2D Fourier Transform Spectroscopy Setup and Ultrafast Dynamics of Porphyrins

The first section of the thesis discusses the development and implementation of a two dimensional Fourier transform spectroscopy setup, that permits the recording of electronic 2D spectra in the visible regime. A hollow core fiber was used to generate broadband pulses, compressed down to sub-15 fs, allowing high spectral and temporal resolution measurements. The design relies on basic optical components (no diffractive optics or liquid crystal display) with pair-wise manipulation of the beams, which lead to reduction of the signal modulation to the difference between the transition frequency and the laser frequency. The required timing precision as well as the mechanical stability is reduced due to the used geometry. For testing the integrity of the setup, stability measurements over several hours are presented as well as measurements on rhodamine 101 dye and Pentacene thin films. The photophysics of porphyrins has been widely investigated because of their importance in biology and their relevance in a wide range of applications such as light harvesting applications, molecular electronics, and gas sensors. The energy of the photon absorbed by these systems is converted into electronic and vibrational energy, eventually triggering photochemical processes such as charge transfer, energy transfer, and bond breaking. Deep understanding of the specific early relaxation mechanism and nuclear wavepacket motion occurring in this family of molecules is therefore fundamental for further comprehension of the role of porphyrins in nature and future application using porphyrin-based molecular devices. In the third chapter we discuss the impulsive heating of free-base porphyrins and the electronic and vibrational relaxation dynamics upon photo-excitation. Transient absorption and fluoresce up-conversion spectroscopy techniques with high temporal resolution were utilized to investigate the relaxation processes, and the heating/cooling dynamics. Wavepacket dynamics of free-base porphyrins are discussed in the fourth chapter, where the phase and spectral intensity of the vibrational modes were extracted using Fourier transform spectroscopy. Based on the mode phase and spectral dependent intensity each mode is assigned to being in-plane or out-of-plane mode and to whether it exists in the excited or ground state. In the last chapter, excited state dynamics of triply fused diporphyrins in toluene is investigated using transient absorption spectroscopy. These highly Ï-conjugated organic systems are receiving considerable attention because they incorporate ease of synthesis with tunable chemical structure that can be tailored for various applications, such as molecular wires, mimic light harvesting complexes, and saturable absorbers dyes. These porphyrin tapes can chelate different metal centers, changing their optical and electronic properties. In this chapter a comparison between free-base, Zn, and Pt based triply fused diporphyrins is done in order to understand the role of the metal in the relaxation dynamics of these systems. By further comparing these systems with earlier studies, the peripheral substituents effects are also discussed. In the end, we show that the high ISC yield, long triplet lifetime, and high cross-section of Pt-3DP makes it a perfect candidate to be used as NIR sensitizer for photochemical up-conversion via triplet-triplet annihilation

Ultrafast Single-Particle Imaging with Intense X-Ray Pulses

Ultrafast single-particle imaging with intense x-ray pulses from free-electron laser sources provides a new approach for visualizing structure and dynamics on the nanoscale. After a short introduction to the novel free-electron laser sources and methods, we highlight selected applications and discuss how ultrafast imaging flourishes from method development to early applications in physics and biology to opportunities for chemical sciences

Enhanced ultrafast X-ray diffraction by transient resonances

Diffraction-before-destruction imaging with single ultrashort X-ray pulses has the potential to visualise non-equilibrium processes, such as chemical reactions, at the nanoscale with sub-femtosecond resolution in the native environment without the need of crystallization. Here, a nanospecimen partially diffracts a single X-ray flash before sample damage occurs. The structural information of the sample can be reconstructed from the coherent X-ray interference image. State-of-art spatial resolution of such snapshots from individual heavy element nanoparticles is limited to a few nanometers. Further improvement of spatial resolution requires higher image brightness which is ultimately limited by bleaching effects of the sample. We compared snapshots from individual 100 nm Xe nanoparticles as a function of the X-ray pulse duration and incoming X-ray intensity in the vicinity of the Xe M-shell resonance. Surprisingly, images recorded with few femtosecond and sub-femtosecond pulses are up to 10 times brighter than the static linear model predicts. Our Monte-Carlo simulation and statistical analysis of the entire data set confirms these findings and attributes the effect to transient resonances. Our simulation suggests that ultrafast form factor changes during the exposure can increase the brightness of X-ray images by several orders of magnitude. Our study guides the way towards imaging with unprecedented combination of spatial and temporal resolution at the nanoscale

Quantifying Photoinduced Polaronic Distortions in Inorganic Lead Halide Perovskites Nanocrystals

The development of next generation perovskite-based optoelectronic devices relies critically on the understanding of the interaction between charge carriers and the polar lattice in out-of-equilibrium conditions. While it has become increasingly evident for CsPbBr3 perovskites that the Pb-Br framework flexibility plays a key role in their light-activated functionality, the corresponding local structural rearrangement has not yet been unambiguously identified. In this work, we demonstrate that the photoinduced lattice changes in the system are due to a specific polaronic distortion, associated with the activation of a longitudinal optical phonon mode at 18 meV by electron-phonon coupling, and we quantify the associated structural changes with atomic-level precision. Key to this achievement is the combination of time-resolved and temperature-dependent studies at Br K-edge and Pb L3-edge X-ray absorption with refined ab-initio simulations, which fully account for the screened core-hole final state effects on the X-ray absorption spectra. From the temporal kinetics, we show that carrier recombination reversibly unlocks the structural deformation at both Br and Pb sites. The comparison with the temperature-dependent XAS results rules out thermal effects as the primary source of distortion of the Pb-Br bonding motif during photoexcitation. Our work provides a comprehensive description of the CsPbBr3 perovskites photophysics, offering novel insights on the light-induced response of the system and its exceptional optoelectronic properties.Comment: Main: 27 pages, 4 figures SI: 16 pages, 8 figure

Antimicrobial resistance among migrants in Europe: a systematic review and meta-analysis

BACKGROUND: Rates of antimicrobial resistance (AMR) are rising globally and there is concern that increased migration is contributing to the burden of antibiotic resistance in Europe. However, the effect of migration on the burden of AMR in Europe has not yet been comprehensively examined. Therefore, we did a systematic review and meta-analysis to identify and synthesise data for AMR carriage or infection in migrants to Europe to examine differences in patterns of AMR across migrant groups and in different settings. METHODS: For this systematic review and meta-analysis, we searched MEDLINE, Embase, PubMed, and Scopus with no language restrictions from Jan 1, 2000, to Jan 18, 2017, for primary data from observational studies reporting antibacterial resistance in common bacterial pathogens among migrants to 21 European Union-15 and European Economic Area countries. To be eligible for inclusion, studies had to report data on carriage or infection with laboratory-confirmed antibiotic-resistant organisms in migrant populations. We extracted data from eligible studies and assessed quality using piloted, standardised forms. We did not examine drug resistance in tuberculosis and excluded articles solely reporting on this parameter. We also excluded articles in which migrant status was determined by ethnicity, country of birth of participants' parents, or was not defined, and articles in which data were not disaggregated by migrant status. Outcomes were carriage of or infection with antibiotic-resistant organisms. We used random-effects models to calculate the pooled prevalence of each outcome. The study protocol is registered with PROSPERO, number CRD42016043681. FINDINGS: We identified 2274 articles, of which 23 observational studies reporting on antibiotic resistance in 2319 migrants were included. The pooled prevalence of any AMR carriage or AMR infection in migrants was 25·4% (95% CI 19·1-31·8; I2 =98%), including meticillin-resistant Staphylococcus aureus (7·8%, 4·8-10·7; I2 =92%) and antibiotic-resistant Gram-negative bacteria (27·2%, 17·6-36·8; I2 =94%). The pooled prevalence of any AMR carriage or infection was higher in refugees and asylum seekers (33·0%, 18·3-47·6; I2 =98%) than in other migrant groups (6·6%, 1·8-11·3; I2 =92%). The pooled prevalence of antibiotic-resistant organisms was slightly higher in high-migrant community settings (33·1%, 11·1-55·1; I2 =96%) than in migrants in hospitals (24·3%, 16·1-32·6; I2 =98%). We did not find evidence of high rates of transmission of AMR from migrant to host populations. INTERPRETATION: Migrants are exposed to conditions favouring the emergence of drug resistance during transit and in host countries in Europe. Increased antibiotic resistance among refugees and asylum seekers and in high-migrant community settings (such as refugee camps and detention facilities) highlights the need for improved living conditions, access to health care, and initiatives to facilitate detection of and appropriate high-quality treatment for antibiotic-resistant infections during transit and in host countries. Protocols for the prevention and control of infection and for antibiotic surveillance need to be integrated in all aspects of health care, which should be accessible for all migrant groups, and should target determinants of AMR before, during, and after migration. FUNDING: UK National Institute for Health Research Imperial Biomedical Research Centre, Imperial College Healthcare Charity, the Wellcome Trust, and UK National Institute for Health Research Health Protection Research Unit in Healthcare-associated Infections and Antimictobial Resistance at Imperial College London

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment