Phylogenetic analysis of full-length, early infection, hepatitis C virus genomes among people with intravenous drug use: the InC3 Study.

Cross-continental phylogenetic analysis is important to understand subtle molecular differences of currently circulating hepatitis C virus (HCV) subtypes. Existence of such differences can be crucial in pursuing a universal hepatitis C vaccine. We characterized molecular epidemiology of early HCV infections identified across nine cohorts [North America (n=4), Australia (n=4) and Europe (n=1)] in the International Collaborative of Incident HIV and Hepatitis C in Injecting Cohorts (InC3 ). One hundred and ninety-two full-length HCV genomes were amplified from plasma of incident infections and subjected to next generation sequencing to establish the largest cross-continental, full-length acute HCV genomic data set available to date. Genomes from the most common subtypes (1a: n=94, 2b: n=15 and 3a: n=68) were used in phylogenetic analysis. Using full genome trees, 78 sequences (44%) were found to lie within 29 phylogenetic clusters/pairs defined on the basis of molecular similarity of consensus sequences. Of these, 26 each had exclusively Australian or North American sequences indicating a strong geographical bias for molecular similarity. On further analysis of behavioural and demographic associations, binary logistic regression analysis showed that older age and non-Caucasian ethnicity were significantly associated with clustering. HCV probably evolves in micro-epidemics within geographically isolated communities.

Analysis of resistance-associated substitutions in acute hepatitis C virus infection by deep sequencing across six genotypes and three continents.

Several direct-acting antivirals (DAAs) have been approved for the treatment of chronic hepatitis C virus (HCV) infections, opening the door to highly effective interferon-free treatment regimens. Resistance-associated substitutions (RASs) have been reported both in treatment-naïve patients and following treatment with protease (NS3), phosphoprotein (NS5A) and polymerase (NS5B) inhibitors. The prevalence of naturally occurring RASs in untreated HCV-infected individuals has mostly been analysed in those infected with genotype 1 (GT1), in the late phase of infection, and only within limited regions of the genome. Furthermore, the geographic distribution of RASs remains poorly characterized. In this study, we used next-generation sequencing to analyse full-length HCV genomes for the prevalence of RASs in acute HCV infections identified in nine international prospective cohorts. RASs were analysed in 179 participants infected with all six major HCV genotypes (GT1-GT6), and the geographic distribution of RASs was assessed in 107 GT1a and GT3a samples. While RASs were detected at varied frequencies across the three genomic regions, and between genotypes, RASs relevant to multiple DAAs in the leading IFN-free regimens were rarely detected in combination. Low-frequency RASs (<10% of the viral population) were also shown to have a GT-specific distribution. The main RASs with geographic associations were NS3 Q80K in GT1a samples and NS5B N142T in GT3a. These data provide the backdrop for prospective surveillance of RASs during DAA treatment scale-up.

Response to treatment following recently acquired hepatitis C virus infection in a multicentre collaborative cohort.

Pegylated interferon therapy is highly effective in recently acquired HCV. The optimal timing of treatment, regimen and influence of host factors remains unclear. We aimed to measure sustained virological response (SVR) during recent HCV infection and identify predictors of response. Data were from five prospective cohorts of high-risk individuals in Australia, Canada, Germany and the United States. Individuals with acute or early chronic HCV who commenced pegylated interferon therapy were included. The main outcome was SVR, and predictors were assessed using logistic regression. Among 516 with documented recent HCV infection, 237 were treated (pegylated interferon n = 161; pegylated interferon/ribavirin n = 76) (30% female, median age 35 years, 56% ever injected drugs, median duration of infection 6.2 months). Sixteen per cent (n = 38) were HIV/HCV co-infected. SVR among those with HCV mono-infection was 64% by intention to treat; SVR was 68% among HCV/HIV co-infection. Independent predictors of SVR in HCV mono-infection were duration of HCV infection (the odds of SVR declined by 8% per month of infection, aOR 0.92, 95% CI 0.85-0.99, P = 0.033), IFNL4 genotype (adjusted OR 2.27, 95% CI 1.13-4.56, P = 0.021), baseline HCV RNA <400 000 IU/mL (aOR 2.06, 95% CI 1.03-4.12, P = 0.041) and age ≥40 years (vs <30: aOR 2.92, 95% CI 1.31-6.49, P = 0.009), with no difference by drug regimen, HCV genotype, symptomatic infection or gender. The effect of infection duration on odds of SVR was greater among genotype-1 infection. Interferon-based HCV treatment is highly effective in recent HCV infection. Duration of infection, IFNL4 genotype and baseline HCV RNA levels can predict virological response and may inform clinical decision-making.

The transport of exogenous cholesterol in the rabbit. I. Role of cholesterol ester of lymph chylomicra and lymph very low density lipoproteins in absorption.

Thoracic lymph duct cannulations were performed shortly after a meal in rabbits trained to ingest a moderate fat, low cholesterol diet. A tracer dose of cholesterol-(3)H was administered to label exogenous (dietary) cholesterol during absorption. Sequential lymph samples were collected up to 24 hr postprandially, after which ultracentrifugal fractionation of lymph lipoproteins was carried out. The d < 1.006 lipoproteins were separated into two classes, chylomicra and very low density lipoproteins (VLDL).A comparison was made between chylomicra and VLDL of lymph in the transport of exogenous cholesterol after ingestion of a single meal. The per cent of exogenous cholesterol present in VLDL of sequential lymph collections progressively increased with time after a meal and by 18 hr had reached a value of 80% or greater. In chylomicra the per cent of exogenous cholesterol of sequential lymph collections progressively decreased. Therefore, exogenous cholesterol was preferentially transported in VLDL compared with chylomicra. Cholesterol ester specific activity (CESA) of lymph chylomicra and VLDL increased at a more rapid rate than free cholesterol specific activity (FCSA). CESA of VLDL was three times higher than FCSA at the maximum. Exogenous cholesterol which appeared in both chylomicra and VLDL was consistently 80% esterified. while the per cent of total cholesterol esterified decreased with time and was significantly lower than that for exogenous cholesterol from 6 to 24 hr postprandially. These results demonstrate preferential esterification of exogenous cholesterol during absorption and indicate that a mechanism exists within the intestinal mucosal cell to maintain both free and esterified exogenous cholesterol in a chemically distinct pool from endogenous cholesterol during incorporation into both chylomicra and VLDL.

Numerical simulations of subsurface probing in diffusely scattering media using spatially offset Raman spectroscopy.

We present the first elementary model predicting how Raman intensities vary for a range of experimental variables for spatially offset Raman spectroscopy (SORS), a recently proposed technique for the effective retrieval of Raman spectra of subsurface layers in diffusely scattering media. The model was able to reproduce the key observations made from the first SORS experiments, namely the dependence of Raman signal intensities on the spatial offset between the illumination and collection points and the relative contributions to the overall spectrum from the top layer and sub-layer. The application of the SORS concept to a three-layer system is also discussed. The model also clearly indicates that an annular geometry, rather than a point-collection geometry, which was used in the earlier experiments, would yield much improved data.

Subsurface probing in diffusely scattering media using spatially offset Raman spectroscopy.

We describe a simple methodology for the effective retrieval of Raman spectra of subsurface layers in diffusely scattering media. The technique is based on the collection of Raman scattered light from surface regions that are laterally offset away from the excitation laser spot on the sample. The Raman spectra obtained in this way exhibit a variation in relative spectral intensities of the surface and subsurface layers of the sample being investigated. The data set is processed using a multivariate data analysis to yield pure Raman spectra of the individual sample layers, providing a method for the effective elimination of surface Raman scatter. The methodology is applicable to the retrieval of pure Raman spectra from depths well in excess of those accessible with conventional confocal microscopy. In this first feasibility study we have differentiated between surface and subsurface Raman signals within a diffusely scattering sample composed of two layers: trans-stilbene powder beneath a 1 mm thick over-layer of PMMA (poly(methyl methacrylate)) powder. The improvement in contrast of the subsurface trans-stilbene layer without numerical processing was 19 times. The potential applications include biomedical subsurface probing of specific tissues through different overlying tissues such as assessment of bone quality through skin, providing an effective noninvasive means of screening for bone degeneration, other skeletal disease diagnosis, and dermatology studies, as well as materials and catalyst research.

A cell-kinetics model for radiation-induced myelopoiesis.

A mathematical model of time-dependent cellular damage, repair, killing and repopulation of bone marrow following treatments with ionizing radiations is described. Effects from variable dose rates, multiple exposures, different radiation sources and arbitrary intervals between treatments can be modeled by ordinary differential equations. Of several unique features, the most unusual is that rate constants for injury, repair, killing and proliferation of cells are evaluated by likelihood analysis of animal mortality data. Results indicate that a relatively radioresistant pool of bone marrow cells mediates the proliferation of the hematopoietic stem cells. Applications include modeling of 1) myelopoietic integrity as a function of time and dose rate, 2) the whole-body survival curve (at any point in the treatment protocol) for cells critical to myelopoiesis, 3) a prompt dose equivalence from any completed portion of a therapeutic schedule and 4) potential gain from schedule changes during the course of the treatment.

A longitudinal study of hepatitis C virus testing and infection status notification on behaviour change in people who inject drugs.

BACKGROUND: Hepatitis C virus (HCV) testing and counselling have the potential to impact individual behaviour and transmission dynamics at the population level. Evidence of the impact of an HCV-positive status notification on injection risk reduction is limited. The objective of our study was to (1) assess drug and alcohol use and injection risk behaviours following notification; (2) to compare behaviour change in people who inject drugs (PWID) who received a positive test result and those who remained negative; and (3) to assess the effect of age on risk behaviour. METHODS: Data from the International Collaboration of Incident HIV and HCV Infection in Injecting Cohorts (InC3 Study) were analysed. Participants who were initially HCV seronegative were followed prospectively with periodic HCV blood testing and post-test disclosure and interview-administered questionnaires assessing drug use and injection behaviours. Multivariable generalised estimating equations were used to assess behavioural changes over time. RESULTS: Notification of an HCV-positive test was independently associated with a small increase in alcohol use relative to notification of a negative test. No significant differences in postnotification injection drug use, receptive sharing of ancillary injecting equipment and syringe borrowing postnotification were observed between diagnosis groups. Younger PWID receiving a positive HCV test notification demonstrated a significant increase in subsequent alcohol use compared with younger HCV negative. CONCLUSIONS: The proportion of PWID reporting alcohol use increased among those receiving an HCV-positive notification, increased the frequency of alcohol use postnotification, while no reduction in injection drug use behaviours was observed between notification groups. These findings underscore the need to develop novel communication strategies during post-test notification to improve their impact on subsequent alcohol use and risk behaviours.

Determination of cholesterol using o-phthalaldehyde.

A simple, rapid method for the determination of cholesterol in plasma and tissue using o-phthalaldehyde is presented. Comparison of this method with the FeCl(3) method gave identical results. However, the o-phthalaldehyde determination is three times more sensitive than the FeCl(3) determination (molar extinction coefficients of 11,610 and 33,440 for FeCl(3) and o-phthalaldehyde, respectively), it takes less time to complete, and the color developed is more stable. The o-phthalaldehyde method can be used to assay free and esterified cholesterol directly after thin-layer chromatographic separation.

A polymorphism in the cystatin C gene is a novel risk factor for late-onset Alzheimer's disease.

OBJECTIVE: To investigate whether or not a coding polymorphism in the cystatin C gene (CST3) contributes risk for AD. DESIGN: A case-control genetic association study of a Caucasian dataset of 309 clinic- and community-based cases and 134 community-based controls. RESULTS: The authors find a signficant interaction between the GG genotype of CST3 and age/age of onset on risk for AD, such that in the over-80 age group the GG genotype contributes two-fold increased risk for the disease. The authors also see a trend toward interaction between APOE epsilon4-carrying genotype and age/age of onset in this dataset, but in the case of APOE the risk decreases with age. Analysis of only the community-based cases versus controls reveals a significant three-way interaction between APOE, CST3 and age/age of onset. CONCLUSION: The reduced or absent risk for AD conferred by APOE in older populations has been well reported in the literature, prompting the suggestion that additional genetic risk factors confer risk for later-onset AD. In the author's dataset the opposite effects of APOE and CST3 genotype on risk for AD with increasing age suggest that CST3 is one of the risk factors for later-onset AD. Although the functional significance of this coding polymorphism has not yet been reported, several hypotheses can be proposed as to how variation in an amyloidogenic cysteine protease inhibitor may have pathologic consequences for AD.

Mathematical models of marrow cell kinetics: differential effects of protracted irradiations on stromal and stem cells in mice.

UNLABELLED: It is known that hematopoiesis is supported by bone-marrow stem cells, but those cells must seed and grow on a stromal microenvironment. Typically, studies have shown that a surviving fraction of about 30 hematopoietic stem cells (HSCs) (i.e., about 0.04%) correspond to the LD50, although other studies have shown that marrow can repopulate from a single viable cell under strong regiments of antibiotics and infusions of irradiated blood elements. PURPOSE: This paper describes comparisons between our results (from maximum-likelihood estimation techniques for cellular damage, repair, and compensatory repopulation) and published experimental data on marrow stromal cells. METHODS AND MATERIALS: After biophysical consideration of the rate constants that were derived by maximizing the likelihood function (a consideration necessary to extend the model to cell populations not indicated by the model as "critical" for recovery), the rate constants for cellular damage to stem cells are fitted to experimental data. Rate constants for repair and proliferation of stem cells are assigned based on published data on repair/proliferation half-times, and these assignments affect the evaluation of the rate constants for cellular damage. From the two models, that is one for "critical" cells (having radiosensitive and repopulation characteristics similar to stromal cells) and another for stem cells, effects on two cell populations of different radiosensitivities and repopulation rates can be demonstrated for complex schedules of protracted irradiations which could reduce either cell population below a critical need for marrow repopulation. RESULTS: Our analysis of animal mortality data has indicated that recovery of an animal from potentially lethal irradiation is dominantly regulated by cells with survival and repopulation characteristics similar to those of stroma cells. CONCLUSION: In contrast to the surviving fraction of hematopoietic stem cells, it appears that the probability of an animal's recovery is high if the "critical" population of cells is above 1% (our "best" maximum likelihood estimate, from mouse data, with the corresponding lower confidence bound at about 0.2%). Of course, a few stem cells--perhaps only one--must maintain a potential for repopulation of blood and marrow.

Modeling marrow damage from response data: evolution from radiation biology to benzene toxicity.

Consensus principles from radiation biology were used to describe a generic set of nonlinear, first-order differential equations for modeling toxicity-induced compensatory cell kinetics in terms of sublethal injury, repair, direct killing, killing of cells with unrepaired sublethal injury, and repopulation. This cellular model was linked to a probit model of hematopoietic mortality that describes death from infection and/or hemorrhage between 5 and 30 days. Mortality data from 27 experiments with 851 dose-response groups, in which doses were protracted by rate and/or fractionation, were used to simultaneously estimate all rate constants by maximum-likelihood methods. Data used represented 18,940 test animals: 12,827 mice, 2925 rats, 1676 sheep, 829 swine, 479 dogs, and 204 burros. Although a long-term, repopulating hematopoietic stem cell is ancestral to all lineages needed to restore normal homeostasis, the dose-response data from the protracted irradiations indicate clearly that the particular lineage that is critical to hematopoietic recovery does not resemble stemlike cells with regard to radiosensitivity and repopulation rates. Instead, the weakest link in the chain of hematopoiesis was found to have an intrinsic radioresistance equal to or greater than stromal cells and to repopulate at the same rates. Model validation has been achieved by predicting the LD50 and/or fractional group mortality in 38 protracted-dose experiments (rats and mice) that were not used in fitting of model coefficients.

The effect of morphine on fear extinction in rats.

Rats were trained on an appetitive discretetrial discriminated-punishment task in which they learned to suppress responding when an intense flashing light predicting punishment was present and to respond rapidly on trials when the flashing light was absent. Once animals were performing discriminatively, 0.75, 3.0, or 6.0 mg/kg of morphine (base) was administered and a fear extinction session consisting of 60 nonshocked presentations of the flashing light was given. Two saline control groups, one that received fear extinction and one that did not, were also included in the experiment. On the day following fear extinction, all rats were tested in the undrugged state on the discriminated punishment problem, but without shock. The rats receiving 3.0 and 6.0 mg/kg of morphine before the fear extinction session were suppressed by the flashing light more than the saline extinction group or the 0.75 mg/kg morphine treatment group. Moreover, the two higher dose morphine groups were suppressed as readily as the saline group that received no fear extinction. These results are attributed to the antiemotionality effects of morphine.

A mathematical model for radiation-induced myelopoiesis.

A model for damage, repair, killing, and repopulation of myelopoietic marrow is presented. Evaluation produces time and dose-rate profiles during and following any complex irradiation. Equations model variable dose rates, multiple exposures, different sources, and arbitrary intervals between treatments. If factors which dominate the control of biological processes can be demonstrated, an option is to set biological rate constants to experimentally determined values. Previously, knowledge did not permit identification of dominating biological processes and their temporal rates. But a unique feature of this study is that unspecified lesions for killing and injury of cells are evaluated from mortality data on the animal species of choice. "Unspecified" is used to indicate a condition of assumption-free modeling of molecular processes, whereby rate constants for cellular effects are simply computed directly from animal mortality data. Coefficients (estimated by maximum-likelihood methods for nonspecific processes) are compared with experimental values for specific processes. The model has many uses, including modeling of the myelopoietic potential as a function of time. Another option is to calculate the whole-body survival curve for cells that control myelopoiesis as a result of the treatment schedule. Also through simple extensions of the model, an extremely complex protocol can be identified with an equivalent prompt dose value--even for partial-body, fractionated exposures.

Estimation of coefficients in a model of radiation-induced myelopoiesis from mortality data for mice following X-ray exposure.

The rate coefficients in the model of cell kinetics and mortality introduced by Jones et al. (Radiat. Res. 128, 258-266 (1991)) are estimated using mortality data from several mouse experiments. The evaluated model fits data from a large variety of prompt, protracted, and fractionated irradiations with 250-k Vp X rays with good fidelity. Although the maximum-likelihood estimates are not unique, all estimates lead to greater cell survival than that observed in in vitro experiments on nonterminally differentiated reproducing cells from the marrow.

A cell kinetics model of radiation-induced myelopoiesis: rate coefficient estimates for mouse, rat, sheep, swine, dog, and burro irradiated by photons.

Rate coefficients in the model of cell kinetics and mortality introduced by Jones et al. (Radiat. Res. 128, 258-266, 1991) are estimated using mortality data from 27 animal experiments. Adjustments are made for the six species and three nominal classes of gamma radiation represented in these studies. The model fits most of the mortality data quite well when the rate coefficient representing cellular proliferation is fitted to individual species and each of the other coefficients is given a single value across the entire data set. Results are qualitatively similar to those reported by Morris et al. (Radiat. Res. 128, 267-275, 1991) who estimated the rate coefficients from a limited number of mouse studies involving only 250 kVp X rays. As in the earlier study, estimates here lead to greater cell survival than is observed for marrow cells in the amplification division compartment.

Forebrain noradrenaline depletion blocks the release by chlordiazepoxide of behavioral extinction in the rat.

The interaction between chlordiazepoxide (CDP) and forebrain noradrenaline (NA) was investigated in rats with bilateral radiofrequency lesions of the noradrenergic dorsal tegmental bundle (DTB). Forebrain NA was reduced to 35% of control by the DTB lesions; hypothalamic NA and dopamine were unchanged. Rats were trained on a straight alley runway task for food reward. During extinction of the runway task, CDP significantly increased extinction responding in sham lesion animals but not in DTB lesion animals. Thus, CDP was ineffective in increasing resistance to extinction responding in the runway task in animals with significant depletion of forebrain NA.

Guest editorial: special section on biomedical applications of vibrational spectroscopic imaging.

This Special Section Guest Editorial provides an overview of the topical area and an introduction to the articles featured in the special section.

Application of vibrational spectroscopy to the study of mineralized tissues (review).

The infrared and Raman spectroscopy of bone and teeth tissues are reviewed. Characteristic spectra are obtained for both the mineral and protein components of these tissues. Vibrational spectroscopy is used to study the mineralization process, to define the chemical structure changes accompanying bone diseases, and to characterize interactions between prosthetic implants and tissues. Microspectroscopy allows acquisition of spatially resolved spectra, with micron scale resolution. Recently developed imaging modalities allow tissue imaging with chemical composition contrast.

Spatial distribution of phosphate species in mature and newly generated Mammalian bone by hyperspectral Raman imaging.

Hyperspectral Raman images of mineral components of trabecular and cortical bone at 3 µm spatial resolution are presented. Contrast is generated from Raman spectra acquired over the 600-1400 cm-1 Raman shift range. Factor analysis on the ensemble of Raman spectra is used to generate descriptors of mineral components. In trabecular bone independent phosphate (PO4-3) and monohydrogen phosphate (HPO4-2) factors are observed. Phosphate and monohydrogen phosphate gradients extend from trabecular packets into the interior of a rod. The gradients are sharply defined in newly regenerated bone. There, HPO4-2 content maximizes near a trabecular packet and decreases to a minimum value over as little as a 20 µm distance. Incomplete mineralization is clearly visible. In cortical bone, factor analysis yields only a single mineral factor containing both PO4-3 and HPO4-2 signatures and this implies uniform distribution of these ions in the region imaged. Uniform PO4-3 and HPO4-2 distribution is verified by spectral band integration. © 1999 Society of Photo-Optical Instrumentation Engineers.