In Vitro Assessment of Optical Properties of Blood by Applying the Extended Huygens-Fresnel Principle to Time-Domain Optical Coherence Tomography Signal at 1300 nm

A direct method for the measurement of the optical attenuation coefficient and the scattering anisotropy parameter based on applying the extended Huygens-Fresnel principle to optical coherence tomography images of blood is demonstrated. The images are acquired with a low-power probing beam at the wavelength of 1300 nm. Values of 12.15 mm−1 and 0.95 are found for the total attenuation coefficient and the scattering anisotropy factor, respectively. Also, as a preliminary step, the optical refraction index is determined with a precision of two decimal numbers directly from optical coherence images. The total attenuation coefficient and the scattering anisotropy factor are determined with precisions within experimental error margins of 5% and 2%, respectively. Readable OCT signal is obtained for a maximum propagation of light into blood of 0.25 mm. At the maximum probed depth, the measured signal is almost 103 smaller than its initial intensity when entering the sample

Diagnosis and Monitoring of Gingivitis in vivo Using Non-Invasive Technology - Infrared Spectroscopy

Peer reviewed: YesNRC publication: Ye

Classification of burn injuries using near-infrared spectroscopy.

Early surgical management of those burn injuries that will not heal spontaneously is critical. The decision to excise and graft is based on a visual assessment that is often inaccurate but yet continues to be the primary means of grading the injury. Superficial and intermediate partial-thickness injuries generally heal with appropriate wound care while deep partial- and full-thickness injuries generally require surgery. This study explores the possibility of using near-infrared spectroscopy to provide an objective and accurate means of distinguishing shallow injuries from deeper burns that require surgery. Twenty burn injuries are studied in five animals, with burns covering <1% of the total body surface area. Carefully controlled superficial, intermediate, and deep partial-thickness injuries as well as full-thickness injuries could be studied with this model. Near-infrared reflectance spectroscopy was used to evaluate these injuries 1 to 3 hours after the insult. A probabilistic model employing partial least-squares logistic regression was used to determine the degree of injury, shallow (superficial or intermediate partial) from deep (deep partial and full thickness), based on the reflectance spectrum of the wound. A leave-animal-out cross-validation strategy was used to test the predictive ability of a 2-latent variable, partial least-squares logistic regression model to distinguish deep burn injuries from shallow injuries. The model displayed reasonable ranking quality as summarized by the area under the receiver operator characteristics curve, AUC = 0.879. Fixing the threshold for the class boundaries at 0.5 probability, the model sensitivity (true positive fraction) to separate deep from shallow burns was 0.90, while model specificity (true negative fraction) was 0.83. Using an acute porcine model of thermal burn injuries, the potential of near-infrared spectroscopy to distinguish between shallow healing burns and deeper burn injuries was demonstrated. While these results should be considered as preliminary and require clinical validation, a probabilistic model capable of differentiating these classes of burns would be a significant aid to the burn specialist

Surface expression, peptide repertoire, and thermostability of chicken class I molecules correlate with peptide transporter specificity.

The chicken major histocompatibility complex (MHC) has strong genetic associations with resistance and susceptibility to certain infectious pathogens. The cell surface expression level of MHC class I molecules varies as much as 10-fold between chicken haplotypes and is inversely correlated with diversity of peptide repertoire and with resistance to Marek's disease caused by an oncogenic herpesvirus. Here we show that the average thermostability of class I molecules isolated from cells also varies, being higher for high-expressing MHC haplotypes. However, we find roughly the same amount of class I protein synthesized by high- and low-expressing MHC haplotypes, with movement to the cell surface responsible for the difference in expression. Previous data show that chicken TAP genes have high allelic polymorphism, with peptide translocation specific for each MHC haplotype. Here we use assembly assays with peptide libraries to show that high-expressing B15 class I molecules can bind a much wider variety of peptides than are found on the cell surface, with the B15 TAPs restricting the peptides available. In contrast, the translocation specificity of TAPs from the low-expressing B21 haplotype is even more permissive than the promiscuous binding shown by the dominantly expressed class I molecule. B15/B21 heterozygote cells show much greater expression of B15 class I molecules than B15/B15 homozygote cells, presumably as a result of receiving additional peptides from the B21 TAPs. Thus, chicken MHC haplotypes vary in several correlated attributes, with the most obvious candidate linking all these properties being molecular interactions within the peptide-loading complex (PLC).This work was originally supported by core funding to the Basel Institute for Immunology (which was founded and supported by F. Hoffmann-La Roche & Co. Ltd., CH-4005 Basel, Switzerland), then by core funding to the Institute for Animal Health [now re-branded the Pirbright Institute, sponsored by the Biotechnology and Biological Sciences Research Council (BBSRC) of the UK] and finally by programme grant 089305 from the Wellcome Trust to JK.This is the author accepted manuscript. The final version is available from PNAS via http://dx.doi.org/10.1073/pnas.151185911

Ex vivo detection and characterization of early dental caries by optical coherence tomography and Raman spectroscopy.

Early dental caries detection will facilitate implementation of nonsurgical methods for arresting caries progression and promoting tooth remineralization. We present a method that combines optical coherence tomography (OCT) and Raman spectroscopy to provide morphological information and biochemical specificity for detecting and characterizing incipient carious lesions found in extracted human teeth. OCT imaging of tooth samples demonstrated increased light backscattering intensity at sites of carious lesions as compared to the sound enamel. The observed lesion depth on an OCT image was approximately 290 mm matching those previously documented for incipient caries. Using Raman microspectroscopy and fiber-optic- based Raman spectroscopy to characterize the caries further, spectral changes were observed in PO 42 vibrations arising from hydroxyapa- tite of mineralized tooth tissue. Examination of various ratios of PO 42 n 2 , n 3 , n 4 vibrations against the n 1 vibration showed consistent in- creases in carious lesions compared to sound enamel. The changes were attributed to demineralization-induced alterations of enamel crystallite morphology and/or orientation. OCT imaging is useful for screening carious sites and determining lesion depth, with Raman spectroscopy providing biochemical confirmation of caries. The com- bination has potential for development into a new fiber-optic diagnos- tic tool enabling dentists to identify early caries lesions with greater sensitivity and specificity. © 2005 Society of Photo-Optical Instrumentation Engi

Forecasting the combined effects of anticipated climate change and agricultural conservation practices on fish recruitment dynamics in Lake Erie

Many aquatic ecosystems are experiencing multiple anthropogenic stressors that threaten their ability to support ecologically and economically important fish species. Two of the most ubiquitous stressors are climate change and non- point source nutrient pollution.Agricultural conservation practices (ACPs, i.e. farming practices that reduce runoff, prevent erosion, and curb excessive nutrient loading) offer a potential means to mitigate the negative effects of non- point source pollution on fish populations. However, our understanding of how ACP implementation amidst a changing climate will affect fish production in large ecosystems that receive substantial upstream sediment and nutrient inputs remains incomplete.Towards this end, we explored how anticipated climate change and the implementation of realistic ACPs might alter the recruitment dynamics of three fish populations (native walleye Sander vitreus and yellow perch Perca flavescens and invasive white perch Morone americana) in the highly productive, dynamic west basin of Lake Erie. We projected future (2020- 2065) recruitment under different combinations of anticipated climate change (n = 2 levels) and ACP implementation (n = 4 levels) in the western Lake Erie catchment using predictive biological models driven by forecasted winter severity, spring warming rate, and Maumee River total phosphorus loads that were generated from linked climate, catchment- hydrology, and agricultural- practice- simulation models.In general, our models projected reduced walleye and yellow perch recruitment whereas invasive white perch recruitment was projected to remain stable or increase relative to the recent past. Our modelling also suggests the potential for trade- offs, as ACP implementation was projected to reduce yellow perch recruitment with anticipated climate change.Overall, our study presents a useful modelling framework to forecast fish recruitment in Lake Erie and elsewhere, as well as offering projections and new avenues of research that could help resource management agencies and policy- makers develop adaptive and resilient management strategies in the face of anticipated climate and land- management change.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/156436/2/fwb13515.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/156436/1/fwb13515_am.pd

Fish Species of Greatest Conservation Need in Wadeable Iowa Streams: Current Status and Effectiveness of Aquatic Gap Program Distribution Models

Effective conservation of fish species of greatest conservation need (SGCN) requires an understanding of species– habitat relationships and distributional trends. Thus, modeling the distribution of fish species across large spatial scales may be a valuable tool for conservation planning. Our goals were to evaluate the status of 10 fish SGCN in wadeable Iowa streams and to test the effectiveness of IowaAquatic Gap Analysis Project (IAGAP) species distribution models. We sampled fish assemblages from 86 wadeable stream segments in the Mississippi River drainage of Iowa during 2009 and 2010 to provide contemporary, independent fish species presence–absence data. The frequencies of occurrence in stream segments where species were historically documented varied from 0.0% for redfin shiner Lythrurus umbratilis to 100.0% for American brook lamprey Lampetra appendix, with a mean of 53.0%, suggesting that the status of Iowa fish SGCN is highly variable. Cohen’s kappa values and other model performance measures were calculated by comparing field-collected presence–absence data with IAGAP model–predicted presences and absences for 12 fish SGCN. Kappa values varied from 0.00 to 0.50, with a mean of 0.15. The models only predicted the occurrences of banded darter Etheostoma zonale, southern redbelly dace Phoxinus erythrogaster, and longnose dace Rhinichthys cataractae more accurately than would be expected by chance. Overall, the accuracy of the twelve models was low, with a mean correct classification rate of 58.3%. Poor model performance probably reflects the difficulties associated with modeling the distribution of rare species and the inability of the large-scale habitat variables used in IAGAP models to explain the variation in fish species occurrences. Our results highlight the importance of quantifying the confidence in species distribution model predictions with an independent data set and the need for long-term monitoring to better understand the distributional trends and habitat associations of fish SGCN

Habitat Associations of Fish Species of Greatest Conservation Need at Multiple Spatial Scales in Wadeable Iowa Streams

Fish and habitat data were collected from 84 wadeable stream reaches in the Mississippi River drainage of Iowa to predict the occurrences of seven fish species of greatest conservation need and to identify the relative importance of habitat variables measured at small (e.g., depth, velocity, and substrate) and large (e.g., stream order, elevation, and gradient) scales in terms of their influence on species occurrences. Multiple logistic regression analysis was used to predict fish species occurrences, starting with all possible combinations of variables (5 large-scale variables, 13 small-scale variables, and all 18 variables) but limiting the final models to a maximum of five variables. Akaike’s information criterion was used to rank candidate models, weight model parameters, and calculate model-averaged predictions. On average, the correct classification rate (CCR = 80%) and Cohen’s kappa (κ = 0.59) were greatest for multiple-scale models (i.e., those including both large-scale and small-scale variables), intermediate for small-scale models (CCR = 75%; κ = 0.49), and lowest for large-scale models (CCR = 73%; κ = 0.44). The occurrence of each species was associated with a unique combination of large-scale and small-scale variables. Our results support the necessity of understanding factors that constrain the distribution of fishes across spatial scales to ensure that management decisions and actions occur at the appropriate scale

Multiple identities in decentralized Spain: The case of Catalonia

Publicado en Regional and Federal Studies, vol. 8, nº 3, 1998, pp. 65-88.The persistence of a dual self-identification expressed by citizens in the Spanish Comunidades Autónomas (nationalities and regions) is one of the main features of centre-periphery relations in democratic Spain. This 'dual identity' or 'compound nationality' incorporates -in variable proportions, individually or subjectively asserted- both state/national and ethnoterritorial identities with no apparent exclusion. It characterises the ambivalent and dynamic nature of spatial politics in decentralized Spain. A succinct review of the main developments in Spain's contemporary history is carried out in order to provide a background for the discussion of the various identities expressed by citizens in Catalonia. A segmentation analysis reviews the various forms of Catalan self-identification, among which ‘duality’ is to be underlined.Peer reviewe