Movements of Gulf Sturgeon (Acipenser oxyrinchus desotoi) in Nearshore Habitat as Determined by Acoustic Telemetry

Gulf sturgeon were tagged with telemetry tags and were tracked and relocated in fall and early winter of 1996 and 1998 to determine migration patterns and winter feeding habitats after they emigrated from the Suwannee River, Florida, into the Gulf of Mexico. We hypothesized that their migration would generally follow the drowned Suwannee River channel across the West Florida shelf. Fish left the river in late Oct. or early Nov., about the time river water temperatures fell below 20 C. Tracked and relocated fish moved slowly and remained offshore of Suwannee Sound in nearby shallow (\u3c6 m) marine-estuarine habitats until at least mid or late Dec. The relatively small area (~115km2) within which fish were consistently relocated in 1998 probably is a critically important feeding habitat because adult Gulf sturgeon, which do not feed while in the river, occupy it for up to half their short (4-5 mo) marine residency. The fish left the area in late Dec. or early Jan., most likely in response to powerful cold front-generated weather conditions (under which, boat-based acoustic tracking is infeasible). A large (1,760 km2) adjacent area was searched for sonic-tagged sturgeon in early Jan. 1999, but only one was relocated (~50 km northwest of the Nov.-Dec. area). Although we were unable to address the hypothesis that their migration follows the Suwannee paleochannel, the results do indicate that Gulf sturgeon move to yet unknown, distant, late-winter feeding areas of the Gulf of Mexico before returning to the river in spring

White matter during concussion recovery: Comparing diffusion tensor imaging (DTI) and neurite orientation dispersion and density imaging (NODDI)

Concussion pathophysiology in humans remains incompletely understood. Diffusion tensor imaging (DTI) has identified microstructural abnormalities in otherwise normal appearing brain tissue, using measures of fractional anisotropy (FA), axial diffusivity (AD), and radial diffusivity (RD). The results of prior DTI studies suggest that acute alterations in microstructure persist beyond medical clearance to return to play (RTP), but these measures lack specificity. To better understand the observed effects, this study combined DTI with neurite orientation dispersion and density imaging (NODDI), which employs a more sophisticated description of water diffusion in the brain. A total of 66 athletes were recruited, including 33 concussed athletes, scanned within 7 days after concussion and at RTP, along with 33 matched controls. Both univariate and multivariate methods identified DTI and NODDI parameters showing effects of concussion on white matter. Spatially extensive decreases in FA and increases in AD and RD were associated with reduced intra-neurite water volume, at both the symptomatic phase of injury and RTP, indicating that effects persist beyond medical clearance. Subsequent analyses also demonstrated that concussed athletes with higher symptom burden and a longer recovery time had greater reductions in FA and increased AD, RD, along with increased neurite dispersion. This study provides the first longitudinal evaluation of concussion from acute injury to RTP using combined DTI and NODDI, significantly enhancing our understanding of the effects of concussion on white matter microstructure

Lipid metabolism in patients infected with Nef-deficient HIV-1 strain

Background: HIV protein Nef plays a key role in impairing cholesterol metabolism in both HIV infected and bystander cells. The existence of a small cohort of patients infected with Nef-deficient strain of HIV presented a unique opportunity to test the effect of Nef on lipid metabolism in a clinical setting. Methods: Here we report the results of a study comparing six patients infected with Nef-deficient strain of HIV (Delta NefHIV) with six treatment-naive patients infected with wild-type HIV (WT HIV). Lipoprotein profile, size and functionality of high density lipoprotein (HDL) particles as well as lipidomic and microRNA profiles of patient plasma were analyzed. Results: We found that patients infected with Delta NefHIV had lower proportion of subjects with plasma HDL-C levels < 1 mmol/l compared to patients infected with WT HIV. Furthermore, compared to a reference group of HIV-negative subjects, there was higher abundance of smaller under-lipidated HDL particles in plasma of patients infected with WT HIV, but not in those infected with Delta NefHIV. Lipidomic analysis of plasma revealed differences in abundance of phosphatidylserine and sphingolipids between patients infected with Delta NefHIV and WT HIV. MicroRNA profiling revealed that plasma abundance of 24 miRNAs, many of those involved in regulation of lipid metabolism, was differentially regulated by WT HIV and Delta NefHIV. Conclusion: Our findings are consistent with HIV protein Nef playing a significant role in pathogenesis of lipid-related metabolic complications of HIV disease

Quasi-coherent fluctuations limiting the pedestal growth on Alcator C-Mod: experiment and modelling

Performance predictions for future fusion devices rely on an accurate model of the pedestal structure. The candidate for predictive pedestal structure is EPED, and it is imperative to test the underlying hypotheses to further gain confidence for ITER projections. Here, we present experimental work testing one of the EPED hypotheses, namely the existence of a soft limit set by microinstabilities such as the kinetic ballooning mode. This work extends recent work on Alactor C-Mod (Diallo et al 2014 Phys. Rev. Lett. 112 115001), to include detailed measurements of the edge fluctuations and comparisons of edge simulation codes and experimental observations

Lipid metabolism in patients infected with Nef-deficient HIV-1 strain.

BACKGROUND: HIV protein Nef plays a key role in impairing cholesterol metabolism in both HIV infected and bystander cells. The existence of a small cohort of patients infected with Nef-deficient strain of HIV presented a unique opportunity to test the effect of Nef on lipid metabolism in a clinical setting. METHODS: Here we report the results of a study comparing six patients infected with Nef-deficient strain of HIV (ΔNefHIV) with six treatment-naïve patients infected with wild-type HIV (WT HIV). Lipoprotein profile, size and functionality of high density lipoprotein (HDL) particles as well as lipidomic and microRNA profiles of patient plasma were analyzed. RESULTS: We found that patients infected with ΔNefHIV had lower proportion of subjects with plasma HDL-C levels/l compared to patients infected with WT HIV. Furthermore, compared to a reference group of HIV-negative subjects, there was higher abundance of smaller under-lipidated HDL particles in plasma of patients infected with WT HIV, but not in those infected with ΔNefHIV. Lipidomic analysis of plasma revealed differences in abundance of phosphatidylserine and sphingolipids between patients infected with ΔNefHIV and WT HIV. MicroRNA profiling revealed that plasma abundance of 24 miRNAs, many of those involved in regulation of lipid metabolism, was differentially regulated by WT HIV and ΔNefHIV. CONCLUSION: Our findings are consistent with HIV protein Nef playing a significant role in pathogenesis of lipid-related metabolic complications of HIV disease

A multi-tissue full lifespan epigenetic clock for mice.

Human DNA-methylation data have been used to develop highly accurate biomarkers of aging ( epigenetic clocks ). Recent studies demonstrate that similar epigenetic clocks for mice (Mus Musculus) can be slowed by gold standard anti-aging interventions such as calorie restriction and growth hormone receptor knock-outs. Using DNA methylation data from previous publications with data collected in house for a total 1189 samples spanning 193,651 CpG sites, we developed 4 novel epigenetic clocks by choosing different regression models (elastic net- versus ridge regression) and by considering different sets of CpGs (all CpGs vs highly conserved CpGs). We demonstrate that accurate age estimators can be built on the basis of highly conserved CpGs. However, the most accurate clock results from applying elastic net regression to all CpGs. While the anti-aging effect of calorie restriction could be detected with all types of epigenetic clocks, only ridge regression based clocks replicated the finding of slow epigenetic aging effects in dwarf mice. Overall, this study demonstrates that there are trade-offs when it comes to epigenetic clocks in mice. Highly accurate clocks might not be optimal for detecting the beneficial effects of anti-aging interventions

Management Outcomes in Splenic Injury: A Statewide Trauma Center Review

OBJECTIVE: Clinical pathways now highlight both observation and operation as acceptable initial therapeutic options for the management of patients with splenic injury. The purpose of this study was to evaluate treatment trends for splenic injury in all North Carolina trauma centers over a 6-year period. METHODS: Splenic injuries in adults over a 6-year period (January 1988-December 1993) were identified in the North Carolina Trauma Registry using ICD-9-CM codes. Patients were divided into four groups by method of management: 1) no spleen operation, 2) splenectomy, 3) definitive splenorrhaphy, and 4) splenorrhaphy failure followed by splenectomy. The authors examined age, mechanism of injury, admitting blood pressure, and severity of injury by trauma score and injury severity score. SUMMARY BACKGROUND DATA: Comparisons were made between adult (17-64 years of age) and geriatric (older than 65 years of age) patients and between patients with blunt and penetrating injury. Resource utilization (length of stay, hospital charges) and outcome (mortality) were compared. RESULTS: One thousand two hundred fifty-five patients were identified with splenic injury. Rate of splenic preservation increased over time and was achieved in more than 50% of patients through nonoperative management (40%) and splenorrhaphy (12%). Splenorrhaphy was not used commonly in either blunt or penetrating injury. Overall mortality was 13%. Geriatric patients had a higher mortality and resource utilization regardless of their mechanism of injury or method of management. CONCLUSIONS: Nonoperative management represents the prevailing method of splenic preservation in both the adult and geriatric population in North Carolina trauma center hospitals. Satisfactory outcomes and economic advantages accompany nonoperative management in this adult population

A Search for Time Variation of the Fine Structure Constant

A method offering an order of magnitude sensitivity gain is described for using quasar spectra to investigate possible time or space variation in the fine structure constant, alpha. Applying the technique to a sample of 30 absorption systems, spanning redshifts 0.5 < z< 1.6, obtained with the Keck I telescope, we derive limits on variations in alpha over a wide range of epochs. For the whole sample Delta(alpha)/alpha = -1.1 +/- 0.4 x 10^{-5}. This deviation is dominated by measurements at z > 1, where Delta(alpha)/alpha = -1.9 +/- 0.5 x 10^{-5}. For z < 1, Delta(alpha)/alpha = -0.2 +/- 0.4 x 10^{-5}, consistent with other known constraints. Whilst these results are consistent with a time-varying alpha, further work is required to explore possible systematic errors in the data, although careful searches have so far not revealed any.Comment: 4 pages, 1 figure, accepted for publication in Physical Review Letter

HIV-1 predisposed to acquiring resistance to maraviroc (MVC) and other CCR5 antagonists in vitro has an inherent, low-level ability to utilize MVC-bound CCR5 for entry

<p>Abstract</p> <p>Background</p> <p>Maraviroc (MVC) and other CCR5 antagonists are HIV-1 entry inhibitors that bind to- and alter the conformation of CCR5, such that CCR5 is no longer recognized by the viral gp120 envelope (Env) glycoproteins. Resistance to CCR5 antagonists results from HIV-1 Env acquiring the ability to utilize the drug-bound conformation of CCR5. Selecting for HIV-1 resistance to CCR5-antagonists <it>in vitro </it>is relatively difficult. However, the CCR5-using CC1/85 strain appears to be uniquely predisposed to acquiring resistance to several CCR5 antagonists <it>in vitro </it>including MVC, vicriviroc and AD101.</p> <p>Findings</p> <p>Here, we show that Env derived from the parental CC1/85 strain is inherently capable of a low affinity interaction with MVC-bound CCR5. However, this phenotype was only revealed in 293-Affinofile cells and NP2-CD4/CCR5 cells that express very high levels of CCR5, and was masked in TZM-bl, JC53 and U87-CD4/CCR5 cells as well as PBMC, which express comparatively lower levels of CCR5 and which are more commonly used to detect resistance to CCR5 antagonists.</p> <p>Conclusions</p> <p>Env derived from the CC1/85 strain of HIV-1 is inherently capable of a low-affinity interaction with MVC-bound CCR5, which helps explain the relative ease in which CC1/85 can acquire resistance to CCR5 antagonists <it>in vitro</it>. The detection of similar phenotypes in patients may identify those who could be at higher risk of virological failure on MVC.</p

SEESAW: detecting isoform-level allelic imbalance accounting for inferential uncertainty.

Detecting allelic imbalance at the isoform level requires accounting for inferential uncertainty, caused by multi-mapping of RNA-seq reads. Our proposed method, SEESAW, uses Salmon and Swish to offer analysis at various levels of resolution, including gene, isoform, and aggregating isoforms to groups by transcription start site. The aggregation strategies strengthen the signal for transcripts with high uncertainty. The SEESAW suite of methods is shown to have higher power than other allelic imbalance methods when there is isoform-level allelic imbalance. We also introduce a new test for detecting imbalance that varies across a covariate, such as time