Tracking the changes in virus taxonomy

A database and website ( http://www.ictvonline.org/taxonomyReleases.asp ) have been established where the history of changes in virus taxonomy from 1971 to the present day can easily be traced. Each change is linked to a source document confirming the change or, for most changes since 2002, to the taxonomic proposal approved by the International Committee on Taxonomy of Viruses (ICTV).

Invasive crayfish as vectors of mercury in freshwater food webs of the Pacific Northwest

Invasive species are important drivers of environmental change in aquatic ecosystems and can alter habitat characteristics, community composition, and ecosystem energetics. Such changes have important implications for many ecosystem processes, including the bioaccumulation and biomagnification of contaminants through food webs. Mercury concentrations were measured in 2 nonnative and 1 native crayfish species from western Oregon (USA). Nonnative red swamp crayfish had mercury concentrations similar to those in native signal crayfish (0.29 ± 0.05 µg/g dry wt and 0.36 ± 0.06 µg/g dry wt, respectively), whereas the nonnative ringed crayfish had lower mercury concentrations (0.10 ± 0.02 µg/g dry wt) than either of the other species. The mean energy content of muscle was similar between the native signal crayfish and nonnative ringed crayfish but was significantly higher in the nonnative red swamp crayfish. Across species, mercury concentrations were negatively correlated with energy density. Such energetic differences could exacerbate changes in mercury transfer through trophic pathways of food webs, especially via alterations to the growth dynamics of consumers. Thus, it is important to consider the role of energy content in determining effective mercury exposure even when mercury concentrations on a per-unit mass basis do not differ between species. Environ Toxicol Chem 2014;33:2639-2645. Published 2014 Wiley Periodicals, Inc. on behalf of SETAC. This article is a US Government work and as such, is in the public domain in the United States of America.

Mechanical properties of alginate hydrogels manufactured using external gelation

Alginate hydrogels are commonly used in biomedical applications such as scaffolds for tissue engineering, drug delivery, and as a medium for cell immobilisation. Multivalent cations are often employed to create physical crosslinks between carboxyl and hydroxyl moieties on neighbouring polysaccharide chains, creating hydrogels with a range of mechanical properties. This work describes the manufacture and characterisation of sodium alginate hydrogels using the divalent cations Mg(2+), Ca(2+) and Sr(2+) to promote gelation via non-covalent crosslinks. Gelation time and Young׳s modulus are characterised as a function of cation and alginate concentrations. The implications of this work towards the use of environmental elasticity to control stem cell differentiation are discussed.

Roles of patch characteristics, drought frequency, and restoration in long-term trends of a widespread amphibian

Despite the high profile of amphibian declines and the increasing threat of drought and fragmentation to aquatic ecosystems, few studies have examined long-term rates of change for a single species across a large geographic area. We analyzed growth in annual egg-mass counts of the Columbia spotted frog (Rana luteiventris) across the northwestern United States, an area encompassing 3 genetic clades. On the basis of data collected by multiple partners from 98 water bodies between 1991 and 2011, we used state-space and linear-regression models to measure effects of patch characteristics, frequency of summer drought, and wetland restoration on population growth. Abundance increased in the 2 clades with greatest decline history, but declined where populations are considered most secure. Population growth was negatively associated with temporary hydroperiods and landscape modification (measured by the human footprint index), but was similar in modified and natural water bodies. The effect of drought was mediated by the size of the water body: populations in large water bodies maintained positive growth despite drought, whereas drought magnified declines in small water bodies. Rapid growth in restored wetlands in areas of historical population declines provided strong evidence of successful management. Our results highlight the importance of maintaining large areas of habitat and underscore the greater vulnerability of small areas of habitat to environmental stochasticity. Similar long-term growth rates in modified and natural water bodies and rapid, positive responses to restoration suggest pond construction and other forms of management can effectively increase population growth. These tools are likely to become increasingly important to mitigate effects of increased drought expected from global climate change. Papeles de las Características del Fragmento, Frecuencia de Sequía y Restauración en las Tendencias a Largo Plazo de un Anfibio Ampliamente Distribuido.

The risk of bleeding with duloxetine treatment in patients who use nonsteroidal anti-inflammatory drugs (NSAIDs): analysis of placebo-controlled trials and post-marketing adverse event reports

Purpose

To assess the safety of duloxetine with regards to bleeding-related events in patients who concomitantly did, versus did not, use nonsteroidal anti-inflammatory drugs (NSAIDs), including aspirin.

Methods

Safety data from all placebo-controlled trials of duloxetine conducted between December 1993 and December 2010, and post-marketing reports from duloxetine-treated patients in the US Food and Drug Administration Adverse Event Reporting System (FAERS), were searched for bleeding-related treatment-emergent adverse events (TEAEs). The percentage of patients with bleeding-related TEAEs was summarized and compared between treatment groups in all the placebo-controlled studies. Differences between NSAID user and non-user subgroups from clinical trial data were analyzed by a logistic regression model that included therapy, NSAID use, and therapy-by-NSAID subgroup interaction. In addition, to determine if higher duloxetine doses are associated with an increased incidence of bleeding-related TEAEs, and whether the use of concomitant NSAIDs might influence the dose effect if one exists, placebo-controlled clinical trials with duloxetine fixed doses of 60 mg, 120 mg, and placebo were analyzed. Also, the incidence of bleeding-related TEAEs reported for duloxetine alone was compared with the incidence in patients treated with duloxetine and concomitant NSAIDs. Finally, the number of bleeding-related cases reported for duloxetine in the FAERS database was compared with the numbers reported for all other drugs.

Results

Across duloxetine clinical trials, there was a significantly greater incidence of bleeding-related TEAEs in duloxetine- versus placebo-treated patients overall and also in those patients who did not take concomitant NSAIDS, but no significant difference was seen among those patients who did take concomitant NSAIDS. There was no significant difference in the incidence of bleeding-related TEAEs in the subset of patients treated with duloxetine 120 mg once daily versus those treated with 60 mg once daily regardless of concomitant NSAID use. The combination of duloxetine and NSAIDs was associated with a statistically significantly higher incidence of bleeding-related TEAEs compared with duloxetine alone. A similarly higher incidence of bleeding-related TEAEs was seen in patients treated with placebo and concomitant NSAIDs compared with placebo alone. Bleeding-related TEAEs reported in the FAERS database were disproportionally more frequent for duloxetine taken with NSAIDs compared with the full FAERS background, but there was no difference in the reporting of bleeding-related TEAEs when the cases reported for duloxetine taken with NSAIDs were compared against the cases reported for NSAIDs alone.

Conclusion

Concomitant use of NSAIDs was associated with a higher incidence of bleeding-related TEAEs in clinical trials regardless of whether patients were taking duloxetine or placebo; bleeding-related TEAEs did not appear to increase along with duloxetine dose regardless of NSAID use. In spontaneously reported post-marketing data, the combination of duloxetine and NSAID use was not associated with an increased reporting of bleeding-related events when compared to NSAID use alone.

Selection pressure and founder effects constrain genetic variation in differentiated populations of soilborne bymovirus Wheat yellow mosaic virus (Potyviridae) in China

To study the population genetic structure and forces driving the evolution of Wheat yellow mosaic virus (WYMV), the nucleotide sequences encoding the coat protein (CP) (297 sequences) or the genome-linked virion protein (VPg) (87 sequences) were determined from wheat plants growing at 11 different locations distributed in five provinces in China. There were close phylogenetic relationships between all sequences but clustering on the phylogenetic trees was congruent with their provenance, suggesting an origin-dependent population genetic structure. There were low levels of genetic diversity, ranging from 0.00035 ± 0.00019 to 0.01536 ± 0.00043 (CP), and 0.00086 ± 0.00039 to 0.00573 ± 0.00111 (VPg), indicating genetic stability or recent emergence of WYMV in China. The results may suggest that founder effects play a role in shaping the genetic structure of WYMV. Between-population diversity was consistently higher than within-population diversity, suggesting limited gene flow between subpopulations (average FST 0.6241 for the CP and 0.7981 for the VPg). Consistent amino acid substitutions correlated with the provenance of the sequences were observed at nine positions in the CP (but none in the VPg), indicating an advanced stage in population structuring. Strong negative (purifying) selection was implicated on both the CP and VPg but positive selection on a few codons in the CP, indicating an ongoing molecular adaptation.

Genetic and environmental contributions to the expression of handedness in chimpanzees (Pan troglodytes)

Most humans are right-handed and, like many behavioral traits, there is good evidence that genetic factors play a role in handedness. Many researchers have argued that non-human animal limb or hand preferences are not under genetic control but instead are determined by random, non-genetic factors. We used quantitative genetic analyses to estimate the genetic and environmental contributions to three measures of chimpanzee handedness. Results revealed significant population-level handedness for two of the three measures-the tube task and manual gestures. Furthermore, significant additive genetic effects for the direction and strength of handedness were found for all three measures, with some modulation due to early social rearing experiences. These findings challenge historical and contemporary views of the mechanisms underlying handedness in non-human animals.

Tunable microwave signal generator with an optically-injected 1310 nm QD-DFB laser

Tunable microwave signal generation with frequencies ranging from below 1 GHz to values over 40 GHz is demonstrated experimentally with a 1310 nm Quantum Dot (QD) Distributed-Feedback (DFB) laser. Microwave signal generation is achieved using the period 1 dynamics induced in the QD DFB under optical injection. Continuous tuning in the positive detuning frequency range of the quantum dot's unique stability map is demonstrated. The simplicity of the experimental configuration offers promise for novel uses of these nanostructure lasers in Radio-over-Fiber (RoF) applications and future mobile networks.

Male reproductive health disorders among Aboriginal and Torres Strait Islander men: a hidden problem?

OBJECTIVE

To better understand help-seeking behaviours and reproductive health disorders among Aboriginal and Torres Strait Islander men.

DESIGN, SETTING AND PARTICIPANTS

A cross-sectional mixed-methods study conducted from 1 May 2004 to 30 April 2005 of 293 Aboriginal and Torres Strait Islander men aged 18 years and over from urban, rural and remote communities in the Northern Territory and Queensland.

MAIN OUTCOME MEASURES

Subscale of the International Index of Erectile Function, self-reported help-seeking behaviours for erectile dysfunction (ED) and prostate disease, thematic analysis of semi-structured interviews and focus groups.

RESULTS

The prevalence of moderate-to-severe ED increased across age groups, from about 10% in younger men (under 35 years) to 28% in men aged 55-74 years. Moderate-to-severe ED was strongly associated with reporting a chronic condition (odds ratio [OR], 3.67) and residing in a remote area (OR, 2.94). Aboriginal and Torres Strait Islander men aged 40-59 years showed similar low levels of help-seeking behaviours compared with non-Indigenous men from a comparable population-based study. About half of the men with ED saw a doctor or received treatment for ED in each population. While prostate cancer rates were low in both studies, testing for prostate problems was less frequent in Aboriginal and Torres Strait Islander men (11.4%) than in non-Indigenous men (34.1%, P < 0.001), despite similar levels of concern about prostate cancer. Barriers to help-seeking included shame, culturally inappropriate services and lack of awareness.

CONCLUSION

This study, the first to investigate reproductive health of Aboriginal and Torres Strait Islander men, found low levels of help-seeking behaviours for reproductive health disorders, with implications for missing a predictor of chronic disease and late diagnosis of prostate disease.

Ribosomal DNA analyses reveal greater sequence variation in Polymyxa species than previously thought and indicate the possibility of new ribotype-host-virus associations

Polymyxa species transmit viruses to many important crops. They are poorly understood obligate parasites occupying a distinct position in the Tree of Life. To better understand the potential for spread of Polymyxa-vectored diseases, ribosomal DNA was analysed from isolates covering a wide range of geographical locations, virus associations and hosts. Internal transcribed spacer 2 structure analysis indicated that Polymyxa graminis isolates could represent many species and there was more sequence variation within the known subgroups (ribotypes) than previously described. In cereal crops and soils from temperate climates Polymyxa isolates were usually ribotype I or II, but their host specificities or preferences were unclear. For the first time, there was evidence that ribotype I (in addition to ribotype II) could transmit SBWMV/SBCMV. Different ribotypes often occurred together in the same soil or plant. New hosts were identified for particular ribotypes, including the first detection of the sugar beet-infecting Polymyxa betae, in wheat. Unexpectedly, ribotype III-like sequences, usually restricted to crops in the tropics, were found in wheat from the USA. P. betae isolates showed limited variation (≤ 2%) and the recent change in susceptibility of sugar beet varieties to BNYVV in the USA is unlikely to be due to changes in P. betae.

Risk of cardiovascular disease in HIV, hepatitis C, or HIV/hepatitis C patients compared to the general population

BACKGROUND

As a result of effective antiretroviral therapy HIV patients are living longer, and their risk of cardiovascular disease (CVD) is a growing concern. It remains unknown whether coinfection with hepatitis C (HCV) changes an HIV person's CVD risk, and how the risks compare to the general population. The objective of this study was to compare the Framingham Risk Score (FRS) and vascular age differences in persons with HIV, HCV or HIV/HCV disease to the general population.

METHODS

HIV, HCV, and HIV/HCV patients with clinic visits between 2004 and 2009 were sampled from medical clinics in Rochester, NY. Uninfected persons were randomly selected from the National Health and Nutrition Examination Survey (NHANES), and individually matched on gender, race, and age. We stratified by infection group and conducted separate multivariable linear regression analyses between each infection group and the gender, race, and age matched participants from NHANES.

RESULTS

Rochester patients (HIV = 239, HCV = 167, HIV/HCV = 182) were compared 3 : 1 with the NHANES participants. After controlling for weight, marital status, current pharmacotherapies and the matching variables of gender, race, and age, HIV/HCV patients had a 2% higher general FRS compared with the general population (p = 0.03), and vascular age differences that were 4.1 years greater (p = .01). HCV patients had a 2.4% higher general FRS than the general population (p < .001), and vascular age differences that were 4.4 years greater (p < .001). CVD risk was elevated but not significantly different between HIV patients and the general population.

CONCLUSION

Cardiovascular disease risk is elevated among HIV/HCV and HCV infected persons compared with the general population.

Finger pad friction and its role in grip and touch

Many aspects of both grip function and tactile perception depend on complex frictional interactions occurring in the contact zone of the finger pad, which is the subject of the current review. While it is well established that friction plays a crucial role in grip function, its exact contribution for discriminatory touch involving the sliding of a finger pad is more elusive. For texture discrimination, it is clear that vibrotaction plays an important role in the discriminatory mechanisms. Among other factors, friction impacts the nature of the vibrations generated by the relative movement of the fingertip skin against a probed object. Friction also has a major influence on the perceived tactile pleasantness of a surface. The contact mechanics of a finger pad is governed by the fingerprint ridges and the sweat that is exuded from pores located on these ridges. Counterintuitively, the coefficient of friction can increase by an order of magnitude in a period of tens of seconds when in contact with an impermeably smooth surface, such as glass. In contrast, the value will decrease for a porous surface, such as paper. The increase in friction is attributed to an occlusion mechanism and can be described by first-order kinetics. Surprisingly, the sensitivity of the coefficient of friction to the normal load and sliding velocity is comparatively of second order, yet these dependencies provide the main basis of theoretical models which, to-date, largely ignore the time evolution of the frictional dynamics. One well-known effect on taction is the possibility of inducing stick-slip if the friction decreases with increasing sliding velocity. Moreover, the initial slip of a finger pad occurs by the propagation of an annulus of failure from the perimeter of the contact zone and this phenomenon could be important in tactile perception and grip function.

Short communication: risk of elevated total cholesterol/high-density lipoprotein cholesterol ratio after antiretroviral therapy in HIV/hepatitis C virus patients

Dyslipidemia from highly active antiretroviral therapy (HAART) use has been reported to be less severe among persons with HIV and hepatitis C (HCV) compared to those with HIV monoinfection. However, the effect on lipoprotein ratios is less clear. The total cholesterol/high-density lipoprotein ratio (TC/HDL-C ratio) is a robust measure of cardiovascular disease (CVD) risk but has not been examined in the context of HIV/HCV-coinfected patients. We compared the TC/HDL-C ratio before HAART initiation and after at least 6 months on HAART between patients monoinfected with HIV and coinfected with HIV and HCV. Pre- and post-HAART TC, HDL-C, and non-HDL-C were also assessed. Although TC, HDL-C, and non-HDL-C significantly increased after HAART initiation in both HIV and HIV/HCV patients, the TC/HDL-C ratio did not. In addition, although the pre- and post-HAART TC, HDL-C, non-HDL-C, and TC/HDL-C ratio were significantly different between HIV and HIV/HCV patients, the magnitude in the change from pre- to post-HAART was not significantly different between infection groups. These results persisted after controlling for age, sex, race, current pharmacotherapy for lipoproteins, body mass index, and current CD4 cell count. The magnitude of change in the TC/HDL-C ratio after HAART initiation is not significantly different between HIV and HIV/HCV patients, suggesting subsequent CVD risk in HIV/HCV patients may be greater than currently appreciated.

Stability of the nonlinear dynamics of an optically injected VCSEL

Automated protocols have been developed to characterize time series data in terms of stability. These techniques are applied to the output power time series of an optically injected vertical cavity surface emitting laser (VCSEL) subject to varying injection strength and optical frequency detuning between master and slave lasers. Dynamic maps, generated from high resolution, computer controlled experiments, identify regions of dynamic instability in the parameter space.

Optically-pumped dilute nitride spin-VCSEL

We report the first room temperature optical spin-injection of a dilute nitride 1300 nm vertical-cavity surface-emitting laser (VCSEL) under continuous-wave optical pumping. We also present a novel experimental protocol for the investigation of optical spin-injection with a fiber setup. The experimental results indicate that the VCSEL polarization can be controlled by the pump polarization, and the measured behavior is in excellent agreement with theoretical predictions using the spin flip model. The ability to control the polarization of a long-wavelength VCSEL at room temperature emitting at the wavelength of 1.3 µm opens up a new exciting research avenue for novel uses in disparate fields of technology ranging from spintronics to optical telecommunication networks.