Radiotherapy optimAl Design: An Academic Radiotherapy Treatment Design System

Optimally designing radiotherapy and radiosurgery treatments to increase the likelihood of a successful recovery from cancer is an important application of operations research. Researchers have been hindered by the lack of academic software that supports head-to-head comparisons of different techniques, and this article addresses the inherent difficulties of designing and implementing an academic treatment planning system. In particular, this article details the algorithms and the software design of Radiotherapy optimAl Design (RAD)

Massively distributed authorship of academic papers

Wiki-like or crowdsourcing models of collaboration can provide a number of benefits to academic work. These techniques may engage expertise from different disciplines, and potentially increase productivity. This paper presents a model of massively distributed collaborative authorship of academic papers. This model, developed by a collective of thirty authors, identifies key tools and techniques that would be necessary or useful to the writing process. The process of collaboratively writing this paper was used to discover, negotiate, and document issues in massively authored scholarship. Our work provides the first extensive discussion of the experiential aspects of large-scale collaborative researc

Analysis of chloroplast genomes and a supermatrix inform reclassification of the Rhodomelaceae (Rhodophyta).

With over a thousand species, the Rhodomelaceae is the most species-rich family of red algae. While its genera have been assigned to 14 tribes, the high-level classification of the family has never been evaluated with a molecular phylogeny. Here, we reassess its classification by integrating genome-scale phylogenetic analysis with observations of the morphological characters of clades. In order to resolve relationships among the main lineages of the family we constructed a phylogeny with 55 chloroplast genomes (52 newly determined). The majority of branches were resolved with full bootstrap support. We then added 266 rbcL, 125 18S rRNA gene and 143 cox1 sequences to construct a comprehensive phylogeny containing nearly half of all known species in the family (407 species in 89 genera). These analyses suggest the same subdivision into higher-level lineages, but included many branches with moderate or poor support. The circumscription for nine of the 13 previously described tribes was supported, but the Lophothalieae, Polysiphonieae, Pterosiphonieae and Herposiphonieae required revision, and five new tribes and one resurrected tribe were segregated from them. Rhizoid anatomy is highlighted as a key diagnostic character for the morphological delineation of several lineages. This work provides the most extensive phylogenetic analysis of the Rhodomelaceae to date and successfully resolves the relationships among major clades of the family. Our data show that organellar genomes obtained through high-throughput sequencing produce well-resolved phylogenies of difficult groups, and their more general application in algal systematics will likely permit deciphering questions about classification at many taxonomic levels

Analysis of chloroplast genomes and a supermatrix inform reclassification of the Rhodomelaceae (Rhodophyta).

With over a thousand species, the Rhodomelaceae is the most species-rich family of red algae. While its genera have been assigned to 14 tribes, the high-level classification of the family has never been evaluated with a molecular phylogeny. Here, we reassess its classification by integrating genome-scale phylogenetic analysis with observations of the morphological characters of clades. In order to resolve relationships among the main lineages of the family we constructed a phylogeny with 55 chloroplast genomes (52 newly determined). The majority of branches were resolved with full bootstrap support. We then added 266 rbcL, 125 18S rRNA gene and 143 cox1 sequences to construct a comprehensive phylogeny containing nearly half of all known species in the family (407 species in 89 genera). These analyses suggest the same subdivision into higher-level lineages, but included many branches with moderate or poor support. The circumscription for nine of the 13 previously described tribes was supported, but the Lophothalieae, Polysiphonieae, Pterosiphonieae and Herposiphonieae required revision, and five new tribes and one resurrected tribe were segregated from them. Rhizoid anatomy is highlighted as a key diagnostic character for the morphological delineation of several lineages. This work provides the most extensive phylogenetic analysis of the Rhodomelaceae to date and successfully resolves the relationships among major clades of the family. Our data show that organellar genomes obtained through high-throughput sequencing produce well-resolved phylogenies of difficult groups, and their more general application in algal systematics will likely permit deciphering questions about classification at many taxonomic levels

Simultaneous observation of mesospheric gravity waves and sprites generated by a Midwestern thunderstorm

Abstract The present report investigates using simultaneous observations of coincident gravity waves and sprites to establish an upper limit on sprite-associated thermal energy deposition in the mesosphere. The University of Alaska operated a variety of optical imagers and photometers at two ground sites in support of the NASA Sprites99 balloon campaign. One site was atop a US Forest Service lookout tower on Bear Mt. in the Black Hills, in western South Dakota. On the night of 18 August 1999 we obtained from this site simultaneous images of sprites and OH airglow modulated by gravity waves emanating from a very active sprite producing thunderstorm over Nebraska, to the Southeast of Bear Mt. Using 25 s exposures with a bare CCD camera equipped with a red ÿlter, we were able to coincidentally record both short duration (¡10 ms) but bright (¿3 MR) N2 1PG red emissions from sprites and much weaker (∼1 kR), but persistent, OH Meinel nightglow emissions. A time lapse movie created from images revealed short period, complete 360 • concentric wave structures emanating radially outward from a central excitation region directly above the storm. During the initial stages of the storm outwardly expanding waves possessed a period of ≈10 min and wavelength ≈50 km. Over a 1 h interval the waves gradually changed to longer period ≈11 min and shorter wavelength ≈40 km. Over the full 2 h observation time, about two dozen bright sprites generated by the underlying thunderstorm were recorded near the center of the outwardly radiating gravity wave pattern. No distinctive OH brightness signatures uniquely associated with the sprites were detected at the level of 2% of the ambient background brightness, establishing an associated upper limit of approximately T . 0:5 K for a neutral temperature perturbation over the volume of the sprites. The corresponding total thermal energy deposited by the sprite is bounded by these measurements to be less than ∼1 GJ. This value is well above the total energy deposited into the medium by the sprite, estimated by several independent methods to be on the order of ∼1-10 MJ

Non-crossing dependencies: Least effort, not grammar

The use of null hypotheses (in a statistical sense) is common in hard sciences but not in theoretical linguistics. Here the null hypothesis that the low frequency of syntactic dependency crossings is expected by an arbitrary ordering of words is rejected. It is shown that this would require star dependency structures, which are both unrealistic and too restrictive. The hypothesis of the limited resources of the human brain is revisited. Stronger null hypotheses taking into account actual dependency lengths for the likelihood of crossings are presented. Those hypotheses suggests that crossings are likely to reduce when dependencies are shortened. A hypothesis based on pressure to reduce dependency lengths is more parsimonious than a principle of minimization of crossings or a grammatical ban that is totally dissociated from the general and non-linguistic principle of economy.Postprint (author's final draft

Personality, posttraumatic stress and trauma type: factors contributing to posttraumatic growth and its domains in a Turkish community sample

Background: Posttraumatic growth (PTG) is conceptualized as a positive transformation resulting from coping with and processing traumatic life events. This study examined the contributory roles of personality traits, posttraumatic stress (PTS) severity and their interactions on PTG and its domains, as assessed with the Posttraumatic Growth Inventory Turkish form (PTGI-T). The study also examined the differences in PTG domains between survivors of accidents, natural disasters and unexpected loss of a loved one. Methods: The Basic Personality Traits Inventory, Posttraumatic Diagnostic Scale, and PTGI-T were administered to a large stratified cluster community sample of 969 Turkish adults in their home settings. Results: The results showed that conscientiousness, agreeableness, and openness to experience significantly related to the total PTG and most of the domains. The effects of extraversion, neuroticism and openness to experience were moderated by the PTS severity for some domains. PTG in relating to others and appreciation of life domains was lower for the bereaved group. Conclusion: Further research should examine the mediating role of coping between personality and PTG using a longitudinal design

Olfactory and solitary chemosensory cells: two different chemosensory systems in the nasal cavity of the American alligator, Alligator mississippiensis

<p>Abstract</p> <p>Background</p> <p>The nasal cavity of all vertebrates houses multiple chemosensors, either innervated by the Ist (olfactory) or the Vth (trigeminal) cranial nerve. Various types of receptor cells are present, either segregated in different compartments (e.g. in rodents) or mingled in one epithelium (e.g. fish). In addition, solitary chemosensory cells have been reported for several species. Alligators which seek their prey both above and under water have only one nasal compartment. Information about their olfactory epithelium is limited. Since alligators seem to detect both volatile and water-soluble odour cues, I tested whether different sensory cell types are present in the olfactory epithelium.</p> <p>Results</p> <p>Electron microscopy and immunocytochemistry were used to examine the sensory epithelium of the nasal cavity of the American alligator. Almost the entire nasal cavity is lined with olfactory (sensory) epithelium. Two types of olfactory sensory neurons are present. Both types bear cilia as well as microvilli at their apical endings and express the typical markers for olfactory neurons. The density of these olfactory neurons varies along the nasal cavity. In addition, solitary chemosensory cells innervated by trigeminal nerve fibres, are intermingled with olfactory sensory neurons. Solitary chemosensory cells express components of the PLC-transduction cascade found in solitary chemosensory cells in rodents.</p> <p>Conclusion</p> <p>The nasal cavity of the American alligator contains two different chemosensory systems incorporated in the same sensory epithelium: the olfactory system proper and solitary chemosensory cells. The olfactory system contains two morphological distinct types of ciliated olfactory receptor neurons.</p