Ultrafast spatio-temporal dynamics of terahertz generation by ionizing two-color femtosecond pulses in gases

We present a combined theoretical and experimental study of spatio-temporal propagation effects in terahertz (THz) generation in gases using two-color ionizing laser pulses. The observed strong broadening of the THz spectra with increasing gas pressure reveals the prominent role of spatio-temporal reshaping and of a plasma-induced blue-shift of the pump pulses in the generation process. Results obtained from (3+1)-dimensional simulations are in good agreement with experimental findings and clarify the mechanisms responsible for THz emission

Quantum-mechanical wavepacket transport in quantum cascade laser structures

We present a viewpoint of the transport process in quantum cascade laser structures in which spatial transport of charge through the structure is a property of coherent quantum-mechanical wavefunctions. In contrast, scattering processes redistribute particles in energy and momentum but do not directly cause spatial motion of charge.Comment: 6 pages, 5 figures included in tex, to appear in Physical Review

Vibronic excitations of large molecules in solution studied by two-color pump–probe experiments on the 20 fs time scale

The ultrafast vibronic response of organic dye molecules in solution is studied in pump–probe experiments with 30 fs excitation pulses resonant to S0–Sn transitions. The molecular dynamics is probed either by pulses at the same spectral position or by 20 fs pulses overlapping with both the S0–S1 absorption and emission bands. Three contributions on distinctly different time scales are observed in the temporally and spectrally resolved two-color measurements. In the regime below 50 fs, a strong coherent coupling of the S0–Sn and the S0–S1 transitions occurs that is due to coherent vibrational motions in the electronic ground state. This signal is superimposed on the fast bleaching of the electronic ground state, resulting in a steplike increase of transmission. In the range of the S0–S1 emission band, one finds a subsequent picosecond rise of transmission that is due to stimulated emission from vibronic S1 states. The data demonstrate that the relaxation of Sn states directly populated by the pump pulses is much faster than the buildup of stimulated emission. This gives insight into different steps of intramolecular vibronic redistribution and is compared to the Sn–S1 relaxation in other molecules

Terahertz radiative coupling and damping in multilayer graphene

The nonlinear interaction between intense terahertz (THz) pulses and epitaxial multilayer graphene is studied by field-resolved THz pump-probe spectroscopy. THz excitation results in a transient induced absorption with decay times of a few picoseconds, much faster than carrier recombination in single graphene layers. The decay times increase with decreasing temperature and increasing amplitude of the excitation. This behaviour originates from the predominant coupling of electrons to the electromagnetic field via the very strong interband dipole moment while scattering processes with phonons and impurities play a minor role. The nonlinear response at field amplitudes above 1 kV cm-1 is in the carrier-wave Rabi flopping regime with a pronounced coupling of the graphene layers via the radiation field. Theoretical calculations account for the experimental results

Inherently Interpretable Multi-Label Classification Using Class-Specific Counterfactuals

Interpretability is essential for machine learning algorithms in high-stakes application fields such as medical image analysis. However, high-performing black-box neural networks do not provide explanations for their predictions, which can lead to mistrust and suboptimal human-ML collaboration. Post-hoc explanation techniques, which are widely used in practice, have been shown to suffer from severe conceptual problems. Furthermore, as we show in this paper, current explanation techniques do not perform adequately in the multi-label scenario, in which multiple medical findings may co-occur in a single image. We propose Attri-Net, an inherently interpretable model for multi-label classification. Attri-Net is a powerful classifier that provides transparent, trustworthy, and human-understandable explanations. The model first generates class-specific attribution maps based on counterfactuals to identify which image regions correspond to certain medical findings. Then a simple logistic regression classifier is used to make predictions based solely on these attribution maps. We compare Attri-Net to five post-hoc explanation techniques and one inherently interpretable classifier on three chest X-ray datasets. We find that Attri-Net produces high-quality multi-label explanations consistent with clinical knowledge and has comparable classification performance to state-of-the-art classification models.Comment: Accepted to MIDL 202

Ultrafast modulation of electronic structure by coherent phonon excitations

Femtosecond x-ray absorption spectroscopy with a laser-driven high-harmonic source is used to map ultrafast changes of x-ray absorption by femtometer- scale coherent phonon displacements. In LiBH4, displacements along an Ag phonon mode at 10 THz are induced by impulsive Raman excitation and give rise to oscillatory changes of x-ray absorption at the Li K edge. Electron density maps from femtosecond x-ray diffraction data show that the electric field of the pump pulse induces a charge transfer from the BH4− to neighboring Li+ ions, resulting in a differential Coulomb force that drives lattice vibrations in this virtual transition state

Transition from ballistic to drift motion in high-field transport in GaAs

With strong THz pulses, we measure ultrafast transport of electrons, holes, and an electron-hole plasma in GaAs. The transition from ballistic to drift-like transport is strongly influenced by electron-hole scattering

Frameshift mutations in coding repeats of protein tyrosine phosphatase genes in colorectal tumors with microsatellite instability

<p>Abstract</p> <p>Background</p> <p>Protein tyrosine phosphatases (PTPs) like their antagonizing protein tyrosine kinases are key regulators of signal transduction thereby assuring normal control of cellular growth and differentiation. Increasing evidence suggests that mutations in PTP genes are associated with human malignancies. For example, mutational analysis of the tyrosine phosphatase (PTP) gene superfamily uncovered genetic alterations in about 26% of colorectal tumors. Since in these studies tumors have not been stratified according to genetic instability status we hypothesized that colorectal tumors characterized by high-level of microsatellite instability (MSI-H) might show an increased frequency of frameshift mutations in those PTP genes that harbor long mononucleotide repeats in their coding region (cMNR).</p> <p>Results</p> <p>Using bioinformatic analysis we identified 16 PTP candidate genes with long cMNRs that were examined for genetic alterations in 19 MSI-H colon cell lines, 54 MSI-H colorectal cancers, and 17 MSI-H colorectal adenomas. Frameshift mutations were identified only in 6 PTP genes, of which PTPN21 show the highest mutation frequency at all in MSI-H tumors (17%).</p> <p>Conclusion</p> <p>Although about 32% of MSI-H tumors showed at least one affected PTP gene, and cMNR mutation rates in PTPN21, PTPRS, and PTPN5 are higher than the mean mutation frequency of MNRs of the same length, mutations within PTP genes do not seem to play a common role in MSI tumorigenesis, since no cMNR mutation frequency reached statistical significance and therefore, failed prediction as a Positive Selective Target Gene.</p

SelTarbase, a database of human mononucleotide-microsatellite mutations and their potential impact to tumorigenesis and immunology

About 15% of human colorectal cancers and, at varying degrees, other tumor entities as well as nearly all tumors related to Lynch syndrome are hallmarked by microsatellite instability (MSI) as a result of a defective mismatch repair system. The functional impact of resulting mutations depends on their genomic localization. Alterations within coding mononucleotide repeat tracts (MNRs) can lead to protein truncation and formation of neopeptides, whereas alterations within untranslated MNRs can alter transcription level or transcript stability. These mutations may provide selective advantage or disadvantage to affected cells. They may further concern the biology of microsatellite unstable cells, e.g. by generating immunogenic peptides induced by frameshifts mutations. The Selective Targets database (http://www.seltarbase.org) is a curated database of a growing number of public MNR mutation data in microsatellite unstable human tumors. Regression calculations for various MSI–H tumor entities indicating statistically deviant mutation frequencies predict TGFBR2, BAX, ACVR2A and others that are shown or highly suspected to be involved in MSI tumorigenesis. Many useful tools for further analyzing genomic DNA, derived wild-type and mutated cDNAs and peptides are integrated. A comprehensive database of all human coding, untranslated, non-coding RNA- and intronic MNRs (MNR_ensembl) is also included. Herewith, SelTarbase presents as a plenty instrument for MSI-carcinogenesis-related research, diagnostics and therapy