Breeding dispersal and parental care in blue tits (Cyanistes caeruleus)

Behaviour varies between individuals and is often thought to be adaptive. Behaviours are predicted to vary according to the circumstances of the individual, to decrease their risk of mortality or that of their offspring, or to reduce the costs associated with certain behaviours, such as territory establishment, foraging or nestling provisioning. Two of the most important behaviours determining reproductive success, and thus having potential to be adaptive, are breeding dispersal and parental care. Individual birds should be under selection pressure to minimise the costs related to these behaviours, and likely to do so in response to aspects of habitat quality, individual quality, and their own prior experience. This study examined the relative importance of these factors upon breeding dispersal and parental care in blue tits (Cyanistes caeruleus), additionally using repeatability analysis as a novel means to indirectly assess the influence of both individual quality and habitat. Specifically, this study explored the influence of habitat quality and individual-specific experience upon nest-site occupancy, breeding dispersal and reproductive success. It also estimated repeatability of the breeding parameters and examined the reproductive outcome of dispersal. Mixed models suggested that nestbox occupancy increased with population density but not habitat quality, and that the probability of dispersing varied by sex, with females more likely to disperse than males, and both more likely to disperse after breeding in noisier territories. Dispersal distance was not influenced by individual or habitat quality and did not influence reproductive success. Repeatability analyses suggested that habitat quality significantly influenced reproductive success. Furthermore, clutch size was strongly repeatable for females, but not males, whereas fledging success was repeatable between individual males but not females. If individual quality is consistent through their lifetime then these results suggest that female quality is important early in the breeding attempt, but that male quality exerts a stronger influence upon final fledging success. Both males and females increased their provisioning rate to larger broods, however, the other variables influencing each sex differed. Male provisioning rates decreased as both they, and their partner, aged, but increased when a mate was retained between breeding attempts. Females increased their provisioning rate in response to their partner’s effort and provisioned at a higher rate after retaining their nest-site. However, retaining mate or nest-site did not result in higher reproductive success for either sex. The repeatability analysis suggested that females responded to the requirements of their brood, and the effort of their partner, whereas male care was less flexible. Additionally, total and male provisioning rates were repeatable for each nestbox, suggesting an influence of habitat quality. Overall, different behaviours and decisions were found to be varyingly influenced by individual, and habitat, quality and the repeatability analyses aided in assessing the relative contribution of each of these

Biomarker changes with systolic anterior motion of the mitral valve in cats with hypertrophic cardiomyopathy.

BACKGROUND: N-terminal pro B-type natriuretic peptide (NT-proBNP) and cardiac troponin-I (cTnI) are biomarkers commonly evaluated in cats with suspected heart disease. Many cats with hypertrophic cardiomyopathy (HCM) have systolic anterior motion of the mitral valve (SAM), but its influence on circulating NT-proBNP or cTnI concentrations is currently unknown. HYPOTHESIS/OBJECTIVES: Cats with HCM and SAM (HCMSAM+ ) have higher NT-proBNP and cTnI concentrations than do cats with HCM but without SAM (HCMSAM- ). ANIMALS: One hundred forty cats with HCM: 70 with SAM and 70 without SAM. METHODS: Retrospective case-to-case study. Cats were recruited if diagnosed with HCM by echocardiography and results were available for NT-proBNP or cTnI concentrations or both. Cats with SAM were matched to those without SAM for clinical presentation, left atrial (LA) size and left ventricular (LV) fractional shortening. RESULTS: A total of 119 NT-proBNP and 123 cTnI results were available. The HCMSAM+ cats had higher median concentrations than did HCMSAM- cats for NT-proBNP (729 pmoL/L; interquartile range [IQR], 275-1467 versus 65 pmoL/L; IQR, 25-271; P < .001) and cTnI (0.27 ng/mL; IQR, 0.10-0.81 versus 0.07 ng/mL; IQR, 0.01-0.43; P = .002). In general linear models for both NT-proBNP and cTnI, the independent explanatory variables were SAM, congestive heart failure, maximal LV wall thickness, and LA size. CONCLUSIONS AND CLINICAL IMPORTANCE: For cats with HCM and equivalent LA size and LV systolic function, those with SAM had higher NT-proBNP and cTnI concentrations than did those without SAM. Presence of SAM should be considered when interpreting biomarker concentrations in cats with HCM

Discovery of A New Retrograde Trans-Neptunian Object: Hint of A Common Orbital Plane for Low Semi-Major Axis, High Inclination TNOs and Centaurs

Although the majority of Centaurs are thought to have originated in the scattered disk, with the high-inclination members coming from the Oort cloud, the origin of the high inclination component of trans-Neptunian objects (TNOs) remains uncertain. We report the discovery of a retrograde TNO, which we nickname "Niku", detected by the Pan-STARRS 1 Outer Solar System Survey. Our numerical integrations show that the orbital dynamics of Niku are very similar to that of 2008 KV$_{42}$ (Drac), with a half-life of $\sim 500$ Myr. Comparing similar high inclination TNOs and Centaurs ($q > 10$ AU, $a 60^\circ$), we find that these objects exhibit a surprising clustering of ascending node, and occupy a common orbital plane. This orbital configuration has high statistical significance: 3.8-$\sigma$. An unknown mechanism is required to explain the observed clustering. This discovery may provide a pathway to investigate a possible reservoir of high-inclination objects.Comment: 18 pages, 4 figures, 1 table, accepted for publication in ApJ Letter

You say Potato, I say Po-Data:Physical Template Tools for Authoring Visualizations

Data visualization authoring tools for the general public remains an ongoing challenge. Inspired by block-printing, we explore how visualization stamps as a physical tool for authoring visualizations could leverage both visual freedom and ease of repetition. We conducted two workshops where participants authored visualizations on paper using hand-carved stamps made from potatoes and sponges. The low-fidelity medium freed participants to test new stamp patterns and accept mistakes. From the created visualizations, we observed several unique traits and uses of block-printing tools for authoring visualizations, including: modularity of patterns; annotation guides; creation of multiple patterns from one stamp; and various techniques to apply data onto paper. We discuss issues around expressivity and effectiveness of block-printing stamps in authoring visualizations, and identify implications for the design and assembly of primitives in potential visualization stamp kits, as well as applications for future use in non-digital environments

Replication and Meta-Analysis of 13,000 Cases Defines the Risk for Interleukin-23 Receptor and Autophagy-Related 16-Like 1 Variants in Crohn’s Disease

BACKGROUND/OBJECTIVE: Variants in the interleukin-23 receptor (IL23R) and the autophagy-related 16-like 1 (ATG16L1) genes have been associated with an increased risk of Crohn’s disease (CD). Both genes were identified through genome-wide association scans and subsequent studies have validated these associations. To assess the effect size of these variants, an independent case-control association study and meta-analysis were performed. METHODS: British Caucasian subjects with inflammatory bowel disease (n=500) and 877 ethnically matched controls were genotyped for the disease-associated variants in IL23R and ATG16L1. In addition, meta-analyses of 12,991 patients and 14,598 controls, and 11,909 patients and 15,798 controls, were conducted on independently published data for the associations between IL23R and ATG16L1 variants and CD, respectively. RESULTS: In the present cohort, both susceptibility variants showed highly significant associations, including IL23R (rs11209026, P=0.0006; OR 0.37; 95% CI 0.21 to 0.67) and ATG16L1 (rs2241880, P=0.0017; OR 1.36; 95% CI 1.12 to 1.66). The meta-analysis based on the random effects model showed similar combined effects for rs11209026 (n=26, OR 0.41; 95% CI 0.37 to 0.46) and rs2241880 (n=25, OR 1.33; 95% CI 1.28 to 1.39). There was no statistically significant gene-gene interaction between caspase recruitment domain (CARD15) variants and the IL23R or ATG16L1 polymorphisms (P=0.44 and P=0.24, respectively). CONCLUSION: The present cohort and meta-analysis provides strong evidence that, in addition to CARD15, polymorphisms in both IL23R and ATG16L1 alter susceptibility to CD and that these effects are consistent across all populations of European ancestry; however, only ATG16L1 is relevant to inflammatory bowel disease in the Asian population

HIV Gag mimics the Tsg101-recruiting activity of the human Hrs protein

The HIV-1 Gag protein recruits the cellular factor Tsg101 to facilitate the final stages of virus budding. A conserved P(S/T)AP tetrapeptide motif within Gag (the “late domain”) binds directly to the NH2-terminal ubiquitin E2 variant (UEV) domain of Tsg101. In the cell, Tsg101 is required for biogenesis of vesicles that bud into the lumen of late endosomal compartments called multivesicular bodies (MVBs). However, the mechanism by which Tsg101 is recruited from the cytoplasm onto the endosomal membrane has not been known. Now, we report that Tsg101 binds the COOH-terminal region of the endosomal protein hepatocyte growth factor–regulated tyrosine kinase substrate (Hrs; residues 222–777). This interaction is mediated, in part, by binding of the Tsg101 UEV domain to the Hrs 348PSAP351 motif. Importantly, Hrs222–777 can recruit Tsg101 and rescue the budding of virus-like Gag particles that are missing native late domains. These observations indicate that Hrs normally functions to recruit Tsg101 to the endosomal membrane. HIV-1 Gag apparently mimics this Hrs activity, and thereby usurps Tsg101 and other components of the MVB vesicle fission machinery to facilitate viral budding

Slow development of woodland vegetation and bird communities during 33 years of passive rewilding in open farmland

Passive rewilding is a potential tool for expanding woodland cover and restoring biodiversity by abandoning land management and allowing natural vegetation succession to occur. Land can be abandoned to passive rewilding deliberately or due to socio-economic change. Despite abandonment being a major driver of land use change, few have studied the long-term outcomes for vegetation and biodiversity in Western Europe. Studies are also biased towards sites that are close to seed sources and favourable to woodland colonisation. In this case-study, we reconstruct a time series of passive rewilding over 33 years on 25 ha of former farmland that had been subject to soil tipping, far from woodland seed sources. Natural colonisation by shrubs and trees was surveyed at three points during the time series, using field mapping and lidar. Breeding birds were surveyed at three time points, and compared with surveys from nearby farmland. Results showed that natural colonisation of woody vegetation was slow, with open grassland dominating the old fields for two decades, and small wetlands developing spontaneously. After 33 years, thorny shrub thickets covered 53% of the site and former hedgerows became subsumed or degraded, but trees remained scarce. However, the resulting habitat mosaic of shrubland, grassland and wetland supported a locally distinctive bird community. Farmland bird species declined as passive rewilding progressed, but this was countered by relatively more wetland birds and an increase in woodland birds, particularly songbirds, compared to nearby farmland. Alongside biodiversity benefits, shrubland establishment by passive rewilding could potentially provide ecosystem services via abundant blossom resources for pollinators, and recreation and berry-gathering opportunities for people. Although closed-canopy woodland remained a distant prospect even after 33 years, the habitat mosaic arising from passive rewilding could be considered a valuable outcome, which could contribute to nature recovery and provision of ecosystem services

A UMLS-based spell checker for natural language processing in vaccine safety

BACKGROUND: The Institute of Medicine has identified patient safety as a key goal for health care in the United States. Detecting vaccine adverse events is an important public health activity that contributes to patient safety. Reports about adverse events following immunization (AEFI) from surveillance systems contain free-text components that can be analyzed using natural language processing. To extract Unified Medical Language System (UMLS) concepts from free text and classify AEFI reports based on concepts they contain, we first needed to clean the text by expanding abbreviations and shortcuts and correcting spelling errors. Our objective in this paper was to create a UMLS-based spelling error correction tool as a first step in the natural language processing (NLP) pipeline for AEFI reports. METHODS: We developed spell checking algorithms using open source tools. We used de-identified AEFI surveillance reports to create free-text data sets for analysis. After expansion of abbreviated clinical terms and shortcuts, we performed spelling correction in four steps: (1) error detection, (2) word list generation, (3) word list disambiguation and (4) error correction. We then measured the performance of the resulting spell checker by comparing it to manual correction. RESULTS: We used 12,056 words to train the spell checker and tested its performance on 8,131 words. During testing, sensitivity, specificity, and positive predictive value (PPV) for the spell checker were 74% (95% CI: 74–75), 100% (95% CI: 100–100), and 47% (95% CI: 46%–48%), respectively. CONCLUSION: We created a prototype spell checker that can be used to process AEFI reports. We used the UMLS Specialist Lexicon as the primary source of dictionary terms and the WordNet lexicon as a secondary source. We used the UMLS as a domain-specific source of dictionary terms to compare potentially misspelled words in the corpus. The prototype sensitivity was comparable to currently available tools, but the specificity was much superior. The slow processing speed may be improved by trimming it down to the most useful component algorithms. Other investigators may find the methods we developed useful for cleaning text using lexicons specific to their area of interest