Ecology of Neotropical Arboreal Snakes and Behavior of New World Mollusk-Eating Snakes

The Neotropics is a biologically diverse region that provides man opportunities for ecological and behavioral studies. I utilized the speciose ophidian fauna of central Panama to explore the general ecology of arboreal snakes, the defensive behaviors of the snake community, and the diet of mollusk-eating snakes. I studied arboreal species to understand interspecilic relationships in several morphometric characters and to examine preferences in habitat. There were significant morphometric differences in relative length of jaw, mass, tail length, and size at midbody. The arboreal realm was partitioned among species by distance to ground, distance to water, and diameter of the perch. Correlations were found in some species between body mass or length and distance to the ground and leaf length. Additionally, man arboreal species have been documented to bridge gaps in vegetation, but few studies have investigated this hehavior systematically. I tested average bridging ability of five Neotropical arboreal snakes and investigated morphological elements underlying differences in relative cantilevering ability. I found significant interspecific differences in average and maximum distances bridged. Species with the relative heaviest mass had the lowest cantilever ratios. Defensive behaviors which are employed for protection from predators, also were evaluated. I document interspecific differences in these behaviors at the community level. With knowledge gained from the ophidian community in Panama, I further documented on the defensive behaviors of other New World mollusk-eating snakes. Finally, I studied the diet of selected mollusk-eating snakes. I evaluated fecal samples of Dipsas and Sibon and found that their diet is broader than mollusks alone. In fact, a majority of Dipsas in central Panama were feeding on oligochaetes. Some species of Sibon were feeding on mollusks, whereas others fed primarily on amphibian eggs and oligochaetes. The discovery of a broader diet in these taxa may have conservation implications as populations of amphibians and terrestrial mollusks decline worldwide. The expansion of our knowledge of the natural history, ecology, and behavior of Neotropical snakes has provided information that will be important for future studies of community- and ecosystem-level interactions and for the conservation of the biota of central Panama

Knowledge and Confidence of Speech-Language Pathologists Regarding Autism

The increased prevalence rate of autism has immense implications for speech language pathologists (SLPs) who are directly involved in the education and service delivery for students with autism. However, few studies have documented the effectiveness of the knowledge and confidence of SLPs regarding autism. The purpose of this study was to measure the knowledge and confidence of SLPs regarding autism and the extent to which their educational and professional training prepared them to work effectively with this population. An online survey was administered to and returned by 336 SLPs nation-wide. Two multiple linear regressions were conducted to determine the variables that explained overall knowledge and confidence. The number of students with autism on one's caseload explained most of the variance. Independent sample t-test results depicted knowledge and confidence scores of SLPs who were behaviorally trained versus those who were not behaviorally trained. SLPs who were behaviorally trained had higher mean scores on measures of knowledge and confidence when compared to those without formal behavioral training. Finally, a bivariate correlation was conducted to explore the relationship between knowledge and confidence of SLPs, however, results were not statistically significant

Infrared-Faint Radio Sources: A New Population of High-redshift Radio Galaxies

We present a sample of 1317 Infrared-Faint Radio Sources (IFRSs) that, for the first time, are reliably detected in the infrared, generated by cross-correlating the Wide-Field Infrared Survey Explorer (WISE) all-sky survey with major radio surveys. Our IFRSs are brighter in both radio and infrared than the first generation IFRSs that were undetected in the infrared by the Spitzer Space Telescope. We present the first spectroscopic redshifts of IFRSs, and find that all but one of the IFRSs with spectroscopy has z > 2. We also report the first X-ray counterparts of IFRSs, and present an analysis of radio spectra and polarization, and show that they include Gigahertz-Peaked Spectrum, Compact Steep Spectrum, and Ultra-Steep Spectrum sources. These results, together with their WISE infrared colours and radio morphologies, imply that our sample of IFRSs represents a population of radio-loud Active Galactic Nuclei at z > 2. We conclude that our sample consists of lower-redshift counterparts of the extreme first generation IFRSs, suggesting that the fainter IFRSs are at even higher redshift.Comment: 23 pages, 17 figures. Submitted to MNRA

Radio galaxies and their magnetic fields out to z <= 3

We present polarization properties at 1.4 GHz of two separate extragalactic source populations: passive quiescent galaxies and luminous quasar-like galaxies. We use data from the Wide-Field Infrared Survey Explorer to determine the host galaxy population of the polarized extragalactic radio sources. The quiescent galaxies have higher percentage polarization, smaller radio linear size, and 1.4 GHz luminosity of 6 × 1021 < L1.4 < 7 × 1025 W Hz−1, while the quasar-like galaxies have smaller percentage polarization, larger radio linear size at radio wavelengths, and a 1.4 GHz luminosity of 9 × 1023 < L1.4 < 7 × 1028 W Hz−1, suggesting that the environment of the quasar-like galaxies is responsible for the lower percentage polarization. Our results confirm previous studies that found an inverse correlation between percentage polarization and total flux density at 1.4 GHz. We suggest that the population change between the polarized extragalactic radio sources is the origin of this inverse correlation and suggest a cosmic evolution of the space density of quiescent galaxies. Finally, we find that the extragalactic contributions to the rotation measures (RMs) of the nearby passive galaxies and the distant quasar-like galaxies are different. After accounting for the RM contributions by cosmological large-scale structure and intervening Mg II absorbers we show that the distribution of intrinsic RMs of the distant quasar-like sources is at most four times as wide as the RM distribution of the nearby quiescent galaxies, if the distribution of intrinsic RMs of the WISE–Star sources itself is at least several rad m−2 wide

Benefits of Automated Crystallization Plate Tracking, Imaging, and Analysis

SummaryWe describe the design of a database and software for managing and organizing protein crystallization data. We also outline the considerations behind the design of a fast web interface linking protein production data, crystallization images, and automated image analysis. The database and associated interfaces underpin the Oxford Protein Production Facility (OPPF) crystallization laboratory, collecting, in a routine and automatic manner, up to 100,000 images per day. Over 17 million separate images are currently held in this database. We discuss the substantial scientific benefits automated tracking, imaging, and analysis of crystallizations offers to the structural biologist: analysis of the time course of the trial and easy analysis of trials with related crystallization conditions. Features of this system address requirements common to many crystallographic laboratories that are currently setting up (semi-)automated crystallization imaging systems

Alterations of immune response of non-small lung cancer with azacytidine

Innovative therapies are needed for advanced Non-Small Cell Lung Cancer (NSCLC). We have undertaken a genomics based, hypothesis driving, approach to query an emerging potential that epigenetic therapy may sensitize to immune checkpoint therapy targeting PD-L1/PD-1 interaction. NSCLC cell lines were treated with the DNA hypomethylating agent azacytidine (AZA - Vidaza) and genes and pathways altered were mapped by genome-wide expression and DNA methylation analyses. AZA-induced pathways were analyzed in The Cancer Genome Atlas (TCGA) project by mapping the derived gene signatures in hundreds of lung adeno (LUAD) and squamous cell carcinoma (LUSC) samples. AZA up-regulates genes and pathways related to both innate and adaptive immunity and genes related to immune evasion in a several NSCLC lines. DNA hypermethylation and low expression of IRF7, an interferon transcription factor, tracks with this signature particularly in LUSC. In concert with these events, AZA up-regulates PD-L1 transcripts and protein, a key ligand-mediator of immune tolerance. Analysis of TCGA samples demonstrates that a significant proportion of primary NSCLC have low expression of AZA-induced immune genes, including PD-L1. We hypothesize that epigenetic therapy combined with blockade of immune checkpoints - in particular the PD-1/PD-L1 pathway - may augment response of NSCLC by shifting the balance between immune activation and immune inhibition, particularly in a subset of NSCLC with low expression of these pathways. Our studies define a biomarker strategy for response in a recently initiated trial to examine the potential of epigenetic therapy to sensitize patients with NSCLC to PD-1 immune checkpoint blockade

Developments in Agricultural Soil Quality and Health: Reflections by the Research Committee on Soil Organic Matter Management

The North Central Education and Research Activity Committee (NCERA-59) was formed in 1952 to address how soil organic matter formation and management practices affect soil structure and productivity. It is in this capacity that we comment on the science supporting soil quality and associated soil health assessment for agricultural lands with the goal of hastening progress in this important field. Even though the suite of soil quality indicators being applied by U.S. soil health efforts closely mirrors the “minimum data set” we developed and recommended in the mid-1990s, we question whether the methods or means for their selection and development are sufficient to meet current and emerging soil health challenges. The rush to enshrine a standard suite of dated measures may be incompatible with longer-term goals. Legitimate study of soil health considers soil change accrued over years to decades that influence on- and off-site function. Tailoring of methods to local conditions is needed to effectively apply and interpret indicators for different soil resource regions and land uses. Adherence to a set suite of methods selected by subjective criteria should be avoided, particularly when we do not yet have adequate data or agreed upon interpretive frameworks for many so-called “Tier 1” biological indicators used in soil health assessment. While pooling data collected by producer-groups is one of the most exciting new trends in soil health, standardizing methods to meet broad inventory goals could compromise indicator use for site or application-specific problem solving. Changes in our nation’s research landscape are shifting responsibility for soil stewardship from national and state government backed entities to public-private partnerships. As a result, it is critical to ensure that the data needed to assess soil health are generated by reproducible methods selected through a transparent process, and that data are readily available for public and private sector use. Appropriate methods for engagement need to be applied by public-private research partnerships as they establish and expand coordinated research enterprises that can deliver fact-based interpretation of soil quality indicators within the type of normative soil health framework conceived by USDA over 20 years ago. We look to existing examples as we consider how to put soil health information into the hands of practitioners in a manner that protects soils’ services

Developments in Agricultural Soil Quality and Health: Reflections by the Research Committee on Soil Organic Matter Management

The North Central Education and Research Activity Committee (NCERA-59) was formed in 1952 to address how soil organic matter formation and management practices affect soil structure and productivity. It is in this capacity that we comment on the science supporting soil quality and associated soil health assessment for agricultural lands with the goal of hastening progress in this important field. Even though the suite of soil quality indicators being applied by U.S. soil health efforts closely mirrors the “minimum data set” we developed and recommended in the mid-1990s, we question whether the methods or means for their selection and development are sufficient to meet current and emerging soil health challenges. The rush to enshrine a standard suite of dated measures may be incompatible with longer-term goals. Legitimate study of soil health considers soil change accrued over years to decades that influence on- and off-site function. Tailoring of methods to local conditions is needed to effectively apply and interpret indicators for different soil resource regions and land uses. Adherence to a set suite of methods selected by subjective criteria should be avoided, particularly when we do not yet have adequate data or agreed upon interpretive frameworks for many so-called “Tier 1” biological indicators used in soil health assessment. While pooling data collected by producer-groups is one of the most exciting new trends in soil health, standardizing methods to meet broad inventory goals could compromise indicator use for site or application-specific problem solving. Changes in our nation’s research landscape are shifting responsibility for soil stewardship from national and state government backed entities to public-private partnerships. As a result, it is critical to ensure that the data needed to assess soil health are generated by reproducible methods selected through a transparent process, and that data are readily available for public and private sector use. Appropriate methods for engagement need to be applied by public-private research partnerships as they establish and expand coordinated research enterprises that can deliver fact-based interpretation of soil quality indicators within the type of normative soil health framework conceived by USDA over 20 years ago. We look to existing examples as we consider how to put soil health information into the hands of practitioners in a manner that protects soils’ services

Radio Galaxy Zoo: compact and extended radio source classification with deep learning

Machine learning techniques have been increasingly useful in astronomical applications overthe last few years, for example in the morphological classification of galaxies. Convolutionalneural networks have proven to be highly effective in classifying objects in image data. Inthe context of radio-interferometric imaging in astronomy, we looked for ways to identifymultiple components of individual sources. To this effect, we design a convolutional neuralnetwork to differentiate between different morphology classes using sources from the RadioGalaxy Zoo (RGZ) citizen science project. In this first step, we focus on exploring the factorsthat affect the performance of such neural networks, such as the amount of training data, number and nature of layers, and the hyperparameters. We begin with a simple experiment inwhich we only differentiate between two extreme morphologies, using compact and multiplecomponentextended sources. We found that a three-convolutional layer architecture yieldedvery good results, achieving a classification accuracy of 97.4 per cent on a test data set. The same architecture was then tested on a four-class problem where we let the networkclassify sources into compact and three classes of extended sources, achieving a test accuracyof 93.5 per cent. The best-performing convolutional neural network set-up has been verifiedagainst RGZ Data Release 1 where a final test accuracy of 94.8 per cent was obtained, usingboth original and augmented images. The use of sigma clipping does not offer a significantbenefit overall, except in cases with a small number of training images.JKB acknowledges financial support from the Australian Research Council Centre of Excellence for All-sky Astrophysics (CAASTRO), through project number CE110001020