2,390 research outputs found
Climate and nitrogen controls on the geography and timescales of terrestrial biogeochemical cycling
We used the terrestrial ecosystem model âCenturyâ to evaluate the relative roles of water and nitrogen limitation of net primary productivity, spatially and in response to climate variability. Within ecology, there has been considerable confusion and controversy over the large-scale significance of limitation of net primary production (NPP) by nutrients versus biophysical quantities (e.g., heat, water, and sunlight) with considerable evidence supporting both views. The Century model, run to a quasi-steady state condition, predicts âequilibrationâ of water with nutrient limitation, because carbon fixation and nitrogen fluxes (inputs and losses) are controlled by water fluxes, and the capture of nitrogen into organic matter is governed by carbon fixation. Patterns in the coupled water, nitrogen, and carbon cycles are modified substantially by ecosystem type or species-specific controls over resource use efficiency (water and nitrogen used per unit NPP), detrital chemistry, and soil water holding capacity. We also examined the coupling between water and nutrients during several temperature perturbation experiments. Model experiments forced by satellite-observed temperatures suggest that climate anomalies can result in significant changes to terrestrial carbon dynamics. The cooling associated with the Mount Pinatubo eruption aerosol injection may have transiently increased terrestrial carbon storage. However, because processes in the water, carbon, and nitrogen cycles have different response times, model behavior during the return to steady state following perturbation was complex and extended for decades after 1- to 5-year perturbations. Thus consequences of climate anomalies are influenced by the climatic conditions of the preceding years, and climate-carbon correlations may not be simple to interpret
Systemic ablation of Camkk2 impairs metastatic colonization and improves insulin sensitivity in TRAMP mice : Evidence for cancer cell-extrinsic CAMKK2 functions in prostate cancer
Despite early studies linking calcium-calmodulin protein kinase kinase 2 (CAMKK2) to prostate cancer cell migration and invasion, the role of CAMKK2 in metastasis in vivo remains unclear. Moreover, while CAMKK2 is known to regulate systemic metabolism, whether CAMKK2âs effects on whole-body metabolism would impact prostate cancer progression and/or related comorbidities is not known. Here, we demonstrate that germline ablation of Camkk2 slows, but does not stop, primary prostate tumorigenesis in the TRansgenic Adenocarcinoma Mouse Prostate (TRAMP) genetic mouse model. Consistent with prior epidemiological reports supporting a link between obesity and prostate cancer aggressiveness, TRAMP mice fed a high-fat diet exhibited a pronounced increase in the colonization of lung metastases. We demonstrated that this effect on the metastatic spread was dependent on CAMKK2. Notably, diet-induced lung metastases exhibited a highly aggressive neuroendocrine phenotype. Concurrently, Camkk2 deletion improved insulin sensitivity in the same mice. Histological analyses revealed that cancer cells were smaller in the TRAMP;Camkk2â/â mice compared to TRAMP;Camkk2+/+ controls. Given the differences in circulating insulin levels, a known regulator of cell growth, we hypothesized that systemic CAMKK2 could promote prostate cancer cell growth and disease progression in part through cancer cell-extrinsic mechanisms. Accordingly, host deletion of Camkk2 impaired the growth of syngeneic murine prostate tumors in vivo, confirming nonautonomous roles for CAMKK2 in prostate cancer. Cancer cell size and mTOR signaling was diminished in tumors propagated in Camkk2-null mice. Together, these data indicate that, in addition to cancer cell-intrinsic roles, CAMKK2 mediates prostate cancer progression via tumor-extrinsic mechanisms. Further, we propose that CAMKK2 inhibition may also help combat common metabolic comorbidities in men with advanced prostate cancer
The Pandora multi-algorithm approach to automated pattern recognition of cosmic-ray muon and neutrino events in the MicroBooNE detector
The development and operation of Liquid-Argon Time-Projection Chambers for
neutrino physics has created a need for new approaches to pattern recognition
in order to fully exploit the imaging capabilities offered by this technology.
Whereas the human brain can excel at identifying features in the recorded
events, it is a significant challenge to develop an automated, algorithmic
solution. The Pandora Software Development Kit provides functionality to aid
the design and implementation of pattern-recognition algorithms. It promotes
the use of a multi-algorithm approach to pattern recognition, in which
individual algorithms each address a specific task in a particular topology.
Many tens of algorithms then carefully build up a picture of the event and,
together, provide a robust automated pattern-recognition solution. This paper
describes details of the chain of over one hundred Pandora algorithms and tools
used to reconstruct cosmic-ray muon and neutrino events in the MicroBooNE
detector. Metrics that assess the current pattern-recognition performance are
presented for simulated MicroBooNE events, using a selection of final-state
event topologies.Comment: Preprint to be submitted to The European Physical Journal
Ionization Electron Signal Processing in Single Phase LArTPCs II. Data/Simulation Comparison and Performance in MicroBooNE
The single-phase liquid argon time projection chamber (LArTPC) provides a
large amount of detailed information in the form of fine-grained drifted
ionization charge from particle traces. To fully utilize this information, the
deposited charge must be accurately extracted from the raw digitized waveforms
via a robust signal processing chain. Enabled by the ultra-low noise levels
associated with cryogenic electronics in the MicroBooNE detector, the precise
extraction of ionization charge from the induction wire planes in a
single-phase LArTPC is qualitatively demonstrated on MicroBooNE data with event
display images, and quantitatively demonstrated via waveform-level and
track-level metrics. Improved performance of induction plane calorimetry is
demonstrated through the agreement of extracted ionization charge measurements
across different wire planes for various event topologies. In addition to the
comprehensive waveform-level comparison of data and simulation, a calibration
of the cryogenic electronics response is presented and solutions to various
MicroBooNE-specific TPC issues are discussed. This work presents an important
improvement in LArTPC signal processing, the foundation of reconstruction and
therefore physics analyses in MicroBooNE.Comment: 54 pages, 36 figures; the first part of this work can be found at
arXiv:1802.0870
Convolutional Neural Networks Applied to Neutrino Events in a Liquid Argon Time Projection Chamber
We present several studies of convolutional neural networks applied to data
coming from the MicroBooNE detector, a liquid argon time projection chamber
(LArTPC). The algorithms studied include the classification of single particle
images, the localization of single particle and neutrino interactions in an
image, and the detection of a simulated neutrino event overlaid with cosmic ray
backgrounds taken from real detector data. These studies demonstrate the
potential of convolutional neural networks for particle identification or event
detection on simulated neutrino interactions. We also address technical issues
that arise when applying this technique to data from a large LArTPC at or near
ground level
Noise Characterization and Filtering in the MicroBooNE Liquid Argon TPC
The low-noise operation of readout electronics in a liquid argon time
projection chamber (LArTPC) is critical to properly extract the distribution of
ionization charge deposited on the wire planes of the TPC, especially for the
induction planes. This paper describes the characteristics and mitigation of
the observed noise in the MicroBooNE detector. The MicroBooNE's single-phase
LArTPC comprises two induction planes and one collection sense wire plane with
a total of 8256 wires. Current induced on each TPC wire is amplified and shaped
by custom low-power, low-noise ASICs immersed in the liquid argon. The
digitization of the signal waveform occurs outside the cryostat. Using data
from the first year of MicroBooNE operations, several excess noise sources in
the TPC were identified and mitigated. The residual equivalent noise charge
(ENC) after noise filtering varies with wire length and is found to be below
400 electrons for the longest wires (4.7 m). The response is consistent with
the cold electronics design expectations and is found to be stable with time
and uniform over the functioning channels. This noise level is significantly
lower than previous experiments utilizing warm front-end electronics.Comment: 36 pages, 20 figure
How to make epidemiological training infectious
CITATION: Bellan, S. E. et al. 2012. How to make epidemiological training infectious. PLoS Biology, 10(4): e1001295, doi:10.1371/journal.pbio.1001295.The original publication is available at http://journals.plos.org/plosbiologyModern infectious disease epidemiology builds on two independently developed fields: classical epidemiology and dynamical epidemiology. Over the past decade, integration of the two fields has increased in research practice, but training options within the fields remain distinct with few opportunities for integration in the classroom. The annual Clinic on the Meaningful Modeling of Epidemiological Data (MMED) at the African Institute for Mathematical Sciences has begun to address this gap. MMED offers participants exposure to a broad range of concepts and techniques from both epidemiological traditions. During MMED 2010 we developed a pedagogical approach that bridges the traditional distinction between classical and dynamical epidemiology and can be used at multiple educational levels, from high school to graduate level courses. The approach is hands-on, consisting of a real-time simulation of a stochastic outbreak in course participants, including realistic data reporting, followed by a variety of mathematical and statistical analyses, stemming from both epidemiological traditions. During the exercise, dynamical epidemiologists developed empirical skills such as study design and learned concepts of bias while classical epidemiologists were trained in systems thinking and began to understand epidemics as dynamic nonlinear processes. We believe this type of integrated educational tool will prove extremely valuable in the training of future infectious disease epidemiologists. We also believe that such interdisciplinary training will be critical for local capacity building in analytical epidemiology as Africa continues to produce new cohorts of well-trained mathematicians, statisticians, and scientists. And because the lessons draw on skills and concepts from many fields in biologyâfrom pathogen biology, evolutionary dynamics of hostâpathogen interactions, and the ecology of infectious disease to bioinformatics, computational biology, and statisticsâthis exercise can be incorporated into a broad array of life sciences courses.http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001295Publisher's versio
Design and construction of the MicroBooNE Cosmic Ray Tagger system
The MicroBooNE detector utilizes a liquid argon time projection chamber
(LArTPC) with an 85 t active mass to study neutrino interactions along the
Booster Neutrino Beam (BNB) at Fermilab. With a deployment location near ground
level, the detector records many cosmic muon tracks in each beam-related
detector trigger that can be misidentified as signals of interest. To reduce
these cosmogenic backgrounds, we have designed and constructed a TPC-external
Cosmic Ray Tagger (CRT). This sub-system was developed by the Laboratory for
High Energy Physics (LHEP), Albert Einstein center for fundamental physics,
University of Bern. The system utilizes plastic scintillation modules to
provide precise time and position information for TPC-traversing particles.
Successful matching of TPC tracks and CRT data will allow us to reduce
cosmogenic background and better characterize the light collection system and
LArTPC data using cosmic muons. In this paper we describe the design and
installation of the MicroBooNE CRT system and provide an overview of a series
of tests done to verify the proper operation of the system and its components
during installation, commissioning, and physics data-taking
Measurement of cosmic-ray reconstruction efficiencies in the MicroBooNE LArTPC using a small external cosmic-ray counter
The MicroBooNE detector is a liquid argon time projection chamber at Fermilab
designed to study short-baseline neutrino oscillations and neutrino-argon
interaction cross-section. Due to its location near the surface, a good
understanding of cosmic muons as a source of backgrounds is of fundamental
importance for the experiment. We present a method of using an external 0.5 m
(L) x 0.5 m (W) muon counter stack, installed above the main detector, to
determine the cosmic-ray reconstruction efficiency in MicroBooNE. Data are
acquired with this external muon counter stack placed in three different
positions, corresponding to cosmic rays intersecting different parts of the
detector. The data reconstruction efficiency of tracks in the detector is found
to be , in good agreement with the Monte Carlo reconstruction
efficiency . This analysis represents
a small-scale demonstration of the method that can be used with future data
coming from a recently installed cosmic-ray tagger system, which will be able
to tag of the cosmic rays passing through the MicroBooNE
detector.Comment: 19 pages, 12 figure
Ionization Electron Signal Processing in Single Phase LArTPCs I. Algorithm Description and Quantitative Evaluation with MicroBooNE Simulation
We describe the concept and procedure of drifted-charge extraction developed
in the MicroBooNE experiment, a single-phase liquid argon time projection
chamber (LArTPC). This technique converts the raw digitized TPC waveform to the
number of ionization electrons passing through a wire plane at a given time. A
robust recovery of the number of ionization electrons from both induction and
collection anode wire planes will augment the 3D reconstruction, and is
particularly important for tomographic reconstruction algorithms. A number of
building blocks of the overall procedure are described. The performance of the
signal processing is quantitatively evaluated by comparing extracted charge
with the true charge through a detailed TPC detector simulation taking into
account position-dependent induced current inside a single wire region and
across multiple wires. Some areas for further improvement of the performance of
the charge extraction procedure are also discussed.Comment: 60 pages, 36 figures. The second part of this work can be found at
arXiv:1804.0258
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