Geological structure as a control on floodplain groundwater dynamics

Groundwater in upland floodplains has an important function in regulating river flows and controlling the coupling of hillslope runoff with rivers, with complex interaction between surface waters and groundwaters throughout floodplain width and depth. Heterogeneity is a key feature of upland floodplain hydrogeology and influences catchment water flows, but it is difficult to characterise and therefore is often simplified or overlooked. An upland floodplain and adjacent hillslope in the Eddleston catchment, southern Scotland (UK), has been studied through detailed three-dimensional geological characterisation, the monitoring of ten carefully sited piezometers, and analysis of locally collected rainfall and river data. Lateral aquifer heterogeneity produces different patterns of groundwater level fluctuation across the floodplain. Much of the aquifer is strongly hydraulically connected to the river, with rapid groundwater level rise and recession over hours. Near the floodplain edge, however, the aquifer is more strongly coupled with subsurface hillslope inflows, facilitated by highly permeable solifluction deposits in the hillslope–floodplain transition zone. Here, groundwater level rise is slower but high heads can be maintained for weeks, sometimes with artesian conditions, with important implications for drainage and infrastructure development. Vertical heterogeneity in floodplain aquifer properties, to depths of at least 12 m, can create local aquifer compartmentalisation with upward hydraulic gradients, influencing groundwater mixing and hydrogeochemical evolution. Understanding the geological processes controlling aquifer heterogeneity, which are common to formerly glaciated valleys across northern latitudes, provides key insights into the hydrogeology and wider hydrological behaviour of upland floodplains

Dynamics of a small neutrally buoyant sphere in a fluid and targeting in Hamiltonian systems

We show that, even in the most favorable case, the motion of a small spherical tracer suspended in a fluid of the same density may differ from the corresponding motion of an ideal passive particle. We demonstrate furthermore how its dynamics may be applied to target trajectories in Hamiltonian systems.Comment: See home page http://lec.ugr.es/~julya

Capture and inception of bubbles near line vortices

Motivated by the need to predict vortex cavitation inception, a study has been conducted to investigate bubble capture by a concentrated line vortex of core size rcrc and circulation Γ0Γ0 under noncavitating and cavitating conditions. Direct numerical simulations that solve simultaneously for the two phase flow field, as well as a simpler one-way coupled point-particle-tracking model (PTM) were used to investigate the capture process. The capture times were compared to experimental observations. It was found that the point-particle-tracking model can successfully predict the capture of noncavitating small nuclei by a line vortex released far from the vortex axis. The nucleus grows very slowly during capture until the late stages of the process, where bubble/vortex interaction and bubble deformation become important. Consequently, PTM can be used to study the capture of cavitating nuclei by dividing the process into the noncavitating capture of the nucleus, and then the growth of the nucleus in the low-pressure core region. Bubble growth and deformation act to speed up the capture process.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/87832/2/022105_1.pd

Smartphone-based remote monitoring for chronic heart failure: mixed methods analysis of user experience from patient and nurse perspectives

BACKGROUND: Community-based management by heart failure specialist nurses (HFSNs) is key to improving self-care in heart failure with reduced ejection fraction. Remote monitoring (RM) can aid nurse-led management, but in the literature, user feedback evaluation is skewed in favor of the patient rather than nursing user experience. Furthermore, the ways in which different groups use the same RM platform at the same time are rarely directly compared in the literature. We present a balanced semantic analysis of user feedback from patient and nurse perspectives of Luscii, a smartphone-based RM strategy combining self-measurement of vital signs, instant messaging, and e-learning. OBJECTIVE: This study aims to (1) evaluate how patients and nurses use this type of RM (usage type), (2) evaluate patients' and nurses' user feedback on this type of RM (user experience), and (3) directly compare the usage type and user experience of patients and nurses using the same type of RM platform at the same time. METHODS: We performed a retrospective usage type and user experience evaluation of the RM platform from the perspective of both patients with heart failure with reduced ejection fraction and the HFSNs using the platform to manage them. We conducted semantic analysis of written patient feedback provided via the platform and a focus group of 6 HFSNs. Additionally, as an indirect measure of tablet adherence, self-measured vital signs (blood pressure, heart rate, and body mass) were extracted from the RM platform at onboarding and 3 months later. Paired 2-tailed t tests were used to evaluate differences between mean scores across the 2 timepoints. RESULTS: A total of 79 patients (mean age 62 years; 35%, 28/79 female) were included. Semantic analysis of usage type revealed extensive, bidirectional information exchange between patients and HFSNs using the platform. Semantic analysis of user experience demonstrates a range of positive and negative perspectives. Positive impacts included increased patient engagement, convenience for both user groups, and continuity of care. Negative impacts included information overload for patients and increased workload for nurses. After the patients used the platform for 3 months, they showed significant reductions in heart rate (P=.004) and blood pressure (P=.008) but not body mass (P=.97) compared with onboarding. CONCLUSIONS: Smartphone-based RM with messaging and e-learning facilitates bilateral information sharing between patients and nurses on a range of topics. Patient and nurse user experience is largely positive and symmetrical, but there are possible negative impacts on patient attention and nurse workload. We recommend RM providers involve patient and nurse users in platform development, including recognition of RM usage in nursing job plans

The variant call format and VCFtools

Summary: The variant call format (VCF) is a generic format for storing DNA polymorphism data such as SNPs, insertions, deletions and structural variants, together with rich annotations. VCF is usually stored in a compressed manner and can be indexed for fast data retrieval of variants from a range of positions on the reference genome. The format was developed for the 1000 Genomes Project, and has also been adopted by other projects such as UK10K, dbSNP and the NHLBI Exome Project. VCFtools is a software suite that implements various utilities for processing VCF files, including validation, merging, comparing and also provides a general Perl API

Genomics of Divergence along a Continuum of Parapatric Population Differentiation

MM received funding from the Max Planck innovation funds for this project. PGDF was supported by a Marie Curie European Reintegration Grant (proposal nr 270891). CE was supported by German Science Foundation grants (DFG, EI 841/4-1 and EI 841/6-1)

A Model-Based Analysis of GC-Biased Gene Conversion in the Human and Chimpanzee Genomes

GC-biased gene conversion (gBGC) is a recombination-associated process that favors the fixation of G/C alleles over A/T alleles. In mammals, gBGC is hypothesized to contribute to variation in GC content, rapidly evolving sequences, and the fixation of deleterious mutations, but its prevalence and general functional consequences remain poorly understood. gBGC is difficult to incorporate into models of molecular evolution and so far has primarily been studied using summary statistics from genomic comparisons. Here, we introduce a new probabilistic model that captures the joint effects of natural selection and gBGC on nucleotide substitution patterns, while allowing for correlations along the genome in these effects. We implemented our model in a computer program, called phastBias, that can accurately detect gBGC tracts about 1 kilobase or longer in simulated sequence alignments. When applied to real primate genome sequences, phastBias predicts gBGC tracts that cover roughly 0.3% of the human and chimpanzee genomes and account for 1.2% of human-chimpanzee nucleotide differences. These tracts fall in clusters, particularly in subtelomeric regions; they are enriched for recombination hotspots and fast-evolving sequences; and they display an ongoing fixation preference for G and C alleles. They are also significantly enriched for disease-associated polymorphisms, suggesting that they contribute to the fixation of deleterious alleles. The gBGC tracts provide a unique window into historical recombination processes along the human and chimpanzee lineages. They supply additional evidence of long-term conservation of megabase-scale recombination rates accompanied by rapid turnover of hotspots. Together, these findings shed new light on the evolutionary, functional, and disease implications of gBGC. The phastBias program and our predicted tracts are freely available. © 2013 Capra et al

The geography of recent genetic ancestry across Europe

The recent genealogical history of human populations is a complex mosaic formed by individual migration, large-scale population movements, and other demographic events. Population genomics datasets can provide a window into this recent history, as rare traces of recent shared genetic ancestry are detectable due to long segments of shared genomic material. We make use of genomic data for 2,257 Europeans (the POPRES dataset) to conduct one of the first surveys of recent genealogical ancestry over the past three thousand years at a continental scale. We detected 1.9 million shared genomic segments, and used the lengths of these to infer the distribution of shared ancestors across time and geography. We find that a pair of modern Europeans living in neighboring populations share around 10-50 genetic common ancestors from the last 1500 years, and upwards of 500 genetic ancestors from the previous 1000 years. These numbers drop off exponentially with geographic distance, but since genetic ancestry is rare, individuals from opposite ends of Europe are still expected to share millions of common genealogical ancestors over the last 1000 years. There is substantial regional variation in the number of shared genetic ancestors: especially high numbers of common ancestors between many eastern populations likely date to the Slavic and/or Hunnic expansions, while much lower levels of common ancestry in the Italian and Iberian peninsulas may indicate weaker demographic effects of Germanic expansions into these areas and/or more stably structured populations. Recent shared ancestry in modern Europeans is ubiquitous, and clearly shows the impact of both small-scale migration and large historical events. Population genomic datasets have considerable power to uncover recent demographic history, and will allow a much fuller picture of the close genealogical kinship of individuals across the world.Comment: Full size figures available from http://www.eve.ucdavis.edu/~plralph/research.html; or html version at http://ralphlab.usc.edu/ibd/ibd-paper/ibd-writeup.xhtm

Finding a moral homeground: appropriately critical religious education and transmission of spiritual values

Values-inspired issues remain an important part of the British school curriculum. Avoiding moral relativism while fostering enthusiasm for spiritual values and applying them to non-curricular learning such as school ethos or children's home lives are challenges where spiritual, moral, social and cultural (SMSC) development might benefit from leadership by critical religious education (RE). Whether the school's model of spirituality is that of an individual spiritual tradition (schools of a particular religious character) or universal pluralistic religiosity (schools of plural religious character), the pedagogy of RE thought capable of leading SMSC development would be the dialogical approach with examples of successful implementation described by Gates, Ipgrave and Skeie. Marton's phenomenography, is thought to provide a valuable framework to allow the teacher to be appropriately critical in the transmission of spiritual values in schools of a particular religious character as evidenced by Hella's work in Lutheran schools