Effects of integrated application of plant-based compost and urea on soil food web, soil properties, and yield and quality of a processing carrot cultivar

Soil nutrient management system characterized by reduced input of inorganic fertilizers integrated with organic amendments is one of the alternatives for reducing deleterious environmental impact of synthetic fertilizers, suppressing soil-borne pests and diseases, and improving soil health and crop yield. A hypothesis of the present study was that lower rates of urea mixed with higher rates of plant compost (PC) would improve nematode community structure, soil food web condition, soil biological, and physiochemical properties, and yield and quality of a processing carrot (Daucus carota) cultivar. Urea and PC were each applied at 135 kg nitrogen (N)/ha alone or at 3:1, 1:1, and 1:3 ratios annually during the 2012 to 2014 growing seasons. A non-amended check served as a control. Nematode community was analyzed from soil samples collected approximately 4-week intervals from planting to 133 days after planting each year. Soil respiration, as a measure of soil biological activity, and soil physiochemical properties were determined from soils collected at planting and at harvest in 2012 and 2013. Results showed that PC alone, and U1:PC1 resulted in soil food web structure significantly above 50 at harvest in 2014. Urea significantly decreased end-of-season soil pH, but increased NO3-N compared with the other treatments. While the herbivore population density was low, abundances of Tylenchus and Malenchus were negatively correlated with carrot fresh weight of marketable carrot. Overall, results suggest that integrating lower rates of urea and higher rates of PC are likely to increase soil biological activity, soil pH, and phosphorus content.

Intrapatient viral diversity and treatment outcome in patients with genotype 3a hepatitis C virus infection on sofosbuvir-containing regimens

Treatment with the direct-acting antiviral agent (DAA) sofosbuvir (SOF), an NS5B inhibitor, and velpatasvir (VEL), an NS5A inhibitor, demonstrates viral cure rates of ≥95% in hepatitis C virus (HCV) genotypes (GT) 1-6. Here, we investigated intrapatient HCV diversity in NS5A and NS5B using Shannon entropy to examine the relationship between viral diversity and treatment outcome. At baseline, HCV diversity was lowest in patients infected with HCV GT3 as compared to the other GTs, and viral diversity was greater in NS5A than NS5B (P < .0001). Treatment outcome with SOF/VEL or the comparator regimen of SOF with ribavirin (RBV) was not correlated with baseline diversity. However, among persons treated with SOF/VEL, a decrease in diversity from baseline was observed at relapse in the majority virologic failures, consistent with a viral bottleneck event at relapse. In contrast, an increase in diversity was observed in 27% of SOF+RBV virologic failures. We investigated whether the increase in diversity was due to an increase in the transition rate, one mode of potential RBV-mediated mutagenesis; however, we found no evidence of this mechanism. Overall, we did not observe that viral diversity at baseline influenced treatment outcome, but the diversity changes observed at relapse can improve our understanding of RBV viral suppression in vivo.

Evolution of the HCV viral population from a patient with S282T detected at relapse after sofosbuvir monotherapy

Clinical phase II/III studies of the nucleotide analogue HCV NS5B inhibitor sofosbuvir (SOF) have demonstrated high efficacy in HCV-infected patients in combination therapy. To date, resistance to SOF (S282T in NS5B) has rarely been detected in patients. In this study, we investigated the evolution of S282T viral variants detected in one HCV genotype 2b-infected patient who relapsed following 12 weeks of SOF monotherapy. Deep sequencing of the NS5B gene was performed on longitudinal plasma samples at baseline, days 2 and 3 on SOF, and longitudinal samples post-SOF treatment through week 48. Intrapatient HCV evolution was analysed by maximum-likelihood phylogenetic analysis. Deep sequencing analysis revealed a low level pre-existence of S282T at 0.05% of viral sequences (4/7755 reads) at baseline and 0.03% (6/23 415 reads) at day 2 on SOF. Viral relapse was detected at week 4 post-treatment where 99.8% of the viral population harboured S282T. Follow-up analysis determined that S282T levels diminished post-treatment reaching undetectable levels 24-48 weeks post-SOF. Phylogenetic analysis together with the persistence of unique post-treatment mutations in all post-SOF samples suggested that growth of wild type resulted from reversion of the S282T mutant to a wild type and not outgrowth of the baseline wild-type population. Our data suggest that a very low level of pre-existing S282T at baseline in this patient was enriched and transiently detected following SOF monotherapy. Despite relapse with drug resistance to SOF, this patient was successfully retreated with SOF plus ribavirin for 12 weeks and is now cured from HCV infection.

Center surround receptive field structure of cone bipolar cells in primate retina

In non-mammalian vertebrates, retinal bipolar cells show center-surround receptive field organization. In mammals, recordings from bipolar cells are rare and have not revealed a clear surround. Here we report center-surround receptive fields of identified cone bipolar cells in the macaque monkey retina. In the peripheral retina, cone bipolar cell nuclei were labeled in vitro with diamidino-phenylindole (DAPI), targeted for recording under microscopic control, and anatomically identified by intracellular staining. Identified cells included 'diffuse' bipolar cells, which contact multiple cones, and 'midget' bipolar cells, which contact a single cone. Responses to flickering spots and annuli revealed a clear surround: both hyperpolarizing (OFF) and depolarizing (ON) cells responded with reversed polarity to annular stimuli. Center and surround dimensions were calculated for 12 bipolar cells from the spatial frequency response to drifting, sinusoidal luminance modulated gratings. The frequency response was bandpass and well fit by a difference of Gaussians receptive field model. Center diameters were all two to three times larger than known dendritic tree diameters for both diffuse and midget bipolar cells in the retinal periphery. In one instance intracellular staining revealed tracer spread between a recorded cell and its nearest neighbors, suggesting that homotypic electrical coupling may contribute to receptive field center size. Surrounds were around ten times larger in diameter than centers and in most cases the ratio of center to surround strength was approximately 1. We suggest that the center-surround receptive fields of the major primate ganglion cell types are established at the bipolar cell, probably by the circuitry of the outer retina.

Long-term outcome of inpatients with tuberculosis assigned to outpatient therapy at a local clinic in New Orleans

BACKGROUND

To characterize the New Orleans tuberculosis (TB) patient population and determine what factors might influence outcome, we followed inpatients with active disease at a large, public hospital who then received outpatient treatment at a public clinic.

METHODS

A total of 61 patients were enrolled from January 1, 1993 through July 1994 and followed until no patients were actively receiving treatment. Demographic and psychosocial data were collected and associated with the number of months of treatment received and final outcome.

RESULTS

Of the 61 patients, 26 (43%) completed treatment, 15 (25%) were lost to follow-up, 11 (18%) died, and 9 (14%) were referred out of the area during treatment. Among those lost to follow-up, 60% received only one month of treatment. Homelessness was the only factor significantly related to whether or not a patient completed outpatient therapy (p = .02) with almost 60% of all homeless patients becoming lost to follow-up. Assignment to directly observed therapy (DOT) did not significantly raise compliance rates. HIV status did not significantly alter the duration of treatment, but these patients had a mortality rate 3 times that of the other patients.

CONCLUSIONS

Efforts to improve TB control should focus on increasing compliance, particularly among the homeless. Although expansion of DOT is essential, raising therapy completion rates to acceptable levels may require additional social services, financial incentives and enforceable legal remedies for noncompliance. More rigorous treatment guidelines are needed to assure consistent management of patients who receive interrupted treatment.

Color, contrast sensitivity, and the cone mosaic

This paper evaluates the role of various stages in the human visual system in the detection of spatial patterns. Contrast sensitivity measurements were made for interference fringe stimuli in three directions in color space with a psychophysical technique that avoided blurring by the eye's optics including chromatic aberration. These measurements were compared with the performance of an ideal observer that incorporated optical factors, such as photon catch in the cone mosaic, that influence the detection of interference fringes. The comparison of human and ideal observer performance showed that neural factors influence the shape as well as the height of the foveal contrast sensitivity function for all color directions, including those that involve luminance modulation. Furthermore, when optical factors are taken into account, the neural visual system has the same contrast sensitivity for isoluminant stimuli seen by the middle-wavelength-sensitive (M) and long-wavelength-sensitive (L) cones and isoluminant stimuli seen by the short-wavelength-sensitive (S) cones. Though the cone submosaics that feed these chromatic mechanisms have very different spatial properties, the later neural stages apparently have similar spatial properties. Finally, we review the evidence that cone sampling can produce aliasing distortion for gratings with spatial frequencies exceeding the resolution limit. Aliasing can be observed with gratings modulated in any of the three directions in color space we used. We discuss mechanisms that prevent aliasing in most ordinary viewing conditions.