Multidecadal variability in hydro-climate of Okavango river system, southwest Africa, in the past and under future climate

The focus of this paper is to understand the multi-decadal oscillatory component of variability in the Okavango River system, in southwestern Africa, and its potential evolution through the 21st century under climate change scenarios. Statistical analyses and hydrological modelling are used to show that the observed multi-decadal wet and dry phases in the Okavango River and Delta result from multi-decadal oscillations in rainfall, which are likely to be related to processes of internal variability in the climate system, rather than external natural or anthropogenic forcing. Analyses of changes in this aspect of variability under projected climate change scenarios are based on data from a multi-model ensemble of 19 General Circulation Models, which are used to drive hydrological models of the Okavango River and Delta. Projections for the 21st century indicate a progressive shift towards drier conditions attributed to the influence of increasing temperatures on water balance. It is, however, highly likely that multi-decadal oscillations, possibly of similar magnitude to that of 20th century, will be superimposed on the overall trend. These may periodically offset or amplify the mean drying trend. This effect should be accounted for in water and catchment management and climate change adaptation strategies

Highly variable friction and slip observed at Antarctic ice stream bed

The slip of glaciers over the underlying bed is the dominant mechanism governing the migration of ice from land into the oceans, with accelerating slip contributing to sea-level rise. Yet glacier slip remains poorly understood, and observational constraints are sparse. Here we use passive seismic observations to measure both frictional shear stress and slip at the bed of the Rutford Ice Stream in Antarctica using 100,000 repetitive stick-slip icequakes. We find that basal shear stresses and slip rates vary from 10$^4$ to 10$^7$ Pa and 0.2 to 1.5 m per day, respectively. Friction and slip vary temporally over the order of hours, and spatially over 10s of metres, due to corresponding variations in effective normal stress and ice–bed interface material. Our findings suggest that the bed is substantially more complex than currently assumed in ice stream models and that basal effective normal stresses may be significantly higher than previously thought. Our observations can provide constraints on the basal boundary conditions for ice-dynamics models. This is critical for constraining the primary contribution of ice mass loss in Antarctica and hence for reducing uncertainty in sea-level rise projections

Effects of Noise on Ecological Invasion Processes: Bacteriophage-mediated Competition in Bacteria

Pathogen-mediated competition, through which an invasive species carrying and transmitting a pathogen can be a superior competitor to a more vulnerable resident species, is one of the principle driving forces influencing biodiversity in nature. Using an experimental system of bacteriophage-mediated competition in bacterial populations and a deterministic model, we have shown in [Joo et al 2005] that the competitive advantage conferred by the phage depends only on the relative phage pathology and is independent of the initial phage concentration and other phage and host parameters such as the infection-causing contact rate, the spontaneous and infection-induced lysis rates, and the phage burst size. Here we investigate the effects of stochastic fluctuations on bacterial invasion facilitated by bacteriophage, and examine the validity of the deterministic approach. We use both numerical and analytical methods of stochastic processes to identify the source of noise and assess its magnitude. We show that the conclusions obtained from the deterministic model are robust against stochastic fluctuations, yet deviations become prominently large when the phage are more pathological to the invading bacterial strain.Comment: 39 pages, 7 figure

Patient-Reported Outcomes in ATLAS and FLAIR Participants on Long-Acting Regimens of Cabotegravir and Rilpivirine Over 48 Weeks

The phase 3 ATLAS and FLAIR studies demonstrated that maintenance with Long-Acting (LA) intramuscular cabotegravir and rilpivirine is non-inferior in efficacy to current antiretroviral (CAR) oral therapy. Both studies utilized Patient-Reported Outcome instruments to measure treatment satisfaction (HIVTSQ) and acceptance (ACCEPT general domain), health status (SF-12), injection tolerability/acceptance (PIN), and treatment preference. In pooled analyses, LA-treated patients (n = 591) demonstrated greater mean improvements from baseline than the CAR group (n = 591) in treatment satisfaction (Week 44, + 3.9 vs. +0.5 HIVTSQs-points; p /= 97% of LA group participants with recorded data preferred LA treatment compared with prior oral therapy. These results further support the potential of a monthly injectable option for people living with HIV seeking an alternative to daily oral treatment

Orbits of Near-Earth Asteroid Triples 2001 SN263 and 1994 CC: Properties, Origin, and Evolution

Three-body model fits to Arecibo and Goldstone radar data reveal the nature of two near-Earth asteroid triples. Triple-asteroid system 2001 SN263 is characterized by a primary of ~10^13 kg, an inner satellite ~1% as massive orbiting at ~3 primary radii in ~0.7 days, and an outer satellite ~2.5% as massive orbiting at ~13 primary radii in ~6.2 days. 1994 CC is a smaller system with a primary of mass ~2.6 \times 10^11 kg and two satellites ~2% and ~1% as massive orbiting at distances of ~5.5 and ~19.5 primary radii. Their orbital periods are ~1.2 and ~8.4 days. Examination of resonant arguments shows that the satellites are not currently in a mean-motion resonance. Precession of the apses and nodes are detected in both systems (2001 SN263 inner body: d{\varpi}/dt ~1.1 deg/day, 1994 CC inner body: d{\varpi}/dt ~ -0.2 deg/day), which is in agreement with analytical predictions of the secular evolution due to mutually interacting orbits and primary oblateness. Nonzero mutual inclinations between the orbital planes of the satellites provide the best fits to the data in both systems (2001 SN263: ~14 degrees, 1994 CC: ~16 degrees). Our best-fit orbits are consistent with nearly circular motion, except for 1994 CC's outer satellite which has an eccentric orbit of e ~ 0.19. We examine several processes that can generate the observed eccentricity and inclinations, including the Kozai and evection resonances, past mean-motion resonance crossings, and close encounters with terrestrial planets. In particular, we find that close planetary encounters can easily excite the eccentricities and mutual inclinations of the satellites' orbits to the currently observed values.Comment: 17 pages, accepted to Astronomical Journa

Genome-to-genome analysis highlights the effect of the human innate and adaptive immune systems on the hepatitis C virus

Outcomes of hepatitis C virus (HCV) infection and treatment depend on viral and host genetic factors. Here we use human genome-wide genotyping arrays and new whole-genome HCV viral sequencing technologies to perform a systematic genome-to-genome study of 542 individuals who were chronically infected with HCV, predominantly genotype 3. We show that both alleles of genes encoding human leukocyte antigen molecules and genes encoding components of the interferon lambda innate immune system drive viral polymorphism. Additionally, we show that IFNL4 genotypes determine HCV viral load through a mechanism dependent on a specific amino acid residue in the HCV NS5A protein. These findings highlight the interplay between the innate immune system and the viral genome in HCV control

SMARTPOP: Inferring the impact of social dynamics on genetic diversity through high speed simulations

Background: Social behavior has long been known to influence patterns of genetic diversity, but the effect of social processes on population genetics remains poorly quantified - partly due to limited community-level genetic sampling (which is increasingly being remedied), and partly to a lack of fast simulation software to jointly model genetic evolution and complex social behavior, such as marriage rules.Results: To fill this gap, we have developed SMARTPOP - a fast, forward-in-time genetic simulator - to facilitate large-scale statistical inference on interactions between social factors, such as mating systems, and population genetic diversity. By simultaneously modeling genetic inheritance and dynamic social processes at the level of the individual, SMARTPOP can simulate a wide range of genetic systems (autosomal, X-linked, Y chromosomal and mitochondrial DNA) under a range of mating systems and demographic models. Specifically designed to enable resource-intensive statistical inference tasks, such as Approximate Bayesian Computation, SMARTPOP has been coded in C++ and is heavily optimized for speed and reduced memory usage.Conclusion: SMARTPOP rapidly simulates population genetic data under a wide range of demographic scenarios and social behaviors, thus allowing quantitative analyses to address complex socio-ecological questions. © 2014 Guillot and Cox; licensee BioMed Central Ltd

Prevalence of Disorders Recorded in Dogs Attending Primary-Care Veterinary Practices in England

Purebred dog health is thought to be compromised by an increasing occurence of inherited diseases but inadequate prevalence data on common disorders have hampered efforts to prioritise health reforms. Analysis of primary veterinary practice clinical data has been proposed for reliable estimation of disorder prevalence in dogs. Electronic patient record (EPR) data were collected on 148,741 dogs attending 93 clinics across central and south-eastern England. Analysis in detail of a random sample of EPRs relating to 3,884 dogs from 89 clinics identified the most frequently recorded disorders as otitis externa (prevalence 10.2%, 95% CI: 9.1-11.3), periodontal disease (9.3%, 95% CI: 8.3-10.3) and anal sac impaction (7.1%, 95% CI: 6.1-8.1). Using syndromic classification, the most prevalent body location affected was the head-and-neck (32.8%, 95% CI: 30.7-34.9), the most prevalent organ system affected was the integument (36.3%, 95% CI: 33.9-38.6) and the most prevalent pathophysiologic process diagnosed was inflammation (32.1%, 95% CI: 29.8-34.3). Among the twenty most-frequently recorded disorders, purebred dogs had a significantly higher prevalence compared with crossbreds for three: otitis externa (P = 0.001), obesity (P = 0.006) and skin mass lesion (P = 0.033), and popular breeds differed significantly from each other in their prevalence for five: periodontal disease (P = 0.002), overgrown nails (P = 0.004), degenerative joint disease (P = 0.005), obesity (P = 0.001) and lipoma (P = 0.003). These results fill a crucial data gap in disorder prevalence information and assist with disorder prioritisation. The results suggest that, for maximal impact, breeding reforms should target commonly-diagnosed complex disorders that are amenable to genetic improvement and should place special focus on at-risk breeds. Future studies evaluating disorder severity and duration will augment the usefulness of the disorder prevalence information reported herein

Immunochip analysis identifies multiple susceptibility loci for systemic sclerosis

In this study, 1,833 systemic sclerosis (SSc) cases and 3,466 controls were genotyped with the Immunochip array. Classical alleles, amino acid residues, and SNPs across the human leukocyte antigen (HLA) region were imputed and tested. These analyses resulted in a model composed of six polymorphic amino acid positions and seven SNPs that explained the observed significant associations in the region. In addition, a replication step comprising 4,017 SSc cases and 5,935 controls was carried out for several selected non-HLA variants, reaching a total of 5,850 cases and 9,401 controls of European ancestry. Following this strategy, we identified and validated three SSc risk loci, including DNASE1L3 at 3p14, the SCHIP1-IL12A locus at 3q25, and ATG5 at 6q21, as well as a suggested association of the TREH-DDX6 locus at 11q23. The associations of several previously reported SSc risk loci were validated and further refined, and the observed peak of association in PXK was related to DNASE1L3. Our study has increased the number of known genetic associations with SSc, provided further insight into the pleiotropic effects of shared autoimmune risk factors, and highlighted the power of dense mapping for detecting previously overlooked susceptibility loci