Parametric survival models for interval-censored data with time-dependent covariates

We present a parametric family of regression models for interval-censored event-time (survival) data that accomodates both fixed (e.g. baseline) and time-dependent covariates. The model employs a three-parameter family of survival distributions that includes the Weibull, negative binomial, and log-logistic distributions as special cases, and can be applied to data with left, right, interval, or non-censored event times. Standard methods, such as Newton-Raphson, can be employed to estimate the model and the resulting estimates have an asymptotically normal distribution about the true values with a covariance matrix that is consistently estimated by the information function. The deviance function is described to assess model fit and a robust sandwich estimate of the covariance may also be employed to provide asymptotically robust inferences when the model assumptions do not apply. Spline functions may also be employed to allow for non-linear covariates. The model is applied to data from a long-term study of type 1 diabetes to describe the effects of longitudinal measures of glycemia (HbA1c) over time (the time-dependent covariate) on the risk of progression of diabetic retinopathy (eye disease), an interval-censored event-time outcome.     

Recurrent laryngeal nerve activity exhibits a 5-HT-mediated long-term facilitation and enhanced response to hypoxia following acute intermittent hypoxia in rat

A progressive and sustained increase in inspiratory-related motor output ("long-term facilitation") and an augmented ventilatory response to hypoxia occur following acute intermittent hypoxia (AIH). To date, acute plasticity in respiratory motor outputs active in the postinspiratory and expiratory phases has not been studied. The recurrent laryngeal nerve (RLN) innervates laryngeal abductor muscles that widen the glottic aperture during inspiration. Other efferent fibers in the RLN innervate adductor muscles that partially narrow the glottic aperture during postinspiration. The aim of this study was to investigate whether or not AIH elicits a serotonin-mediated long-term facilitation of laryngeal abductor muscles, and if recruitment of adductor muscle activity occurs following AIH. Urethane anesthetized, paralyzed, unilaterally vagotomized, and artificially ventilated adult male Sprague-Dawley rats were subjected to 10 exposures of hypoxia (10% O(2) in N(2), 45 s, separated by 5 min, n = 7). At 60 min post-AIH, phrenic nerve activity and inspiratory RLN activity were elevated (39 ± 11 and 23 ± 6% above baseline, respectively). These responses were abolished by pretreatment with the serotonin-receptor antagonist, methysergide (n = 4). No increase occurred in time control animals (n = 7). Animals that did not exhibit postinspiratory RLN activity at baseline did not show recruitment of this activity post-AIH (n = 6). A repeat hypoxia 60 min after AIH produced a significantly greater peak response in both phrenic and RLN activity, accompanied by a prolonged recovery time that was also prevented by pretreatment with methysergide. We conclude that AIH induces neural plasticity in laryngeal motoneurons, via serotonin-mediated mechanisms similar to that observed in phrenic motoneurons: the so-called "Q-pathway". We also provide evidence that the augmented responsiveness to repeat hypoxia following AIH also involves a serotonergic mechanism.     

Evolutionary history of the genus Trisopterus

The group of small poor cods and pouts from the genus Trisopterus, belonging to the Gadidae family, comprises four described benthopelagic species that occur across the North-eastern Atlantic, from the Baltic Sea to the coast of Morocco, and the Mediterranean. Here, we combined molecular data from mitochondrial (cytochrome b) and nuclear (rhodopsin) genes to confirm the taxonomic status of the described species and to disentangle the evolutionary history of the genus. Our analyses supported the monophyly of the genus Trisopterus and confirmed the recently described species Trisopterus capelanus. A relaxed molecular clock analysis estimated an Oligocene origin for the group (∼30 million years ago; mya) indicating this genus as one of the most ancestral within the Gadidae family. The closure and re-opening of the Strait of Gibraltar after the Messinian Salinity Crisis (MSC) probably triggered the speciation process that resulted in the recently described T. capelanus.     

Role of hepatic macrophages during the viral haemorrhagic fever induced by African Swine Fever Virus

To ascertain the role played by the various liver monocyte-macrophage populations in the course of a viral hemorrhagic fever, fifteen pigs were inoculated intramuscularly with the highly virulent isolate of African Swine Fever Virus (ASFV) Espa?a-70 and slaughtered at 1-7 days post-inoculation (dpi). Samples of liver were fixed in different solutions and routinely processed for morphological, immunohistochemical and ultrastructural studies. Viral antigen (vp73) was detected from 3 dpi onward, mainly in circulating monocytes of sinusoid and Kupffer's cells (KC), as well as in portal macrophages and hepatocytes from 5 dpi. Anti-SWC3 immunolabelled cells were increased from 1 dpi, peaking between 3 and 5 dpi, thereafter declining until the end of the experiment. The significant increase in the number of sinusoidal circulating monocytes and KC expressing IL-1alpha, TNFalpha and IL-6 from 1 dpi, confirmed the secretory activation of these cells. The results show that in the course of an ASFV-induced hemorrhagic syndrome, hepatic macrophage populations undergo major quantitative and biosynthetic changes prior to virus detection, suggesting the existence of a mechanism by which the virus concentrates infectable cells, which subsequently spread the virus around the body.     

Proteomic approaches to identifying carbonylated proteins in brain tissue

Oxidative stress plays a critical role in the pathogenesis of a number of diseases. The carbonyl end products of protein oxidation are among the most commonly measured markers of oxidation in biological samples. Protein carbonyl functional groups may be derivatized with 2,4-dinitrophenylhydrazine (DNPH) to render a stable 2,4-dinitrophenylhydrazone-protein (DNP-protein) and the carbonyl contents of individual proteins then determined by two-dimensional electrophoresis followed by immunoblotting using specific anti-DNP antibodies. Unfortunately, derivatization of proteins with DNPH could affect their mass spectrometry (MS) identification. This problem can be overcome using nontreated samples for protein identification. Nevertheless, derivatization could also affect their mobility, which might be solved by performing the derivatization step after the initial electrophoresis. Here, we compare two-dimensional redox proteome maps of mouse cerebellum acquired by performing the DNPH derivatization step before or after electrophoresis and detect differences in protein patterns. When the same approach is used for protein detection and identification, both methods were found to be useful to identify carbonylated proteins. However, whereas pre-DNPH derivatized proteins were successfully analyzed, high background staining complicated the analysis when the DNPH reaction was performed after transblotting. Comparative data on protein identification using both methods are provided.     

Molecular phylogeny and morphological homoplasy in fruitbats.

The present study evaluates the evolutionary framework of the Old World fruitbats based on the cytochrome b and 16S rRNA mitochondrial gene sequences from a wide range of taxa. Phylogenetic analyses indicated that morphology-based subfamilies and most suprageneric groups are nonnatural assemblages. They also support the existence of an endemic African clade of fruitbats. The discrepancy between the evolutionary relationships yielded by molecular and morphological data sets may be, at least in part, explained by the recurrent retention of primitive morphology (Rousettus-like) across different lineages. The maintenance of primitive characters in different groups of flying foxes, as well as morphological convergence in nectar-feeding bats and possibly also in short-muzzle bats, may have led to high levels of homoplasy, resulting in misleading taxonomic arrangements. This may be particularly so with respect to high taxonomic levels based on morphological characters.     

A quantitative study of enterotoxin production by sheep milk staphylococci

Of 124 staphylococcal strains isolated from sheep milk, 78 produced enterotoxin A, B, C, or D when evaluated by an enzyme-linked immunosorbent assay. Enterotoxins A and D, elaborated by 44 and 43 strains, respectively, showed the highest incidence. Enterotoxin production by coagulase-negative strains (one Staphylococcus cohnii, three S. epidermidis, five S. haemolyticus, and four S. xylosus) was detected. Linear and logarithmic-logarithmic regressions of optical density on enterotoxin concentration yielded the best-fitting equations for enterotoxin quantitation. A significantly higher incidence of enterotoxin producers and significantly higher levels of enterotoxins produced were recorded for coagulase-positive, thermostable nuclease-positive, hemolysis-positive, or mannitol-positive strains. Mannitol utilization was the best test for discriminating between enterotoxigenic and nonenterotoxigenic staphylococci.     

Extraction, purification and characterization of the plant-produced HPV16 subunit vaccine candidate E7 GGG

Several studies indicated that biopharmaceuticals based on the recombinant protein E7 of human papillomavirus (HPV) can serve as therapeutic vaccines preventing the development of cancer in women infected with high-risk types of HPV such as HPV16. Here, we report effective extraction and purification of a plant-produced E7GGG-lichenase fusion protein, an HPV16 subunit vaccine candidate, from Nicotiana benthamiana plants, to a high yield. The target contains the modified HPV16 E7 protein internally fused to the surface loop of a truncated, hexa-His- and KDEL-tagged variant of bacterial lichenase, and has been previously shown to possess anti-cancer activity in an animal model. We purified the protein using a combination of immobilized metal-ion affinity chromatography and gel filtration. The achieved purity of the final product was 99% as confirmed by Coomassie or SYPRO Ruby staining after sodium dodecyl sulfate-polyacrylamide gel electrophoresis and by analytical size exclusion chromatography coupled with multi-angle laser light scattering. The overall yield was 50% corresponding to 0.1g of protein per 1 kg plant biomass. Only slight changes in these parameters were observed during the process scale-up from 50 g to 1 kg of processed leaf biomass.