Fresh Air

In this “Subterranean fiction” novella, a young woman named Ena Henders is faced with taking over the leadership of her underground civilization early, due to the unexpected death of her father. She is forced to take drastic measures to save her people when their subterranean city begins to collapse. She faces vocal opponents within her community who underestimate her and how dangerous the Underground can get. There is something mysterious, though, that lurks in her city and threatens to destroy them all, which Ena has yet to discover. This project was inspired by my previous goal to spend a full semester writing “female-focused fantasy,” which resulted in two short stories, and one novel-in-progress on the theme. This piece continues that exploration of women in positions of power in alternate-universes. The motivation for this theme is part escapism, because it is currently easier to envision women in places of power within different universes that have different centers of morality than it is in the world as it is. It is also motivated by optimism, though. Following the advice of author Toni Morrison, who stated that “If there's a book that you want to read, but it hasn't been written yet, then you must write it,”[1] I have done just that. There is a lack of female-led fantasy in the popular media, and this story’s themes address that. While there are some male authors in the genre who write female protagonists in positions of power, there is a lack of female authors or female-led fantasy novels (with a few exceptions). This novella attempts to address this gap in American popular media. This piece is written for a young-adult, primarily female, audience. It addresses issues of insecurity, family conflicts, and the universal intricacies that young adults face when coming of age within a fantastic, yet grounded, universe in which the heroine has claws and other unusual physical attributes. This story also specifically addresses the over-sexualization of young female characters in novels by attributing physical characteristics of utility instead of aestheticism to its characters of all genders. It is unfortunately rare to see women described by what they do with their bodies, and not by what those bodies look like, isolated from the character’s feelings or abilities. This story seeks to correct that trend as much as is possible. Finally, although romance is not the focus of this story, the normalization of non-heterosexual relationships is attempted through subtle romantic attachments that Ena forms throughout the novella, which, although not developed by the story’s stopping point, percolate in the background behind the action. They allow the character to develop as an adult in a subtle way, alongside the external action. This story deals with feminist themes while exploring the genre that is “Subterranean fiction” in a fantasy setting. Ultimately, despite the other-worldly setting, the story remains grounded in family and individual responsibility. [1] https://goo.gl/WyhHtF- Toni Morrison and Junot Día

Modelling growth, recruitment and mortality to describe and simulate dynamics of subtropical rainforests following different levels of disturbance

The capacity of rainforests to recover from logging disturbance is difficult to model due to the compounding interactions between long-term disturbance effects, natural dynamics, site characteristics and tree species regeneration strategies. The aim of this study was to develop a quantitative model using over three decades of data from stands subjected to various levels of disturbance ranging from natural, through increasing intensities of tree removal to intensive logging. Data for trees >10 cm diameter at 1.3 m above the ground (dbh) in subtropical rainforest of north-east New South Wales, Australia were used. Botanical identity of trees at species level, species-specific shade tolerance and size at maturity were used to classify 117 species into five groups. These groups include the emergent and shade tolerant main canopy species, shade tolerant mid canopy species, shade tolerant understorey species, moderate shade tolerant species, and shade intolerant tree species. Multilevel nonlinear regression was used to estimate growth, recruitment and mortality parameters, based on the assumption of variations in tree species performance at both the plot and tree levels. The species group, tree size and competition from larger trees accounted for most variation at the tree level. Significant stand level variables included topography (elevation, slope and aspect), stand basal area, and time since the disturbance. The final model is a classical matrix management-oriented model with an ecological basis and maximum size-dependent parameters of ingrowth and outgrowth. The model provides a tool to simulate stand performance after logging and to assess silvicultural prescriptions before they are applied. Simulations with estimated parameters indicate that moderate harvesting (47% overstorey basal area (BA) removal) in a checkerboard of logged and unlogged patches (group selection) on a 120-year cycle could enable sustainable timber production without compromising the ecological integrity in these rainforests. This is due to reduced logging damage in group selection, which also released retained stems and facilitated recruitment of both shade tolerant and intolerant trees. Single-tree selection (35% BA removal) created small canopy gaps that resulted in low recruitment, a slight increase in the growth of retained stems and recovery time of 150 years. Intensive single-tree selection (50% BA removal) resulted in high logging damage that increased recovery time to 180 years. Intensive logging (65-80% BA removal) decreased the stem density and created larger canopy gaps allowing for high growth rates and recruitment of both shade tolerant and intolerant trees. However, few retained stems and high mortality of recruits, increased the recovery time to 180-220 years. Pre-harvest climber cutting coupled with poisoning of nontimber species followed by logging could allow harvesting on a 300-year cycle. Shorter logging cycles may lead to changes in species composition as well as in the forest structure

Functional distinctiveness of major plant lineages

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/106060/1/jec12208.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/106060/2/jec12208-sup-0001-Supp_Info.pd

Detection of long repeat expansions from PCR-free whole-genome sequence data

Identifying large expansions of short tandem repeats (STRs) such as those that cause amyotrophic lateral sclerosis (ALS) and fragile X syndrome is challenging for short-read whole-genome sequencing (WGS) data. A solution to this problem is an important step towards integrating WGS into precision medicine. We have developed a software tool called ExpansionHunter that, using PCR-free WGS short-read data, can genotype repeats at the locus of interest, even if the expanded repeat is larger than the read length. We applied our algorithm to WGS data from 3,001 ALS patients who have been tested for the presence of the C9orf72 repeat expansion with repeat-primed PCR (RP-PCR). Compared against this truth data, ExpansionHunter correctly classified all (212/212, 95% CI [0.98, 1.00]) of the expanded samples as either expansions (208) or potential expansions (4). Additionally, 99.9% (2,786/2,789, 95% CI [0.997, 1.00]) of the wild type samples were correctly classified as wild type by this method with the remaining three samples identified as possible expansions. We further applied our algorithm to a set of 152 samples where every sample had one of eight different pathogenic repeat expansions including those associated with fragile X syndrome, Friedreich's ataxia and Huntington's disease and correctly flagged all but one of the known repeat expansions. Thus, ExpansionHunter can be used to accurately detect known pathogenic repeat expansions and provides researchers with a tool that can be used to identify new pathogenic repeat expansions. The software is licensed under GPL v3.0 and the source code is freely available on GitHub

Cheek Tooth Morphology and Ancient Mitochondrial DNA of Late Pleistocene Horses from the Western Interior of North America: Implications for the Taxonomy of North American Late Pleistocene Equus

Horses were a dominant component of North American Pleistocene land mammal communities and their remains are well represented in the fossil record. Despite the abundant material available for study, there is still considerable disagreement over the number of species of Equus that inhabited the different regions of the continent and on their taxonomic nomenclature. In this study, we investigated cheek tooth morphology and ancient mtDNA of late Pleistocene Equus specimens from the Western Interior of North America, with the objective of clarifying the species that lived in this region prior to the end-Pleistocene extinction. Based on the morphological and molecular data analyzed, a caballine (Equus ferus) and a non-caballine (E. conversidens) species were identified from different localities across most of the Western Interior. A second non-caballine species (E. cedralensis) was recognized from southern localities based exclusively on the morphological analyses of the cheek teeth. Notably the separation into caballine and non-caballine species was observed in the Bayesian phylogenetic analysis of ancient mtDNA as well as in the geometric morphometric analyses of the upper and lower premolars. Teeth morphologically identified as E. conversidens that yielded ancient mtDNA fall within the New World stilt-legged clade recognized in previous studies and this is the name we apply to this group. Geographic variation in morphology in the caballine species is indicated by statistically different occlusal enamel patterns in the specimens from Bluefish Caves, Yukon Territory, relative to the specimens from the other geographic regions. Whether this represents ecomorphological variation and/or a certain degree of geographic and genetic isolation of these Arctic populations requires further study

Does Diving Limit Brain Size in Cetaceans?

We test the longstanding hypothesis, known as the dive constraint hypothesis, that the oxygenation demands of diving pose a constraint on aquatic mammal brain size.Using a sample of 23 cetacean species we examine the relationship among six different measures of relative brain size, body size, and maximum diving duration. Unlike previous tests we include body size as a covariate and perform independent contrast analyses to control for phylogeny. We show that diving does not limit brain size in cetaceans and therefore provide no support for the dive constraint hypothesis. Instead, body size is the main predictor of maximum diving duration in cetaceans. Furthermore, our findings show that it is important to conduct robust tests of evolutionary hypotheses by employing a variety of measures of the dependent variable, in this case, relative brain size

Following a foraging fish-finder : diel habitat use of Blainville's beaked whales revealed by echolocation

© The Author(s), 2011. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 6 (2011): e28353, doi:10.1371/journal.pone.0028353.Simultaneous high resolution sampling of predator behavior and habitat characteristics is often difficult to achieve despite its importance in understanding the foraging decisions and habitat use of predators. Here we tap into the biosonar system of Blainville's beaked whales, Mesoplodon densirostris, using sound and orientation recording tags to uncover prey-finding cues available to echolocating predators in the deep-sea. Echolocation sounds indicate where whales search and encounter prey, as well as the altitude of whales above the sea-floor and the density of organisms around them, providing a link between foraging activity and the bio-physical environment. Tagged whales (n = 9) hunted exclusively at depth, investing most of their search time either in the lower part of the deep scattering layer (DSL) or near the sea-floor with little diel change. At least 43% (420/974) of recorded prey-capture attempts were performed within the benthic boundary layer despite a wide range of dive depths, and many dives included both meso- and bentho-pelagic foraging. Blainville's beaked whales only initiate searching when already deep in the descent and encounter prey suitable for capture within 2 min of the start of echolocation, suggesting that these whales are accessing prey in reliable vertical strata. Moreover, these prey resources are sufficiently dense to feed the animals in what is effectively four hours of hunting per day enabling a strategy in which long dives to exploit numerous deep-prey with low nutritional value require protracted recovery periods (average 1.5 h) between dives. This apparent searching efficiency maybe aided by inhabiting steep undersea slopes with access to both the DSL and the sea-floor over small spatial scales. Aggregations of prey in these biotopes are located using biosonar-derived landmarks and represent stable and abundant resources for Blainville's beaked whales in the otherwise food-limited deep-ocean.The work was funded by the Office of Naval Research and the National Ocean Partnership Program (US), by a consortium consisting of the Canary Islands Government, the Spanish Ministry of Environment and the Spanish Ministry of Defense, and by the European environmental funding LIFE-INDEMARES program for the inventory and designation of the Natura 2000 network in marine areas of the Spanish territory, headed by Fundacion Biodiversidad, with additional support from the Cabildo Insular of El Hierro. PA is currently supported by the National Research Project: Cetacean, Oceanography and Biodiversity from La Palma and El Hierro (CGL2009-13112) of the Spanish Ministry of Science and NAS by a Marie Curie fellowship from the 7th European Frame Program. MJ was supported by grants from the Strategic Environmental Research Development Program and from the National Ocean Partnership Program. PTM was supported by frame grants from the National Danish Science Foundation