The Effect of Focusing and Caustics on Exit Phenomena in Systems Lacking Detailed Balance

We study the trajectories followed by a particle subjected to weak noise when escaping from the domain of attraction of a stable fixed point. If detailed balance is absent, a _focus_ may occur along the most probable exit path, leading to a breakdown of symmetry (if present). The exit trajectory bifurcates, and the exit location distribution may become `skewed' (non-Gaussian). The weak-noise asymptotics of the mean escape time are strongly affected. Our methods extend to the study of skewed exit location distributions in stochastic models without symmetry.Comment: REVTEX macros (latest version). Two accompanying PS figures, one of which is large (over 600K unpacked

Continuing Progress towards a Phylogeny of Tachinidae

Readers of this newsletter are likely familiar with our ongoing project to establish a framework phylogeny of world Tachinidae (see articles in The Tachinid Times 26 and 27). This collaborative project, involving myself, Jim O’Hara, Kevin Moulton, Pierfilippo Cerretti, Isaac Winkler and a long list of collaborating tachinidophiles was initiated in 2012 with funding from the U.S. National Science Foundation. Our goal is to produce a robust phylogenetic framework of Tachinidae that can be used to inform tachinid taxonomy, systematics research, and the patterns of tachinid evolution. In previous issues of The Tachinid Times we summarized our progress to date in terms of obtaining taxa (e.g., Cerretti et al. 2013, O’Hara et al. 2014) and some of our preliminary phylogenetic findings (Stireman et al. 2013, Winkler et al. 2014). Here, we provide a brief update on some of our recent progress and associated products

Statistical techniques to construct assays for identifying likely responders to a treatment under evaluation from cell line genomic data

<p>Abstract</p> <p>Background</p> <p>Developing the right drugs for the right patients has become a mantra of drug development. In practice, it is very difficult to identify subsets of patients who will respond to a drug under evaluation. Most of the time, no single diagnostic will be available, and more complex decision rules will be required to define a sensitive population, using, for instance, mRNA expression, protein expression or DNA copy number. Moreover, diagnostic development will often begin with in-vitro cell-line data and a high-dimensional exploratory platform, only later to be transferred to a diagnostic assay for use with patient samples. In this manuscript, we present a novel approach to developing robust genomic predictors that are not only capable of generalizing from in-vitro to patient, but are also amenable to clinically validated assays such as qRT-PCR.</p> <p>Methods</p> <p>Using our approach, we constructed a predictor of sensitivity to dacetuzumab, an investigational drug for CD40-expressing malignancies such as lymphoma using genomic measurements of cell lines treated with dacetuzumab. Additionally, we evaluated several state-of-the-art prediction methods by independently pairing the feature selection and classification components of the predictor. In this way, we constructed several predictors that we validated on an independent DLBCL patient dataset. Similar analyses were performed on genomic measurements of breast cancer cell lines and patients to construct a predictor of estrogen receptor (ER) status.</p> <p>Results</p> <p>The best dacetuzumab sensitivity predictors involved ten or fewer genes and accurately classified lymphoma patients by their survival and known prognostic subtypes. The best ER status classifiers involved one or two genes and led to accurate ER status predictions more than 85% of the time. The novel method we proposed performed as well or better than other methods evaluated.</p> <p>Conclusions</p> <p>We demonstrated the feasibility of combining feature selection techniques with classification methods to develop assays using cell line genomic measurements that performed well in patient data. In both case studies, we constructed parsimonious models that generalized well from cell lines to patients.</p

Remarkable fly (Diptera) diversity in a patch of Costa Rican cloud forest : Why inventory is a vital science

Study of all flies (Diptera) collected for one year from a four-hectare (150 x 266 meter) patch of cloud forest at 1,600 meters above sea level at Zurqui de Moravia, San Jose Province, Costa Rica (hereafter referred to as Zurqui), revealed an astounding 4,332 species. This amounts to more than half the number of named species of flies for all of Central America. Specimens were collected with two Malaise traps running continuously and with a wide array of supplementary collecting methods for three days of each month. All morphospecies from all 73 families recorded were fully curated by technicians before submission to an international team of 59 taxonomic experts for identification. Overall, a Malaise trap on the forest edge captured 1,988 species or 51% of all collected dipteran taxa (other than of Phoridae, subsampled only from this and one other Malaise trap). A Malaise trap in the forest sampled 906 species. Of other sampling methods, the combination of four other Malaise traps and an intercept trap, aerial/hand collecting, 10 emergence traps, and four CDC light traps added the greatest number of species to our inventory. This complement of sampling methods was an effective combination for retrieving substantial numbers of species of Diptera. Comparison of select sampling methods (considering 3,487 species of non-phorid Diptera) provided further details regarding how many species were sampled by various methods. Comparison of species numbers from each of two permanent Malaise traps from Zurqui with those of single Malaise traps at each of Tapanti and Las Alturas, 40 and 180 km distant from Zurqui respectively, suggested significant species turnover. Comparison of the greater number of species collected in all traps from Zurqui did not markedly change the degree of similarity between the three sites, although the actual number of species shared did increase. Comparisons of the total number of named and unnamed species of Diptera from four hectares at Zurqui is equivalent to 51% of all flies named from Central America, greater than all the named fly fauna of Colombia, equivalent to 14% of named Neotropical species and equal to about 2.7% of all named Diptera worldwide. Clearly the number of species of Diptera in tropical regions has been severely underestimated and the actual number may surpass the number of species of Coleoptera. Various published extrapolations from limited data to estimate total numbers of species of larger taxonomic categories (e.g., Hexapoda, Arthropoda, Eukaryota, etc.) are highly questionable, and certainly will remain uncertain until we have more exhaustive surveys of all and diverse taxa (like Diptera) from multiple tropical sites. Morphological characterization of species in inventories provides identifications placed in the context of taxonomy, phylogeny, form, and ecology. DNA barcoding species is a valuable tool to estimate species numbers but used alone fails to provide a broader context for the species identified.Peer reviewe

Evolution and Biogeography of the Tachinid Flies with Focus on the Tribe Blondeliini (Insecta: Diptera: Tachinidae)

1. The large Diptera family Tachinidae is a diverse and recent group of koinobiont endoparasitoids feeding on a wide range of insects and some other arthropods. 2. Unfortunately, taxonomic confusion and poor understanding of tropical faunas has made difficulties for both basic and derived ecological research on tachinid flies. 3. Here I present evolutionary and ecological hypotheses for tachinid flies, with focus on the large tribe Blondeliini. Chapter 2 summarizes evidence for a latitudinal gradient in tachinid fly species richness within the Americas, using 7 survey data sets within both the temperate zone and tropics. In Chapter 3, I use several nuclear genes to construct a phylogenic framework for the tribe Blondeliini. Despite overall low support values, it was possible to infer several genus groups as well as describe overall evolutionary trends in host use and biogeography in the tribe. Chapter 4 is a conspectus of the Blondelia group of genera, which are distinctive for the female keel and piercer oviposition device. Both genetic and morphological evidence were used to delimit the included genera and species groups of Eucelatoria. Chapter 5 is a revision of the Eucelatoria ferox species group, the females of which are distinctive for their elongate piercers. Total ecological, morphological, and genetic evidence were used to describe previously named species as well as 17 species new to science

Evolution and Biogeography of the Tachinid Flies with Focus on the Tribe Blondeliini (Insecta: Diptera: Tachinidae).

1. The large Diptera family Tachinidae is a diverse and recent group of koinobiont endoparasitoids feeding on a wide range of insects and some other arthropods. 2. Unfortunately, taxonomic confusion and poor understanding of tropical faunas has made difficulties for both basic and derived ecological research on tachinid flies. 3. Here I present evolutionary and ecological hypotheses for tachinid flies, with focus on the large tribe Blondeliini. Chapter 2 summarizes evidence for a latitudinal gradient in tachinid fly species richness within the Americas, using 7 survey data sets within both the temperate zone and tropics. In Chapter 3, I use several nuclear genes to construct a phylogenic framework for the tribe Blondeliini. Despite overall low support values, it was possible to infer several genus groups as well as describe overall evolutionary trends in host use and biogeography in the tribe. Chapter 4 is a conspectus of the Blondelia group of genera, which are distinctive for the female keel and piercer oviposition device. Both genetic and morphological evidence were used to delimit the included genera and species groups of Eucelatoria. Chapter 5 is a revision of the Eucelatoria ferox species group, the females of which are distinctive for their elongate piercers. Total ecological, morphological, and genetic evidence were used to describe previously named species as well as 17 species new to science

A Phylogenetic Framework for the Tachinid Fly Tribe Blondeliini (Diptera: Tachinidae: Exoristinae)

Much of the great Neotropical species richness of the parasitoid fly family Tachinidae (Diptera) is found within the exoristine tribe Blondeliini. This species diversity is particularly concentrated within a number of genera, including the piercer-possessing genera of the “Blondelia genus group”. Unfortunately, the blondeliines are plagued with a history of taxonomic inflation, poor descriptions, and confusing morphology, thus making it unclear whether these intriguing oviposition structures are homologous or convergent. We therefore present a molecular phylogeny for the Blondeliini using three informative nuclear genes, which resolves the relationships between the key centers of diversity in the tribe and the monophyly of the Blondelia group. This framework will serve as a baseline for future taxonomic work within the tribe

A Phylogenetic Framework for the Tachinid Fly Tribe Blondeliini (Diptera: Tachinidae: Exoristinae)

Much of the great Neotropical species richness of the parasitoid fly family Tachinidae (Diptera) is found within the exoristine tribe Blondeliini. This species diversity is particularly concentrated within a number of genera, including the piercer-possessing genera of the “Blondelia genus group”. Unfortunately, the blondeliines are plagued with a history of taxonomic inflation, poor descriptions, and confusing morphology, thus making it unclear whether these intriguing oviposition structures are homologous or convergent. We therefore present a molecular phylogeny for the Blondeliini using three informative nuclear genes, which resolves the relationships between the key centers of diversity in the tribe and the monophyly of the Blondelia group. This framework will serve as a baseline for future taxonomic work within the tribe