Common datastream permutations of animal social network data are not appropriate for hypothesis testing using regression models

1. Social network methods have become a key tool for describing, modelling and testing hypotheses about the social structures of animals. However, due to the non-independence of network data and the presence of confounds, specialised statistical techniques are often needed to test hypotheses in these networks. Datastream permutations, originally developed to test the null hypothesis of random social structure, have become a popular tool for testing a wide array of null hypotheses in animal social networks. In particular, they have been used to test whether exogenous factors are related to network structure by interfacing these permutations with regression models.2. Here, we show that these datastream permutations typically do not represent the null hypothesis of interest to researchers interfacing animal social network analysis with regression modelling, and use simulations to demonstrate the potential pitfalls of using this methodology.3. Our simulations show that, if used to indicate whether a relationship exists between network structure and a covariate, datastream permutations can result in extremely high type I error rates, in some cases approaching 50%. In the same set of simulations, traditional node-label permutations produced appropriate type I error rates (~5%).4. Our analysis shows that datastream permutations do not represent the appropriate null hypothesis for these analyses. We suggest that potential alternatives to this procedure may be found in regarding the problems of non-independence of network data and unreliability of observations separately. If biases introduced during data collection can be corrected, either prior to model fitting or within the model itself, node-label permutations then serve as a useful test for interfacing animal social network analysis with regression modelling

A Cell-Free System for Regulated Exocytosis in Pc12 Cells

We have developed a cell-free system for regulated exocytosis in the PC12 neuroendocrine cell line. Secretory vesicles were preloaded with acridine orange in intact cells, and the cells were sonicated to produce flat, carrier-supported plasma membrane patches with attached vesicles. Exocytosis resulted in the release of acridine orange which was visible as a disappearance of labeled vesicles and, under optimal conditions, produced light flashes by fluorescence dequenching. Exocytosis in vitro requires cytosol and Ca2+ at concentrations in the micromolar range, and is sensitive to Tetanus toxin. Imaging of membrane patches at diffraction- limited resolution revealed that 42% of docked granules were released in a Ca2+-dependent manner dur- ing 1 min of stimulation. Electron microscopy of membrane patches confirmed the presence of dense-core vesicles. Imaging of membrane patches by atomic force microscopy revealed the presence of numerous particles attached to the membrane patches which decreased in number upon stimula- tion. Thus, exocytotic membrane fusion of single vesicles can be monitored with high temporal and spatial resolution, while providing access to the site of exocytosis for biochemical and molecular tools

Human cases of simultaneous echinococcosis and tuberculosis - significance and extent in China

During analysis of retrospective community survey data, we identified two patients from Xiji County, south Ningxia Hui Autonomous Region with simultaneous echinococcosis and tuberculosis (TB), representing the first such reports for China. As the echinococcosis chronicity increased, the immune profile in both subjects changed from a Th1 to Th2 response, as shown by a TB skin test, originally positive, becoming negative. Such an elevated Th2 immune profile, with subsequent suppression of the Th1 immune response, is a common feature of chronic helminth infections. Given the difficulties in definitive diagnosis, and the potential increased susceptibility for TB infection in patients with advanced echinococcosis, we suggest that combined TB/echinococcosis surveys be undertaken in this area in the future. This would allow early diagnosis of both TB and echinococcosis cases with better prognosis for effective and sustainable treatment outcomes, ultimately reducing associated morbidity and mortality, and also the overall financial costs to the individual and the public health care system in this under developed part of China

Red Sea fish market assessments indicate high species diversity and potential overexploitation

In many parts of the world, particularly remote and underdeveloped regions, reports of fisheries catch, effort, and landing data are limited. In order to implement effective fishing regulations to protect natural stocks, understanding fishing pressure, key target species, catch composition, and value of each species is vital. In regions where published data is limited, and the sampling of numerous small boats and landing sites is not feasible, fish market surveys represent an opportunity to obtain key fisheries data. This study therefore aims to obtain species-specific prices and market composition for fish landed in the central Red Sea by surveying local fish markets. We conducted 11 surveys at two major Red Sea fish markets to ascertain key fisheries metrics using market data as a proxy for catch data. Results indicate that a high proportion of the market composition is generated by 46 species from six family-level groups, Serranidae, Labridae, scarine labrids, Carangidae, Lethrinidae, and Lutjanidae, contributing to 87 % of the total market biomass. Species-specific values ranged from 4.50 USD/kg to 26.44 USD/kg, with market surveys highlighting the economic value of three local serranid species: Plectropomus pessuliferus marisrubri, Plectropomus areolatus and Variola louti, all valued at more than 25 USD/kg, and a labrid: Cheilinus undulatus, valued at 26.44 USD/kg. The Serranidae family represents 47 % of the total biomass and 55 % of the potential revenue in the market, while also indicating potentially overfished reefs due to the high occurrence of smaller species and undersized individuals of higher priced serranid species. Many of the high-valued serranids were below the size at sexual maturity. Target species exhibited small body size and decreasing abundance, potentially indicating a “shrinking baseline” scenario occurring in the Saudi Arabian artisanal coral reef fishery. These results indicate that introducing effective fisheries legislation and management is necessary for the longevity and sustainability of the reef-based fishery in the Saudi Arabian Red Sea. Implementing catch quotas, size limits, and seasonal restrictions are potential mechanisms that could be used to facilitate positive change within this vulnerable fishery

Metabolomics and lipidomics reveal perturbation of sphingolipid metabolism by a novel anti-trypanosomal 3-(oxazolo[4,5-b]pyridine-2-yl)anilide

Introduction: Trypanosoma brucei is the causative agent of human African trypanosomiasis, which is responsible for thousands of deaths every year. Current therapies are limited and there is an urgent need to develop new drugs. The anti-trypanosomal compound, 3-(oxazolo[4,5-b]pyridine-2-yl)anilide (OXPA), was initially identified in a phenotypic screen and subsequently optimized by structure–activity directed medicinal chemistry. It has been shown to be non-toxic and to be active against a number of trypanosomatid parasites. However, nothing is known about its mechanism of action. Objective: Here, we have utilized an untargeted metabolomics approach to investigate the biochemical effects and potential mode of action of this compound in T. brucei. Methods: Total metabolite extracts were analysed by HILIC-chromatography coupled to high resolution mass spectrometry. Results: Significant accumulation of ceramides was observed in OXPA-treated T. brucei. To further understand drug-induced changes in lipid metabolism, a lipidomics method was developed which enables the measurement of hundreds of lipids with high throughput and precision. The application of this LC–MS based approach to cultured bloodstream-form T. brucei putatively identified over 500 lipids in the parasite including glycerophospholipids, sphingolipids and fatty acyls, and confirmed the OXPA-induced accumulation of ceramides. Labelling with BODIPY-ceramide further confirmed the ceramide accumulation following drug treatment. Conclusion: These findings clearly demonstrate perturbation of ceramide metabolism by OXPA and indicate that the sphingolipid pathway is a promising drug target in T. brucei.No Full Tex

Successful recovery of motile and viable boar sperm after vitrification with different methods (pearls and mini straws) using sucrose as a cryoprotectant

Vitrification of sperm by direct contact with liquid nitrogen is increasing in popularity as an alternative to conventional (slow) freezing. Although slow freezing is very challenging in boar sperm cryopreservation, this is currently the standard method used. We compared vitrification in “pearls” and in “mini straws” using the in vitro fertilization media Porcine Gamete Media with 0.3 M sucrose with the standard (slow) method used to preserve boar sperm. Both vitrification methods reduced the viability of the sperm sample more than slow freezing (42.2 ± 4.3% total motility and 71.4 ± 2.3% alive), however, both protocols allowed for the successful recovery of the sperm samples. By comparing two different methods of vitrification and two different methods of post-thaw preparation we were able to determine the optimal vitrification-thaw protocol for boar sperm. When comparing pearls and mini-straws, the smaller liquid volume associated with pearls had a positive effect on the survivability of the samples, reducing sperm DNA damage (1.2 ± 0.2% vs. 5.1 ± 0.1.7%) and preserving motility (26.15 ± 2.8% vs 9.39 ± 0.9%) after thawing. In conclusion, the pearl method was the most suitable of the vitrification techniques for use with boar sperm

Digital tools for brownfield redevelopment: Stakeholder perspectives and opportunities

Brownfield redevelopment is a complex process often involving a wide range of stakeholders holding differing priorities and opinions. The use of digital systems and products for decision making, modelling, and supporting discussion has been recognised throughout literature and industry. The inclusion of stakeholder preferences is an important consideration in the design and development of impactful digital tools and decision support systems. In this study, we present findings from stakeholder consultation with professionals from the UK brownfield sector with the aim of informing the design of future digital tools and systems. Our research investigates two broad themes; digitalisation and the use of digital tools across the sector; and perceptions of key brownfield challenge areas where digital tools could help better inform decision-makers. The methodology employed for this study comprises the collection of data and information using a combination of interviews and an online questionnaire. The results from these methods were evaluated both qualitatively and quantitatively. Findings reveal a disparity in levels of digital capability between stakeholder groups including between technical stakeholder types, and that cross-discipline communication of important issues may be aided by the development of carefully designed digital tools. To this end, we present seven core principles to guide the design and implementation of future digital tools for the brownfield sector. These principles are that future digital tools should be: (1) Stakeholder driven, (2) Problem centred, (3) Visual, (4) Intuitive, (5) Interactive, (6) Interoperable, and (7) Geospatial data driven

The DEEP2 Galaxy Redshift Survey: Spectral classification of galaxies at z~1

We present a Principal Component Analysis (PCA)-based spectral classification, eta, for the first 5600 galaxies observed in the DEEP2 Redshift Survey. This parameter provides a very pronounced separation between absorption and emission dominated galaxy spectra - corresponding to passively evolving and actively star-forming galaxies in the survey respectively. In addition it is shown that despite the high resolution of the observed spectra, this parameter alone can be used to quite accurately reconstruct any given galaxy spectrum, suggesting there are not many `degrees of freedom' in the observed spectra of this galaxy population. It is argued that this form of classification, eta, will be particularly valuable in making future comparisons between high and low-redshift galaxy surveys for which very large spectroscopic samples are now readily available, particularly when used in conjunction with high-resolution spectral synthesis models which will be made public in the near future. We also discuss the relative advantages of this approach to distant galaxy classification compared to other methods such as colors and morphologies. Finally, we compare the classification derived here with that adopted for the 2dF Galaxy Redshift Survey and in so doing show that the two systems are very similar. This will be particularly useful in subsequent analyses when making comparisons between results from each of these surveys to study evolution in the galaxy populations and large-scale structure.Comment: 10 pages, 9 figures, Accepted for publication in Ap

Recovery From Heart Attack, Biomedicalization, and the Production of a Contingent Health Citizenship

In this article, I explore the experience of recovery from a heart attack through an analytic autoethnography. I discuss the tensions inherent in biomedical subjectivities of health and ill-health during cardiac recovery through three key themes: (a) the transfer of responsibility and becoming a subject “at risk,” (b) technologies of biomedicine and the disciplining of subjectivities, and (c) the transformation of a body toward a new pharmaceuticalized bodily normal. Through an analysis driven by the biomedicalization thesis of Clarke, alongside work on biopower and the governmentality of health by Foucault, Rose, and Rabinow, I seek to provide new insights into the process of cardiac recovery and the relationship between individual experience and broader socio-political processes. Key to this analysis is a focus on the contingent subjectivities brought into being through biomedicalization that constitute a new form of health citizenship that is otherwise not accounted for in narratives of recovery

Common datastream permutations of animal social network data are not appropriate for hypothesis testing using regression models

Contains the R code necessary to run the simulations used in the manuscript "Common datastream permutations of animal social network data are not appropriate for hypothesis testing using regression models," in press in Methods in Ecology and Evolution