The performance of permutations and exponential random graph models when analyzing animal networks

This is the author accepted manuscript. The final version is available from Oxford University Press via the DOI in this record.The R code used to simulate and analyze the networks are available as supplemental files. Simulation R code, and necessary summary data and R code to reproduce the analyses reported in this article are provided by (Evans et al. 2020).Social network analysis is a suite of approaches for exploring relational data. Two approaches commonly used to analyze animal social network data are permutation-based tests of significance and exponential random graph models. However, the performance of these approaches when analyzing different types of network data has not been simultaneously evaluated. Here we test both approaches to determine their performance when analyzing a range of biologically realistic simulated animal social networks. We examined the false positive and false negative error rate of an effect of a two-level explanatory variable (e.g., sex) on the number and combined strength of an individual’s network connections. We measured error rates for two types of simulated data collection methods in a range of network structures, and with/without a confounding effect and missing observations. Both methods performed consistently well in networks of dyadic interactions, and worse on networks constructed using observations of individuals in groups. Exponential random graph models had a marginally lower rate of false positives than permutations in most cases. Phenotypic assortativity had a large influence on the false positive rate, and a smaller effect on the false negative rate for both methods in all network types. Aspects of within- and between-group network structure influenced error rates, but not to the same extent. In "grouping event-based" networks, increased sampling effort marginally decreased rates of false negatives, but increased rates of false positives for both analysis methods. These results provide guidelines for biologists analyzing and interpreting their own network data using these methods

Impact of N-myc amplification on median survival in children with neuroblastoma

Background: Neuroblastoma is the most common extracranial malignant solid tumor in children under 5 years, and it is characterized by wide clinical and biological heterogeneity. N-myc oncogene amplification is considered to be one of the most important prognostic factors used to evaluate survival in these patients. Objectives: The aim of our study was to determine amplification of the N-myc oncogene using real-time quantitative polymerase chain reaction (PCR) and to show the influence of N-myc amplified tumors on the overall survival rate. Patients and Methods: This study is an analytical historical cohort study of forty children with neuroblastoma admitted to the Shafa Hospital, Iran from 1999 to 2010. Paraffined blocks of tumoral tissue were analyzed for N-myc amplification by a PCR. The degree of N-myc amplification was derived from the ratio of the N-myc oncogene and the single copy reference gene, NAGK. In the statistical analysis, a Kaplan-Meier survival analysis was used. Results: We found a variable degree of N-myc amplification, from 3 to 2 200, in 32 of the 40 neuroblastomas (80%). NMYC amplification was seen more frequently in patients older than 2.5 years (71.9%), stage 4 (65.6%) and female (53.1%). Median survival time in the males was significantly longer than in the females (P = 0.03). The overall median survival for N-myc amplified tumor patients was 20 months, and 30 months for the non amplified tumors. Conclusions: The N-myc amplified tumors may increase the probability of more aggressive behavior and rapid tumor progression, especially in advanced stages of neuroblastoma. This study confirmed the importance of obtaining correct measurements of oncogene amplification in the early evaluation of neuroblastomas in order to target more aggressive therapies in patients with a higher risk of cancer progression

Reflections and Experiences of a Co-Researcher involved in a Renal Research Study

Background Patient and Public Involvement (PPI) is seen as a prerequisite for health research. However, current Patient and public involvement literature has noted a paucity of recording of patient and public involvement within research studies. There have been calls for more recordings and reflections, specifically on impact. Renal medicine has also had similar criticisms and any reflections on patient and public involvement has usually been from the viewpoint of the researcher. Roles of patient and public involvement can vary greatly from sitting on an Advisory Group to analysing data. Different PPI roles have been described within studies; one being a co-researcher. However, the role of the co-researcher is largely undefined and appears to vary from study to study. Methods The aims of this paper are to share one first time co-researcher's reflections on the impact of PPI within a mixed methods (non-clinical trial) renal research study. A retrospective, reflective approach was taken using data available to the co-researcher as part of the day-to-day research activity. Electronic correspondence and documents such as meeting notes, minutes, interview thematic analysis and comments on documents were re-examined. The co-researcher led on writing this paper. Results This paper offers a broad definition of the role of the co-researcher. The co-researcher reflects on undertaking and leading on the thematic analysis of interview transcripts, something she had not previously done before. The co-researcher identified a number of key themes; the differences in time and responsibility between being a coresearcher and an Advisory Group member; how the role evolved and involvement activities could match the co-researchers strengths (and the need for flexibility); the need for training and support and lastly, the time commitment. It was also noted that it is preferable that a co-researcher needs to be involved from the very beginning of the grant application. Conclusions The reflections, voices and views of those undertaking PPI has been largely underrepresented in the literature. The role of co-researcher was seen to be rewarding but demanding, requiring a large time commitment. It is hoped that the learning from sharing this experience will encourage others to undertake this role, and encourage researchers to reflect on the needs of those involved.Peer reviewedFinal Published versio

Historical geography II: traces remain

The second report in this series turns to focus on the trace in relation to life-writing and biography in historical geography and beyond. Through attention to tracing journeys, located moments and listening to the presence of ghosts (Ogborn, 2005), this report seeks to highlight the range of different ways in which historical geographers have explored lives, deaths, and their transient traces through varied biographical terrains. Continuing to draw attention in historical geography to the darkest of histories, this piece will pivot on moments of discovering the dead to showcase the nuanced ways in which historical geography is opening doors into uncharted lives and unspoken histories

Emergent Quantum Near-Criticality from Baryonic Black Branes

We find new black 3-brane solutions describing the "conifold gauge theory" at nonzero temperature and baryonic chemical potential. Of particular interest is the low-temperature limit where we find a new kind of weakly curved near-horizon geometry; it is a warped product AdS_2 x R^3 x T^{1,1} with warp factors that are powers of the logarithm of the AdS radius. Thus, our solution encodes a new type of emergent quantum near-criticality. We carry out some stability checks for our solutions. We also set up a consistent ansatz for baryonic black 2-branes of M-theory that are asymptotic to AdS_4 x Q^{1,1,1}.Comment: 29 pages, 4 figures; v2 discussion of entropy revised, minor changes; v3 note added, minor improvements, version published in JHE

Pancreatic adenocarcinoma in a patient with Situs Inversus: a case report of this rare coincidence

<p>Abstract</p> <p>Background</p> <p><it>Situs inversus </it>(SI) is a relatively rare occurrence in patients with pancreatic adenocarcinoma. Pancreatic resection in these patients has rarely been described. CT scan imaging is a principle modality for detecting pancreatic cancer and its use in SI patients is seldom reported.</p> <p>Case Presentation</p> <p>We report a 48 year old woman with SI who, despite normal CT scan 8 months earlier, presented with obstructive jaundice and a pancreatic head mass requiring a pancreaticoduodenectomy. The surgical pathology report demonstrated pancreatic adenocarcinoma.</p> <p>Conclusion</p> <p>SI is a rare condition with concurrent pancreatic cancer being even rarer. Despite the rarity, pancreaticoduodenectomy in these patients for resectable lesions is safe as long as special consideration to the anatomy is taken. Additionally, radiographic imaging has significantly improved detection of early pancreatic cancer; however, there continues to be a need for improved detection of small neoplasms.</p

Discovery of the Onset of Rapid Accretion by a Dormant Massive Black Hole

Massive black holes are believed to reside at the centres of most galaxies. They can be- come detectable by accretion of matter, either continuously from a large gas reservoir or impulsively from the tidal disruption of a passing star, and conversion of the gravitational energy of the infalling matter to light. Continuous accretion drives Active Galactic Nuclei (AGN), which are known to be variable but have never been observed to turn on or off. Tidal disruption of stars by dormant massive black holes has been inferred indirectly but the on- set of a tidal disruption event has never been observed. Here we report the first discovery of the onset of a relativistic accretion-powered jet in the new extragalactic transient, Swift J164449.3+573451. The behaviour of this new source differs from both theoretical models of tidal disruption events and observations of the jet-dominated AGN known as blazars. These differences may stem from transient effects associated with the onset of a powerful jet. Such an event in the massive black hole at the centre of our Milky Way galaxy could strongly ionize the upper atmosphere of the Earth, if beamed towards us.Comment: Submitted to Nature. 4 pages, 3 figures (main paper). 26 pages, 13 figures (supplementary information

Performance evaluation of highly admixed Tanzanian smallholder dairy cattle using SNP derived kinship matrix

The main purpose of this study was to understand the type of dairy cattle that can be optimally used by smallholder farmers in various production environments such that they will maximize their yields without increasing the level of inputs. Anecdotal evidence and previous research suggests that the optimal level of taurine inheritance in crossbred animals lies between 50 and 75% when considering total productivity in tropical management clusters. We set out to assess the relationship between breed composition and productivity for various smallholder production systems in Tanzania. We surveyed 654 smallholder dairy households over a 1-year period and grouped them into production clusters. Based on supplementary feeding, milk productivity and sale as well as household wealth status four clusters were described: low-feed–low-output subsistence, medium-feed–low-output subsistence, maize germ intensive semi-commercial and feed intensive commercial management clusters. About 839 crossbred cows were genotyped at approximately 150,000 single nucleotide polymorphism (SNP) loci and their breed composition determined. Percentage dairyness (proportion of genes from international dairy breeds) was estimated through admixture analysis with Holstein, Friesian, Norwegian Red, Jersey, Guernsey, N’Dama, Gir, and Zebu as references. Four breed types were defined as RED–GUE (Norwegian Red/Friesian–Guernsey; Norwegian Red/Friesian–Jersey), RED–HOL (Norwegian Red/Friesian–Holstein), RED–Zebu (Norwegian Red/Friesian–Zebu), Zebu–RED (Zebu–Norwegian Red/Friesian) based on the combination of breeds that make up the top 76% breed composition. A fixed regression model using a genomic kinship matrix was used to analyze milk yield records. The fitted model accounted for year-month-test-date, parity, age, breed type and the production clusters as fixed effects in the model in addition to random effects of animal and permanent environment effect. Results suggested that RED–Zebu breed type with dairyness between 75 and 85% is the most appropriate for a majority of smallholder management clusters. Additionally, for farmers in the feed intensive management group, animals with a Holstein genetic background with at least 75% dairy composition were the best performing. These results indicate that matching breed type to production management group is central to maximizing productivity in smallholder systems. The findings from this study can serve as a basis to inform the development of the dairy sector in Tanzania and beyond.</p

Risks for Acquisition of Bacterial Vaginosis Among Women Who Report Sex with Women: A Cohort Study

Bacterial vaginosis (BV) is common in women who have sex with women. While cross-sectional data support a role for sexual transmission, risks for incident BV have not been prospectively studied in this group. at enrollment conferred reduced risk for subsequent BV (HR 0.18 (0.08–0.4)). Detailed analysis of behavioral data suggested a direct dose-response relationship with increasing number of episodes of receptive oral-vulvovaginal sex (HR 1.02 (95% CI, 1.00–1.04).Vaginal detection of several BVAB in BV-negative women predicted subsequent BV, suggesting that changes in vaginal microbiota precede BV by weeks or months. BV acquisition was associated with report of new partner with BV; associations with sexual practices – specifically, receptive oral sex – require further investigation