A molecular phylogenetic analysis of the genera of fruit doves and allies using dense taxonomic sampling

Fruit doves and their allies are a diverse group within the pigeon and dove family (Aves: Columbidae). Progress towards subfamilial classification of Columbidae relies on identifying major groups and the phylogenetic relationships within these groups. One such recently proposed group is the Raphinae based on previous evidence that the extinct dodo is potentially within what was formerly recognized as the Treroninae (fruit doves and allies). Although several studies have explored the phylogenetic relationships within Columbidae, most have focused either on broad-scale, familial level relationships or finer scale, species level relationships. Here we use mitochondrial and nuclear gene sequences from a diverse taxonomic sample to identify relationships among the genera and species of fruit doves and their allies. In particular our goal is to identify which of these genera should be included within Raphinae (the name which has taxonomic priority over Treroninae), focusing on an inclusive, well-supported monophyletic group. We also use dense taxon sampling to explore relationships among genera and species in this group, expanding on previous studies. In addition, we use resulting phylogenetic hypotheses to reconstruct the ancestral evolutionary history of foraging mode and biogeographic patterns of dispersal within the group. We used two data sets for our phylogenetic analysis: the first consisting of novel sequences generated for this project and the second with additional, previously published sequences from the fruit dove genus (Ptilinopus). Our analyses found support for the monophyly of a clade that contains a large fraction of the genera currently classified within Raphinae and also found several well-supported clades within this group of pigeons and doves. Character reconstruction methods based on the resulting phylogeny recover multiple transitions from a terrestrial to an arboreal foraging mode and evidence for multiple dispersal events from Asia to Africa throughout the history of the clade.is peer reviewedOpe

Organic Anion and Cation Transporter Expression and Function During Embryonic Kidney Development and in Organ Culture Model Systems

Background Organic anion and cation transporters (OATs, OCTs and OCTNs) mediate the proximal tubular secretion of numerous clinically important compounds, including various commonly prescribed pharmaceuticals. Here, we examine the ontogeny of these transporters in rat embryonic kidney in detail, both in vivo and in two in vitro organ culture models of kidney development, whole embryonic kidney (WEK) culture and culture of induced metanephric mesenchyme (MM). Methods We used QPCR to determine expression levels of transporter genes in rat embryonic kidneys on each day of gestation from ed13 to ed18, in induced and un-induced MM, and on each day of one week of WEK culture. We also used uptake of fluorescein as a novel functional assay of organic anion transporter expression in WEK and MM. Results The developmental induction of the various organic anion and cation transporter genes does not occur uniformly: some genes are induced early (e.g., Oat1 and Oat3, potential early markers of proximal tubulogenesis), and others not till kidney development is relatively advanced (e.g., Oct1, a potential marker of terminal differentiation). We also find that the ontogeny of transporter genes in WEK and MM is similar to that observed in vivo, indicating that these organ culture systems may appropriately model the expression of OATs, OCTs and OCTNs. Conclusion We show that WEK and MM cultures may represent convenient in vitro models for study of the developmental induction of organic anion and cation transporters. Functional organic anion transport as measured by fluorescein uptake was evident by accumulation of the fluorescence in the developing tubule in these organ cultures. By demonstrating the mediated uptake of fluorescein in WEK and MM, we have established a novel in vitro functional assay of transporter function. We find that OATs, OCTs, and OCTNs are differentially expressed during proximal tubule development. Our findings on the renal ontogeny of organic anion and cation transporters could carry implications both for the development of more rational therapeutics for premature infants, as well as for our understanding of proximal tubule differentiation

Explain To Me: Salience-Based Explainability for Synthetic Face Detection Models

The performance of convolutional neural networks has continued to improve over the last decade. At the same time, as model complexity grows, it becomes increasingly more difficult to explain model decisions. Such explanations may be of critical importance for reliable operation of human-machine pairing setups, or for model selection when the "best" model among many equally-accurate models must be established. Saliency maps represent one popular way of explaining model decisions by highlighting image regions models deem important when making a prediction. However, examining salience maps at scale is not practical. In this paper, we propose five novel methods of leveraging model salience to explain a model behavior at scale. These methods ask: (a) what is the average entropy for a model's salience maps, (b) how does model salience change when fed out-of-set samples, (c) how closely does model salience follow geometrical transformations, (d) what is the stability of model salience across independent training runs, and (e) how does model salience react to salience-guided image degradations. To assess the proposed measures on a concrete and topical problem, we conducted a series of experiments for the task of synthetic face detection with two types of models: those trained traditionally with cross-entropy loss, and those guided by human salience when training to increase model generalizability. These two types of models are characterized by different, interpretable properties of their salience maps, which allows for the evaluation of the correctness of the proposed measures. We offer source codes for each measure along with this paper.Comment: 13 pages, 10 figure

Electrochemical Cell for Obtaining Oxygen from Carbon Dioxide Atmospheres

To support human life on the Martian surface, an electrochemical device will be required to obtain oxygen from the carbon dioxide rich atmosphere. The electrolyte employed in such a device must be constructed from extremely thin, dense membranes to efficiently acquire the oxygen necessary to support life. A forming process used industrially in the production of multilayer capacitors and electronic substrates was adapted to form the thin membranes required. The process, known as the tape casting, involves the suspension consisting of solvents and binders. The suspension is passed under a blade, resulting in the production of ceramic membranes between 0.1 and 0.5 mm thick. Once fired, the stabilized zirconia membranes were assembled into the cell design by employing a zirconium phosphate solution as the sealing agent. The resulting ceramic-to-ceramic seals were found to be structurally sound and gas-tight. Furthermore, by using a zirconia-based solution to assemble the cell, the problem of a thermal expansion mismatch was alleviated. By adopting an industrial forming process to produce thin membranes, an electrochemical cell for obtaining oxygen from carbon dioxide was produced. The proposed cell design is unique in that it does not require a complicated manifold system for separating the various gases present in this process, nor does it require a series of complex electrical connections. Thus, the device can reliably obtain the vital oxygen supply from the toxic carbon dioxide atmosphere

The late Pleistocene Po River lowstand wedge in the Adriatic Sea : Controls on architecture variability and sediment partitioning

The authors dedicate this study to their colleague Giovanni Bortoluzzi, who passed away in 2015. A special tanks is due to Marco Ligi and Nevio Zitellini for geophysical data acquisition and processing; Marco Pastore and Filippo D'Oriano for their support during the cruise LSD2014 and processing of geophysical data. Elisabetta Campiani provided additional support for processing the multibeam bathymetry. A particular thank goes to Cpt. Emanuele Gentile and the crew of the R/V Urania during cruise LSD 2014. We thank Ronald Steel and an anonymous Reviewer for their constructive comments. This project was funded by ExxonMobil Upstream Research Company and by the Flagship Project RITMARE–The Italian Research for the Sea. We acknowledge the European Union Project PROMESS-1 (contract EVR1-2001-41) for borehole PRAD 1-2. This is ISMAR-CNR contribution number 1959.Peer reviewedPostprin

Counselees’ Perspectives of Genomic Counseling Following Online Receipt of Multiple Actionable Complex Disease and Pharmacogenomic Results: a Qualitative Research Study

Genomic applications raise multiple challenges including the optimization of genomic counseling (GC) services as part of the results delivery process. More information on patients’ motivations, preferences, and informational needs are essential to guide the development of new, more efficient practice delivery models that capitalize on the existing strengths of a limited genetic counseling workforce. Semi‐structured telephone interviews were conducted with a subset of counselees from the Coriell Personalized Medicine Collaborative following online receipt of multiple personalized genomic test reports. Participants previously had either in‐person GC (chronic disease cohort, n = 20; mean age 60 years) or telephone GC (community cohort, n = 31; mean age 46.8 years). Transcripts were analyzed using a Grounded Theory framework. Major themes that emerged from the interviews include 1) primary reasons for seeking GC were to clarify results, put results into perspective relative to other health‐related concerns, and to receive personalized recommendations; 2) there is need for a more participant driven approach in terms of mode of GC communication (in‐person, phone, video), and refining the counseling agenda pre‐session; and 3) there was strong interest in the option of follow up GC. By clarifying counselees’ expectations, views and desired outcomes, we have uncovered a need for a more participant‐driven GC model when potentially actionable genomic results are received online.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/146805/1/jgc40738.pd

How can religions help to avoid a nuclear war?

Abstract not availabl

A Transdisciplinary Collaboration and Innovation Education Model and Experience

As the interconnectedness of the world grows, the need to prepare college students capable of addressing complexity likewise grows. In this context, the University of Dayton has developed and tested a transdisciplinary model for education. This model links multiple classes from different disciplines via a common theme and within a common space. It also employs an educational model premised on the following trajectory: disciplinary content development / transdisciplinary observation (empathy); transdisciplinary disruption leading to “A-Ha” observations which transform the disciplinary directions; and lastly transdisciplinary informed design and research. Central to this model is a 3,500 square foot common space used only by the classes participating in the experience. In this space classes share their reflections and content with other classes via both personal linkages and analog communications. The other classes respond to these from their disciplinary and personal perspectives. Thirteen classes, fourteen faculty, and over three-hundred students participated in a themed experience centered on the addiction crisis in Dayton, Ohio. Participants included faculty in applied creativity, engineering, health and sport science, education, theater, and religious studies. Also serving as co-teacher were community stakeholders. Assessment of the experience revealed variable student takeaways. Most prominent among these was student recognition that the experience had expanded their perspectives of the other disciplines. Most suggested that it had improved their ability to collaborate in a transdisciplinary environment and that it had significantly impacted their career aspirations. Fewer acknowledged the experience had improved their ability to create

Oxidative Release of O-Glycans under Neutral Conditions for Analysis of Glycoconjugates Having Base-Sensitive Substituents

Protein O-glycosylation is one of the most diverse post-translational modifications. A critical step in the analysis of O-glycomes is the release of glycans from glycoconjugates. Current release methods rely mainly on β-elimination, which can result in peeling reactions and loss of base-sensitive functionalities leading to misidentification of glycans. To address this challenge, well-defined synthetic glycopeptides were used to establish a robust workflow for the oxidative release of O-glycans suitable for glycomics. Treatment of O-glycopeptides with neutralized hypochlorite resulted in the selective formation of lactic/glycolic acid glycosides, thereby retaining unique information of the parent amino acid (serine/threonine) that is lost by β-elimination. It locks the glycan in a closed ring configuration, thereby preventing peeling, and furthermore, the carboxylate of the anomeric tag promotes ionization in negative ion mode mass spectrometry, thereby increasing signal intensities. Labile modifications such as sialic acids, sulfates, and acetyl esters are maintained during the release procedure. The promise of the approach was demonstrated by the analysis of O-glycans from bovine submaxillary mucin, which identified mono- and di- O-acetylated sialoglycans as well as previously undetected tri- O-acetylated and sulfated glycans. The use of well-defined glycopeptide standards made it also possible to identify reaction intermediates, which in turn allowed us to postulate a reaction mechanism for oxidative O-glycan release under neutral conditions