XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments.

We present an extensible software model for the genotype and phenotype community, XGAP. Readers can download a standard XGAP (http://www.xgap.org) or auto-generate a custom version using MOLGENIS with programming interfaces to R-software and web-services or user interfaces for biologists. XGAP has simple load formats for any type of genotype, epigenotype, transcript, protein, metabolite or other phenotype data. Current functionality includes tools ranging from eQTL analysis in mouse to genome-wide association studies in humans.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Brain and Spinal Cord Interaction: Protective Effects of Exercise Prior to Spinal Cord Injury

We have investigated the effects of a spinal cord injury on the brain and spinal cord, and whether exercise provided before the injury could organize a protective reaction across the neuroaxis. Animals were exposed to 21 days of voluntary exercise, followed by a full spinal transection (T7–T9) and sacrificed two days later. Here we show that the effects of spinal cord injury go beyond the spinal cord itself and influence the molecular substrates of synaptic plasticity and learning in the brain. The injury reduced BDNF levels in the hippocampus in conjunction with the activated forms of p-synapsin I, p-CREB and p-CaMK II, while exercise prior to injury prevented these reductions. Similar effects of the injury were observed in the lumbar enlargement region of the spinal cord, where exercise prevented the reductions in BDNF, and p-CREB. Furthermore, the response of the hippocampus to the spinal lesion appeared to be coordinated to that of the spinal cord, as evidenced by corresponding injury-related changes in BDNF levels in the brain and spinal cord. These results provide an indication for the increased vulnerability of brain centers after spinal cord injury. These findings also imply that the level of chronic activity prior to a spinal cord injury could determine the level of sensory-motor and cognitive recovery following the injury. In particular, exercise prior to the injury onset appears to foster protective mechanisms in the brain and spinal cord

Enhancing carbon sequestration in soil with coal combustion products: a technology for minimising carbon footprints in coal-power generation and agriculture

Coal-fired power generation and agriculture account for more than half of global greenhouse gas emissions, but the coal fly ash (CFA) produced in the former can be a resource for reducing emissions from agriculture to minimise environmental footprints in both industries. Our aim in this study was to test how acidic and alkaline CFA addition could minimise loss of C and N from acidic soil, with or without added manure. We determined composition and structural characteristics of acidic and alkaline CFA for their capacity to adsorb organic carbon, but observed poor adsorption because of low concentrations of cenospheres and unburnt carbon as the primary absorbents in the ash. Addition of CFA had no impact on the loss of carbon or nitrogen from unmanured soil in which concentrations of these nutrients were low. Loss of carbon from manured soil was reduced by 36% with alkaline ashes and by 3-fold with acidic ashes; while loss of N was 30–50% lower with acidic ashes, but 28% higher with alkaline ashes, compared with no ash treatment. The increases in C sparing with CFA addition were achieved not by direct C absorption but by restraining microbial population and respiration, and potentially emissions. Alkaline CFA increased soil pH and if used to substitute just 10% of lime for ameliorating soil acidity would reduce CO2 emission associated with the mining of the lime and its eventual dissolution in soil by ~ 2.66 Tg or 2.8% of Australia’s annual agricultural emissions. High concentrations of oxides of phosphorus, silicon, titanium and clay particles in acidic ashes, and oxides of cations in alkaline ashes, were associated with potential for promoting C storage and acidity amelioration in soil

Relationship between Spatial Working Memory Performance and Diet Specialization in Two Sympatric Nectar Bats

Behavioural ecologists increasingly recognise spatial memory as one the most influential cognitive traits involved in evolutionary processes. In particular, spatial working memory (SWM), i.e. the ability of animals to store temporarily useful information for current foraging tasks, determines the foraging efficiency of individuals. As a consequence, SWM also has the potential to influence competitive abilities and to affect patterns of sympatric occurrence among closely related species. The present study aims at comparing the efficiency of SWM between generalist (Glossophaga soricina) and specialist (Leptonycteris yerbabuenae) nectarivorous bats at flowering patches. The two species differ in diet – the generalist diet including seasonally fruits and insects with nectar and pollen while the specialist diet is dominated by nectar and pollen yearlong – and in some morphological traits – the specialist being heavier and with proportionally longer rostrum than the generalist. These bats are found sympatrically within part of their range in the Neotropics. We habituated captive individuals to feed on artificial flower patches and we used infrared video recordings to monitor their ability to remember and avoid the spatial location of flowers they emptied in previous visits in the course of 15-min foraging sequences. Experiments revealed that both species rely on SWM as their foraging success attained significantly greater values than random expectations. However, the nectar specialist L. yerbabuenae was significantly more efficient at extracting nectar (+28% in foraging success), and sustained longer foraging bouts (+27% in length of efficient foraging sequences) than the generalist G. soricina. These contrasting SWM performances are discussed in relation to diet specialization and other life history traits

Comparison of Promoter Hypermethylation Pattern in Salivary Rinses Collected with and without an Exfoliating Brush from Patients with HNSCC

Background: Salivary rinses have been recently proposed as a valuable resource for the development of epigenetic biomarkers for detection and monitoring of head and neck squamous cell carcinoma (HNSCC). Both salivary rinses collected with and without an exfoliating brush from patients with HNSCC are used in detection of promoter hypermethylation, yet their correlation of promoter hypermethylation has not been evaluated. This study was to evaluate the concordance of promoter hypermethylation between salivary rinses collected with and without an exfoliating brush from patients with HNSCC. Methodolgy: 57 paired salivary rinses collected with or without an exfoliating brush from identical HNSCC patients were evaluated for promoter hypermethylation status using Quantitative Methylation-Specific PCR. Target tumor suppressor gene promoter regions were selected based on our previous studies describing a panel for HNSCC screening an

Measuring effectiveness, efficiency and equity in a Payments for Ecosystem Services trial.

There is currently a considerable effort to evaluate the performance of payments for ecosystem services (PES) as an environmental management tool. The research presented here contributes to this work by using an experimental design to evaluate PES as a tool for supporting biodiversity conservation in the context of an African protected area. The trial employed a 'before and after' and 'with and without' design. We present the results of social and ecological surveys to investigate the impacts of the PES in terms of its effectiveness, efficiency and equity. We find the PES to be effective at bringing about additional conservation outcomes. However, we also found that increased monitoring is similarly effective in the short term, at lower cost. The major difference - and arguably the significant contribution of the PES - was that it changed the motives for protecting the park and improved local perceptions both of the park and its authority. We discuss the implications of these results for conservation efficiency, arguing that efficiency should not be defined in terms of short-term cost-effectiveness, but also in terms of the sustainability of behavioral motives. This insight helps us to resolve the apparent trade-off between goals of equity and efficiency in PES

Addressing risk factors for child abuse among high risk pregnant women: design of a randomised controlled trial of the nurse family partnership in Dutch preventive health care

<p>Abstract</p> <p>Background</p> <p>Low socio-economic status combined with other risk factors affects a person's physical and psychosocial health from childhood to adulthood. The societal impact of these problems is huge, and the consequences carry on into the next generation(s). Although several studies show these consequences, only a few actually intervene on these issues. In the United States, the Nurse Family Partnership focuses on high risk pregnant women and their children. The main goal of this program is primary prevention of child abuse. The Netherlands is the first country outside the United States allowed to translate and culturally adapt the Nurse Family Partnership into VoorZorg. The aim of the present study is to assess whether VoorZorg is as effective in the Netherland as in the United States.</p> <p>Methods</p> <p>The study consists of three partly overlapping phases. Phase 1 was the translation and cultural adaptation of Nurse Family Partnership and the design of a two-stage selection procedure. Phase 2 was a pilot study to examine the conditions for implementation. Phase 3 is the randomized controlled trial of VoorZorg compared to the care as usual. Primary outcome measures were smoking cessation during pregnancy and after birth, birth outcomes, child development, child abuse and domestic violence. The secondary outcome measure was the number of risk factors present.</p> <p>Discussion</p> <p>This study shows that the Nurse Family Partnership was successfully translated and culturally adapted into the Dutch health care system and that this program fulfills the needs of high-risk pregnant women. We hypothesize that this program will be effective in addressing risk factors that operate during pregnancy and childhood and compromise fetal and child development.</p> <p>Trial registration</p> <p>Current Controlled Trials <a href="http://www.controlled-trials.com/ISRCTN16131117">ISRCTN16131117</a></p

Toward a geography of black internationalism: Bayard Rustin, nonviolence and the promise of Africa

This article charts the trip made by civil rights leader Bayard Rustin to West Africa in 1952, and examines the unpublished ‘Africa Program’ which he subsequently presented to leading American pacifists. I situate Rustin’s writings within the burgeoning literature on black internationalism which, despite its clear geographical registers, geographers themselves have as yet made only a modest contribution towards. The article argues that within this literature there remains a tendency to romanticize cross-cultural connections in lieu of critically interrogating their basic, and often competing, claims. I argue that closer attention to the geographies of black internationalism, however, allows us to shape a more diverse and practiced sense of internationalist encounter and exchange. The article reconstructs the multiplicity of Rustin’s black internationalist geographies which drew eclectically from a range of Pan-African, American and pacifist traditions. Though each of these was profoundly racialized, they conceptualized race in distinctive ways and thereby had differing understandings of what constituted the international as a geographical arena. By blending these forms of internationalism Rustin was able to promote a particular model of civil rights which was characteristically internationalist in outlook, nonviolent in principle and institutional in composition; a model which in selective and uneven ways continues to shape our understanding of the period

A Comparison of Scent Marking between a Monogamous and Promiscuous Species of Peromyscus: Pair Bonded Males Do Not Advertise to Novel Females

Scent marking can provide behavioral and physiological information including territory ownership and mate advertisement. It is unknown how mating status and pair cohabitation influence marking by males from different social systems. We compared the highly territorial and monogamous California mouse (Peromyscus californicus) to the less territorial and promiscuous white-footed mouse (P. leucopus). Single and mated males of both species were assigned to one of the following arenas lined with filter paper: control (unscented arena), male scented (previously scent-marked by a male conspecific), or females present (containing females in small cages). As expected, the territorial P. californicus scent marked and overmarked an unfamiliar male conspecific's scent marks more frequently than P. leucopus. Species differences in responses to novel females were also found based on mating status. The presence of unfamiliar females failed to induce changes in scent marking in pair bonded P. californicus even though virgin males increased marking behavior. Pair bonding appears to reduce male advertisement for novel females. This is in contrast to P. leucopus males that continue to advertise regardless of mating status. Our data suggest that communication through scent-marking can diverge significantly between species based on mating system and that there are physiological mechanisms that can inhibit responsiveness of males to female cues

Neuron-glia cross talk in rat striatum after transient forebrain ischemia

Striatum is highly vulnerable to transient forebrain ischemia induced by the 4 vessel occlusion (4V0) method (Brierley 1976. Pulsinelli et al. 1982, Zini et al. 1990a). Massive degeneration and loss of Nissl-stained neurons occur within 24 hr from an ischemia of long duration (30 min) (Pulsinelli et al. 1982). Neuronal loss is mainly restricted to the lateral part of caudate-putamen (Pulsinelli et al. 1982, Zini et al. 1990a). Cellular alterations include loss of medium-size spiny projection neurons (Pulsinelli et al. 1982, Francis and Pulsinelli 1982), largely corresponding to dopaminoceptive neurons (Benfenati et al. 1989, Zoli et al. 1989), and increase in reactive astrocytes (Pulsinelli et al. 1982, Grimaldi et al. 1990) and microglia (Gehrmann et al. 1982). On the other hand, large cholinergie (Francis and Pulsinelli 1982) and medium-size aspiny somatostatin (SS)/neuropeptide Y (NPY)-containing interneurons are resistant to the ischemic insult (Pulsinelli et al. 1982, Grimaldi et al. 1990). In a few instances, such as in the case of SS and NPY immunoreactivity (IR), the initial loss is followed by full recovery within 7 (SS) or 40 (NPY) days post-ischemia (Grimaldi et al. 1990). However, it is not known whether some kind of recovery is present for the bulk of medium-size spiny projections neurons after the first days post-ischemia