Study of Regions of Extended Homozygosity Provides a Powerful Method to Explore Haplotype Structure of Human Populations

Previous investigations have reported linkage disequilibrium occurring between nearby polymorphisms, a block-like structure for such relationships, some instances where surprisingly few haplotypes are found and regions of extended homozygosity which are especially marked around centromeres and which are especially common on the X chromosome. We investigated the distribution and nature of regions of extended homozygosity in a sample of 1411 subjects included in a genome wide association study. Regions of extended homozygosity over 1Mb are common, with an average of 35.9 occurring per subject, and containing on average 73 homozygous markers. They have a markedly non-random distribution. They are relatively common on the X chromosome and are seen at centromeres but are also concentrated at other chromosomal regions where presumably recombination is rare. They seem to be a consequence of some haplotypes being very common in the population and although sometimes this reflects the effect of a very common haplotype we also note that there are examples of two or three common haplotypes, each very different from each other, underlying this effect. Regions of extended homozygosity are commoner than previously appreciated. They result from the presence of extended haplotypes with high population frequency. Such regions concentrate in particular locations. The haplotypes involved are sometimes markedly disparate from each other. These regions offer a valuable opportunity for further investigation, in particular with regard to their ancestral history

Investigation into the Ability of SNP Chipsets and Microsatellites to Detect Association with a Disease Locus

We wished to investigate the ability of different SNP chipsets to detect association with a disease and to investigate the linkage disequilibrium (LD) relationships between microsatellites and nearby SNPs in order to assess their potential usefulness to detect association

Synthesizing SMOS Zero-Baselines with Aquarius Brightness Temperature Simulator

SMOS [1] and Aquarius [2] are ESA and NASA missions, respectively, to make L-band measurements from the Low Earth Orbit. SMOS makes passive measurements whereas Aquarius measures both passive and active. SMOS was launched in November 2009 and Aquarius in June 2011.The scientific objectives of the missions are overlapping: both missions aim at mapping the global Sea Surface Salinity (SSS). Additionally, SMOS mission produces soil moisture product (however, Aquarius data will eventually be used for retrieving soil moisture too). The consistency of the brightness temperature observations made by the two instruments is essential for long-term studies of SSS and soil moisture. For resolving the consistency, the calibration of the instruments is the key. The basis of the SMOS brightness temperature level is the measurements performed with the so-called zero-baselines [3]; SMOS employs an interferometric measurement technique which forms a brightness temperature image from several baselines constructed by combination of multiple receivers in an array; zero-length baseline defines the overall brightness temperature level. The basis of the Aquarius brightness temperature level is resolved from the brightness temperature simulator combined with ancillary data such as antenna patterns and environmental models [4]. Consistency between the SMOS zero-baseline measurements and the simulator output would provide a robust basis for establishing the overall comparability of the missions

The effect of fresh seaweed and a formulated diet supplemented with seaweed on the growth and gonad quality of the collector sea urchin, Tripneustes gratilla, under farm conditions

This gonad enhancement study investigates the effect of different fresh and formulated feeds and feeding regimes on the growth and gonad quality of wild-collected adult sea urchin, Tripneustes gratilla, under farm conditions for over 18 weeks. In the first 12 weeks (phase 1), urchins were fed fresh Ulva rigida (U); a 50:50 mixture of fresh U. rigida and Gracilaria gracilis (UG); fresh G. gracilis (G) and a formulated diet 20U (containing 20% U. rigida), and in the final 6 weeks (phase 2) of the study, diet was changed to a formulated feed (20U diet). By the end of phase 1, urchins fed the 20U diet produced gonads (50.72 ± 5.4 g) that were significantly heavier (p < .001) than the gonads of urchins fed the fresh seaweed diets (U, UG & G). By the end of phase 2, gonad weight of urchins in treatment groups UG-20U and G-20U were similar to those fed the 20U-20U diet. Gonad colour of urchins in the G-20U treatment became significantly lighter (ANOVA, p = .029) and poorer quality, compared with urchins in the U-20U group. This gonad enhancement study, conducted on wild collected adult T. gratilla, has shown that a formulated feed (20U diet) can enhance gonad growth and produce commercially acceptable gonads. This farm-based study supports previous findings from aquarium-based studies by our group and indicates that short-term sea urchin gonad enhancement can be carried out under farm conditions in South Africa

Determination of Best Low-Frequency Microwave Antenna Approach for Future High Resolution Measurements from Space

Microwave remote sensing measurements at L-band (~1.2-1.6 GHz) of geophysical parameters such as soil moisture will need to be at higher spatial resolution than current systems (SMOS/ SMAP/ Aquarius) in order to meet the requirements of land surface, ocean, and numerical weather prediction models in the near future, which will operate at ~9-15 km global grids and 1-3 km regional grids in the next few years. In order to make progress toward these needed spatial resolutions, advancements in technology are necessary which would lead to improved effective (i.e. equivalent) antenna size. An architecture trade study was conducted to quantitatively define the value and limits of different microwave technology paths, and to select the most appropriate path to achieve the high spatial resolution required by science in the future without sacrificing performance, accuracy, and global coverage

Indium joints for cryogenic gravitational wave detectors

A viable technique for the preparation of highly thermal conductive joints between sapphire components in gravitational wave detectors is presented. The mechanical loss of such a joint was determined to be as low as 2 × 10−3 at 20 K and 2 × 10−2 at 300 K. The thermal noise performance of a typical joint is compared to the requirements of the Japanese gravitational wave detector, KAGRA. It is shown that using such an indium joint in the suspension system allows it to operate with low thermal noise. Additionally, results on the maximum amount of heat which can be extracted via indium joints are presented. It is found that sapphire parts, joined by means of indium, are able to remove the residual heat load in the mirrors of KAGRA

Effects on the immune system associated with living near a pesticide dump site.

In this paper, we report results of the second phase of a larger study designed to evaluate the effects on the immune system of living near a Superfund site containing organochlorine pesticides, volatile organic compounds, and metals. Phase II was conducted to determine whether living near the site, consisting of six locations in Aberdeen, North Carolina, is associated with higher plasma organochlorine levels, immune suppression, or DNA damage. Each of 302 residents of Aberdeen and neighboring communities provided a blood specimen, underwent a skin test, and answered a questionnaire. Blood specimens were analyzed for organochlorine pesticides, immune markers, and micronuclei. Of 20 organochlorines tested, only DDE was detected in the blood of participants (except for one individual). Age-adjusted mean plasma DDE levels were 4.05 ppb for Aberdeen residents and 2.95 ppb (p = 0.01) for residents of neighboring communities. Residents of 40-59 years of age who lived within a mile of any site, but particularly the Farm Chemicals site, had higher plasma DDE levels than residents who lived farther away. Residents who lived near the Farm Chemicals site before versus after 1985 also had higher plasma DDE levels. Overall, there were few differences in immune markers between residents of Aberdeen and the neighboring communities. However, residents who lived closer to the dump sites had statistically significantly lower mitogen-induced lymphoproliferative activity than residents who lived farther away (p < 0.05). Residential location was not consistently associated with frequency of micronuclei or skin test responses. Although some statistically significant differences in immune markers were noted in association with residential location, the magnitude of effects are of uncertain clinical importance

Food for thought: Dietary nootropics for the optimisation of military operators cognitive performance

Nootropics are compounds that enhance cognitive performance and have been highlighted as a medium-term human augmentation technology that could support soldier performance. Given the differing ethical, safety, and legal considerations associated with the pharmaceutical subset of nootropics, this analysis focuses on dietary supplementation which may enhance cognition during training and operations. Numerous supplements have been investigated as possible nootropics, however research is often not context specific or of high quality, leading to questions regarding efficacy. There are many other complex cofactors that may affect the efficacy of any dietary nootropic supplement which is designed to improve cognition, such as external stressors (e.g., sleep deprivation, high physical workloads), task specifics (e.g., cognitive processes required), and other psychological constructs (e.g., placebo/nocebo effect). Moreover, military population considerations, such as prior nutritional knowledge and current supplement consumption (e.g., caffeine), along with other issues such as supplement contamination should be evaluated when considering dietary nootropic use within military populations. However, given the increasing requirement for cognitive capabilities by military personnel to complete role-related tasks, dietary nootropics could be highly beneficial in specific contexts. Whilst current evidence is broadly weak, nutritional nootropic supplements may be of most use to the military end user, during periods of high military specific stress. Currently, caffeine and L-tyrosine are the leading nootropic supplements candidates within the military context. Future military specific research on nootropics should be of high quality and use externally valid methodologies to maximise the translation of research to practice

Recent Advances in SMAP RFI Processing

The measurements made by the Soil Moisture Active/Passive (SMAP) mission are affected by the presence of Radio Frequency Interference (RFI) in the protected 1400-1427 MHz band. In SMAP data processing, the main protection against RFI is a sophisticated RFI detection algorithm which flags sub-samples in time and frequency that are contaminated by RFI and removes them before estimating the brightness temperature. This contribution presents two additional approaches that have been developed to address the RFI concern in SMAP. The first consists in locating sources of RFI; once located, it becomes possible to report RFI sources to spectrum management authorities, which can lead to less RFI being experienced by SMAP in the future. The second is a new RFI detection method that is based on detecting outliers in the spatial distribution of measured antenna temperatures

Developing search strategies for clinical practice guidelines in SUMSearch and Google Scholar and assessing their retrieval performance

<p>Abstract</p> <p>Background</p> <p>Information overload, increasing time constraints, and inappropriate search strategies complicate the detection of clinical practice guidelines (CPGs). The aim of this study was to provide clinicians with recommendations for search strategies to efficiently identify relevant CPGs in SUMSearch and Google Scholar.</p> <p>Methods</p> <p>We compared the retrieval efficiency (retrieval performance) of search strategies to identify CPGs in SUMSearch and Google Scholar. For this purpose, a two-term GLAD (GuideLine And Disease) strategy was developed, combining a defined CPG term with a specific disease term (MeSH term). We used three different CPG terms and nine MeSH terms for nine selected diseases to identify the most efficient GLAD strategy for each search engine. The retrievals for the nine diseases were pooled. To compare GLAD strategies, we used a manual review of all retrievals as a reference standard. The CPGs detected had to fulfil predefined criteria, e.g., the inclusion of therapeutic recommendations. Retrieval performance was evaluated by calculating so-called diagnostic parameters (sensitivity, specificity, and "Number Needed to Read" [NNR]) for search strategies.</p> <p>Results</p> <p>The search yielded a total of 2830 retrievals; 987 (34.9%) in Google Scholar and 1843 (65.1%) in SUMSearch. Altogether, we found 119 unique and relevant guidelines for nine diseases (reference standard). Overall, the GLAD strategies showed a better retrieval performance in SUMSearch than in Google Scholar. The performance pattern between search engines was similar: search strategies including the term "guideline" yielded the highest sensitivity (SUMSearch: 81.5%; Google Scholar: 31.9%), and search strategies including the term "practice guideline" yielded the highest specificity (SUMSearch: 89.5%; Google Scholar: 95.7%), and the lowest NNR (SUMSearch: 7.0; Google Scholar: 9.3).</p> <p>Conclusion</p> <p>SUMSearch is a useful tool to swiftly gain an overview of available CPGs. Its retrieval performance is superior to that of Google Scholar, where a search is more time consuming, as substantially more retrievals have to be reviewed to detect one relevant CPG. In both search engines, the CPG term "guideline" should be used to obtain a comprehensive overview of CPGs, and the term "practice guideline" should be used if a less time consuming approach for the detection of CPGs is desired.</p