Relationships of Cetacea (Artiodactyla) Among Mammals: Increased Taxon Sampling Alters Interpretations of Key Fossils and Character Evolution

BACKGROUND: Integration of diverse data (molecules, fossils) provides the most robust test of the phylogeny of cetaceans. Positioning key fossils is critical for reconstructing the character change from life on land to life in the water. METHODOLOGY/PRINCIPAL FINDINGS: We reexamine relationships of critical extinct taxa that impact our understanding of the origin of Cetacea. We do this in the context of the largest total evidence analysis of morphological and molecular information for Artiodactyla (661 phenotypic characters and 46,587 molecular characters, coded for 33 extant and 48 extinct taxa). We score morphological data for Carnivoramorpha, Creodonta, Lipotyphla, and the raoellid artiodactylan Indohyus and concentrate on determining which fossils are positioned along stem lineages to major artiodactylan crown clades. Shortest trees place Cetacea within Artiodactyla and close to Indohyus, with Mesonychia outside of Artiodactyla. The relationships of Mesonychia and Indohyus are highly unstable, however--in trees only two steps longer than minimum length, Mesonychia falls inside Artiodactyla and displaces Indohyus from a position close to Cetacea. Trees based only on data that fossilize continue to show the classic arrangement of relationships within Artiodactyla with Cetacea grouping outside the clade, a signal incongruent with the molecular data that dominate the total evidence result. CONCLUSIONS/SIGNIFICANCE: Integration of new fossil material of Indohyus impacts placement of another extinct clade Mesonychia, pushing it much farther down the tree. The phylogenetic position of Indohyus suggests that the cetacean stem lineage included herbivorous and carnivorous aquatic species. We also conclude that extinct members of Cetancodonta (whales+hippopotamids) shared a derived ability to hear underwater sounds, even though several cetancodontans lack a pachyostotic auditory bulla. We revise the taxonomy of living and extinct artiodactylans and propose explicit node and stem-based definitions for the ingroup

Modeling and Analysis of the Molecular Basis of Pain in Sensory Neurons

Intracellular calcium dynamics are critical to cellular functions like pain transmission. Extracellular ATP plays an important role in modulating intracellular calcium levels by interacting with the P2 family of surface receptors. In this study, we developed a mechanistic mathematical model of ATP-induced P2 mediated calcium signaling in archetype sensory neurons. The model architecture, which described 90 species connected by 162 interactions, was formulated by aggregating disparate molecular modules from literature. Unlike previous models, only mass action kinetics were used to describe the rate of molecular interactions. Thus, the majority of the 252 unknown model parameters were either association, dissociation or catalytic rate constants. Model parameters were estimated from nine independent data sets taken from multiple laboratories. The training data consisted of both dynamic and steady-state measurements. However, because of the complexity of the calcium network, we were unable to estimate unique model parameters. Instead, we estimated a family or ensemble of probable parameter sets using a multi-objective thermal ensemble method. Each member of the ensemble met an error criterion and was located along or near the optimal trade-off surface between the individual training data sets. The model quantitatively reproduced experimental measurements from dorsal root ganglion neurons as a function of extracellular ATP forcing. Hypothesized architecture linking phosphoinositide regulation with P2X receptor activity explained the inhibition of P2X-mediated current flow by activated metabotropic P2Y receptors. Sensitivity analysis using individual and the whole system outputs suggested which molecular subsystems were most important following P2 activation. Taken together, modeling and analysis of ATP-induced P2 mediated calcium signaling generated qualitative insight into the critical interactions controlling ATP induced calcium dynamics. Understanding these critical interactions may prove useful for the design of the next generation of molecular pain management strategies

Sequencing and de novo assembly of 150 genomes from Denmark as a population reference

Hundreds of thousands of human genomes are now being sequenced to characterize genetic variation and use this information to augment association mapping studies of complex disorders and other phenotypic traits. Genetic variation is identified mainly by mapping short reads to the reference genome or by performing local assembly. However, these approaches are biased against discovery of structural variants and variation in the more complex parts of the genome. Hence, large-scale de novo assembly is needed. Here we show that it is possible to construct excellent de novo assemblies from high-coverage sequencing with mate-pair libraries extending up to 20 kilobases. We report de novo assemblies of 150 individuals (50 trios) from the GenomeDenmark project. The quality of these assemblies is similar to those obtained using the more expensive long-read technology. We use the assemblies to identify a rich set of structural variants including many novel insertions and demonstrate how this variant catalogue enables further deciphering of known association mapping signals. We leverage the assemblies to provide 100 completely resolved major histocompatibility complex haplotypes and to resolve major parts of the Y chromosome. Our study provides a regional reference genome that we expect will improve the power of future association mapping studies and hence pave the way for precision medicine initiatives, which now are being launched in many countries including Denmark

Autologous microsurgical breast reconstruction and coronary artery bypass grafting: an anatomical study and clinical implications

OBJECTIVE: To identify possible avenues of sparing the internal mammary artery (IMA) for coronary artery bypass grafting (CABG) in women undergoing autologous breast reconstruction with deep inferior epigastric artery perforator (DIEP) flaps. BACKGROUND: Optimal autologous reconstruction of the breast and coronary artery bypass grafting (CABG) are often mutually exclusive as they both require utilisation of the IMA as the preferred arterial conduit. Given the prevalence of both breast cancer and coronary artery disease, this is an important issue for women's health as women with DIEP flap reconstructions and women at increased risk of developing coronary artery disease are potentially restricted from receiving this reconstructive option should the other condition arise. METHODS: The largest clinical and cadaveric anatomical study (n=315) to date was performed, investigating four solutions to this predicament by correlating the precise requirements of breast reconstruction and CABG against the anatomical features of the in situ IMAs. This information was supplemented by a thorough literature review. RESULTS: Minimum lengths of the left and right IMA needed for grafting to the left-anterior descending artery are 160.08 and 177.80 mm, respectively. Based on anatomical findings, the suitable options for anastomosis to each intercostals space are offered. In addition, 87-91% of patients have IMA perforator vessels to which DIEP flaps can be anastomosed in the first- and second-intercostal spaces. CONCLUSION: We outline five methods of preserving the IMA for future CABG: (1) lowering the level of DIEP flaps to the fourth- and fifth-intercostals spaces, (2) using the DIEP pedicle as an intermediary for CABG, (3) using IMA perforators to spare the IMA proper, (4) using and end-to-side anastomosis between the DIEP pedicle and IMA and (5) anastomosis of DIEP flaps using retrograde flow from the distal IMA. With careful patient selection, we hypothesize using the IMA for autologous breast reconstruction need not be an absolute contraindication for future CABG

How can Respectfulness in Medical Professionals be Increased? A Complex but Important Question.

Respectfulness is demanded of doctors and predicts more positive patient health-related outcomes but research is scarce on ways to promote it. This study explores two ways to conceptualize unconditional respect from medical students, defined as respect paid to people on the basis of their humanity, in order to inform strategies to increase it. Unconditional respect conceptualized as an attitude suggests that unconditional respect and conditional respect are additive, whereas unconditional respect conceptualized as a personality trait suggests that people who are high on unconditional respect afford equal respect to all humans regardless of their merits. One-hundred and eighty one medical students completed an unconditional respect measure then read a description of a respect-worthy or a non-respect-worthy man and indicated their respect towards him. The study found a main effect for unconditional respect and a main effect for target respect-worthiness but no interaction between the two when respect paid to the target was assessed, supporting the attitude-based conceptualization. This suggests that unconditional respect can be increased through relevant interventions aimed at increasing the relative salience to doctors of the human worth of individuals. Interventions to increase unconditional respect are discussed

Heterostructured approaches to efficient thermoelectric materials

A key challenge for the materials chemist is the development of controllable and straightforward synthetic methodologies that will integrate multiple phases/compositions with scalar designed physical properties. The intent of this Perspective is to give a brief summary of some of the current bulk-scaled approaches that might help guide researchers in the design of optimal heterostructures in large quantity for the further improvement of thermoelectric conversion efficiency. Examples of two-phase combinations on different length scales will be discussed with a focus on the hot carrier filtering effect that results from the selective scattering of carriers with different energies. On the basis of this strategy, heterostructures fabricated by both the bottom-up solution approaches at low temperature and top-down solid-state deposition routes that show promise in improving the thermoelectric figure of merit are highlighted. © 2013 American Chemical Society

Heterostructured approaches to efficient thermoelectric materials

A key challenge for the materials chemist is the development of controllable and straightforward synthetic methodologies that will integrate multiple phases/compositions with scalar designed physical properties. The intent of this Perspective is to give a brief summary of some of the current bulk-scaled approaches that might help guide researchers in the design of optimal heterostructures in large quantity for the further improvement of thermoelectric conversion efficiency. Examples of two-phase combinations on different length scales will be discussed with a focus on the hot carrier filtering effect that results from the selective scattering of carriers with different energies. On the basis of this strategy, heterostructures fabricated by both the bottom-up solution approaches at low temperature and top-down solid-state deposition routes that show promise in improving the thermoelectric figure of merit are highlighted. © 2013 American Chemical Society

The selective high-yield conversion of methane using iodine-catalyzed methane bromination

Methyl bromide is used as feed in a process that converts it to gasoline. It is prepared by the gas-phase reaction of CH4 with Br2, a reaction that produces, besides the desired CH3Br, large amounts of CH2Br2. The latter cokes the catalyst used for gasoline production. The separation of CH2Br2 by distillation makes gasoline production too expensive. It is therefore important to increase the selectivity of the bromination reaction. We show that a small amount of I 2 catalyzes the reaction CH2Br2 + CH 4 → 2CH3Br, which leads to higher CH4 conversion and higher selectivity to CH3Br. These findings are promising for developing a low-cost integrated bromine-iodine based dual-halogen pathway to convert stranded natural gas into fuels and chemicals. © 2013 American Chemical Society