Estimating and correcting mie scattering in synchrotron-based microscopic fourier transform infrared spectra by extended multiplicative signal correction

We present an approach for estimating and correcting Mie scattering occurring in infrared spectra of single cells, at diffraction limited probe size, as in synchrotron based microscopy. The Mie scattering is modeled by extended multiplicative signal correction (EMSC) and subtracted from the vibrational absorption. Because the Mie scattering depends non-linearly on alpha, the product of the radius and the refractive index of the medium/sphere causing it, a new method was developed for estimating the Mie scattering by EMSC for unknown radius and refractive index of the Mie scatterer. The theoretically expected Mie contributions for a range of different alpha values were computed according to the formulae developed by Van de Hulst (1957). The many simulated spectra were then summarized by a six-dimensional subspace model by principal component analysis (PCA). This subspace model was used in EMSC to estimate and correct for Mie scattering, as well as other additive and multiplicative interference effects. The approach was applied to a set of Fourier transform infrared (FT-IR) absorbance spectra measured for individual lung cancer cells in order to remove unwanted interferences and to estimate ranges of important alpha values for each spectrum. The results indicate that several cell components may contribute to the Mie scattering.

The major pathways of carbohydrate metabolism in the ectomycorrhizal basidiomycete Laccaria bicolor S238N

The primary carbohydrate metabolism of an ectomycorrhizal fungus and its transcriptional regulation has never been characterized at the genome scale although it plays a fundamental role in the functioning of the symbiosis. In this study, the genome sequence of the ectomycorrhizal basidiomycete Laccaria bicolor S238N-H82 was explored to construct a comprehensive genome-wide inventory of pathways involved in primary carbohydrate metabolism. Several genes and gene families were annotated, including those of the glycolysis, pentose phosphate pathway, tricarboxylic acid cycle, and trehalose and mannitol metabolism. The transcriptional regulation of these pathways was studied using whole-genome expression oligoarrays and quantitative polymerase chain reaction in free-living mycelium, ectomycorrhizas and fruiting bodies. Pathways of carbohydrate biosynthesis and catabolism are identical in L. bicolor compared with other sequenced saprotrophic basidiomycetes. Ectomycorrhiza and fruiting body development induced the regulation of a restricted set of transcripts of the glycolytic, mannitol and trehalose metabolisms.

Multivariate image analysis of a set of FTIR microspectroscopy images of aged bovine muscle tissue combining image and design information

In this paper we present an algorithm for analysing sets of FTIR microscopic images of tissue sections. The proposed approach allows one to investigate sets of many FTIR tissue images both with respect to sample information (variation from image to image) and spatial variations of tissues (variation within the image). The algorithm is applied to FTIR microscopy images of beef loin muscles containing myofibre and connective tissue regions. The FTIR microscopy images are taken of sub-samples from five different beef loin muscles that were aged for four different lengths of time. The images were investigated regarding variation due to the ageing length and due to the homogeneity of the connective tissue regions. The presented algorithm consists of the following main elements: (1) pre-processing of the spectra to overcome large quality differences in FTIR spectra and differences due to scatter effects, (2) identification of connective tissue regions in every image, (3) labelling of every connective tissue spectrum with respect to its location in the connective tissue region, and (4) analysis of variations in the FTIR microscopic images in regard to ageing time and pixel position of the spectra in the connective tissue region. Important spectral parameters characterising collagen and proteoglycan structure were determined.

Successful Intrauterine Therapy for Congenital Cystic Adenomatoid Malformation of the Lung

Congenital cystic adenomatoid malformation (CCAM) of the lung is a rare abnormality which is amenable to be diagnosed by prenatal ultrasonography. In general, CCAM associated with non-immune hydrops has a poor prognosis unless a fetal intervention is performed. In some series almost 100% of either prenatal or early neonatal deaths are observed without intervention. Recently the cystic adenomatoid malformation volume ratio (CVR) has been proposed as an index to predict the development of hydrops in this condition. If the CVR is >1.6, the risk of hydrops is approximately 75%. We report a case of CCAM (macrocystic type) of the left lung referred to our center at 21 weeks of gestation. Fetal therapy was considered owing to enlargement of the CCAM volume, severe mediastinal shift, right lung compression, polyhydramnios and ascites from 21 to 26 weeks. Thoracoamniotic shunting was performed successfully at 26 weeks with resolution of the cystic mass. At 37 weeks a male infant was born vaginally weighing 3,210 g with Apgar scores of 5 and 10. Resection of the mass was performed uneventfully on day 3. The infant is currently 22 months of age, asymptomatic and in good condition.

FT-IR microspectroscopy for early identification of some clinically relevant pathogens

AIMS

To investigate the potentials and limitations of Fourier transform-infrared (FT-IR) microspectroscopy as a tool to identify, at the level of microcolonies, pathogenic bacteria frequently isolated in the clinical environment.

METHODS AND RESULTS

A total of 1570 FT-IR spectra from 164 gram-positive and gram-negative bacteria isolated from patients were recorded from 6 to 10-h old microcolonies of 50-150 microm size. A classification of 100% was obtained for the most frequent gram-positive bacteria, such as Staphylococcus aureus, Staphylococcus epidermidis, Enterococcus faecalis, and Enterococcus faecium at the species level. An average accuracy of about 80% was reached with Gram negative bacteria from the Enterobacteriaceae and Pseudomonaceae families; Enterobacter aerogenes, Enterobacter cloacae, Klebsiella spp., and Citrobacter koseri; and Proteus mirabilis and Escherichia coli. Results were comparable with FT-IR measurements on dried suspensions from 18-h cultures.

CONCLUSIONS

Early identification of young microcolonies is feasible with FT-IR microscopy with a very high accuracy for gram-positive bacteria. Some improvement in the transfer of microcolonies is necessary to increase the accuracy for gram-negative bacteria.

SIGNIFICANCE AND IMPACT OF THE STUDY

Combination of FT-IR microscopy and multivariate data analysis could be a complementary, rapid, and reliable tool for screening and discriminating, at species and subspecies level, micro-organisms of clinical, food-borne, or environmental origins.

The mycorrhiza helper Pseudomonas fluorescens BBc6R8 has a specific priming effect on the growth, morphology and gene expression of the ectomycorrhizal fungus Laccaria bicolor S238N

The mycorrhiza helper Pseudomonas fluorescens BBc6R8 promotes the presymbiotic survival and growth of the ectomycorrhizal fungus Laccaria bicolor S238N in the soil. An in vitro fungal-bacterial confrontation bioassay mimicking the promoting effects of the bacteria on fungal growth was set up to analyse the fungal morphological and transcriptional changes induced by the helper bacteria at three successive stages of the interaction. The specificity of the P. fluorescens BBc6R8 effect was assessed in comparison with six other rhizobacterial strains possessing mycorrhiza helper or pathogen antagonistic abilities. The helper BBc6R8 strain was the only strain to induce increases in the radial growth of the colony, hyphal apex density and branching angle. These morphological modifications were coupled with pleiotropic alterations of the fungal transcriptome, which varied throughout the interaction. Early stage-responsive genes were presumably involved in recognition processes and transcription regulation, while late stage-responsive genes encoded proteins of primary metabolism. Some of the responsive genes were partly specific to the interaction with P. fluorescens BBc6R8, whereas others were mutually regulated by different rhizobacteria. The results highlight the fact that the helper BBc6R8 strain has a specific priming effect on growth, morphology and gene expression of its fungal associate L. bicolor S238N.

The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)

We report the draft genome of the black cottonwood tree, Populus trichocarpa. Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. More than 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages. Nucleotide substitution, tandem gene duplication, and gross chromosomal rearrangement appear to proceed substantially more slowly in Populus than in Arabidopsis. Populus has more protein-coding genes than Arabidopsis, ranging on average from 1.4 to 1.6 putative Populus homologs for each Arabidopsis gene. However, the relative frequency of protein domains in the two genomes is similar. Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport.

Physics-based multiplicative scatter correction approaches for improving the performance of calibration models

Light scattering effects pose a major problem in the estimation of chemical properties of particulate systems such as blood, tissue, and pharmaceutical solids. Recently, Martens et al. proposed an extended multiplicative signal correction (EMSC) approach where light-scattering effects were taken into account in an empirical manner. It is possible to include causal, first-principles mathematical models based on the physics of light scattering into the EMSC framework. This could lead to significant improvements in the separation of absorption and scattering effects. A preconditioning step prior to application of EMSC, whereby a transformation based on the physics of light scattering is used to convert the spectra into a form where the absorption and scattering effects are separable (an underlying assumption of EMSC), is proposed. Results indicate that the transformation followed by EMSC gives better calibration models than the direct application of EMSC to the absorbance spectra.

Extended multiplicative signal correction as a tool for separation and characterization of physical and chemical information in Fourier transform infrared microscopy images of cryo-sections of beef loin

Extended multiplicative signal correction (EMSC) is used to separate and to characterize physical and chemical information in spectra from Fourier transform infrared (FT-IR) microscopy. This appears especially useful for applications in infrared spectroscopy where the scatter variance in spectra changes with the chemical variance in the sample set. In these cases the chemical information of specific bands that are assigned to functional groups is easier to interpret when the scatter information is removed from the spectra. We show that scatter (physical) information in FT-IR spectra of heat-treated beef loin is related to chemical changes due to heat treatment. This information is caused by textural changes induced by the heat treatment and expressed by physical effects as the optical path length. The chemical absorbance changes introduced in the FT-IR spectra due to heat treatment are shifts in the protein region of the infrared spectrum caused by changes in the secondary structure of the proteins. If the scatter and the chemical information is not separated properly, scatter information may erroneously be interpreted as chemical information.

Monitoring of denaturation processes in aged beef loin by Fourier transform infrared microspectroscopy

We present the results of a Fourier transform infrared (FT-IR) microspectroscopic study using conventional FT-IR microscopy and FT-IR imaging to detect the denaturation process during four different heating temperatures (raw, 45, 60, and 70 degrees C) spatially resolved in bovine cryosections from longissimus dorsi muscle. FT-IR imaging, employing a focal plane array detector, which allowed the simultaneous collection of spectra at 4096 pixels, enabled the investigation of the heat-induced changes in the two major meat constituents, i.e., myofibrillar and connective tissue proteins, spatially resolved. The infrared spectra of both compounds revealed that the major spectral changes involved an increase in beta-sheet and a decrease in alpha-helical structures, which appeared to be much more pronounced for the myofibers than for the connective tissue. These conformational changes could be correlated to the denaturation of the major meat proteins, such as myosin, actin, and collagen.

Trace element carriers in combined sewer during dry and wet weather: an electron microscope investigation

The nature of trace element carriers contained in sewage and combined sewer overflow (CSO) was investigated by TEM-EDX-Electron diffraction and SEM-EDX. During dry weather, chalcophile elements were found to accumulate in sewer sediments as early diagenetic sulfide phases. The sulfurization of some metal alloys was also evidenced. Other heavy metal carriers detected in sewage include metal alloys, some iron oxihydroxide phases and neoformed phosphate minerals such as anapaite. During rain events, the detailed characterization of individual mineral species allowed to differentiate the contributions from various specific sources. Metal plating particles, barite from automobile brake, or rare earth oxides from catalytic exhaust pipes, originate from road runoff, whereas PbSn alloys and lead carbonates are attributed to zinc-works from roofs and paint from building siding. Soil contribution can be traced by the presence of clay minerals, iron oxihydroxides, zircons and rare earth phosphates. However, the most abundant heavy metal carriers in CSO samples were the sulfide particles eroded from sewer sediments. The evolution of relative abundances of trace element carriers during a single storm event, suggests that the pollution due to the "first flush" effect principally results from the sewer stock of sulfides and previously deposited metal alloys, rather than from urban surface runoff.

The role of fetal nuchal translucency and ductus venosus Doppler at 11-14 weeks of gestation in the detection of major congenital heart defects

OBJECTIVE

To determine whether, in a selected high-risk population, Doppler velocimetry of the ductus venosus can improve the predictive capacity of increased nuchal translucency in the detection of major congenital heart defects in chromosomally normal fetuses at 11-14 weeks of gestation.

METHODS

Ductus venosus Doppler ultrasound blood velocity waveforms were obtained prospectively at 11-14 weeks of gestation in 1040 consecutive singleton pregnancies. Waveforms were classified either as normal in the presence of a positive A-wave, or as abnormal if the A-wave was absent or negative. All cases were screened for chromosomal defects by a combination of maternal age and fetal nuchal translucency thickness. In 484 cases karyotyping was performed. Those fetuses found to be chromosomally normal by prenatal cytogenetic analysis, and which had abnormally increased nuchal translucency and/or abnormal ductus venosus Doppler velocimetry, underwent fetal echocardiography at 14-16 weeks of gestation. Ultrasound examination was repeated at 22-24 weeks of gestation in all women. The sensitivity, specificity and positive and negative predictive values for the detection of major cardiac defects of increased nuchal translucency thickness alone, ductus venosus Doppler alone and increased nuchal translucency thickness in association with abnormal ductus venosus Doppler were determined.

RESULTS

In 29 of 998 fetuses presumed to be chromosomally normal, reversed or absent flow during atrial contraction was associated with increased (> 95(th) centile for crown-rump length) nuchal translucency. Major cardiac defects were observed in 9 of these 29 fetuses. No other major cardiac abnormalities were found in chromosomally normal fetuses in spite of the presence of either increased nuchal translucency alone or abnormal ductus venosus velocimetry. A total of 25 cardiac malformations were observed in the population. Fifteen were associated with aneuploidy and 10 fetuses had a normal karyotype. Nine of the 10 had major cardiac anomalies and one had a ventricular septal defect. The nine cases with normal karyotype and major cardiac anomalies had both increased nuchal translucency and abnormal ductus venosus flow velocity waveforms.

CONCLUSION

In chromosomally normal fetuses with increased nuchal translucency, assessment of ductus venosus blood flow velocimetry could improve the predictive capacity for an underlying major cardiac defect.

Parametric correlations of the energy levels of ray-splitting billiards

Parameter-dependent statistical properties of the spectra of ray-splitting billiards are studied experimentally and theoretically. The autocorrelation functions c(x) and c(omega,x) of level velocities as well as the generalized conductance C(0) are calculated for two different classically chaotic ray-splitting billiards. Experimentally a modified Sinai ray-splitting billiard is studied consisting of a thin microwave rectangular cavity with two quarter-circle-shaped Teflon inserts. The length of the cavity serves as the experimentally adjustable parameter. For the theoretical estimates of the parametric correlations we compute the quantum spectrum of a scaling triangular ray-splitting billiard. Our experimental and numerical results are compared with each other and with the predictions of random matrix theory.

[Current indications for the treatment with botulin toxin]

Botulinum toxin is more and more frequently used as a therapeutic agent. The toxin blocks selectively and reversibly the neuromuscular junction, causing a muscle relaxation. Indications are mainly muscular hypercontraction, such as dystonia, blepharospasm, focal spasticity, strabismus or tics. The range of action extend to focal hyperhydrosis, palmar, axillary or plantar. It seems now that some painful syndrome such as migraine or tension headache may benefit from toxin injections. Esthetic indications constitute an extension to the pure medical indications.

Image analysis of particle dispersions in microscopy images of cryo-sectioned sausages

Two feature extraction methods, the three-dimensional (3-D) local box-counting method and the area distribution method, are presented to describe the fat dispersion pattern on digital microscopy images of cryo-sectioned sausages. Both methods calculate whole arrays of variables for each microscopy image. The 3-D box-counting method calculates scale dependent (local) dimensions. This is in contrast to common fractal methods, which are univariate. Principal component analysis (PCA) was used to show that different sausages yield different fat dispersion patterns. Partial least square regression (PLS) shows that there is a correlation between the variables gained with both methods and the fat content.

Exercise test in muscle channelopathies and other muscle disorders

We studied the percentage change in compound muscle action potential (CMAP) amplitude and area during and after a 5-min maximal contraction of the muscle. The exercise test (ET) was performed on 64 patients with different muscle disorders and on 46 normal controls. The range of normal ET values was defined as the mean + 2 SD of the control values. The mean sensitivity of the test was 63% in the whole group with ion channel muscle disorders, the highest sensitivity being seen in primary periodic paralysis (81%) and the lowest in chloride channelopathies (17%). In thyrotoxic periodic paralysis, the ET was abnormal in the three of the four patients studied. In patients with myotonic dystrophy, a smaller than normal increase in CMAP amplitude occurred during and after exercise, whereas in proximal myotonic myopathy a normal initial increase in CMAP amplitude was followed by an abnormal decrement. We conclude that the ET can be of use in confirming abnormal muscle membrane excitability in patients with calcium and sodium channelopathies and thyrotoxic periodic paralysis. In chloride channelopathy, the test may also be abnormal, but shows no, or only a small, increase in amplitude or area in the immediate postexercise period. The test may also be abnormal in proximal myotonic myopathy, but is normal in myotonic dystrophy.

Proximal myotonic myopathy: clinical, electrophysiological and pathological findings in a family

Proximal myotonic myopathy (PROMM) is an autosomal dominant muscle disorder characterized by proximal weakness, myotonia, muscle pain and cataract. It resembles Steinert myotonic dystrophy (MD), but weakness is proximal, without facial muscle involvement, and the chromosome 19 CTG trinucleotide repeat expansion characteristic of MD is not present. We describe a further family with PROMM. Affected members complained of weakness of lower limbs or of myotonia. EMG revealed diffuse myotonic discharges. Muscle histology showed dystrophic abnormalities. The PROMM phenotype varies, even in the same pedigree, and may mimic MD or limb-girdle muscle dystrophy. EMG is particularly useful, since it may disclose myotonic discharges even in the absence of overt myotonia. Thus far it is not known whether PROMM is a single entity, or if it represents a heterogeneous group of disorders. This question will probably soon be settled through genetic analysis.

Autocorrelation function of level velocities for ray-splitting billiards

We study experimentally and theoretically the autocorrelation function of level velocities c(x) and the generalized conductance C(0) for classically chaotic ray-splitting systems. Experimentally, a Sinai ray-splitting billiard was simulated by a thin microwave rectangular cavity with a quarter-circle Teflon insert. For the theoretical estimates of the autocorrelator c(x) and the conductance C(0) we made parameter-dependent quantum calculations of eigenenergies of an annular ray-splitting billiard. Our experimental and numerical results are compared to theoretical predictions of systems based on the Gaussian orthogonal ensemble in random matrix theory.

Intima-like smooth muscle cells: developmental link between endothelium and media?

The presence of non-contractile smooth muscle cells within the arterial wall raises questions as to their origin and function. These cells abound within the aortae of murine and porcine neonates, but are also present within the intimal and medial layers of adult arteries. They are largely devoid of smooth muscle-associated proteins and manifest an epithelioid form. Their morphological resemblance to endothelial cells prompted us to explore this potential relationship and to investigate their angiogenic properties in three-dimensional collagen gels. Using well-characterized smooth muscle cell lines, displaying either the intima-like (epithelioid) or media-like (spindle-shaped) morphology, we were able to show that intima-like cells share several features in common with endothelial ones and can transform into a media-like phenotype, whereby they irreversibly lose their characteristic pattern of protein expression. Intima-like, but not media-like, vascular smooth muscle cells are capable of forming capillary tubes, and, in co-cultures, can induce media-like ones to participate in this process. Such capillaries consist of a randomly-organized, mixed population of endothelial cells with intima-like or media-like smooth muscle ones. The functional significance of this diversity in smooth muscle cell type is not well understood, but phenotypic plasticity could conceivably figure as an important adaptive response to changes in the local environment.