of a short lived transient state with decoupled electronic and lattice degree of freedom in magnetite. The excitation and relaxation mechanism for X-ray pumping is discussed within a simple model leading to the conclusion that within the first 10 fs the original photoexcitation decays into low-energy electronic excitations comparable to what is achieved by optical pump pulse excitation. Our findings show on which time scales dynamical decoupling of degrees of freedom in functional oxides can be expected and how to probe this selectively with soft X-ray pulses. Results can be expected to provide crucial information for theories for ultrafast behavior of materials and help to develop concepts for novel switching devices.

A sensitive EUV Schwarzschild microscope for plasma studies with sub-micrometer resolution.

We present an extreme ultraviolet (EUV) microscope using a Schwarzschild objective which is optimized for single-shot sub-micrometer imaging of laser-plasma targets. The microscope has been designed and constructed for imaging the scattering from an EUV-heated solid-density hydrogen jet. Imaging of a cryogenic hydrogen target was demonstrated using single pulses of the free-electron laser in Hamburg (FLASH) free-electron laser at a wavelength of 13.5 nm. In a single exposure, we observe a hydrogen jet with ice fragments with a spatial resolution in the sub-micrometer range. In situ EUV imaging is expected to enable novel experimental capabilities for warm dense matter studies of micrometer-sized samples in laser-plasma experiments.

XUV photodesorption of carbon cluster ions and ionic photofragments from a mixed methane-water ice.

The photochemical processing of a CH4 : D2O 1 : 3.3 ice mixture adsorbed on an HOPG surface in the XUV regime was investigated using pulses obtained from the Free-electron LASer in Hamburg (FLASH) facility. Ice films were exposed to femtosecond pulses with a photon energy of hν = 40.8 eV, consistent with the HeII resonance line. Cationic species desorbing directly from the ice films were detected using time-of-flight (ToF) mass spectrometry. Simple ions formed through the fragmentation of the parent molecules and subsequent recombination reactions were detected and are consistent with efficient D+ and H+ ejection from the parent species, similar to the case for low energy electron irradiation. The FEL fluence dependencies of these ions are linear or exhibit a non-linear order of up to 3. In addition, a series of Cn+ cluster ions (with n up to 12) were also identified. These ions display a highly non-linear desorption yield with respect to the FEL fluence, having an order of 6-10, suggesting a complex multi-step process involving the primary products of CH4 fragmentation. Two-pulse correlation measurements were performed to gain further insight into the underlying reaction dynamics of the photo-chemical reactions. The yield of the D2O derived products displayed a different temporal behaviour with respect to the Cn+ ions, indicating the presence of very different reaction pathways to the two families of ionic products.

Reference point insensitive molecular data analysis.

MOTIVATION: In biomedicine, every molecular measurement is relative to a reference point, like a fixed aliquot of RNA extracted from a tissue, a defined number of blood cells, or a defined volume of biofluid. Reference points are often chosen for practical reasons. For example, we might want to assess the metabolome of a diseased organ but can only measure metabolites in blood or urine. In this case, the observable data only indirectly reflects the disease state. The statistical implications of these discrepancies in reference points have not yet been discussed. RESULTS: Here, we show that reference point discrepancies compromise the performance of regression models like the LASSO. As an alternative, we suggest zero-sum regression for a reference point insensitive analysis. We show that zero-sum regression is superior to the LASSO in case of a poor choice of reference point both in simulations and in an application that integrates intestinal microbiome analysis with metabolomics. Moreover, we describe a novel coordinate descent based algorithm to fit zero-sum elastic nets. AVAILABILITY AND IMPLEMENTATION: The R-package "zeroSum" can be downloaded at https://github.com/rehbergT/zeroSum Moreover, we provide all R-scripts and data used to produce the results of this manuscript as Supplementary Material CONTACT: Michael.Altenbuchinger@ukr.de, Thorsten.Rehberg@ukr.de and Rainer.Spang@ukr.deSupplementary information: Supplementary material is available at Bioinformatics online.

Near-isogenic lines of Triticum aestivum with distinct modes of resistance exhibit dissimilar transcriptional regulation during Diuraphis noxia feeding.

Russian wheat aphid (Diuraphis noxia, Kurdjumov) feeding on susceptible Triticum aestivum L. leads to leaf rolling, chlorosis and plant death - symptoms not present in resistant lines. Although the effects of several D. noxia (Dn) resistance genes are known, none have been isolated or characterized. Wheat varieties expressing different Dn genes exhibit distinct modes of D. noxia resistance, such as antibiosis (Dn1), tolerance (Dn2), and antixenosis (Dn5). However, the mechanism whereby feeding aphids are perceived, and how subsequent transcriptional responses are partitioned into resistance categories, remains unclear. Here we report on downstream events in near-isogenic wheat lines containing different Dn genes after D. noxia biotype SA1 feeding. Transcripts involved in stress, signal transduction, photosynthesis, metabolism and gene regulation were differentially regulated during D. noxia feeding. Expression analyses using RT-qPCR and RNA hybridization, as well as enzyme activity profiling, provide evidence that the timing and intensity of pathways induced are critical in the development of particular modes of resistance. Pathways involved include the generation of kinase signalling cascades that lead to a sustained oxidative burst, and a hypersensitive response that is active during antibiosis. Tolerance is a passive resistance mechanism that acts through repair or de novo synthesis of photosystem proteins. Results further suggest that ethylene-mediated pathways are possibly involved in generating volatile compounds and cell wall fortification during the antixenosic response.

Equilibration dynamics and conductivity of warm dense hydrogen.

We investigate subpicosecond dynamics of warm dense hydrogen at the XUV free-electron laser facility (FLASH) at DESY (Hamburg). Ultrafast impulsive electron heating is initiated by a ≤ 300-fs short x-ray burst of 92-eV photon energy. A second pulse probes the sample via x-ray scattering at jitter-free variable time delay. We show that the initial molecular structure dissociates within (0.9 ± 0.2) ps, allowing us to infer the energy transfer rate between electrons and ions. We evaluate Saha and Thomas-Fermi ionization models in radiation hydrodynamics simulations, predicting plasma parameters that are subsequently used to calculate the static structure factor. A conductivity model for partially ionized plasma is validated by two-temperature density-functional theory coupled to molecular dynamic simulations and agrees with the experimental data. Our results provide important insights and the needed experimental data on transport properties of dense plasmas.

Electron rearrangement dynamics in dissociating I(2)

The charge rearrangement in dissociating I_{2}^{n+} molecules is measured as a function of the internuclear distance R using extreme ultraviolet pulses delivered by the free-electron laser in Hamburg. Within an extreme ultraviolet pump-probe scheme, the first pulse initiates dissociation by multiply ionizing I_{2}, and the delayed probe pulse further ionizes one of the two fragments at a given time, thus triggering charge rearrangement at a well-defined R. The electron transfer between the fragments is monitored by analyzing the delay-dependent ion kinetic energies and charge states. The experimental results are in very good agreement with predictions of the classical over-the-barrier model demonstrating its validity in a thus far unexplored quasimolecular regime relevant for free-electron laser, plasma, and chemistry applications.

Tunable two-color hard x-ray multilayer Bragg mirrors.

A tunable two-color multilayer Bragg coating capable of simultaneously reflecting the fundamental and the third harmonic of an x-ray free-electron laser at the same angle and with high reflectance R>0.70 is presented. The novel coating will enable two-color x-ray pump/x-ray probe experiments. This mirror consists of a Si substrate that is coated with two different types of multilayer systems, Mo/B4C layers with a periodicity of d=3. nm directly on the substrate and Ni/B4C layers with a periodicity of d=11.85 nm on top. Fundamental radiation with photon energies between 3 and 9 keV is reflected by a Ni/B4C multilayer system while the third harmonic (9 keV

Resolving ultrafast heating of dense cryogenic hydrogen.

We report on the dynamics of ultrafast heating in cryogenic hydrogen initiated by a ≲300 fs, 92 eV free electron laser x-ray burst. The rise of the x-ray scattering amplitude from a second x-ray pulse probes the transition from dense cryogenic molecular hydrogen to a nearly uncorrelated plasmalike structure, indicating an electron-ion equilibration time of ∼0.9 ps. The rise time agrees with radiation hydrodynamics simulations based on a conductivity model for partially ionized plasma that is validated by two-temperature density-functional theory.

Reactive scattering of H2 from Cu(100): comparison of dynamics calculations based on the specific reaction parameter approach to density functional theory with experiment.

We present new experimental and theoretical results for reactive scattering of dihydrogen from Cu(100). In the new experiments, the associative desorption of H(2) is studied in a velocity resolved and final rovibrational state selected manner, using time-of-flight techniques in combination with resonance-enhanced multi-photon ionization laser detection. Average desorption energies and rotational quadrupole alignment parameters were obtained in this way for a number of (v = 0, 1) rotational states, v being the vibrational quantum number. Results of quantum dynamics calculations based on a potential energy surface computed with a specific reaction parameter (SRP) density functional, which was derived earlier for dihydrogen interacting with Cu(111), are compared with the results of the new experiments and with the results of previous molecular beam experiments on sticking of H(2) and on rovibrationally elastic and inelastic scattering of H(2) and D(2) from Cu(100). The calculations use the Born-Oppenheimer and static surface approximations. With the functional derived semi-empirically for dihydrogen + Cu(111), a chemically accurate description is obtained of the molecular beam experiments on sticking of H(2) on Cu(100), and a highly accurate description is obtained of rovibrationally elastic and inelastic scattering of D(2) from Cu(100) and of the orientational dependence of the reaction of (v = 1, j = 2 - 4) H(2) on Cu(100). This suggests that a SRP density functional derived for H(2) interacting with a specific low index face of a metal will yield accurate results for H(2) reactively scattering from another low index face of the same metal, and that it may also yield accurate results for H(2) interacting with a defected (e.g., stepped) surface of that same metal, in a system of catalytic interest. However, the description that was obtained of the average desorption energies, of rovibrationally elastic and inelastic scattering of H(2) from Cu(100), and of the orientational dependence of reaction of (v = 0, j = 3 - 5, 8) H(2) on Cu(100) compares less well with the available experiments. More research is needed to establish whether more accurate SRP-density functional theory dynamics results can be obtained for these observables if surface atom motion is added to the dynamical model. The experimentally and theoretically found dependence of the rotational quadrupole alignment parameter on the rotational quantum number provides evidence for rotational enhancement of reaction at low translational energies.

Electronic structure of spatially aligned graphene nanoribbons on Au(788).

We report on a bottom-up approach of the selective and precise growth of subnanometer wide straight and chevron-type armchair nanoribbons (GNRs) on a stepped Au(788) surface using different specific molecular precursors. This process creates spatially well-aligned GNRs, as characterized by STM. High-resolution direct and inverse photoemission spectroscopy of occupied and unoccupied states allows the determination of the energetic position and momentum dispersion of electronic states revealing the existence of band gaps of several electron volts for straight 7-armchair, 13-armchair, and chevron-type GNRs in the electronic structure.

Spin selectivity in electron transmission through self-assembled monolayers of double-stranded DNA.

In electron-transfer processes, spin effects normally are seen either in magnetic materials or in systems containing heavy atoms that facilitate spin-orbit coupling. We report spin-selective transmission of electrons through self-assembled monolayers of double-stranded DNA on gold. By directly measuring the spin of the transmitted electrons with a Mott polarimeter, we found spin polarizations exceeding 60% at room temperature. The spin-polarized photoelectrons were observed even when the photoelectrons were generated with unpolarized light. The observed spin selectivity at room temperature was extremely high as compared with other known spin filters. The spin filtration efficiency depended on the length of the DNA in the monolayer and its organization.

Site specificity in femtosecond laser desorption of neutral H atoms from graphite(0001).

Femtosecond laser excitation and density functional theory reveal site and vibrational state specificity in neutral atomic hydrogen desorption from graphite induced by multiple electronic transitions. Multimodal velocity distributions witness the participation of ortho and para pair states of chemisorbed hydrogen in the desorption process. Very slow velocities of 700 and 400 ms^{-1} for H and D atoms are associated with the desorption out of the highest vibrational state of a barrierless potential.

Desorption of ionic species from ice/graphite by femtosecond XUV free-electron laser pulses.

We report results of laser desorption from water ice surfaces using XUV pulses from the free-electron laser in Hamburg (FLASH). This XUV to soft x-ray FEL provides femtosecond pulses at 20-200 eV photon energy with pulse energies up to 100 µJ. The interaction of this intense soft x-ray radiation with ice (H2O, D2O) adsorbed on highly oriented pyrolytic graphite (HOPG) yields the desorption of various ions, particularly H (+) (D (+) ), O (+) , O2 (+) and others. For H (+) and O (+) ions linear desorption yields are observed, while for O2 (+) a highly nonlinear desorption yield with n = (2.5 ± 0.2) is found. Kinetic energies of 1.8 eV, 559 meV and 390 meV for H (+) , O (+) , and O2 (+) , respectively, account for only a small part of the available excess energy.