Matrix Effects of Urine Marker Substances in LC-MS/MS Analysis of Drug of Abuse.

BACKGROUND: Analysis of drug abuse is frequently performed using high-performance liquid chromatography with an MS/MS detector and electrospray ionization. In this context, matrix effects, like signal reduction by ion suppression of individual analytes, play an important role. In this study, the authors evaluated the matrix effect caused by polyethylene glycol (PEG) with chain lengths ranging from 6 to 12 repeating units in drug analysis by LC-MS/MS. Selected chain lengths were used in the Ruma urine marker system. METHODS AND RESULTS: Amphetamines, opiates, opioids, antidepressants, psychotics, benzodiazepines, z-substances, and individual drugs, including THCCOOH, cocaine, LSD, and some of their metabolites were investigated. The matrix effect was investigated at PEG concentrations of 500 mcg/mL and 20 mcg/mL. The effect of each PEG molecule was determined. Furthermore, the effects of different common sample preparations on the PEG matrix effects were evaluated. There was a strong correlation between the retention time of PEG and the drug that was ion-suppressed by PEG. The matrix effect decreased to the point where it was within an acceptable range at the lower PEG concentrations investigated in this study. CONCLUSIONS: Matrix effects were observed for drugs with approximately the same retention times as the individual PEGs. The influence of the different workup methods was not as clear, which may be because of the similar solubilities of the PEGs and some analytes. At low PEG concentrations, the matrix effect was always below 60%, except for nortilidine. All the drugs were detectable. The effect on quantification was less than 15% for substances with deuterated analytes as internal standards and less than 32% for analytes without their own internal standards.

Mitigation of transverse mode instability by modal birefringence in polarization-maintaining fibers.

The effect of transverse mode instability (TMI) poses a fundamental obstacle for a further scaling of diffraction-limited, high-power fiber laser systems. In this work we present a theoretical and experimental study on the mitigation of TMI by modal birefringence in a polarization maintaining (PM) fiber. With the help of comprehensive simulations, we show that the thermally-induced refractive index grating responsible for TMI can be modified and washed out when light is coupled with a polarization input angle detuned from the main axes of the fiber. To confirm the theoretical predictions, we have designed and manufactured an Yb-doped large-mode-area PM fiber. Using this fiber, we have systematically investigated the dependence of the TMI threshold on the polarization input angle of the seed laser. We experimentally demonstrate that when the polarization input angle of the seed is aligned at 50° with respect to the slow-axis, the TMI threshold increases by a factor of 2, verifying the theory and the numerical simulations. A high speed polarization mode-resolved analysis of the output beam is presented, which reveals that at the onset of TMI both polarization axes fluctuates simultaneously.

TMI and polarization static energy transfer in Yb-doped low-NA PM fibers.

In this work, we conduct experimental investigations of transverse mode instabilities (TMI) in a large mode area ultra-low numerical aperture polarization maintaining fiber amplifier. This fiber is few mode in the slow-axis (conventional operation mode), but single mode in the fast-axis. We test the stability of the output beam by changing the input polarization angle and systematically investigate the transverse mode instability threshold in the two principal polarization axes. The lowest TMI threshold at 300 W was found when the input polarization angle was aligned parallel to the slow-axis. Detuning the input polarization angle from the slow-axis led to increased TMI thresholds. For input polarization angle of 90° (parallel to the fast-axis), the output signal was stable up to 475 W and further scaling was limited by the available pump power. However, for fast-axis operation a lower polarization ratio compared to slow-axis operation was observed as well as an unexpected static energy transfer from the fast-axis into the slow-axis above 400 W.

Polarization-resolved mode evolution in TMI-limited Yb-doped fiber amplifiers using a novel high-speed Stokes polarimeter.

In this work we have developed a high-speed Stokes polarimeter method based on simultaneous 4-channel imaging with a high-speed camera. Thus, current speed limitations of imaging polarimeters for wavelengths around 1 µm can be overcome, allowing a sub-ms polarization-resolved characterization of transverse mode instability (TMI). Additionally, the Stokes parameters of each individual mode are calculated by a simultaneous 4-beam mode reconstruction algorithm during post-processing and can be analyzed with unprecedented temporal resolution. We demonstrate the measurement capabilities of this polarimeter setup by characterizing TMI of a large-mode-area Yb-doped polarization maintaining (PM) fiber amplifier with 30 kHz video frame rate. Upon thorough characterization, we have found for the first time that at the onset of TMI in a PM fiber, the modal polarization states begin to oscillate on circular and elliptical trajectories at the same frequencies as the modal energy transfer occurs. The ability to measure the modal polarization states with sub-ms temporal resolution is key to developing a fundamental understanding and subsequently possible mitigation strategies of TMI in PM-fiber lasers.

Experimental analysis of Raman-induced transverse mode instability in a core-pumped Raman fiber amplifier.

The effect of transverse mode instability is a limitation for the power scaling of fiber laser systems, that can originate due to heat caused by stimulated Raman scattering. In this contribution, we experimentally investigate the threshold of transverse mode instability caused by stimulated Raman scattering in a passive fiber. Both, the Stokes seed power and the fiber length of a core-pumped Raman fiber amplifier are varied to systematically study this effect. Mode resolved measurements reveal that the threshold occurs at approximately the same Stokes output power for all tested configurations, independent of the total Raman conversion efficiency. These results increase the understanding of this type of mode instability and show which parameters are important for a further power scaling of high-power Raman fiber amplifiers.

Transverse mode instability in a passive fiber induced by stimulated Raman scattering.

Transverse mode instabilities are a major limitation for power scaling of fiber lasers but have so far only been observed in laser-active fibers. In this contribution we present experimental observations of transverse mode instabilities in a passive fiber. In this fiber, stimulated Raman scattering acted as heat source. To demonstrate the effect, a kW-level ytterbium-doped fiber laser was used as pump for a Raman amplifier. Transverse mode instabilities were only observed in the case with high Raman amplification. Frequency resolved stability measurements at various fiber positions as well as spectral and mode resolved measurements pin their origin to the passive fiber. This observation might help to gain further understanding of transverse mode instabilities and shows limitations of high-power Raman amplifiers.

Extremely robust femtosecond written fiber Bragg gratings for an ytterbium-doped fiber oscillator with 5 kW output power.

We present highly robust fiber Bragg gratings (FBGs) in passive large-mode-area fibers for kilowatt fiber laser systems. The gratings were inscribed directly through the fiber coating using near-infrared femtosecond laser pulses and then implemented in an all-fiber ytterbium-doped single-mode oscillator setup reaching up to 5 kW signal output power. The untreated cooled FBGs showed thermal coefficients as low as ${1}\;{\rm K}\;{{\rm kW}^{ - 1}}$1KkW-1, proving excellent qualification for the implementation into robust high-power fiber laser setups.

Experimental investigations on the TMI thresholds of low-NA Yb-doped single-mode fibers.

In this contribution we investigate the transversal mode instability behavior of a ytterbium-doped commercial 20/400 fiber and obtain 2.9 kW of output power after optimizing the influencing parameters. In this context, we evaluate the influence of the bend diameter and the pump wavelength within the scope of the absorption length and the length of the fiber. Furthermore, with a newly developed fiber we report on 4.4 kW of single-mode output power at 40 cm bend diameter.

Simultaneous identification of long similar substrings in large sets of sequences.

BACKGROUND: Sequence comparison faces new challenges today, with many complete genomes and large libraries of transcripts known. Gene annotation pipelines match these sequences in order to identify genes and their alternative splice forms. However, the software currently available cannot simultaneously compare sets of sequences as large as necessary especially if errors must be considered. RESULTS: We therefore present a new algorithm for the identification of almost perfectly matching substrings in very large sets of sequences. Its implementation, called ClustDB, is considerably faster and can handle 16 times more data than VMATCH, the most memory efficient exact program known today. ClustDB simultaneously generates large sets of exactly matching substrings of a given minimum length as seeds for a novel method of match extension with errors. It generates alignments of maximum length with a considered maximum number of errors within each overlapping window of a given size. Such alignments are not optimal in the usual sense but faster to calculate and often more appropriate than traditional alignments for genomic sequence comparisons, EST and full-length cDNA matching, and genomic sequence assembly. The method is used to check the overlaps and to reveal possible assembly errors for 1377 Medicago truncatula BAC-size sequences published at http://www.medicago.org/genome/assembly_table.php?chr=1. CONCLUSION: The program ClustDB proves that window alignment is an efficient way to find long sequence sections of homogenous alignment quality, as expected in case of random errors, and to detect systematic errors resulting from sequence contaminations. Such inserts are systematically overlooked in long alignments controlled by only tuning penalties for mismatches and gaps. ClustDB is freely available for academic use.

A structural genomics approach to the regulation of apoptosis: chimp vs. human.

After the sequencing of the human genome, the publication of the genome of our nearest relative, the chimpanzee (Pan troglodytes) provided groundbreaking data improving the understanding of the recent human evolution. There are about forty million changes, most of them single nucleotide substitutions, which teach us about ourselves, both in terms of similarities and differences with chimpanzees. From a medical point of view differences in incidence and severity of diseases are of special importance to pinpoint novel targets and to develop innovative therapies. This analysis focuses on the cognition that chimpanzees rarely suffer from cancer. To elucidate possible reasons for this finding, we compare differences regarding apoptosis and DNA-repair on different levels of chromosome organization, gene structure, post-transcriptional and post-translational modifications to functional changes in protein structures. The result is a complex pattern of subtle variances and a few large-scale changes.

Self-alignments to detect mutually exclusive exon usage.

The surprisingly low number of about 25,000 genes in the human genome [1] confirmed a fairly accurate estimate given by King and Jukes in 1969 based on population genetical arguments [2]. On the other hand, the number of different transcripts vastly exceeds gene number. This fact intensified the search for alternatively spliced genes. Recent results [1,3,4-7] suggest that more than 60% of the human genes are alternatively spliced, some of them with a myriad of different splice forms. Alternative splicing is found in all higher eukaryotic species in varying frequency. In this paper we focus on a particular form of alternative splicing, the so-called mutually exclusive exon usage (MEEU). In most known examples mutually exclusive exons are arranged in cassettes of highly similar exons suggesting that they have been derived by exon duplication [8-10]. Since classical gene-finding programs may fail to correctly predict such genes [11-16], we present a method, which is based on local similarity of exons, to detect gene candidates with mutually exclusive exon usage. We have screened the entire genome of D. melanogaster and found five new genes with MEEU in addition to eight previously described cases. Additional 1703 candidate regions of putative mutually exclusive exons were identified.

Genome comparison without alignment using shortest unique substrings.

BACKGROUND: Sequence comparison by alignment is a fundamental tool of molecular biology. In this paper we show how a number of sequence comparison tasks, including the detection of unique genomic regions, can be accomplished efficiently without an alignment step. Our procedure for nucleotide sequence comparison is based on shortest unique substrings. These are substrings which occur only once within the sequence or set of sequences analysed and which cannot be further reduced in length without losing the property of uniqueness. Such substrings can be detected using generalized suffix trees. RESULTS: We find that the shortest unique substrings in Caenorhabditis elegans, human and mouse are no longer than 11 bp in the autosomes of these organisms. In mouse and human these unique substrings are significantly clustered in upstream regions of known genes. Moreover, the probability of finding such short unique substrings in the genomes of human or mouse by chance is extremely small. We derive an analytical expression for the null distribution of shortest unique substrings, given the GC-content of the query sequences. Furthermore, we apply our method to rapidly detect unique genomic regions in the genome of Staphylococcus aureus strain MSSA476 compared to four other staphylococcal genomes. CONCLUSION: We combine a method to rapidly search for shortest unique substrings in DNA sequences and a derivation of their null distribution. We show that unique regions in an arbitrary sample of genomes can be efficiently detected with this method. The corresponding programs shustring (SHortest Unique subSTRING) and shulen are written in C and available at http://adenine.biz.fh-weihenstephan.de/shustring/.