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

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

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

Assessing the impact of Bacillus strains mixture probiotic on water quality, growth performance, blood profile and intestinal morphology of Nile tilapia, Oreochromis niloticus

The aim of this study was to assess the impact of a commercial probiotic, Sanolife PRO‐F, on water quality, growth performance, blood profiles and intestinal morphometry of monosex Nile tilapia. A field trial was conducted for 10 weeks in which tilapia fingerlings (20 ± 1.26 g) were randomly distributed into three replicate ponds which were subdivided into three treatment groups, receiving Sanolife PRO‐F at 0 (B0), 0.1 (B1) and 0.2 (B2) g/kg diet, respectively. The results showed a significant improvement in growth performance, feed conversion ratio and blood profiles in tilapia fed on treated diets. The whole intestinal lengths, anterior and terminal intestinal villi heights and anterior goblet cells count were greater in tilapia fed on treated diets. There were no noticeable differences in growth and intestinal morphology between tilapia fed on B1 and B2 diets. The ammonia concentration in water was lower with B1 diet while electric conductivity, salinity and total dissolved solids were higher with the B2 diet. The pH level of pond water was enhanced by both diets, B1 and B2. In conclusion, application of Sanolife PRO‐F at 0.1–0.2 g/kg diet might have beneficial effects on growth, immunity, stress responses and gut health and function as well as the water quality of farmed Nile tilapia

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

Signaling via interleukin-4, receptor alpha chain is required for successful vaccination against schistosomiasis in BALB/c mice

Radiation-attenuated (RA) schistosome larvae are potent stimulators of innate immune responses at the skin site of exposure (pinna) that are likely to be important factors in the development of Th1-mediated protective immunity. In addition to causing an influx of neutrophils, macrophages, and dendritic cells (DCs) into the dermis, RA larvae induced a cascade of chemokine and cytokine secretion following in vitro culture of pinna biopsy samples. While macrophage inflammatory protein 1 and interleukin-1 (IL-1) were produced transiently within the first few days, the Th1-promoting cytokines IL-12 and IL-18 were secreted at high levels until at least day 14. Assay of C3H/HeJ mice confirmed that IL-12 secretion was not due to lipopolysaccharide contaminants binding Toll-like receptor 4. Significantly, IL-12 p40 secretion was sustained in pinnae from vaccinated mice but not in those from nonprotected infected mice. In contrast, IL-10 was produced from both vaccinated and infected mice. This cytokine regulates IL-12-associated dermal inflammation, since in vaccinated IL-10/ mice, pinna thickness was greatly increased concurrent with elevated levels of IL-12 p40. A significant number of IL-12 p40 cells were detected as emigrants from in vitro-cultured pinnae, and most were within a population of rare large granular cells that were Ia, consistent with their being antigen-presenting cells. Labeling of IL-12 cells for CD11c, CD205, CD8, CD11b, and F4/80 indicated that the majority were myeloid DCs, although a proportion were CD11c F4/80, suggesting that macrophages were an additional source of IL-12 in the skin

CanRisk-Prostate: A Comprehensive, Externally Validated Risk Model for the Prediction of Future Prostate Cancer.

PURPOSE: Prostate cancer (PCa) is highly heritable. No validated PCa risk model currently exists. We therefore sought to develop a genetic risk model that can provide personalized predicted PCa risks on the basis of known moderate- to high-risk pathogenic variants, low-risk common genetic variants, and explicit cancer family history, and to externally validate the model in an independent prospective cohort. MATERIALS AND METHODS: We developed a risk model using a kin-cohort comprising individuals from 16,633 PCa families ascertained in the United Kingdom from 1993 to 2017 from the UK Genetic Prostate Cancer Study, and complex segregation analysis adjusting for ascertainment. The model was externally validated in 170,850 unaffected men (7,624 incident PCas) recruited from 2006 to 2010 to the independent UK Biobank prospective cohort study. RESULTS: The most parsimonious model included the effects of pathogenic variants in BRCA2, HOXB13, and BRCA1, and a polygenic score on the basis of 268 common low-risk variants. Residual familial risk was modeled by a hypothetical recessively inherited variant and a polygenic component whose standard deviation decreased log-linearly with age. The model predicted familial risks that were consistent with those reported in previous observational studies. In the validation cohort, the model discriminated well between unaffected men and men with incident PCas within 5 years (C-index, 0.790; 95% CI, 0.783 to 0.797) and 10 years (C-index, 0.772; 95% CI, 0.768 to 0.777). The 50% of men with highest predicted risks captured 86.3% of PCa cases within 10 years. CONCLUSION: To our knowledge, this is the first validated risk model offering personalized PCa risks. The model will assist in counseling men concerned about their risk and can facilitate future risk-stratified population screening approaches

The condition-dependent transcriptional landscape of Burkholderia pseudomallei

This is the final version of the article. Available from the publisher via the DOI in this record.Burkholderia pseudomallei (Bp), the causative agent of the often-deadly infectious disease melioidosis, contains one of the largest prokaryotic genomes sequenced to date, at 7.2 Mb with two large circular chromosomes (1 and 2). To comprehensively delineate the Bp transcriptome, we integrated whole-genome tiling array expression data of Bp exposed to >80 diverse physical, chemical, and biological conditions. Our results provide direct experimental support for the strand-specific expression of 5,467 Sanger protein-coding genes, 1,041 operons, and 766 non-coding RNAs. A large proportion of these transcripts displayed condition-dependent expression, consistent with them playing functional roles. The two Bp chromosomes exhibited dramatically different transcriptional landscapes--Chr 1 genes were highly and constitutively expressed, while Chr 2 genes exhibited mosaic expression where distinct subsets were expressed in a strongly condition-dependent manner. We identified dozens of cis-regulatory motifs associated with specific condition-dependent expression programs, and used the condition compendium to elucidate key biological processes associated with two complex pathogen phenotypes--quorum sensing and in vivo infection. Our results demonstrate the utility of a Bp condition-compendium as a community resource for biological discovery. Moreover, the observation that significant portions of the Bp virulence machinery can be activated by specific in vitro cues provides insights into Bp's capacity as an "accidental pathogen", where genetic pathways used by the bacterium to survive in environmental niches may have also facilitated its ability to colonize human hosts.This work was funded by a core grant provided by the Agency for Science, Technology and Research to the Genome Institute of Singapore, and funding from the Defence Medical and Environmental Research Institute, Singapore. This work was supported in part through NIAID contract HHSN266200400035C to BWS. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Vector control strategies in Brazil: a qualitative investigation into community knowledge, attitudes and perceptions following the 2015-2016 Zika virus epidemic.

OBJECTIVE: The World Health Organization declared a Public Health Emergency of International Concern following the rapid emergence of neonatal microcephaly in Brazil during the 2015-2016 Zika virus (ZIKV) epidemic. In response, a national campaign sought to control Aedes mosquito populations and reduce ZIKV transmission. Achieving adherence to vector control or mosquito-bite reduction behaviours, including the use of topical mosquito repellents, is challenging. Coproduction of research at the community level is needed to understand and mitigate social determinants of lower engagement with Aedes preventive measures, particularly within disempowered groups. DESIGN: In 2017, the Zika Preparedness Latin America Network (ZikaPLAN) conducted a qualitative study to understand individual and community level experiences of ZIKV and other mosquito-borne disease outbreaks. Presented here is a thematic analysis of 33 transcripts from community focus groups and semistructured interviews, applying the Health Belief Model (HBM) to elaborate knowledge, attitudes and perceptions of ZIKV and vector control strategies. PARTICIPANTS: 120 purposively sampled adults of approximate reproductive age (18-45); 103 women participated in focus groups and 17 men in semistructured interviews. SETTING: Two sociopolitically and epidemiologically distinct cities in Brazil: Jundiaí (57 km north of São Paolo) and Salvador (Bahia state capital). RESULTS: Four key and 12 major themes emerged from the analysis: (1) knowledge and cues to action; (2) attitudes and normative beliefs (perceived threat, barriers, benefits and self-efficacy); (3) behaviour change (household prevention and community participation); and (4) community preferences for novel repellent tools, vector control strategies and ZIKV messaging. CONCLUSIONS: Common barriers to repellent adherence were accessibility, appearance and effectiveness. A strong case is made for the transferability of the HBM to inform epidemic preparedness for mosquito-borne disease outbreaks at the community level. Nationally, a health campaign targeting men is recommended, in addition to local mobilisation of funding to strengthen surveillance, risk communication and community engagement

Asexuality: Classification and characterization

This is a post-print version of the article. The official published version can be obtaineed at the link below.The term “asexual” has been defined in many different ways and asexuality has received very little research attention. In a small qualitative study (N = 4), individuals who self-identified as asexual were interviewed to help formulate hypotheses for a larger study. The second larger study was an online survey drawn from a convenience sample designed to better characterize asexuality and to test predictors of asexual identity. A convenience sample of 1,146 individuals (N = 41 self-identified asexual) completed online questionnaires assessing sexual history, sexual inhibition and excitation, sexual desire, and an open-response questionnaire concerning asexual identity. Asexuals reported significantly less desire for sex with a partner, lower sexual arousability, and lower sexual excitation but did not differ consistently from non-asexuals in their sexual inhibition scores or their desire to masturbate. Content analyses supported the idea that low sexual desire is the primary feature predicting asexual identity