Polygenic prediction of major depressive disorder and related traits in African ancestries UK Biobank participants

Introduction

Genome-Wide Association Studies (GWAS) over-represent European ancestries compared to the global population, neglecting all other ancestry groups and low-income nations. Consequently, polygenic risk scores (PRS) more accurately predict complex traits in Europeans than African Ancestries groups. Very few studies have looked at the transferability of European-derived PRS for behavioural and mental health phenotypes to non-Europeans. We assessed the comparative accuracy of PRS for Major Depressive Disorder (MDD) trained on European and African Ancestries GWAS studies to predict MDD and related traits in African Ancestries participants from the UK Biobank.

Methods

UK Biobank participants were selected based on Principal component analysis (PCA) clustering with an African genetic similarity reference population and MDD was assessed with the Composite International Diagnostic Interview (CIDI). Polygenic Risk Scores (PRS) were computed using PRSice2 using either European or African Ancestries GWAS summary statistics.

Results

PRS trained on European ancestry samples (246,363 cases) predicted case control status in Africans of the UK Biobank with similar accuracies (190 cases, R2=2%) to PRS trained on far much smaller samples of African Ancestries participants from 23andMe, Inc. (5045 cases, R2=1.8%). This suggests that prediction of MDD status from Africans to Africans had greater efficiency per unit increase in the discovery sample size than prediction of MDD from Europeans to Africans. Prediction of MDD status in African UK Biobank participants using GWAS findings of causal risk factors from European ancestries was non-significant.

Conclusion

GWAS studies of MDD in European ancestries are an inefficient means of improving polygenic prediction accuracy in African samples.

IgG fractions from patients with antiphospholipid syndrome and systemic lupus erythematosus bind to platelets, but do not affect collagen-induced platelet activation

Anti-beta-2 glycoprotein 1 (anti-β2GP1) is an antiphospholipid antibody found in patients with antiphospholipid syndrome (APS) and systemic lupus erythematosus (SLE). Its presence commonly is associated with thrombosis; however, the mechanisms of interaction of anti-β2GP1 antibodies and platelets remain unclear. We investigated the effects of APS and SLE patient-derived IgG fractions on collagen-mediated platelet aggregation and examined the binding of patient-derived IgG to platelets before and after activation by collagen. IgG fractions, 150, 200, 300 or 350 µg/ml, isolated from 11 patients with APS and SLE were incubated with two sets of platelet-rich plasma (PRP) in the incubation wells of an aggregometer. The first set was activated by collagen and the other set was incubated for an additional 10 min. All platelets were collected by centrifugation and fixed in cell blocks. We assessed binding of IgG to platelets using immunocytochemistry (ICC). Patient-derived IgG fractions did not affect collagen-induced platelet aggregation. ICC staining using anti-human IgG antibodies demonstrated that patient-derived IgG fractions had greater affinity for non-activated platelets than those activated by 0.75 µg/ml collagen. Patient-derived IgG fractions bound to the surface of platelets and potentially could be internalized by platelets. IgG fractions from APS and SLE patients may sensitize non-activated platelets, which could increase platelet reactivity and thrombotic risk in patients. We did not detect secondary effects of patient-derived IgG fractions.

A universal scaling law of mammalian touch

For most mammals, touch is the first sense to develop. They must feel vibrations on the surface of their skin to enable them to respond to various stimuli in their environment, a process called vibrotaction. But how do mammals perceive these vibrations? Through mathematical modeling of the skin and touch receptors, we show that vibrotaction is dominated by "surface" Rayleigh waves traveling cooperatively through all layers of the skin and bone. Applying our model to experimental data, we identify a universal scaling law for the depth of touch receptors across multiple species, indicating an evolutionarily conserved constant in the sensation of vibrations.

Coronavirus (COVID-19), Coagulation, and Exercise: Interactions That May Influence Health Outcomes

The proinflammatory cytokine storm associated with coronavirus disease 2019 (COVID-19) negatively affects the hematological system, leading to coagulation activation and endothelial dysfunction and thereby increasing the risk of venous and arterial thrombosis. Coagulopathy has been reported as associated with mortality in people with COVID-19 and is partially reflected by enhanced D-dimer levels. Poor vascular health, which is associated with the cardiometabolic health conditions frequently reported in people with severer forms of COVID-19, might exacerbate the risk of coagulopathy and mortality. Sedentary lifestyles might also contribute to the development of coagulopathy, and physical activity participation has been inherently lowered due to at-home regulations established to slow the spread of this highly infectious disease. It is possible that COVID-19, coagulation, and reduced physical activity may contribute to generate a “perfect storm,” where each fuels the other and potentially increases mortality risk. Several pharmaceutical agents are being explored to treat COVID-19, but potential negative consequences are associated with their use. Exercise is known to mitigate many of the identified side effects from the pharmaceutical agents being trialled but has not yet been considered as part of management for COVID-19. From the limited available evidence in people with cardiometabolic health conditions, low- to moderate-intensity exercise might have the potential to positively influence biochemical markers of coagulopathy, whereas high-intensity exercise is likely to increase thrombotic risk. Therefore, low- to moderate-intensity exercise could be an adjuvant therapy for people with mild-to-moderate COVID-19 and reduce the risk of developing severe symptoms of illness that are associated with enhanced mortality.

High-frequency dynamics of evanescently-coupled nanowire lasers

We analyse the dynamics and conditions for stability in an array of two laterally-coupled nanowire lasers in terms of their separation, difference in resonant frequencies and pumping rate under conditions of weak coupling. We find that the regions of stability are very small and are found close to zero frequency offset between the lasers. Outside these regions various forms of instability including periodic oscillation, chaos and complex dynamics are predicted. Importantly, the analysis of the frequency of periodic oscillations for realistic laser separations and pumping yields values of order 100 GHz thus underlining the significant potential of nanowire laser arrays for ultra-high frequency on-chip systems with very low foot-print and energy requirements.

Roller compaction: Ribbon splitting and sticking

Roller compaction is the main technique employed in dry granulation. Ribbon sticking and splitting are among the major factors that can hinder the use of this process for some formulations. Ribbon splitting can occur either transversally (through the ribbon thickness) or longitudinally (through the ribbon width). It was observed that transverse splitting is commonly associated with sticking of the split ribbons to the rollers and results in an inferior performance of the process. Longitudinal splitting is associated with an across-width distribution of the ribbon density so that there may an adverse effect on the mechanical strength and dissolution properties of the tablets formed from the milled granules. The aim of the current work was to elucidate the mechanisms of splitting by an experimental study involving single component powders with a range of yield strengths, including those that are commonly used as excipients. Both smooth and knurled rollers were employed without and with lubrication by applying magnesium stearate to the rollers. The minimum gap was fixed and the maximum roll stress was varied. The observed trends for the smooth rollers were rationalised in terms of a splitting index, which is a measure of the residual stresses driving crack growth relative to the tensile strength of the ribbons. There was a lower limit at which splitting was observed but the occurrence of transverse splitting decreased and that for longitudinal splitting increased with increasing values of the index, which was accompanied by an increase in mixed transverse-longitudinal splitting. Transverse splitting was always associated with sticking to the rollers and was prevented by external lubrication. The main difference with the knurled rollers was that in some cases transverse splitting occurred without sticking to the rollers. A detailed discussion of the mechanisms involved is presented.

Acquired and Genetic Thrombotic Risk Factors in the Athlete

While athletes are often considered the epitome of health due to their physique and lowered potential for metabolic and cardiovascular diseases, they may also be at risk for the onset and development of venous thromboembolism (VTE). In an attempt to achieve and remain competitive, athletes are frequently exposed to numerous athlete-specific risk factors, which may predispose them to VTE through the disruption of factors associated with Virchow's triad (i.e., hypercoagulability, venous stasis, and vessel wall injury). Indeed, hypercoagulability within an athletic population has been well documented to occur due to a combination of multiple factors including exercise, dehydration, and polycythemia. Furthermore, venous stasis within an athletic population may occur as a direct result of prolonged periods of immobilization experienced when undertaking long-distance travels for training and competition, recovery from injury, and overdevelopment of musculature. While all components of Virchow's triad are disrupted, injury to the vessel wall has emerged as the most important factor contributing to thrombosis formation within an athletic population, due to its ability to influence multiple hemostatic mechanisms. Vessel wall injury within an athletic population is often related to repetitive microtrauma to the venous and arterial walls as a direct result of sport-dependent trauma, in addition to high metabolic rates and repetitive blood monitoring. Although disturbances to Virchow's triad may not be detrimental to most individuals, approximately 1 in 1,000 athletes will experience a potentially fatal post-exercise thrombotic incidence. When acquired factors are considered in conjunction with genetic predispositions to hypercoagulability present in some athletes, an overall increased risk for VTE is present.

Mapping bifurcation structure and parameter dependence in quantum dot spin-VCSELs

We consider a modified version of the spin-flip model (SFM) that describes optically pumped quantum dot (QD) spin-polarized vertical-cavity surface-emitting lasers (VCSELs). Maps showing different dynamical regions and those consisting of various key bifurcations are constructed by direct numerical simulations and a numerical path continuation technique, respectively. A comparison between them clarifies the physical mechanism that governs the underlying dynamics as well as routes to chaos in QD spin-VCSELs. Detailed numerical simulations illustrate the role played by the capture rate from wetting layer (WL) to QD ground state, the gain parameter, and the amplitude-phase coupling. By tuning the aforementioned key parameters in turn we show how the dynamical regions evolve as a function of the intensity and polarization of the optical pump, as well as in the plane of the spin relaxation rate and linear birefringence rate, which is of importance in the design of spin lasers promising potential applications. By increasing the capture rate from WL to QD our simulation accurately describes the transition from the QD spin-VCSEL to the quantum well case, in agreement with a previous mathematical derivation, and thus validates the modified SFM equations.

Nonlinear dynamics of solitary and optically injected two-element laser arrays with four different waveguide structures: a numerical study

We study the nonlinear dynamics of solitary and optically injected two-element laser arrays with a range of waveguide structures. The analysis is performed with a detailed direct numerical simulation, where high-resolution dynamic maps are generated to identify regions of dynamic instability in the parameter space of interest. Our combined one- and two-parameter bifurcation analysis uncovers globally diverse dynamical regimes (steady-state, oscillation, and chaos) in the solitary laser arrays, which are greatly influenced by static design waveguiding structures, the amplitude-phase coupling factor of the electric field, i.e. the linewidth-enhancement factor, as well as the control parameter, e.g. the pump rate. When external optical injection is introduced to one element of the arrays, we show that the whole system can be either injection-locked simultaneously or display rich, different dynamics outside the locking region. The effect of optical injection is to significantly modify the nature and the regions of nonlinear dynamics from those found in the solitary case. We also show similarities and differences (asymmetry) between the oscillation amplitude of the two elements of the array in specific well-defined regions, which hold for all the waveguiding structures considered. Our findings pave the way to a better understanding of dynamic instability in large arrays of lasers.

Time of day and short-duration high-intensity exercise influences on coagulation and fibrinolysis

Exercise has been demonstrated to have considerable effects upon haemostasis, with activation dependent upon the duration and intensity of the exercise bout. In addition, markers of coagulation and fibrinolysis have been shown to possess circadian rhythms, peaking within the morning (0600-1200 h). Therefore, the time of day in which exercise is performed may influence the activation of the coagulation and fibrinolytic systems. This study aimed to examine coagulation and fibrinolytic responses to short-duration high-intensity exercise when completed at different times of the day. Fifteen male cyclists (VO_2max: 60.3 ± 8.1 ml kg^-1 min^-1) completed a 4-km cycling time trial (TT) on five separate occasions at 0830, 1130, 1430, 1730 and 2030. Venous blood samples were obtained pre- and immediately post-exercise, and analysed for tissue factor (TF), tissue factor pathway inhibitor (TFPI), thrombin-anti-thrombin complexes (TAT) and D-Dimer. Exercise significantly increased plasma concentrations of TF (p < .0005), TFPI (p < .0006), TAT complexes (p < .0012) and D-Dimer (p < .0003). There was a time-of-day effect in pre-exercise TF (p = .004) and TFPI (p = .031), with 0830 greater than 1730 (p  .001), while 1730 was less than 2030 h (p = .008), respectively. There was no significant effect of time of day for TAT (p = .364) and D-Dimer (p = .228). Power output, TT time and heart rate were not significantly different between TTs (p > .05); however, percentage VO_2max was greater at 1730 when compared to 2030 (p = .04). Due to a time-of-day effect present within TF, peaking at 0830, caution should be applied when prescribing short-duration high-intensity exercise bout within the morning in populations predisposed to hypercoagulability.

Locking bandwidth of two laterally-coupled semiconductor lasers subject to optical injection

We report here for the first time (to our knowledge), a new and universal mechanism by which a two-element laser array is locked to external optical injection and admits stably injection-locked states within a nontrivial trapezoidal region. The rate equations for the system are studied both analytically and numerically. We derive a simple mathematical expression for the locking conditions, which reveals that two parallel saddle-node bifurcation branches, not reported for conventional single lasers subject to optical injection, delimit the injection locking range and its width. Important parameters are the linewidth enhancement factor, the laser separation, and the frequency offset between the two laterally-coupled lasers; the influence of these parameters on locking conditions is explored comprehensively. Our analytic approximations are validated numerically by using a path continuation technique as well as direct numerical integration of the rate equations. More importantly, our results are not restricted by waveguiding structures and uncover a generic locking behavior in the lateral arrays in the presence of injection.

Heterogeneous responses of temperate-zone amphibian populations to climate change complicates conservation planning

The pervasive and unabated nature of global amphibian declines suggests common demographic responses to a given driver, and quantification of major drivers and responses could inform broad-scale conservation actions. We explored the influence of climate on demographic parameters (i.e., changes in the probabilities of survival and recruitment) using 31 datasets from temperate zone amphibian populations (North America and Europe) with more than a decade of observations each. There was evidence for an influence of climate on population demographic rates, but the direction and magnitude of responses to climate drivers was highly variable among taxa and among populations within taxa. These results reveal that climate drivers interact with variation in life-history traits and population-specific attributes resulting in a diversity of responses. This heterogeneity complicates the identification of conservation 'rules of thumb' for these taxa, and supports the notion of local focus as the most effective approach to overcome global-scale conservation challenges.

Secure communication systems based on chaos in optically pumped spin-VCSELs

We report on a master and slave configuration consisting of two optically pumped spin-vertical-cavity surface-emitting lasers for chaos synchronization and secure communication. Under appropriate conditions, high-quality chaos synchronization is achieved. We propose two encryption schemes, where either the pump magnitude or polarization is modulated. The results show that these allow for Gb/s transmission of secure data, but exhibit different features: one indicates that the message can be recovered by the total intensity, but not the polarization components, whereas the other shows that the message can be better or exclusively retrieved from the polarization components at high bit rates.

Do regional brain volumes and major depressive disorder share genetic architecture? A study of Generation Scotland (n=19 762), UK Biobank (n=24 048) and the English Longitudinal Study of Ageing (n=5766)

Major depressive disorder (MDD) is a heritable and highly debilitating condition. It is commonly associated with subcortical volumetric abnormalities, the most replicated of these being reduced hippocampal volume. Using the most recent published data from Enhancing Neuroimaging Genetics through Meta-analysis (ENIGMA) consortium's genome-wide association study of regional brain volume, we sought to test whether there is shared genetic architecture between seven subcortical brain volumes and intracranial volume (ICV) and MDD. We explored this using linkage disequilibrium score regression, polygenic risk scoring (PRS) techniques, Mendelian randomisation (MR) analysis and BUHMBOX. Utilising summary statistics from ENIGMA and Psychiatric Genomics Consortium, we demonstrated that hippocampal volume was positively genetically correlated with MDD (r_G=0.46, P=0.02), although this did not survive multiple comparison testing. None of the other six brain regions studied were genetically correlated and amygdala volume heritability was too low for analysis. Using PRS analysis, no regional volumetric PRS demonstrated a significant association with MDD or recurrent MDD. MR analysis in hippocampal volume and MDD identified no causal association, however, BUHMBOX analysis identified genetic subgrouping in GS:SFHS MDD cases only (P=0.00281). In this study, we provide some evidence that hippocampal volume and MDD may share genetic architecture in a subgroup of individuals, albeit the genetic correlation did not survive multiple testing correction and genetic subgroup heterogeneity was not replicated. In contrast, we found no evidence to support a shared genetic architecture between MDD and other regional subcortical volumes or ICV.

High frequency continuous birefringence-induced oscillations in spin-polarized vertical-cavity surface-emitting lasers

Sustained, large amplitude and tunable birefringence-induced oscillations are obtained in a spin-vertical cavity surface-emitting laser (spin-VCSEL). Experimental evidence is provided using a spin-VCSEL operating at 1300 nm, under continuous-wave optical pumping and at room temperature. Numerical and stability analyses are performed to interpret the experiments and to identify the combined effects of pump ellipticity, spin relaxation rate, and cavity birefringence. Importantly, the frequency of the induced oscillations is determined by the device's birefringence rate, which can be tuned to very large values. This opens the path for ultrafast spin-lasers operating at record frequencies exceeding those possible in traditional semiconductor lasers and with ample expected impact in disparate disciplines (e.g., datacomms, spectroscopy).

Intelligence and neuroticism in relation to depression and psychological distress: Evidence from two large population cohorts

Background

Neuroticism is a risk factor for selected mental and physical illnesses and is inversely associated with intelligence. Intelligence appears to interact with neuroticism and mitigate its detrimental effects on physical health and mortality. However, the inter-relationships of neuroticism and intelligence for major depressive disorder (MDD) and psychological distress has not been well examined.

Methods

Associations and interactions between neuroticism and general intelligence (g) on MDD, self-reported depression, and psychological distress were examined in two population-based cohorts: Generation Scotland: Scottish Family Health Study (GS:SFHS, n = 19,200) and UK Biobank (n = 90,529). The Eysenck Personality Scale Short Form-Revised measured neuroticism and g was extracted from multiple cognitive ability tests in each cohort. Family structure was adjusted for in GS:SFHS.

Results

Neuroticism was strongly associated with increased risk for depression and higher psychological distress in both samples. Although intelligence conferred no consistent independent effects on depression, it did increase the risk for depression across samples once neuroticism was adjusted for. Results suggest that higher intelligence may ameliorate the association between neuroticism and self-reported depression although no significant interaction was found for clinical MDD. Intelligence was inversely associated with psychological distress across cohorts. A small interaction was found across samples such that lower psychological distress associates with higher intelligence and lower neuroticism, although effect sizes were small.

Conclusions

From two large cohort studies, our findings suggest intelligence acts a protective factor in mitigating the effects of neuroticism on psychological distress. Intelligence does not confer protection against diagnosis of depression in those high in neuroticism.

Dissection of major depressive disorder using polygenic risk scores for schizophrenia in two independent cohorts

Major depressive disorder (MDD) is known for its substantial clinical and suspected causal heterogeneity. It is characterized by low mood, psychomotor slowing and increased levels of the personality trait neuroticism; factors also associated with schizophrenia (SCZ). It is possible that some cases of MDD may have a substantial genetic loading for SCZ. The presence of SCZ-like MDD subgroups would be indicated by an interaction between MDD status and polygenic risk of SCZ on cognitive, personality and mood measures. Here, we hypothesized that higher SCZ polygenic risk would define larger MDD case-control differences in cognitive ability, and smaller differences in distress and neuroticism. Polygenic risk scores (PRSs) for SCZ and their association with cognitive variables, neuroticism, mood and psychological distress were estimated in a large population-based cohort (Generation Scotland: Scottish Family Health Study, GS:SFHS). The individuals were divided into those with, and without, depression (n=2587 and n=16 764, respectively) to test for the interactions between MDD status and schizophrenia risk. Replication was sought in UK Biobank (UKB; n=6049 and n=27 476 cases and controls, respectively). In both the cohorts, we found significant interactions between SCZ-PRS and MDD status for measures of psychological distress (βGS=-0.04, PGS=0.014 and βUKB=-0.09, PUKB⩽0.001 for GS:SFHS and UKB, respectively) and neuroticism (βGS=-0.04, PGS=0.002 and βUKB=-0.06, PUKB=0.023). In both the cohorts, there was a reduction of case-control differences on a background of higher genetic risk of SCZ. These findings suggest that depression on a background of high genetic risk for SCZ may show attenuated associations with distress and neuroticism. This may represent a causally distinct form of MDD more closely related to SCZ.

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).

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.

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.

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.

Impaired control of the tissue factor pathway of blood coagulation in systemic lupus erythematosus

Thrombosis is a frequent manifestation in patients with systemic lupus erythematosus (SLE), although precise mechanisms remain unclear. This study investigated whether the major physiological trigger of blood coagulation, the tissue factor (TF) pathway, was altered in SLE patients. Furthermore, we investigated potential associations between the TF pathway, the presence of antiphospholipid (APL) antibodies and other abnormalities present in SLE. A total of 101 participants (40 SLE patients and 61 age- and sex-matched controls) were recruited from Tasmania, Australia. Markers of the TF pathway, hypercoagulability, inflammation and endothelial cell damage were measured in plasma. Serum levels of APL antibodies (anti-cardiolipin antibodies [ACL], lupus anticoagulants [LAC], anti-beta2-glycoprotein-1 [anti-β2GP1] and anti-prothrombin antibodies) were also determined. Despite similar TF and TF pathway inhibitor (TFPI) total antigen levels, SLE patients had significantly increased levels of TFPI free antigen (patients vs controls; mean ± SD) (11.6 ± 0.9 ng/mL vs 6.4 ± 0.4 ng/mL; p < 0.001) but significantly reduced TFPI activity (0.66 ± 0.07 U/mL vs 1.22 ± 0.03 U/mL; p < 0.001), compared with healthy controls. Anti-TFPI activity, designated as the ability of isolated IgG fractions to inhibit TFPI activity in normal plasma, was detected in 19/40 (47.5%) of SLE patients and 3/40 (7.5%) of healthy controls. The significant reduction in TFPI activity in SLE patients reflects impaired functional control of the TF pathway. Moreover, SLE patients with a history of thrombosis demonstrated higher levels of TFPI activity compared with patients without a previous thrombotic event (0.97 ± 0.07 U/mL vs 0.53 ± 0.14 U/mL; p = 0.0026). Changes to the TF pathway were not associated with manifestations of SLE such as inflammation or endothelial cell damage. The results from this study suggest hypercoagulability in SLE may (in part) be due to reduced TFPI activity, a mechanism that appears to be independent of other abnormalities in SLE.

Indirect genetics effects and evolutionary constraint: an analysis of social dominance in red deer, Cervus elaphus

By determining access to limited resources, social dominance is often an important determinant of fitness. Thus, if heritable, standard theory predicts mean dominance should evolve. However, dominance is usually inferred from the tendency to win contests, and given one winner and one loser in any dyadic contest, the mean proportion won will always equal 0.5. Here, we argue that the apparent conflict between quantitative genetic theory and common sense is resolved by recognition of indirect genetic effects (IGEs). We estimate selection on, and genetic (co)variance structures for, social dominance, in a wild population of red deer Cervus elaphus, on the Scottish island of Rum. While dominance is heritable and positively correlated with lifetime fitness, contest outcomes depend as much on the genes carried by an opponent as on the genotype of a focal individual. We show how this dependency imposes an absolute evolutionary constraint on the phenotypic mean, thus reconciling theoretical predictions with common sense. More generally, we argue that IGEs likely provide a widespread but poorly recognized source of evolutionary constraint for traits influenced by competition.

Nonlinear semiconductor lasers and amplifiers for all-optical information processing

The nonlinear properties of semiconductor lasers and laser amplifiers when subject to optical injection are reviewed and new results are presented for multisection lasers, vertical cavity semiconductor optical amplifiers, and surface-emitting lasers. The main underlying material parameters are outlined and the key design approaches are discussed for both edge-emitting and vertical cavity devices. An overview of theoretical modeling approaches is discussed and a summary of key experimental results is presented. The practical use of optically injected edge-emitting and vertical cavity semiconductor lasers and laser amplifiers is illustrated with examples of applications including, among others, optical logic and chaotic communication.

Analysis of the outcome in male and female patients using a unisex total knee replacement system

Gender-specific total knee replacement has generated much interest recently. We reviewed 1970 Sigma knees implanted in 920 women and 592 men with a mean age of 69.7 years. At a mean follow-up of 7.3 years (minimum, five years), we found minimal differences in the outcome between genders. At the final follow-up, men had a higher overall Knee Society score and more osteolysis (3.8% vs 1.1%). However, there were no significant differences between men and women in terms of complications or improvements in knee function, pain score or range of movement. The estimated ten-year survivorship was 97% in women and 98% in men (p = 0.96). We concluded that there was little difference in outcome between the genders treated by a modern unisex design of total knee replacement in this large multicentre study.

Mutual optical injection in coupled DBR laser pairs

We report an experimental study of nonlinear effects, characteristic of mutual optical coupling, in an ultra-short coupling regime observed in a distributed Bragg reflector laser pair fabricated on the same chip. Optical feedback is amplified via a double pass through a common on-chip optical amplifier, which introduces further nonlinear phenomena. Optical coupling has been introduced via back reflection from a cleave-ended fibre. The coupling may be varied in strength by varying the distance of the fibre from the output of the chip, without significantly affecting the coupling time.

Recent Rice stripe virus Epidemics in Zhejiang Province, China, and Experiments on Sowing Date, Disease-Yield Loss Relationships, and Seedling Susceptibility

Rice stripe virus, transmitted by the small brown planthopper Laodelphax striatellus, has recently reemerged as a major disease in Zhejiang province, eastern China. Intensive surveys during 2003 to 2006 demonstrated how the disease has spread rapidly from the northern to central and eastern regions with increasing incidence each year. In bioassays, the highest proportions of viruliferous vectors were from regions where the disease was most severe. The greatest disease incidence was in the earliest sown plants, and substantial control could be achieved by delaying planting from late May to mid-June. In experiments where different proportions of infected plants were established (by inoculation or varying the sowing date), average yield losses were 0.8% for every 1% increase in disease incidence. In inoculation experiments, young seedlings, particularly those at the three- to five-leaf stage, were the most susceptible, whereas ≤1% of plants inoculated at or after the elongation stage developed symptoms. Recent epidemics appear to have resulted from large populations of viruliferous vectors colonizing rice seedlings at the most susceptible stage. This is probably because of changes in cropping practice, recent warmer winters in Zhejiang province, and the development of resistance or tolerance to the insecticides widely used (triazophos, synthetic pyrethroids, and Imidacloprid).

Analysis of SFM dynamics in solitary and optically-injected VCSELs

The aim of this paper is to use the spin-flip model (SFM) to investigate how the fundamental parameters of birefringence, spin relaxation and pumping affect the dynamics of solitary and optically-injected vertical-cavity surface-emitting lasers (VCSELs). The SFM predicts that a solitary VCSEL can exhibit diverse polarisation behaviour, including elliptical and linear stability, which can be used in polarisation switching. For given values of pumping, spin relaxation and birefringence, we analyse the electric field components, the carrier densities corresponding to spin-up and spin-down, and the relaxation oscillation frequency for a solitary VCSEL and the stability map for an optically-injected VCSEL.

Genomic analysis of rice stripe virus Zhejiang isolate shows the presence of an OTU-like domain in the RNA1 protein and a novel sequence motif conserved within the intergenic regions of ambisense segments of tenuiviruses

The complete genome sequence of the four RNAs of rice stripe virus Zhejiang isolate was determined. In addition to polymerase modules, the pc1 protein encoded on RNA1 harbours an ovarian tumour (OTU) - like cysteine protease signature near its N-terminus, suggesting that the protein might yield the viral polymerase and one or more additional proteins by autoproteolytic cleavage and/or have deubiquitination activity. A novel inverted repeat sequence motif was found to be universal within the intergenic regions of ambisense genome segments of tenuiviruses, supporting the possibility that it may be functionally important, perhaps in regulating transcription termination.

Molecular characterization of the genome segments S4, S6 and S7 of rice gall dwarf virus

Rice gall dwarf virus (RGDV) is a member of the genus Phytoreovirus within the family Reovirdae. Its genome has 12 segments of double-stranded RNA (dsRNA), of which the nucleotide sequences of segments S4, S6, and S7 were determined, providing the first complete genome sequence of RGDV. Each of the segments S4, S6, and S7 contained conserved terminal sequences conforming to the RGDV consensus, 5'-GGXA ... UGAU-3' (X = U or C). Each segment had a single predicted open reading frame encoding proteins with calculated molecular weights of 79.8, 58.6, and 53.3 kDa. These proteins appeared to be homologous to those encoded by the corresponding segments of rice dwarf virus and wound tumor virus, the other known members of the same genus, having about 20-30% amino acid identity to them. It is therefore likely that RGDV S4 and S6 encode non-structural proteins and S7 an inner core protein. Probable homologies between the segments of all known phytoreoviruses are summarized. Beyond these similarities, the RGDV proteins displayed no significant similarity to any other reported viral proteins.

The Sbm1 locus conferring resistance to Soil-borne cereal mosaic virus maps to a gene-rich region on 5DL in wheat

A mosaic disease caused by Soil-borne cereal mosaic virus (SBCMV) is becoming increasingly important, particularly in winter wheat in Europe. As there are currently no effective cultural practices or practical environmentally friendly chemicals for disease control, host plant resistance is an important objective in breeding programs. However, development of resistant cultivars is slow owing to difficulties in germplasm screening for resistance. Therefore, there is a need to identify molecular markers linked to SBCMV-resistance gene(s), so that quick and accurate laboratory-based marker-assisted selection rather than prolonged field-based screens for resistance can be used in developing resistant cultivars. We previously demonstrated that resistance to SBCMV in Triticum aestivum ‘Cadenza’ is controlled by a single locus. In this work, we used AFLP and microsatellite technology to map this resistance locus, with the proposed name Sbm1, to the distal end of chromosome 5DL. Interestingly, several expressed disease-resistance gene analogues also map to this gene-rich region on 5DL. Closely linked (~17 cM interval) markers, BARC110 and WMC765, RRES01 and BARC144, that flank Sbm1 will be very useful in breeding for selection of germplasm carrying Sbm1.

Characterisation of an isolate of Narcissus degeneration virus from Chinese narcissus (Narcissus tazetta var. chinensis)

A potyvirus from Chinese narcissus was transmitted mechanically to three species of Narcissus and to Lycoris radiata but not to 22 other test species. In western blot, the coat protein reacted strongly with Narcissus degeneration virus (UK isolate) antiserum. Antiserum raised to the Chinese virus did not react with eighteen other potyviruses. The complete nucleotide sequence (9816 nt) had the typical genome organisation for a member of the genus Potyvirus. Sequence comparisons and phylogenetic analysis showed that the Chinese virus was different from all previously sequenced potyviruses but distantly related to onion yellow dwarf and shallot yellow stripe viruses.

Narcissus symptomless virus: a new carlavirus of daffodils

A filamentous virus, with particles 600-650 nm long, was purified from Narcissus pseudonarcissus (daffodil) in Hangzhou and an antiserum prepared. After mechanical inoculation, the virus could be detected serologically in Narcissus species but not in some commonly used virus indicators. Infection was symptomless. The complete sequence of the genomic RNA (8281 nt) showed six predicted ORFs typical of carlaviruses. Pairwise comparisons of gene sequences and phylogenetic analysis demonstrated that the new virus should be classified as a carlavirus but that it was not closely related to members of any current species. We propose the name Narcissus symptomless virus (NSV).

Complete nucleotide sequence and affinities of the genomic RNA of Narcissus common latent virus (genus Carlavirus)

The complete sequence of an isolate of Narcissus common latent virus (NCLV) from Zhangzhou city, Fujian, China was determined from amplified fragments of purified viral RNA. Excluding the poly(A) tail, the genomic RNA of NCLV was 8539 nucleotides (nt) long and had the typical organization for a member of the genus Carlavirus. The most closely related species were Potato virus M, Hop latent virus and Aconitum latent virus, which had 58-59% nt identity to NCLV in their entire genomes. These relationships were confirmed by a phylogenetic analysis using a composite nucleotide alignment of all the open reading frames.

Detection and characterisation of a second potyvirus from Thunberg fritillary in China

Plants of Thunberg fritillary (Fritillaria thunbergii Miq.) from Zhejiang Province, were found to be co-infected with two distinct potyviruses. One was an isolate of the recently reported Thunberg fritillary mosaic virus (TFMV; Wei et al., (2005) Arch Virol 150: 1271-1280), while the other was a distinct virus that did not react with TFMV antiserum nor with antisera to 17 other potyviruses, except for a weak reaction with antibodies produced to soybean mosaic virus (SMV) Pinellia strain. Both viruses could be transmitted mechanically to their original host but not to any of a range of commonly used indicator plants. No local lesion host was identified that would enable the viruses to be propagated independently. The complete sequences of both viruses were determined; that of the new virus (9656 nt) had the typical genome organisation and recognised sequence motifs of a potyvirus, encoding a putative polyprotein of 351 kDa. Phylogenetic analysis, sequence comparisons, and the pattern of polyprotein cleavage sites all indicated that it was a member of the Bean common mosaic virus subgroup. The most closely related species are Soybean mosaic virus and Wisteria vein mosaic virus, with 68-69% amino acid identity between their polyproteins. This is sufficiently different for the new virus to be regarded as a distinct species, which we have tentatively named Fritillary virus Y.

Characterisation of the welsh onion isolate of Shallot yellow stripe virus from China

The host range and nucleotide sequence of shallot yellow stripe virus (SYSV) from welsh onion in Shandong province, China is described. Of the plants tested, only shallot and welsh onion became infected but most shallot plants were symptomless. The complete sequence of one isolate (10429 nt) and the 3'-terminal 3540 nts of a second isolate were determined. They had c. 90% nt identity to one another and to published (partial) sequences of SYSV. SYSV was most closely related to onion yellow dwarf virus (OYDV) and resembled it in having a much larger P3 protein than other species in the genus.

A new potyvirus from Thunberg fritillary (Fritillaria thunbergii Miq.) in Zhejiang, China

A potyvirus causing mosaic symptoms in Thunberg fritillary (Fritillaria thunbergii) was found at two sites in Zhejiang province, China. The virus was readily mechanically transmitted to its original host but not to any of 17 other widely used plant virus indicators. A polyclonal antiserum raised to purified virus particles reacted with its homologous virus but not with a range of other viruses (including 16 potyvirus species). In electron microscopy, virus particles and inclusion bodies typical of a potyvirus were seen. The complete nucleotide sequence of an isolate from Ningbo was determined. It was 9723 nt long and sequence analyses predicted the standard potyvirus organisation. The partial sequence (1664 nts at the 3'-terminus) of an isolate from Panan was also determined; the two sequences had 96.9% nt identity. In sequence comparisons and phylogenetic analyses with completely sequenced potyviruses, the new virus was most closely related to Lily mottle virus (53.0% aa identity) and Leek yellow stripe virus. The most closely related incomplete sequence in the international databases was for Lycoris mild mottle virus (72.8% nt identity in their coat proteins). These results suggest that the virus studied is a new species in the genus Potyvirus, which we have tentatively named Thunberg fritillary mosaic virus.

Structure of 6-phosphogluconate dehydrogenase refined at 2 A resolution

The X-ray unliganded structure of 6-phosphogluconate dehydrogenase (E.C. 1.1.1.44) (6-PGDH) from sheep liver has been determined at 2A resolution and refined to a final R-factor of 19.8% for 35 031 unique reflections. The enzyme is dimeric, each subunit being comprised of an N-terminal coenzyme-binding domain with a Rossmann fold, a large all-helical domain and a small C-terminal tail. The model contains 473 residues, three sulfate ions and 346 water molecules; the two best defined sulfates are found in the active site. This structure, based on improved diffraction data, is an extension of the 2.5 A, resolution model reported earlier. It has good geometry with 92% of the residues falling in the most favoured areas of the Ramachandran plot. Several unusual features are discussed: the incorporation of an alanine in place of the second conserved glycine of the dinucleotide-binding fingerprint; a duplicated five-helix motif which is unique to this enzyme; an extended water network at the dimer interface and a C-terminal tail which is incorporated within the second subunit, forming not only a major part of the dimer interface but also part of the active site.

Molecular criteria for genus and species discrimination within the family Potyviridae

A phylogenetic analysis of the optimised nucleotide (nt) alignment of the entire ORFs of a representative of each fully-sequenced species in the family Potyviridae provided strong support for several subgroups within the genus Potyvirus. A complete set of two-way comparisons was done between the sequences for the entire ORF and for each gene amongst all the 187 complete sequences from the family. Most species had 50-55% nt identity to other members of their genus in their ORFs but there were significant groups of more closely related species and species demarcation criteria were <76% nt identity and <82% amino acid identity. The corresponding thresholds for species demaracation using nt identity values for the individual genes ranged from 58% (P1 gene) to 74-78% (other genes) although a few comparisons between different species exceeded these values. For the entire ORF, genus demarcation criteria were <46% nt identity but this did not separate rymoviruses from potyviruses. Comparisons in the CI gene most accurately reflected those for the complete ORF and this region would therefore be the best for diagnostic and taxonomic studies if only a sub-portion of the genome is to be sequenced. Further comparisons were then made using all the 1220 complete capsid protein (CP) genes. These studies suggest that 76-77% nt identity is the optimal species demarcation criterion for the CP. The study has also helped to allocate the correct virus name to some sequences from the international databases that currently have incorrect or redundant names. The taxonomic status of the current genus Rymovirus and of three unassigned species in the family is discussed. Significant discontinuities in the distributions within and between the currently defined species suggest that the continuum of variation that is theoretically available is constrained or disrupted by molecular barriers that must have some biological significance.

The complete sequence of the genomic RNA of an isolate of Lily virus X (genus Potexvirus)

The complete sequence of the genomic RNA of an isolate of Lily virus X (LVX) has been determined for the first time. The isolate from the Netherlands was 5823 nucleotide (nt) long excluding the 3'-poly(A) tail, making it the shortest reported potexvirus sequence. The 5'-non-coding region begins with GGAAAA like that of Scallion virus X (ScaVX) and some isolates of Cymbidium mosaic virus (CymMV), whereas those of other sequenced potexviruses probably all begin with GAAAA. The genome organisation was similar to that of other members of the genus except that a TGBp3-like region lacked a normal AUG start codon. A phylogenetic analysis based on the entire coding sequence showed that LVX was most closely related to Strawberry mild yellow edge virus and belonged in a subgroup of the genus that also contains CymMV, Narcissus mosaic virus, ScaVX, Pepino mosaic virus, Potato aucuba mosaic virus and White clover mosaic virus.

Further molecular characterisation of potyviruses infecting aroid plants for medicinal use in China

Degenerate primers were used to detect and amplify 3'-terminal genome fragments of potyviruses from medicinal aroid plants growing at 16 sites in China. Virus was detected in 7 samples of which six, all of Pinellia ternata, contained a strain of soybean mosaic virus (SMV) similar to that previously reported from this host in China. The complete sequence of one isolate and the P1 protein coding region of the other isolates were also sequenced. In all cases, the P1 proteins resembled isolates of Dasheen mosaic virus (DsMV) more closely than SMV, confirming earlier suggestions of recombination in this region. In a phylogenetic analysis of SMV, DsMV and related sequences, the aroid sequences of SMV formed a distinct group which also included a sequence published as Zantedeschia symptomless virus (AF469171). One of the P. ternata samples was also infected with a second potyvirus, the 3'-terminal sequence of which was similar to DsMV and to some sequences published as Vanilla mosaic virus. The seventh infected sample was Typhonium flagelliforme and the virus from it was identified from its sequence as zantedeschia mosaic virus (ZaMV), providing the first report of this virus from mainland China.

The new plant virus family Flexiviridae and assessment of molecular criteria for species demarcation

The new plant virus family Flexiviridae is described. The family is named because its members have flexuous virions and it includes the existing genera Allexivirus, Capillovirus, Carlavirus, Foveavirus, Potexvirus, Trichovirus and Vitivirus, plus the new genus Mandarivirus together with some related viruses not assigned to any genus. The family is justified from phylogenetic analyses of the polymerase and coat protein (CP) sequences. To help to define suitable molecular criteria for demarcation of species, a complete set of pairwise comparisons was made using the nucleotide (nt) and amino acid (aa) sequences of each fully-sequenced gene from every available accession in the family. Based on the distributions and on inspection of the data, it was concluded that, as a general rule, distinct species have less than ca. 72% identical nt or 80% identical aa between their entire CP or replication protein genes.

Biological and sequence analysis of a novel European isolate of Barley mild mosaic virus that overcomes the barley rym5 resistance gene

A Barley mild mosaic virus (BaMMV) isolate from France (BaMMV-Sil) capable of overcoming rym5-controlled resistance was inoculated to barley genotypes carrying various genes for resistance to the barley mosaic viruses. BaMMV-Sil was unable to infect genotypes carrying rym1, rym4, rym8, rym9, or rym11 but genotypes carrying rym3, rym5, rym6 or no known bymovirus resistance gene were susceptible. Plants carrying rym7 or rym10 showed partial resistance with delayed virus accumulation. The two genomic RNAs of BaMMV-Sil were sequenced and compared to published sequences and those of a further common strain isolate from the UK. Four amino acid differences were observed between BaMMV-Sil and European common strain isolates in the polypeptide encoded by RNA1, the RNA species which determines pathogenicity on the rym5 genotypes. Only two of these differences are likely to be functionally important (His rather than Gln at position1217 in the VPg cistron; His rather than Asp at position 1776 in the NIb cistron). Comparisons with related viruses in the genera Bymovirus and Potyvirus suggest that the change in the VPg, which occurs within a motif conserved amongst all viruses within the family Potyviridae, is the more likely cause of rym5 resistance-breaking.

A new potyvirus from tuberose ( Polianthes tuberosa) in China

Tuberose plants with mild mottle symptoms, growing in a glasshouse in Hangzhou, China, contained virions and inclusion bodies typical of a potyvirus. The virus was mechanically transmitted to tuberose but not to 14 other test plant species. A fragment of 4607 nucleotides, corresponding to the 3'-half of a typical potyvirus was amplified by RT-PCR using degenerate primers and sequenced. The most similar sequence in the databases was that of Tuberose mild mosaic virus (TuMMV) from Taiwan and this was the only virus significantly related to it in phylogenetic analyses. The new sequence had 71.1% nt and 76.6% aa identity to TuMMV in the coat protein. Western blot analyses using antisera raised to expressed coat protein showed that the two viruses were serologically related. Although there are no substantial biological data to distinguish the Hangzhou isolate from TuMMV, the molecular difference between the two virus isolates is similar to, or slightly greater than, that between several pairs of well-established potyvirus species. These results therefore suggest that the Hangzhou isolate should be regarded as a new member of the genus Potyvirus, and we have tentatively named it Tuberose mild mottle virus.

A virus related to soybean mosaic virus from Pinellia ternata in China and its comparison with local soybean SMV isolates

A potyvirus isolated from Pinellia ternata in China was characterised and shown to be related to Soybean mosaic virus (SMV). The virus was pathogenic on P. ternata and some soybean cultivars, whereas the local soybean SMV isolate HH5 did not infect P. ternata. Western blot experiments demonstrated a serological relationship between the virus from Pinellia, SMV and Watermelon mosaic virus (WMV). The complete nucleotide sequences of the Pinellia virus (isolate P-1, 9735 nt) and of the Chinese soybean SMV isolates HH5 (9585 nt) and HZ (9588 nt) were determined. A 1733 nt sequence at the 3'-terminus of a second isolate from Pinellia (isolate P-2) was also determined. The predicted polyprotein of isolate P-1 has 83% amino acid (aa) identity with those of published SMV sequences. In many parts of the genome, aa identity was about 90% but it was much lower in the P1 protein region (24-29%), where it more closely resembled Dasheen mosaic virus (62%). The partial sequence of isolate P-2 had 91% nt identity to P-1 and both isolates resembled a recent sequence in the public databases (AF469171) wrongly named Zantedeschia mosaic virus. The two complete SMV soybean sequences had 93-95% nt identity with those of the previously sequenced isolates and >97% amino acid identity. Phylogenetic analysis and comparisons of coat proteins suggest that the Pinellia, WMV and SMV potyviruses should probably be treated as strains of the same species.