A Novel and Fast Approach for Population Structure Inference Using Kernel-PCA and Optimization (PSIKO)

Population structure is a confounding factor in Genome Wide Association Studies, increasing the rate of false positive associations. In order to correct for it, several model-based algorithms such as ADMIXTURE and STRUCTURE have been proposed. These tend to suffer from the fact that they have a considerable computational burden, limiting their applicability when used with large datasets, such as those produced by Next Generation Sequencing (NGS) techniques. To address this, non-model based approaches such as SNMF and EIGENSTRAT have been proposed, which scale better with larger data. Here we present a novel non-model based approach, PSIKO, which is based on a unique combination of linear kernel-PCA and least-squares optimization and allows for the inference of admixture coefficients, principal components, and number of founder populations of a dataset. PSIKO has been compared against existing leading methods on a variety of simulation scenarios, as well as on real biological data. We found that in addition to producing results of the same quality as other tested methods, PSIKO scales extremely well with dataset size, being considerably (up to 30 times) faster for longer sequences than even state of the art methods such as SNMF. PSIKO and accompanying manual are freely available at https://www.uea.ac.uk/computing/psiko

Scientific Visualization Using the Flow Analysis Software Toolkit (FAST)

Over the past few years the Flow Analysis Software Toolkit (FAST) has matured into a useful tool for visualizing and analyzing scientific data on high-performance graphics workstations. Originally designed for visualizing the results of fluid dynamics research, FAST has demonstrated its flexibility by being used in several other areas of scientific research. These research areas include earth and space sciences, acid rain and ozone modelling, and automotive design, just to name a few. This paper describes the current status of FAST, including the basic concepts, architecture, existing functionality and features, and some of the known applications for which FAST is being used. A few of the applications, by both NASA and non-NASA agencies, are outlined in more detail. Described in the Outlines are the goals of each visualization project, the techniques or 'tricks' used lo produce the desired results, and custom modifications to FAST, if any, done to further enhance the analysis. Some of the future directions for FAST are also described

Density waves theory of the capsid structure of small icosahedral viruses

We apply Landau theory of crystallization to explain and to classify the capsid structures of small viruses with spherical topology and icosahedral symmetry. We develop an explicit method which predicts the positions of centers of mass for the proteins constituting viral capsid shell. Corresponding density distribution function which generates the positions has universal form without any fitting parameter. The theory describes in a uniform way both the structures satisfying the well-known Caspar and Klug geometrical model for capsid construction and those violating it. The quasiequivalence of protein environments in viral capsid and peculiarities of the assembly thermodynamics are also discussed.Comment: 8 pages, 3 figur

Investigation of the Effects of Growth Environment on the Ferric Reducing Antioxidant Power of Selected Plant Species

Metabolism within the human body creates multiple oxidant by-products. These oxidants may cause cell injury, damage to DNA, and other complications leading to the development of chronic disease. Antioxidants are important dietary components which defend against oxidative damage by scavenging the oxidant by-products. Research has shown that diets rich in antioxidants offer protection against various chronic diseases. The goal of this research is to determine the effects of varying growing conditions on the production of antioxidants, and to ultimately find the best possible plant-growth environment for maximum production of antioxidants. Each plant was grown under three different environmental conditions; positive, negative, and control treatment. The positive treatment consisted of supplying water to field capacity with fertilizer, the negative treatment consisted supplying half of the water required to reach field capacity with no fertilizer, and the control treatment consisted of supplying water to field capacity with no fertilizer. Ferric reducing antioxidant levels were then determined. The ferric reducing antioxidant power evaluates antioxidant potential by reducing ferric iron (Fe3+) to its ferrous form (Fe2+). Addition of excess ferric ions result in the development of a Prussian blue color. The ferric reducing antioxidant power of the extracts was measured by reading the absorbance at 750 nm using a spectrophotometer. The ferric reducing antioxidant power assay was performed on extracts of red clover (Trifolium pratense), Amur honeysuckle (Lonicera maackii) and wild garlic (Allium vineale). The differing growing conditions resulted in variation in the production of antioxidants by the plants. The data obtained revealed that the plants grown under the negative treatment produced a significantly lower level of antioxidants when compared to the plants grown under the positive treatment. These results indicate that growing conditions can influence antioxidant production in plants

The use of needs assessment methodologies to focus technical interventions in root and tuber crop post-harvest systems: a case study to improve incomes and reduce losses associated with marketing of fresh cassava from rural areas to Dar es Salaam

The Transfer of Needs Assessment Methodologies and Post-Harvest Technologies for Non-Grain Starch Staple Food Crops (NGSS) in sub-Saharan Africa project was initiated in Tanzania in July 1993 as a collaborative venture between the Natural Resources Institute (NRI) and the Tanzania Food and Nutrition Centre (TFNC). The project was funded by the UK Department For International Development (DFID). The main project involved activities in Ghana and Tanzania but this report deals exclusively with activities in Tanzania focusing on the transfer of needs assessment methodologies, the application of needs assessment in identifying post-harvest problems and technical interventions for NGSS and the identification, validation and dissemination of a technology to improve incomes and reduce post-harvest losses associated with marketing of fresh cassava roots from rural production areas to urban markets in Dar es Salaam. In the first stage of the project a range of needs assessment methodologies were successfully validated under field conditions through the mechanism of three case studies, which were carried out in Lake Zone, Tanga Region and Dar es Salaam of Tanzania. Following the case studies, two training in needs assessment workshops were conducted in Tanzania to disseminate needs assessment technologies to key personnel from research organisations and institutes in Tanzania, Mozambique, Uganda, Kenya, Ghana, Rwanda and Ethiopia. The needs assessment case study in Tanga Region highlighted post-harvest problems as a major constraint facing farmers and traders involved in the marketing of fresh cassava to urban areas, and formed the basis for a more detailed study of the marketing system for fresh cassava from rural production areas to urban markets in Dar es Salaam. Semi structured interviews with key stakeholders in the marketing system demonstrated that reductions in quality resulting from poor handling and delays in marketing lead to serious reductions in income throughout the market chain. Farmers and market personnel identified the criteria for a technical intervention to reduce income losses incurred when marketing fresh cassava. After considering various options a simple low cost storage technique for fresh cassava originally developed by the Centro Internacional de Agricultura Tropical (CIAT) and NRI and later modified with DFID RNRRS funds by the NRI and the Ministry of Food and Agriculture (MoFA) in Ghana was selected for validation in Tanzania. Validation exercises in Tanzania demonstrated that low cost fresh cassava root storage technology had the technical and economic potential to alleviate postharvest problems associated with marketing of fresh cassava and improve the incomes of those involved in the cassava market system. In the final stage of the project a flexible dissemination strategy was developed and used to carry out a limited technical dissemination campaign in the major cassava markets in Dares Salaam and selected villages ofKisarawe and Ruf~i Districts in Pwani (Coast) Region, and to promote wider awareness of the technology throughout Tanzania. Needs assessment techniques were used to develop practical approaches for dissemination and two impact assessments (November 1996 and December1997) were carried out to assess effectiveness of dissemination activities and allow for optimisation ofthe strategy. The first impact assessment (November 1996) was used to highlight the strengths and limitations of the initial dissemination strategy, so that a more effective strategy could be developed in collaboration with representatives of the Agricultural Extension Services and key stakeholders in the market system. In December 1997 a second impact assessment was made to assess the effectiveness of the revised dissemination strategy and to highlight any problems. The wider awareness campaign was found to have been effective and a number of expressions of interest had been received from organisations and individuals interested in fresh cassava within Tanzania. A high level of interest and awareness was found in markets and villages where training activities had taken place, but a number of problems were identified which were hampering uptake of the technology. The two main problems were: (a). to be effective the technology needs to be implemented at all points in the market system but individuals were unwilling to take the risk ofbeing the first to use the technology without proof of the economic benefits of the technology; (b). the market system is dominated by a large open type of package called a lumbesa which is not suitable for application of the technology or for transport of cassava but is used for other reasons related to transport charges. To overcome the first difficulty the project team developed a marketing demonstration to provide a practical demonstration of the financial benefits of low cost :fresh cassava root storage technology to potential beneficiaries within the marketing system. The second difficulty was addressed by representatives of various village governments and market co-operatives in collaboration with the TFNCINRI project team. In November of 1997 the village governments of Jaribu and Bungu villages in Rufiji District enacted bylaws to encourage adoption of close packaging for cassava and adoption of the new storage technology. To support this initiative the Agricultural Extension Service in Rufiji District have agreed to integrate the technology into their extension programmes, and in addition the village government in Jaribu has initiated its own training programme in the sub-villages around Jaribu. In December 1997 the village governments of Masaki, Sungwi and Gumba villages in Kisarawe District villages decided to follow the lead taken by villages in Rufiji District and develop bylaws and training programmes to promote uptake ofthe new technology. The Agricultural Extension Service for Kisarawe District have acknowledged the importance of cassava as a source of income generation in the District, and have agreed to integrate the technology into their extension programmes. If co-operation between the various stakeholders is maintained it seems likely that the technology will start to be adopted during 1998. This case study within the main regional Africa project has demonstrated not only that low cost :fresh cassava root storage technology has the technical and economic potential to reduce post-harvest losses and improve incomes, but has also shown that key stakeholders are genuinely interested in adoption of the technology and are willing to co-operate and spend their own funds to promote uptake of the technology. However, for successful uptake of the technology a wider dissemination at both local and national level is required. It is also clear that lack of funds in rural areas could constrain producers and country buyers from adopting this technology. To meet the needs ofthose involved in marketing of fresh cassava throughout Tanzania a sustained campaign of dissemination is required, involving close collaboration between the Agricultural Extension Services, selected NGOs and key stakeholders involved in marketing of fresh cassava from rural areas to various urban centres in Tanzania. A concept note for wider dissemination of low cost fresh cassava root storage technology in Tanzania is included in this report (Appendix 5). The fmdings of this case study have shown that successful adoption of this technology would improve the quality of cassava reaching urban consumers, and contribute to poverty alleviation by improving the income generating potential of marketing of fresh cassava

EP11 Using machine learning to recover unrecorded prehospital data

Background The recording practices, of electronic patient records for ambulance crews, are continuously developing. South Central Ambulance Service (SCAS) adapted the common AVPU-scale (Alert, Voice, Pain, Unresponsive) in 2019 to include an option for ‘New Confusion’. Progressing to this new AVCPU-scale made comparisons with older data impossible. We demonstrate a method to retrospectively classify patients into the alertness levels most influenced by this update. Methods SCAS provided ~1.6 million Electronic Patient Records, including vital signs, demographics, and presenting complaint free-text, these were split into training, validation, and testing datasets (80%, 10%, 10% respectively), and under sampled to the minority class. These data were used to train and validate predictions of the classes most affected by the modification of the scale (Alert, New Confusion, Voice). A transfer-learning natural language processing (NLP) classifier was used, using a language model described by Smerity et al. (2017) to classify the presenting complaint free-text. A second approach used vital signs, demographics, conveyance, and assessments (30 metrics) for classification. Categorical data were binary encoded and continuous variables were normalised. 20 machine learning algorithms were empirically tested and the best 3 combined into a voting ensemble combining three vital-sign based algorithms (Random Forest, Extra Tree Classifier, Decision Tree) with the NLP classifier using a Random Forest output layer. Results The ensemble method resulted in a weighted F1 of 0.78 for the test set. The sensitivities/specificities for each of the classes are: 84%/ 90% (Alert), 73%/ 89% (Newly Confused) and 68%/ 93% (Voice). Conclusions The ensemble combining free text and vital signs resulted in high sensitivity and specificity when reclassifying the alertness levels of prehospital patients. This study demonstrates the capabilities of machine learning classifiers to recover missing data, allowing the comparison of data collected with different recording standards

Optimisation of Bioluminescent Reporters for Use with Mycobacteria

BACKGROUND: Mycobacterium tuberculosis, the causative agent of tuberculosis, still represents a major public health threat in many countries. Bioluminescence, the production of light by luciferase-catalyzed reactions, is a versatile reporter technology with multiple applications both in vitro and in vivo. In vivo bioluminescence imaging (BLI) represents one of its most outstanding uses by allowing the non-invasive localization of luciferase-expressing cells within a live animal. Despite the extensive use of luminescent reporters in mycobacteria, the resultant luminescent strains have not been fully applied to BLI. METHODOLOGY/PRINCIPAL FINDINGS: One of the main obstacles to the use of bioluminescence for in vivo imaging is the achievement of reporter protein expression levels high enough to obtain a signal that can be detected externally. Therefore, as a first step in the application of this technology to the study of mycobacterial infection in vivo, we have optimised the use of firefly, Gaussia and bacterial luciferases in mycobacteria using a combination of vectors, promoters, and codon-optimised genes. We report for the first time the functional expression of the whole bacterial lux operon in Mycobacterium tuberculosis and M. smegmatis thus allowing the development of auto-luminescent mycobacteria. We demonstrate that the Gaussia luciferase is secreted from bacterial cells and that this secretion does not require a signal sequence. Finally we prove that the signal produced by recombinant mycobacteria expressing either the firefly or bacterial luciferases can be non-invasively detected in the lungs of infected mice by bioluminescence imaging. CONCLUSIONS/SIGNIFICANCE: While much work remains to be done, the finding that both firefly and bacterial luciferases can be detected non-invasively in live mice is an important first step to using these reporters to study the pathogenesis of M. tuberculosis and other mycobacterial species in vivo. Furthermore, the development of auto-luminescent mycobacteria has enormous ramifications for high throughput mycobacterial drug screening assays which are currently carried out either in a destructive manner using LuxAB or the firefly luciferase

Spectroscopy of 28^{28}Na: shell evolution toward the drip line

Excited states in $^{28}$Na have been studied using the $\beta$-decay of implanted $^{28}$Ne ions at GANIL/LISE as well as the in-beam $\gamma$-ray spectroscopy at the NSCL/S800 facility. New states of positive (J$^{\pi}$=3,4$^+$) and negative (J$^{\pi}$=1-5$^-$) parity are proposed. The former arise from the coupling between 0d$\_{5/2}$ protons and a 0d$\_{3/2}$ neutron, while the latter are due to couplings with 1p$\_{3/2}$ or 0f$\_{7/2}$ neutrons. While the relative energies between the J$^{\pi}$=1-4$^+$ states are well reproduced with the USDA interaction in the N=17 isotones, a progressive shift in the ground state binding energy (by about 500 keV) is observed between $^{26}$F and $^{30}$Al. This points to a possible change in the proton-neutron 0d$\_{5/2}$-0d$\_{3/2}$ effective interaction when moving from stability to the drip line. The presence of J$^{\pi}$=1-4$^-$ negative parity states around 1.5 MeV as well as of a candidate for a J$^{\pi}$=5$^-$ state around 2.5 MeV give further support to the collapse of the N=20 gap and to the inversion between the 0f$\_{7/2}$ and 1p$\_{3/2}$ levels below Z=12. These features are discussed in the framework of Shell Model and EDF calculations, leading to predicted negative parity states in the low energy spectra of the $^{26}$F and $^{25}$O nuclei.Comment: Exp\'erience GANIL/LISE et NSCL/S80

Mechanisms of Interference in Vibrotactile Working Memory

In previous studies of interference in vibrotactile working memory, subjects were presented with an interfering distractor stimulus during the delay period between the target and probe stimuli in a delayed match-to-sample task. The accuracy of same/different decisions indicated feature overwriting was the mechanism of interference. However, the distractor was presented late in the delay period, and the distractor may have interfered with the decision-making process, rather than the maintenance of stored information. The present study varies the timing of distractor onset, (either early, in the middle, or late in the delay period), and demonstrates both overwriting and non-overwriting forms of interference

Between platonic love and internet pornography

The article sets out to show how an holistic approach in matters of sexuality is always more helpful than one-sided approaches. On the issue of internet pornography, the authors suggest that the recent anti-masturbation online movement ‘no fapping’ is based on wrong conclusions from insufficient evidence. We suggest that a holistic approach is called for, with emphasis on the embodied human. Abstinence or what is understood by ‘Platonic love’ is not a solution, according to Plato himself. From a phenomenological perspective, we suggest owning up to our strange bodies and habitualising sexual activity