The Dawn of Open Access to Phylogenetic Data

The scientific enterprise depends critically on the preservation of and open access to published data. This basic tenet applies acutely to phylogenies (estimates of evolutionary relationships among species). Increasingly, phylogenies are estimated from increasingly large, genome-scale datasets using increasingly complex statistical methods that require increasing levels of expertise and computational investment. Moreover, the resulting phylogenetic data provide an explicit historical perspective that critically informs research in a vast and growing number of scientific disciplines. One such use is the study of changes in rates of lineage diversification (speciation - extinction) through time. As part of a meta-analysis in this area, we sought to collect phylogenetic data (comprising nucleotide sequence alignment and tree files) from 217 studies published in 46 journals over a 13-year period. We document our attempts to procure those data (from online archives and by direct request to corresponding authors), and report results of analyses (using Bayesian logistic regression) to assess the impact of various factors on the success of our efforts. Overall, complete phylogenetic data for ~60% of these studies are effectively lost to science. Our study indicates that phylogenetic data are more likely to be deposited in online archives and/or shared upon request when: (1) the publishing journal has a strong data-sharing policy; (2) the publishing journal has a higher impact factor, and; (3) the data are requested from faculty rather than students. Although the situation appears dire, our analyses suggest that it is far from hopeless: recent initiatives by the scientific community -- including policy changes by journals and funding agencies -- are improving the state of affairs

Bipolar ablation for deep intra-myocardial circuits: human ex vivo development and in vivo experience.

To access publisher's full text version of this article click on the hyperlink at the bottom of the pageCurrent conventional ablation strategies for ventricular tachycardia (VT) aim to interrupt reentrant circuits by creating ablation lesions. However, the critical components of reentrant VT circuits may be located at deep intramural sites. We hypothesized that bipolar ablations would create deeper lesions than unipolar ablation in human hearts.Ablation was performed on nine explanted human hearts at the time of transplantation. Following explant, the hearts were perfused by using a Langendorff perfusion setup. For bipolar ablation, the endocardial catheter was connected to the generator as the active electrode and the epicardial catheter as the return electrode. Unipolar ablation was performed at 50 W with irrigation of 25 mL/min, with temperature limit of 50°C. Bipolar ablation was performed with the same settings. Subsequently, in a patient with an incessant septal VT, catheters were positioned on the septum from both the ventricles and radiofrequency was delivered with 40 W. In the explanted hearts, there were a total of nine unipolar ablations and four bipolar ablations. The lesion depth was greater with bipolar ablation, 14.8 vs. 6.1 mm (P < 0.01), but the width was not different (9.8 vs. 7.8 mm). All bipolar lesions achieved transmurality in contrast to the unipolar ablations. In the patient with a septal focus, bipolar ablation resulted in termination of VT with no inducible VTs.By using a bipolar ablation technique, we have demonstrated the creation of significantly deeper lesions without increasing the lesion width, compared with standard ablation. Further clinical trials are warranted to detail the risks of this technique

The Role of Device Diagnostic Algorithms in the Assessment and Management of Patients with Systolic Heart Failure: A Review

Hospitalization due to heart failure (HF) exacerbation represents a major burden in health care and portends a poor long-term prognosis for patients. As a result, there is considerable interest to develop novel tools and strategies to better detect onset of volume overload, as HF hospitalizations may be reduced if appropriate interventions can be promptly delivered. One such innovation is the use of device-based diagnostic parameters in HF patients with implantable cardioverter defibrillators (ICD) and/or cardiac resynchronization therapy (CRT) devices. These diagnostic algorithms can effectively monitor and detect changes in patients' HF status, as well as predict one's risk of HF hospitalization. This paper will review the role of these device diagnostics parameters in the assessment and management of HF patients in ambulatory settings. In addition, the integration of these novel algorithms in existing HF disease management models will be discussed

KMT-2018-BLG-1292: A Super-Jovian Microlens Planet in the Galactic Plane

We report the discovery of KMT-2018-BLG-1292Lb, a super-Jovian $M_{\rm planet} = 4.5\pm 1.3\,M_J$ planet orbiting an F or G dwarf $M_{\rm host} = 1.5\pm 0.4\,M_\odot$, which lies physically within {\cal O}(10\,\pc) of the Galactic plane. The source star is a heavily extincted $A_I\sim 5.2$ luminous giant that has the lowest Galactic latitude, $b=-0.28^\circ$, of any planetary microlensing event. The relatively blue blended light is almost certainly either the host or its binary companion, with the first explanation being substantially more likely. This blend dominates the light at $I$ band and completely dominates at $R$ and $V$ bands. Hence, the lens system can be probed by follow-up observations immediately, i.e., long before the lens system and the source separate due to their relative proper motion. The system is well characterized despite the low cadence $\Gamma=0.15$--$0.20\,{\rm hr^{-1}}$ of observations and short viewing windows near the end of the bulge season. This suggests that optical microlensing planet searches can be extended to the Galactic plane at relatively modest cost.Comment: 35 pages, 3 Tables, 8 figure

A global perspective on marine photosynthetic picoeukaryote community structure

A central goal in ecology is to understand the factors affecting the temporal dynamics and spatial distribution of microorganisms and the underlying processes causing differences in community structure and composition. However, little is known in this respect for photosynthetic picoeukaryotes (PPEs), algae that are now recognised as major players in marine CO2 fixation. Here, we analysed dot blot hybridisation and cloning–sequencing data, using the plastid-encoded 16S rRNA gene, from seven research cruises that encompassed all four ocean biomes. We provide insights into global abundance, α- and β-diversity distribution and the environmental factors shaping PPE community structure and composition. At the class level, the most commonly encountered PPEs were Prymnesiophyceae and Chrysophyceae. These taxa displayed complementary distribution patterns, with peak abundances of Prymnesiophyceae and Chrysophyceae in waters of high (25:1) or low (12:1) nitrogen:phosphorus (N:P) ratio, respectively. Significant differences in phylogenetic composition of PPEs were demonstrated for higher taxonomic levels between ocean basins, using Unifrac analyses of clone library sequence data. Differences in composition were generally greater between basins (interbasins) than within a basin (intrabasin). These differences were primarily linked to taxonomic variation in the composition of Prymnesiophyceae and Prasinophyceae whereas Chrysophyceae were phylogenetically similar in all libraries. These data provide better knowledge of PPE community structure across the world ocean and are crucial in assessing their evolution and contribution to CO2 fixation, especially in the context of global climate change

OGLE-2018-BLG-0532Lb: Cold Neptune With Possible Jovian Sibling

We report the discovery of the planet OGLE-2018-BLG-0532Lb, with very obvious signatures in the light curve that lead to an estimate of the planet-host mass ratio $q=M_{\rm planet}/M_{\rm host}\simeq 1\times10^{-4}$. Although there are no obvious systematic residuals to this double-lens/single-source (2L1S) fit, we find that $\chi^2$ can be significantly improved by adding either a third lens (3L1S, $\Delta\chi^2=81$) or second source (2L2S, $\Delta\chi^2=65$) to the lens-source geometry. After thorough investigation, we conclude that we cannot decisively distinguish between these two scenarios and therefore focus on the robustly-detected planet. However, given the possible presence of a second planet, we investigate to what degree and with what probability such additional planets may affect seemingly single-planet light curves. Our best estimates for the properties of the lens star and the secure planet are: a host mass $M\sim 0.25\,M_\odot$, system distance $D_L\sim 1\,$kpc and planet mass $m_{p,1}= 8\,M_\oplus$ with projected separation $a_{1,\perp}=1.4\,$au. However, there is a relatively bright $I=18.6$ (and also relatively blue) star projected within $<50\,$mas of the lens, and if future high-resolution images show that this is coincident with the lens, then it is possible that it is the lens, in which case, the lens would be both more massive and more distant than the best-estimated values above.Comment: 48 pages, 9 figures, 7 table

Reading faces: differential lateral gaze bias in processing canine and human facial expressions in dogs and 4-year-old children

Sensitivity to the emotions of others provides clear biological advantages. However, in the case of heterospecific relationships, such as that existing between dogs and humans, there are additional challenges since some elements of the expression of emotions are species-specific. Given that faces provide important visual cues for communicating emotional state in both humans and dogs, and that processing of emotions is subject to brain lateralisation, we investigated lateral gaze bias in adult dogs when presented with pictures of expressive human and dog faces. Our analysis revealed clear differences in laterality of eye movements in dogs towards conspecific faces according to the emotional valence of the expressions. Differences were also found towards human faces, but to a lesser extent. For comparative purpose, a similar experiment was also run with 4-year-old children and it was observed that they showed differential processing of facial expressions compared to dogs, suggesting a species-dependent engagement of the right or left hemisphere in processing emotions

Spontaneous Eosinophilic Nasal Inflammation in a Genetically-Mutant Mouse: Comparative Study with an Allergic Inflammation Model

Background: Eosinophilic inflammation is a hallmark of chronic rhinosinusitis with nasal polyps. To model this disease process experimentally, nasal sensitization of mice with ovalbumin or aspergillus has been described. Here, we describe a genetically mutant mouse that develops robust spontaneous nasal eosinophilic inflammation. These mice lack the enzyme SHP-1 that down-regulates the IL-4Ra/stat6 signaling pathway. We compared nasal inflammation and inflammatory mediators in SHP-1 deficient mice (mev) and an ovalbumin-induced nasal allergy model. Methods: A novel technique of trans-pharyngeal nasal lavage was developed to obtain samples of inflammatory cells from the nasal passages of allergic and mev mice. Total and differential cell counts were performed on cytospin preparations. Expression of tissue mRNA for IL-4, IL-13, and mouse beta-defensin-1 (MBD-1) was determined by quantitative PCR. Eotaxin in the lavage fluid was assessed by ELISA. Results: Allergic and mev mice had increased total cells and eosinophils compared with controls. Expression of IL-4 was similarly increased in both allergic and mev mice, but expression of IL-13 and eotaxin was significantly greater in the allergic mice than mev mice. Eotaxin was significantly up-regulated in both allergic rhinitis and mev mice. In both models of eosinophilic inflammation, down-regulation of the innate immune marker MBD-1 was observed. Conclusions: The mev mice display spontaneous chronic nasal eosinophilic inflammation with potential utility for chroni