Tracking Charge Migration with Frequency-Matched Strobo-Spectroscopy.

We present frequency-matched strobo-spectroscopy (FMSS) of charge migration (CM) in bromobutadiyne, simulated with time-dependent density functional theory. CM + FMSS is a pump-probe scheme that uses a frequency-matched high harmonic generation (HHG)-driving laser as an independent probe step, following the creation of a localized hole on the bromine atom that induces CM dynamics. We show that the delay-dependent harmonic yield tracks the phase of the CM dynamics through its sensitivity to the amount of electron density on the bromine end of the molecule.

Attochemistry Regulation of Charge Migration.

Charge migration (CM) is a coherent attosecond process that involves the movement of localized holes across a molecule. To determine the relationship between a molecule's structure and the CM dynamics it exhibits, we perform systematic studies of para-functionalized bromobenzene molecules (X-CH-R) using real-time time-dependent density functional theory. We initiate valence-electron dynamics by emulating rapid strong-field ionization leading to a localized hole on the bromine atom.

Investigation of Interferences in Carbon Dioxide through Multidimensional Molecular-Frame High-Harmonic Spectroscopy.

We present molecular-frame high-harmonic spectroscopic measurements of the spectral intensity and group delay of carbon dioxide. Using four different driving wavelengths and a range of intensities at each wavelength for high-harmonic generation, we observe a well-characterized minimum in the harmonic emission that exhibits both a wavelength and intensity dependence. Using the intensity dependence at each driving wavelength, we classify the minimum as due to either a structural two-center interference or dynamic multichannel interference, consistent with previous literature.

Methylated ccfDNA from plasma biomarkers of Alzheimer's disease using targeted bisulfite sequencing.

Noninvasive biomarkers such as methylated ccfDNA from plasma could help to support the diagnosis of Alzheimer's disease (AD). A targeted sequencing protocol was developed to identify candidate biomarkers of AD in methylated ccfDNA extracted from plasma. The authors identified differentially methylated CpGs, regions of which were the same as those identified in previous AD studies.

PIntMF: Penalized Integrative Matrix Factorization method for multi-omics data.

Motivation: It is more and more common to perform multi-omics analyses to explore the genome at diverse levels and not only at a single level. Through integrative statistical methods, multi-omics data have the power to reveal new biological processes, potential biomarkers and subgroups in a cohort. Matrix factorization (MF) is an unsupervised statistical method that allows a clustering of individuals, but also reveals relevant omics variables from the various blocks.

Molecular Modes of Attosecond Charge Migration.

First-principles calculations are employed to elucidate the modes of attosecond charge migration (CM) in halogenated hydrocarbon chains. We use constrained density functional theory (DFT) to emulate the creation of a localized hole on the halogen and follow the subsequent dynamics via time-dependent DFT. We find low-frequency CM modes (∼1  eV) that propagate across the molecule and study their dependence on length, bond order, and halogenation.

Comparison of commercially available whole-genome sequencing kits for variant detection in circulating cell-free DNA.

Circulating cell-free DNA (ccfDNA) has great potential for non-invasive diagnosis, prognosis and monitoring treatment of disease. However, a sensitive and specific whole-genome sequencing (WGS) method is required to identify novel genetic variations (i.e.

Enhanced--COLD-PCR for the Sensitive Detection of Rare DNA Methylation Patterns in Liquid Biopsies.

In the context of precision medicine, the identification of novel biomarkers for the diagnosis of disease, prognosis, predicting treatment outcome and monitoring of treatment success is of great importance. The analysis of methylated circulating-cell free DNA provides great promise to complement or replace genetic markers for these applications, but is associated with substantial challenges. This is particularly true for the detection of rare methylated DNA molecules in a limited amount of sample such as tumor released hypermethylated molecules in the background of DNA fragments from normal cells, especially lymphocytes.

Clustering and variable selection evaluation of 13 unsupervised methods for multi-omics data integration.

Recent advances in NGS sequencing, microarrays and mass spectrometry for omics data production have enabled the generation and collection of different modalities of high-dimensional molecular data. The integration of multiple omics datasets is a statistical challenge, due to the limited number of individuals, the high number of variables and the heterogeneity of the datasets to integrate. Recently, a lot of tools have been developed to solve the problem of integrating omics data including canonical correlation analysis, matrix factorization and SM.

Angle-dependent strong-field ionization of halomethanes.

We study, experimentally and theoretically, the ionization probability of singly halogenated methane molecules, CHCl and CHBr, in intense linearly polarized 800 nm laser pulses as a function of the angle between the molecular axis and the laser polarization. Experimentally, the molecules are exposed to two laser pulses with a relative time delay. The first, weaker pulse induces a nuclear rotational wave packet within the molecules, which are then ionized by the second, stronger pulse.

High-harmonic spectroscopy of transient two-center interference calculated with time-dependent density-functional theory.

We demonstrate high-harmonic spectroscopy in many-electron molecules using time-dependent density-functional theory. We show that a weak attosecond-pulse-train ionization seed that is properly synchronized with the strong driving mid-infrared laser field can produce experimentally relevant high-harmonic generation (HHG) signals, from which we extract both the spectral amplitude and the target-specific phase (group delay). We also show that further processing of the HHG signal can be used to achieve molecular-frame resolution, i.

Probing the interplay between geometric and electronic-structure features via high-harmonic spectroscopy.

We present molecular-frame measurements of the recombination dipole matrix element (RDME) in CO, NO, and carbonyl sulfide (OCS) molecules using high-harmonic spectroscopy. Both the amplitudes and phases of the RDMEs exhibit clear imprints of a two-center interference minimum, which moves in energy with the molecular alignment angle relative to the laser polarization. We find that whereas the angle dependence of this minimum is consistent with the molecular geometry in CO and NO, it behaves very differently in OCS; in particular, the phase shift which accompanies the two-center minimum changes sign for different alignment angles.

Enrichment of methylated molecules using enhanced-ice-co-amplification at lower denaturation temperature-PCR (E-ice-COLD-PCR) for the sensitive detection of disease-related hypermethylation.

Aim: The detection of specific DNA methylation patterns bears great promise as biomarker for personalized management of cancer patients. Co-amplification at lower denaturation temperature-PCR (COLD-PCR) assays are sensitive methods, but have previously only been able to analyze loss of DNA methylation.

Materials & Methods: Enhanced (E)-ice-COLD-PCR reactions starting from 2 ng of bisulfite-converted DNA were developed to analyze methylation patterns in two promoters with locked nucleic acid (LNA) probes blocking amplification of unmethylated CpGs.

Whole-Genome Bisulfite Sequencing for the Analysis of Genome-Wide DNA Methylation and Hydroxymethylation Patterns at Single-Nucleotide Resolution.

The analysis of genome-wide epigenomic alterations including DNA methylation and hydroxymethylation has become a subject of intensive research for many biological and disease-associated investigations. Whole-genome bisulfite sequencing (WGBS) using next-generation sequencing technologies is currently considered as the gold standard for a comprehensive and quantitative analysis of DNA methylation throughout the genome. However, bisulfite conversion does not allow distinguishing between cytosine methylation and hydroxymethylation requiring an additional chemical or enzymatic step to identify hydroxymethylated cytosines.

Search for Neutrinoless Quadruple-β Decay of ^{150}Nd with the NEMO-3 Detector.

We report the results of a first experimental search for lepton number violation by four units in the neutrinoless quadruple-β decay of ^{150}Nd using a total exposure of 0.19 kg yr recorded with the NEMO-3 detector at the Modane Underground Laboratory. We find no evidence of this decay and set lower limits on the half-life in the range T_{1/2}>(1.

Whole-Genome Bisulfite Sequencing Using the Ovation® Ultralow Methyl-Seq Protocol.

The analysis of genome-wide epigenomic alterations including DNA methylation has become a subject of intensive research for many complex diseases. Whole-genome bisulfite sequencing (WGBS) using next-generation sequencing technologies can be considered the gold standard for a comprehensive and quantitative analysis of cytosine methylation throughout the genome. Several approaches including tagmentation- and post bisulfite adaptor tagging (PBAT)-based WGBS have been devised.

Attosecond Charge Migration with TDDFT: Accurate Dynamics from a Well-Defined Initial State.

We investigate the ability of time-dependent density functional theory (TDDFT) to capture attosecond valence electron dynamics resulting from sudden X-ray ionization of a core electron. In this special case the initial state can be constructed unambiguously, allowing for a simple test of the accuracy of the dynamics. The response following nitrogen K-edge ionization in nitrosobenzene shows excellent agreement with fourth-order algebraic diagrammatic construction (ADC(4)) results, suggesting that a properly chosen initial state allows TDDFT to adequately capture attosecond charge migration.

The BiPo-3 detector.

The BiPo-3 detector is a low radioactive detector dedicated to measuring ultra-low natural contaminations of Tl and Bi in thin materials, initially developed to measure the radiopurity of the double β decay source foils of the SuperNEMO experiment at the μBq/kg level. The BiPo-3 technique consists in installing the foil of interest between two thin ultra-radiopure scintillators coupled to low radioactive photomultipliers. The design and performances of the detector are presented.

COLD-PCR Technologies in the Area of Personalized Medicine: Methodology and Applications.

Somatic mutations bear great promise for use as biomarkers for personalized medicine, but are often present only in low abundance in biological material and are therefore difficult to detect. Many assays for mutation analysis in cancer-related genes (hotspots) have been developed to improve diagnosis, prognosis, prediction of drug resistance, and monitoring of the response to treatment. Two major approaches have been developed: mutation-specific amplification methods and methods that enrich and detect mutations without prior knowledge on the exact location and identity of the mutation.

Comparison of the quantification of KRAS mutations by digital PCR and E-ice-COLD-PCR in circulating-cell-free DNA from metastatic colorectal cancer patients.

Circulating cell-free DNA (ccfDNA) bears great promise as biomarker for personalized medicine, but ccfDNA is present only at low levels in the plasma or serum of cancer patients. E-ice-COLD-PCR is a recently developed enrichment method to detect and identify mutations present at low-abundance in clinical samples. However, recent studies have shown the importance to accurately quantify low-abundance mutations as clinically important decisions will depend on certain mutation thresholds.

Angle-dependent strong-field molecular ionization rates with tuned range-separated time-dependent density functional theory.

Strong-field ionization and the resulting electronic dynamics are important for a range of processes such as high harmonic generation, photodamage, charge resonance enhanced ionization, and ionization-triggered charge migration. Modeling ionization dynamics in molecular systems from first-principles can be challenging due to the large spatial extent of the wavefunction which stresses the accuracy of basis sets, and the intense fields which require non-perturbative time-dependent electronic structure methods. In this paper, we develop a time-dependent density functional theory approach which uses a Gaussian-type orbital (GTO) basis set to capture strong-field ionization rates and dynamics in atoms and small molecules.

Recurrent NRAS mutations in pulmonary Langerhans cell histiocytosis.

The mitogen-activated protein kinase (MAPK) pathway is constantly activated in Langerhans cell histiocytosis (LCH). Mutations of the downstream kinases BRAF and MAP2K1 mediate this activation in a subset of LCH lesions. In this study, we attempted to identify other mutations which may explain the MAPK activation in nonmutated BRAF and MAP2K1 LCH lesions.

New technologies for DNA analysis--a review of the READNA Project.

The REvolutionary Approaches and Devices for Nucleic Acid analysis (READNA) project received funding from the European Commission for 41/2 years. The objectives of the project revolved around technological developments in nucleic acid analysis. The project partners have discovered, created and developed a huge body of insights into nucleic acid analysis, ranging from improvements and implementation of current technologies to the most promising sequencing technologies that constitute a 3(rd) and 4(th) generation of sequencing methods with nanopores and in situ sequencing, respectively.