HPLC-Detector Based on Hadamard-Transform Fluorescence Excitation-Emission-Matrix Spectroscopy.

We present a new rapid-acquisition HPLC detector based on a Hadamard-transform (HT) excitation-emission-matrix (EEM) fluorescence spectrometer allowing the acquisition of two-dimensional spectra at a rate faster than 6 spectra per second (<150 ms per spectrum). The instrument uses discrete ultraviolet light emitting diode (UV LED) light sources which are multiplexed using patterns derived from a Hadamard-matrix and affords faster spectral acquisition compared to conventional sequentially scanning EEM spectrometers. This new programmable light source was combined with a commercial fluorescence spectrometer and integrated as a detector into an HPLC system. We characterize the HT-EEM spectrometer by rapidly separating and detecting a mixture of five different coumarin dyes, with all five analytes eluting in under 2 min. A parallel factor analysis (PARAFAC) algorithm was able to readily separate and identify all coumarin fluorophores without any prior knowledge of the system, even decomposing two coeluting analytes into two distinct PARAFAC components. The HT-EEM spectrometer provides a novel and versatile detection technique suited for rapid online analysis and quantification of analytes in separation methods such as HPLC.

Identifying high-confidence capture Hi-C interactions using CHiCANE.

The ability to identify regulatory interactions that mediate gene expression changes through distal elements, such as risk loci, is transforming our understanding of how genomes are spatially organized and regulated. Capture Hi-C (CHi-C) is a powerful tool to delineate such regulatory interactions. However, primary analysis and downstream interpretation of CHi-C profiles remains challenging and relies on disparate tools with ad-hoc input/output formats and specific assumptions for statistical modeling. Here we present a data processing and interaction calling toolkit (CHiCANE), specialized for the analysis and meaningful interpretation of CHi-C assays. In this protocol, we demonstrate applications of CHiCANE to region capture Hi-C (rCHi-C) and promoter capture Hi-C (pCHi-C) libraries, followed by quality assessment of interaction peaks, as well as downstream analysis specific to rCHi-C and pCHi-C to aid functional interpretation. For a typical rCHi-C/pCHi-C dataset this protocol takes up to 3 d for users with a moderate understanding of R programming and statistical concepts, although this is dependent on dataset size and compute power available. CHiCANE is freely available at https://cran.r-project.org/web/packages/chicane .

Multiresponsive Tetradentate Phosphorescent Metal Complexes as Highly Sensitive and Robust Luminescent Oxygen Sensors: Pd(II) Versus Pt(II) and 1,2,3-Triazolyl Versus 1,2,4-Triazolyl.

Two Pd(II) complexes based on tetradentate chelate ligands with either a 1,2,4-triazolyl (Pd1) or 1,2,3-triazolyl (Pd2) unit were synthesized, and their structure-property relationships were studied. Both Pd1 and Pd2 are rare bright deep blue Pd(II) phosphors with contrasting properties. Pd1 displays stimuli-responsive luminescence in response to UV irradiation, concentration, or temperature change, which is ascribed to the facile switching of monomer to excimer emission. In contrast, a similar stimuli-responsive luminescence was not observed for Pd2. Crystal structures and time-dependent density functional theory computational studies established that the excimer formation of Pd1 is caused by electronically favored intermolecular π-π interactions and less steric protection of the Pd core because of the position of its alkyl chains, compared to Pd2. In solution, the excimer emission of Pd1 shows a much greater sensitivity toward oxygen than the monomer emission with a very large Stern-Volmer constant ( Ksv) that is more than twice that of the monomer emission. Both Pd(II) complexes are found to be outstanding oxygen sensors in ethyl cellulose films with superior sensitivity ( Ksvapp = 0.228-0.346 Torr-1) over their Pt(II) equivalents ( Ksvapp = 0.00674-0.0110 Torr-1), owing to their long phosphorescence decay lifetimes. Furthermore, Pd1 shows an excellent photostability, compared to the Pt(II) analogue, making it one of the best and highly robust oxygen sensors based on cyclometalated metal complexes.

Impact of Ferrocene Substitution on the Electronic Properties of BODIPY Derivatives and Analogues.

Bis(ferrocenyl)-functionalized boron dipyrromethene (BODIPY) compound 1 featuring direct Fc-B bonds was obtained via a "prefunctionalization strategy". UV-vis absorption, electrochemical, and transient absorption experiments were performed on compound 1 and its analogues to examine the impact of ferrocenyl substitution on the electronic properties. The ferrocene units were found to have little impact on the absorption spectrum of the BODIPY unit but significantly change the excited-state dynamics.

Spiro-BODIPYs with a Diaryl Chelate: Impact on Aggregation and Luminescence.

Spiro-BODIPYs with a diaryl chelate unit have been found to form J-aggregates in methanol-water solvent mixture and brightly emissive in the solid state. The diaryl chelate unit has a significant impact on J-aggregates and fluorescence of BODIPYs. Crystal structural analysis reveals that the spiro-structures facilitate J-stacking in the solid state.

Towards real-time photon Monte Carlo dose calculation in the cloud.

Near real-time application of Monte Carlo (MC) dose calculation in clinic and research is hindered by the long computational runtimes of established software. Currently, fast MC software solutions are available utilising accelerators such as graphical processing units (GPUs) or clusters based on central processing units (CPUs). Both platforms are expensive in terms of purchase costs and maintenance and, in case of the GPU, provide only limited scalability. In this work we propose a cloud-based MC solution, which offers high scalability of accurate photon dose calculations. The MC simulations run on a private virtual supercomputer that is formed in the cloud. Computational resources can be provisioned dynamically at low cost without upfront investment in expensive hardware. A client-server software solution has been developed which controls the simulations and transports data to and from the cloud efficiently and securely. The client application integrates seamlessly into a treatment planning system. It runs the MC simulation workflow automatically and securely exchanges simulation data with the server side application that controls the virtual supercomputer. Advanced encryption standards were used to add an additional security layer, which encrypts and decrypts patient data on-the-fly at the processor register level. We could show that our cloud-based MC framework enables near real-time dose computation. It delivers excellent linear scaling for high-resolution datasets with absolute runtimes of 1.1 seconds to 10.9 seconds for simulating a clinical prostate and liver case up to 1% statistical uncertainty. The computation runtimes include the transportation of data to and from the cloud as well as process scheduling and synchronisation overhead. Cloud-based MC simulations offer a fast, affordable and easily accessible alternative for near real-time accurate dose calculations to currently used GPU or cluster solutions.

Variational calculation of highly excited rovibrational energy levels of H2O2.

Results are presented for highly accurate ab initio variational calculation of the rotation-vibration energy levels of H2O2 in its electronic ground state. These results use a recently computed potential energy surface and the variational nuclear-motion programs WARV4, which uses an exact kinetic energy operator, and TROVE, which uses a numerical expansion for the kinetic energy. The TROVE calculations are performed for levels with high values of rotational excitation, J up to 35. The purely ab initio calculations of the rovibrational energy levels reproduce the observed levels with a standard deviation of about 1 cm(-1), similar to that of the J = 0 calculation, because the discrepancy between theory and experiment for rotational energies within a given vibrational state is substantially determined by the error in the vibrational band origin. Minor adjustments are made to the ab initio equilibrium geometry and to the height of the torsional barrier. Using these and correcting the band origins using the error in J = 0 states lowers the standard deviation of the observed-calculated energies to only 0.002 cm(-1) for levels up to J = 10 and 0.02 cm(-1) for all experimentally known energy levels, which extend up to J = 35.

Fiber Bragg grating photoacoustic detector for liquid chromatography.

Fiber Bragg Gratings (FBGs) are known to be sensitive acoustic transducers and have previously been used for the photoacoustic detection of small solid samples. Here, we demonstrate the use of an FBG as an on-line detector for liquid chromatography. The FBG was inserted into a silica capillary and the photoacoustic response from the effluent was generated by a 10 ns pulsed laser. The acoustic pulse was quantified by the FBG through a characteristic change in the reflection spectrum. Good repeatability and linear response were obtained over three orders of magnitude (R(2) > 0.99), and the limit of detection of Coumarin 440 was determined to be 5 microM. The technique was successfully coupled to high performance liquid chromatography and applied to on-line analysis of a three-compound solution. Photoacoustic detection in liquid chromatography using FBGs is a label-free method, which can be applied to the detection of any chromogenic compound irrespective of its fluorogenic properties. It is a simple, inexpensive, and inherently micron-sized technique, insensitive to electromagnetic interference.

Calculating energy levels of isomerizing tetra-atomic molecules. II. The vibrational states of acetylene and vinylidene.

A general, full-dimensional computational method for the accurate calculation of rotationally and vibrationally excited states of tetra-atomic molecules is further developed. The resulting computer program may be run in serial and parallel modes and is particularly appropriate for molecules executing wide-amplitude motions and isomerizations. An application to the isomerizing acetylene/vinylidene system is presented. Large-scale calculations using a coordinate system based on orthogonal satellite vectors have been performed in six dimensions and vibrational term values and wave functions for acetylene and vinylidene states up to approximately 23 000 cm(-1) above the potential minimum have been determined. This has permitted the characterization of acetylene and vinylidene states at and above the isomerization barrier. These calculations employ more extensive vibrational basis sets and hence consider a much higher density of states than in any variational calculations reported hitherto for this system. Comparison of the calculated density of states with that determined empirically suggests that our calculations are the most realistic achieved for this system to date. Indeed more states have been converged than in any previous study of this system. Calculations on lower lying excited states of acetylene based on HC-CH diatom-diatom coordinates give nearly identical results to those based on orthogonal satellite vectors. Comparisons are also made with calculations based on HH-CC diatom-diatom coordinates.

Kinetics of mixed function oxygenase induction and retene excretion in retene-exposed rainbow trout (Oncorhynchus mykiss).

The polycyclic aromatic hydrocarbon 7-isopropyl-1-methylphenanthrene (retene) induces mixed function oxygenase (MFO) activity of fish. Bile levels of retene and its metabolite(s) were measured in relation to exposure time, exposure concentration, and induction of MFO activity. Synchronous fluorescence spectrometry provided a rapid means of measuring the amount of retene present in the bile of exposed fish, whereas conventional fluorescence spectrometry was used to quantify the amount of retene metabolites. Based on bile analysis, increased retene exposure resulted in an increased uptake of retene and a curvilinear increase in hepatic MFO activity. Retene was present in the bile within 6 h of initial exposure. However, retene metabolite(s) only appeared in the bile after MFO induction had occurred, 12 h after exposure had commenced, suggesting that MFO activity is required for metabolism. Transfer of fish to clean water after 48 h of exposure resulted in a rapid decrease in the presence of retene and its metabolite(s) in the bile, with a calculated half-life of about 14 h. In vitro additions of retene directly to the ethoxyresorufin O-deethylase assay demonstrated that retene is capable of acting as a competitive inhibitor. Thus, retene contamination of postmitochondrial supernatant (S9 fraction) could result in false-negative results in the MFO assay. The MFO activity in extrahepatic tissues (gills, heart, and kidney) was not significantly induced with retene exposure. Thus, the major site of retene metabolism seems to be in the liver. These results confirm that retene is rapidly taken up, metabolized, and excreted by rainbow trout, and that retene metabolism and excretion are linked to hepatic MFO induction.