A likelihood-based method for haplotype association studies of case-control data with genotyping uncertainty

This paper discusses the associations between traits and haplotypes based on Fl (fluorescent intensity) data sets. We consider a clustering algorithm based on mixtures of t distributions to obtain all possible genotypes of each individual (i.e. "GenoSpec-trum"). We then propose a likelihood-based approach that incorporates the genotyping uncertainty to assessing the associations between traits and haplotypes through a haplotype-based logistic regression model. Simulation studies show that our likelihood-based method can reduce the impact induced by genotyping errors.     

Sub-Doppler and Doppler spectroscopy of DCN isotopomers in the terahertz region: ground and first excited bending states (v1v2v3)=(0 1 0)

The rotational spectra of the deuterium cyanide isotopic species DCN, D¹³CN, DC¹⁵N, and D¹³C¹⁵N were recorded in the vibrational ground and first excited bending state (v₂=1) up to 2 THz. The R-branch transitions from J=3←2 to J=13←12 were measured with sub-Doppler resolution. These very high resolution (∼70 kHz) and precise (±3-10 kHz) saturation dip measurements allowed for resolving the underlying hyperfine structure due to the ¹⁴N nucleus in DCN and D¹³CN for transitions as high as J=10←9. Additional high JR-branch (J=25←24 to J=28←27) transitions around 2 THz and direct l-type (ΔJ=0, J=19 to J=25) transitions from 66 to 118 GHz were recorded in Doppler-limited resolution. For the ground state of D¹³C¹⁵N, the J=1←0 transition was measured for the first time. The transition frequency accuracies for the other deuterated species were significantly improved. These new experimental data, together with the available infrared rovibrational data and previously measured direct l-type transitions, were subjected to a global least squares analysis for each isotopomer. This yielded precise sets of molecular constants for the ground and first excited vibrational states, including the nuclear quadrupole and magnetic spin-rotation coupling constants of the ¹⁴N nucleus for DCN and D¹³CN. The hyperfine structure due to the D, ¹³C, and ¹⁵N nuclei have not been resolved, but led to a broadening of the observed saturation dips.     

Towards cooling of high-intensity ion beams

Buffer gas beam coolers may become excellent beam preparation devices for high-resolution mass separation. The small beam emittance provided makes efficient isobar resolution a realistic goal. In order to fulfill the needs of future facilities providing high-intensity beams of rare isotopes, it is desirable to increase the beam intensity limit of such devices from typically several tens of nanoamperes to microamperes. This requires the usage of high-voltage radiofrequencies in a low-pressure gas environment. A buffer gas beam cooler, dedicated to this purpose, is under development at the NSCL. The study of voltage breakdowns under such conditions and the design of an electrode system minimizing them is mandatory.      

A detailed analysis of the photoemission spectra of basic thioaromatic monolayers on noble metal substrates

Analysis of photoemission spectra of complex thioaromatic self-assembled monolayers (SAMs) requires the knowledge and understanding of such spectra for the basic systems. Keeping this goal in mind, synchrotron-based high-resolution X-ray photoelectron spectroscopy was used to characterize SAMs formed from the simplest thioaromatic compounds, namely thiophenol, 1,1′-biphenyl-4-thiol and 1,1′;4′,1″-terphenyl-4-thiol on evaporated Au(1 1 1) and Ag(1 1 1) substrates. The acquired S 2p and C 1s spectra were analyzed in terms of fine structure and initial and final state effects in the photoemission process. The assignment of the individual spectral features was considered in detail. Conclusions on quality and chemical and structural homogeneity of the investigated SAMs were derived.     

The structure of monolayer SiO2 on Mo(1 1 2): A 2-D [Si-O-Si] network or isolated [SiO4] units?

In this letter, atomically resolved scanning tunneling microscopic (STM) images obtained from monolayer SiO₂/Mo(1 1 2) are presented. The results are consistent with a previously proposed structural model of isolated [SiO₄] units based on vibrational features observed by high-resolution electron energy loss spectroscopy (HREELS) and infrared reflection-absorption spectroscopy (IRAS), and oxygen species identified by ultra-violet photoemission spectroscopy (UPS). These results are inconsistent with a structural model that assumes a two-dimensional (2-D) [Si-O-Si] network. These data illustrate that a metal substrate, although coated with an oxide thin layer, can be directly imaged at the atomic-scale with STM.     

Tetragonal low-temperature structure of LiAl

The cubic face-centered structure of LiAl (, at ) transforms into a tetragonal body-centered structure (I4₁/amd, , at ). This first-order phase transition at about during heating is probably the reason for the so-called “ anomalies” in some physical properties like specific heat, electrical resistivity and nuclear-spin lattice relaxation. This transition seems to be correlated with the composition Li:Al of the alloy and the amount of Li vacancies.     

Metabolic profiling of normal and hypertensive rat kidney tissues by hrMAS-NMR spectroscopy

Intact kidney tissue samples of normal and spontaneously hypertensive rats (SHRs) were analyzed by hrMAS-NMR spectroscopy and principal component analysis (PCA). Radial components (cortex, outer stripe of the outer medulla, inner stripe of the outer medulla, and papilla) were sampled from various regions across the kidney from multiple animals in order to establish inter- and intra-animal variability. The effects of temperature were also measured. Papilla was differentiated from the other tissue types, and this variation by tissue type was greater than the effect of temperature on the samples (spectra were compared from samples at 2 and 30 °C). This study also revealed long term stability issues of tissue storage at -80 °C. The PCA showed that the greatest differentiation between normal rats and SHRs was found in the cortex and the regions in the NMR spectra that were correlated with this variation were identified.Abbreviations hrMAS High-resolution magic angle spinning - NMR Nuclear magnetic resonance - PCA Principal component analysis - CSA Chemical shift anisotropy - DD Dipolar coupling - SHR Spontaneously hypertensive rat     

Determination of aluminum in highly concentrated iron samples: Study of interferences using high-resolution continuum source atomic absorption spectrometry

High-resolution continuum source atomic absorption spectrometry (HR-CS AAS) has been used to investigate spectral and non-spectral interferences found with a conventional line source atomic absorption spectrometer in the determination of aluminum in pharmaceutical products containing elevated iron and sugar concentrations. A transversely heated graphite furnace was used as the atomizer in both spectrometers. The two most sensitive aluminum lines at 309.3 nm and 396.2 nm were investigated and it was found that an iron absorption line at 309.278 nm, in the vicinity of the aluminum line at 309.271 nm, could be responsible for some spectral interference. The simultaneous presence of iron and the organic components of the matrix were responsible for radiation scattering, causing high continuous and also structured background absorption at both wavelengths. The aluminum and iron absorption could not be separated in time, i.e., the iron interference could not be eliminated by optimizing the graphite furnace temperature program. However, an interference-free determination of aluminum was possible carrying out the measurements with HR-CS AAS at 396.152 nm after applying least squares background correction for the elimination of the structured background. Analytical working range and other figures of merit were determined and are presented for both wavelengths using peak volume registration (center pixel ± 1) and the center pixel only. Limits of detection and characteristic masses ranged from 1.1 to 2.5 pg and 13 to 43 pg, respectively. The method was used for the determination of the aluminum contamination in pharmaceutical formulations for iron deficiency treatment, which present iron concentrations from 10 to 50 g l^− 1. Spike recoveries from 89% to 105% show that the proposed method can be satisfactorily used for the quality control of these formulations.     

High-resolution laser ablation-inductively coupled plasma-mass spectrometry imaging of cisplatin-induced nephrotoxic side effects

Two-dimensional elemental mapping (bioimaging) via laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) was performed on 5 μm thick formalin-fixed, paraffin-embedded kidney tissue sections from Cynomolgus monkeys administered with increasing pharmacological doses of cisplatin. Laterally resolved pixels of 1 μm were achieved, enabling elemental analysis on a (sub-)cellular level. Zones of high Pt response were observed in the renal cortex, where proximal tubules are present, the epithelium of which is responsible for partial reabsorption of cisplatin. Histopathological evaluation, of hematoxylin and eosin-stained serial sections, adjacent to the sections probed via LA-ICP-MS, revealed minimal to mild cisplatin-related lesions (<100 μm) in the renal cortex. Necrotic proximal tubules with sloughed epithelial cells in their lumen could be linked directly to the areas with the highest accumulation of cisplatin, indicating a direct link between cellular concentration and toxicity, thereby providing more insight into the mechanisms through which renal damage occurs.     

Accurate mass determination,quantification and determination of detection limits in liquid chromatography–high-resolution time-of-flight mass spectrometry: Challenges and practical solutions

Uniform guidelines for the data processing and validation of qualitative and quantitative multi-residue analysis using full-spectrum high-resolution mass spectrometry are scarce.