Intelligent assistance in scientific data preparation

Scientific data preparation is the process of extracting usable scientific data from raw instrument data. This task involves noise detection (and subsequent noise classification and flagging or removal), extracting data from compressed forms, and construction of derivative or aggregate data (e.g. spectral densities or running averages). A software system called PIPE provides intelligent assistance to users developing scientific data preparation plans using a programming language called Master Plumber. PIPE provides this assistance capability by using a process description to create a dependency model of the scientific data preparation plan. This dependency model can then be used to verify syntactic and semantic constraints on processing steps to perform limited plan validation. PIPE also provides capabilities for using this model to assist in debugging faulty data preparation plans. In this case, the process model is used to focus the developer's attention upon those processing steps and data elements that were used in computing the faulty output values. Finally, the dependency model of a plan can be used to perform plan optimization and run time estimation. These capabilities allow scientists to spend less time developing data preparation procedures and more time on scientific analysis tasks

A massive warm baryonic halo in the Coma cluster

Several deep PSPC observations of the Coma cluster reveal a very large-scale halo of soft X-ray emission, substantially in excess of the well known radiation from the hot intra-cluster medium. The excess emission, previously reported in the central region of the cluster using lower-sensitivity EUVE and ROSAT data, is now evident out to a radius of 2.6 Mpc, demonstrating that the soft excess radiation from clusters is a phenomenon of cosmological significance. The X-ray spectrum at these large radii cannot be modeled non-thermally, but is consistent with the original scenario of thermal emission from warm gas at ~ 10^6 K. The mass of the warm gas is on par with that of the hot X-ray emitting plasma, and significantly more massive if the warm gas resides in low-density filamentary structures. Thus the data lend vital support to current theories of cosmic evolution, which predict that at low redshift \~30-40 % of the baryons reside in warm filaments converging at clusters of galaxies.Comment: Astrophysical Journal, in pres

Parental Impact on Child Physical Activity and Sedentary Time in Appalachian North Carolina

Introduction: Physical activity has positive health benefits across the lifespan including reduced rates of chronic disease. Despite having ample availability of outdoor space for physical activity in the Appalachian Mountain region, there are low rates of physical activity along with high rates of sedentary time and increased prevalence of overweight individuals across all age groups. Therefore, there is a need to understand the factors that influence family’s physical activity and sedentary time. Purpose: To assess whether parental attitudes and behaviors influence children’s physical activity and sedentary time. Methods: The current study was a secondary analysis of the baseline data from a pilot study of a pediatrician prescription program for outdoor physical activity. Parents (N = 70) with children aged 5–13 years living in a county served by a single-pediatrician office completed surveys in the pediatrician’s office during a well-child visit. The survey included questions related to parental attitudes toward children’s physical activity and the physical activity and sedentary time performed by the parent and their child. Results: Parent sedentary time was the only factor that had an impact on child sedentary time, with 18% of the variance in children’s sedentary time being explained by parent sedentary time. No factors predicted children’s physical activity. Implications: To decrease child sedentary time, interventions should focus on reducing parental and joint parent–child sedentary time

Holocene variations in peatland methane cycling associated with the Asian summer monsoon system

Atmospheric methane concentrations decreased during the early to middle Holocene; however, the governing mechanisms remain controversial. Although it has been suggested that the mid-Holocene minimum methane emissions are associated with hydrological change, direct evidence is lacking. Here we report a new independent approach, linking hydrological change in peat sediments from the Tibetan Plateau to changes in archaeal diether concentrations and diploptene delta C-13 values as tracers for methanogenesis and methanotrophy, respectively. A minimum in inferred methanogenesis occurred during the mid-Holocene, which, locally, corresponds with the driest conditions of the Holocene, reflecting a minimum in Asian monsoon precipitation. The close coupling between precipitation and methanogenesis is validated by climate simulations, which also suggest a regionally widespread impact. Importantly, the minimum in methanogenesis is associated with a maximum in methanotrophy. Therefore, methane emissions in the Tibetan Plateau region were apparently lower during the mid-Holocene and partially controlled by interactions of large-scale atmospheric circulation

Response of Amazonian forests to mid-Holocene drought: a model-data comparison

There is major concern for the fate of Amazonia over the coming century in the face of anthropogenic climate change. A key area of uncertainty is the scale of rainforest die-back to be expected under a future, drier climate. In this study, we use the middle Holocene (ca. 6,000 years before present) as an approximate analogue for a drier future, given that palaeoclimate data show much of Amazonia was significantly drier than present at this time. Here, we use an ensemble of climate and vegetation models to explore the sensitivity of Amazonian biomes to mid-Holocene climate change. For this we employ three dynamic vegetation models (JULES, IBIS, and SDGVM) forced by the bias-corrected mid-Holocene climate simulations from seven models that participated in the Paleoclimate Modelling Intercomparison Project 3 (PMIP3). These model outputs are compared with a multi-proxy palaeoecological dataset to gain a better understanding of where in Amazonia we have most confidence in the mid-Holocene vegetation simulations. A robust feature of all simulations and palaeodata is that the central Amazonian rainforest biome is unaffected by mid-Holocene drought. Greater divergence in mid-Holocene simulations exists in ecotonal eastern and southern Amazonia. Vegetation models driven with climate models that simulate a drier mid Holocene (100-150 mm per year decrease) better capture the observed (palaeodata) tropical forest die-back in these areas. Based on the relationship between simulated rainfall decrease and vegetation change, we find indications that in southern Amazonia the rate of tropical forest die-back was ~125,000 km2 per 100 mm rainfall decrease in the mid Holocene. This provides a baseline sensitivity of tropical forests to drought for this region (without human-driven changes to greenhouse gases, fire, and deforestation). We highlight the need for more palaeoecological and palaeoclimate data across lowland Amazonia to constrain model responses

Diet Composition and Body Condition of Northern Continental Divide Grizzly Bears, Montana

From 2009–2013, we documented apparent population health by investigating food use and physiological condition of grizzly bears (Ursus arctos) in the Northern Continental Divide Ecosystem (NCDE), Montana.  We used stable isotope analysis upon hair and blood tissue to obtain information on percent terrestrial meat and plant matter in the diets of NCDE bears.  We also assessed body fat content of grizzly bears via bioelectrical impedance analysis.  Adult females used less meat compared to subadults and adult males (P < 0.0001).  Bears within regions on the southwestern, southern, and eastern periphery of the ecosystem consumed a significantly higher proportion of meat than those in the interior or northwestern periphery (P < 0.0001).  Diets of bears in the Whitefish Mountains and North and South Fork of the Flathead River were, on average, composed of 70% less meat than those on the East Front.  Adult males had significantly higher den entrance body fat contents than adult females and subadults (P < 0.0001).  Average body fat of adult females varied significantly between those in areas of high consumption of meat and those otherwise.  However, we find adult females across all regions enter dens at mean fat levels above those thought to be critical for cub production (i.e., > 20%).  We conclude that, within each region, the quantity and quality of foods appear adequate to meet the needs of reproductively-active adult females.  As truly opportunistic omnivores, grizzly bears in each region of the NCDE exploit diverse combinations of food items to arrive at productive body conditions

Detection of a CMB decrement towards a cluster of mJy radiosources

We present the results of radio, optical and near-infrared observations of the field of TOC J0233.3+3021, a cluster of milliJansky radiosources from the TexOx Cluster survey. In an observation of this field with the Ryle Telescope (RT) at 15 GHz, we measure a decrement in the cosmic microwave background (CMB) of $-675 \pm 95 \mu$Jy on the RT's $\approx$ 0.65 k$\lambda$ baseline. Using optical and infrared imaging with the McDonald 2.7-m Smith Reflector, Calar Alto 3.5-m telescope and UKIRT, we identify the host galaxies of five of the radiosources and measure magnitudes of $R \approx 24$, $J \approx 20$, $K \approx 18$. The CMB decrement is consistent with the Sunyaev-Zel'dovich (SZ) effect of a massive cluster of galaxies, which if modelled as a spherical King profile of core radius $\theta_C = 20^{\prime\prime}$ has a central temperature decrement of $900 \mu$K. The magnitudes and colours of the galaxies are consistent with those of old ellipticals at $z \sim 1$. We therefore conclude that TOC J0233.3+3021 is a massive, high redshift cluster. These observations add to the growing evidence for a significant population of massive clusters at high redshift, and demonstrate the effectiveness of combining searches for AGN `signposts' to clusters with the redshift-independence of the SZ effect.Comment: Six pages; accepted for publication in MNRAS. Version with full-resolution UV plot available from http://www.mrao.cam.ac.uk/~garret/MB185.p

Magnetic unmixing of first-order reversal curve diagrams using principal component analysis

We describe a quantitative magnetic unmixing method based on principal component analysis (PCA) of first-order reversal curve (FORC) diagrams. For PCA we resample FORC distributions on grids that capture diagnostic signatures of single-domain (SD), pseudo-single-domain (PSD), and multi-domain (MD) magnetite, as well as of minerals such as hematite. Individual FORC diagrams are recast as linear combinations of end-member (EM) FORC diagrams, located at user-defined positions in PCA space. The EM selection is guided by constraints derived from physical modeling and imposed by data scatter. We investigate temporal variations of two EMs in bulk North Atlantic sediment cores collected from the Rockall Trough and the Iberian Continental Margin. Sediments from each site contain a mixture of magnetosomes and granulometrically distinct detrital magnetite. We also quantify the spatial variation of three EM components (a coarse silt-sized MD component, a fine silt-sized PSD component, and a mixed clay-sized component containing both SD magnetite and hematite) in surficial sediments along the flow path of the North Atlantic Deep Water (NADW). These samples were separated into granulometric fractions, which helped constrain EM definition. PCA-based unmixing reveals systematic variations in EM relative abundance as a function of distance along NADW flow. Finally, we apply PCA to the combined dataset of Rockall Trough and NADW sediments, which can be recast as a four-EM mixture, providing enhanced discrimination between components. Our method forms the foundation of a general solution to the problem of unmixing multi-component magnetic mixtures, a fundamental task of rock magnetic studies. This article is protected by copyright. All rights reserved

Atmospheric phase correction using CARMA-PACS: high angular resolution observations of the FU Orionis star PP 13S*

We present 0".15 resolution observations of the 227 GHz continuum emission from the circumstellar disk around the FU Orionis star PP 13S*. The data were obtained with the Combined Array for Research in Millimeter-wave Astronomy (CARMA) Paired Antenna Calibration System (C-PACS), which measures and corrects the atmospheric delay fluctuations on the longest baselines of the array in order to improve the sensitivity and angular resolution of the observations. A description of the C-PACS technique and the data reduction procedures are presented. C-PACS was applied to CARMA observations of PP 13S*, which led to a factor of 1.6 increase in the observed peak flux of the source, a 36% reduction in the noise of the image, and a 52% decrease in the measured size of the source major axis. The calibrated complex visibilities were fitted with a theoretical disk model to constrain the disk surface density. The total disk mass from the best-fit model corresponds to 0.06 M_⊙, which is larger than the median mass of a disk around a classical T Tauri star. The disk is optically thick at a wavelength of 1.3 mm for orbital radii less than 48 AU. At larger radii, the inferred surface density of the PP 13S* disk is an order of magnitude lower than that needed to develop a gravitational instability

Impact of Platelet-Rich Plasma on Arthroscopic Repair of Small- to Medium-Sized Rotator Cuff Tears: A Randomized Controlled Trial

© 2016, © The Author(s) 2016. Background: Increased interest in using platelet-rich plasma (PRP) as an augment to rotator cuff repair warrants further investigation, particularly in smaller rotator cuff tears. Purpose: To examine the effectiveness of PRP application in improving perioperative pain and function and promoting healing at 6 months after arthroscopic repair of small- or medium-sized rotator cuff tears. Study Design: Randomized controlled trial; Level of evidence, 1. Methods: This was a double-blinded randomized controlled trial of patients undergoing arthroscopic repair of partial- or full-thickness rotator cuff tears of up to 3 cm who were observed for 6 months. Patients were randomized to either repair and PRP application (study group) or repair only (control group) groups. The patient-oriented outcome measures utilized were the visual analog scale (VAS), the Short Western Ontario Rotator Cuff Index (ShortWORC), the American Shoulder and Elbow Surgeons (ASES) form, and the Constant-Murley Score (CMS). Range of motion (ROM) and inflammatory and coagulation markers were measured before and after surgery. Magnetic resonance imaging was used at 6 months to assess retear and fatty infiltration rate. Results: Eighty-two patients (41 males) with a mean age of 59 ± 8 years were enrolled; 41 patients were included in each group. Both the PRP and control groups showed a significant improvement in their pain level based on the VAS within the first 30 days (P .05), retear (14% vs 18% full retear; P =.44), or fatty infiltration rate (P =.08). Conclusion: The PRP biological augmentation for repair of small- to medium-sized rotator cuff tears has a short-term effect on perioperative pain without any significant impact on patient-oriented outcome measures or structural integrity of the repair compared with control group