scholarly journals Large scale similarity search across digital reconstructions of neural morphology

2021 ◽  
Author(s):  
Bengt Ljungquist ◽  
Masood A Akram ◽  
Giorgio A Ascoli
Keyword(s):  
Similarity Search ◽  
Large Scale ◽  
Principal Component ◽  
Software Tool ◽  
Cell Types ◽  
Brain Regions ◽  
Morphological Comparison ◽  
Data Set ◽  
Qualitative Performance ◽  
The Impact

Most functions of the nervous system depend on neuronal and glial morphology. Continuous advances in microscopic imaging and tracing software have provided an increasingly abundant availability of 3D reconstructions of arborizing dendrites, axons, and processes, allowing their detailed study. However, efficient, large-scale methods to rank neural morphologies by similarity to an archetype are still lacking. Using the NeuroMorpho.Org database, we present a similarity search software enabling fast morphological comparison of hundreds of thousands of neural reconstructions from any species, brain regions, cell types, and preparation protocols. We compared the performance of different morphological measurements: 1) summary morphometrics calculated by L-Measure, 2) persistence vectors, a vectorized descriptor of branching structure, 3) the combination of the two. In all cases, we also investigated the impact of applying dimensionality reduction using principal component analysis (PCA). We assessed qualitative performance by gauging the ability to rank neurons in order of visual similarity. Moreover, we quantified information content by examining explained variance and benchmarked the ability to identify occasional duplicate reconstructions of the same specimen. The results indicate that combining summary morphometrics and persistence vectors with applied PCA provides an information rich characterization that enables efficient and precise comparison of neural morphology. The execution time scaled linearly with data set size, allowing seamless live searching through the entire NeuroMorpho.Org content in fractions of a second. We have deployed the similarity search function as an open-source online software tool both through a user-friendly graphical interface and as an API for programmatic access.

Evaluation of the Aging Behavior of High Density Polyethylene in Thermal Oxidative Environment by Principal Component Analysis

2017 ◽  
Vol 727 ◽  
pp. 447-449 ◽  
Author(s):  
Jun Dai ◽  
Hua Yan ◽  
Jian Jian Yang ◽  
Jun Jun Guo
Keyword(s):  
Principal Component Analysis ◽  
Impact Strength ◽  
High Density Polyethylene ◽  
Tensile Modulus ◽  
Principal Component ◽  
Component Analysis ◽  
High Density ◽  
Aging Behavior ◽  
Data Set ◽  
The Impact

To evaluate the aging behavior of high density polyethylene (HDPE) under an artificial accelerated environment, principal component analysis (PCA) was used to establish a non-dimensional expression Z from a data set of multiple degradation parameters of HDPE. In this study, HDPE samples were exposed to the accelerated thermal oxidative environment for different time intervals up to 64 days. The results showed that the combined evaluating parameter Z was characterized by three-stage changes. The combined evaluating parameter Z increased quickly in the first 16 days of exposure and then leveled off. After 40 days, it began to increase again. Among the 10 degradation parameters, branching degree, carbonyl index and hydroxyl index are strongly associated. The tensile modulus is highly correlated with the impact strength. The tensile strength, tensile modulus and impact strength are negatively correlated with the crystallinity.

scholarly journals Farmers’ Perceptions of Commercial Insect-Based Feed for Sustainable Livestock Production in Kenya

2021 ◽  
Vol 13 (10) ◽  
pp. 5359
Author(s):  
Afrika Onguko Okello ◽  
Jonathan Makau Nzuma ◽  
David Jakinda Otieno ◽  
Michael Kidoido ◽  
Chrysantus Mbi Tanga
Keyword(s):  
Food Systems ◽  
Large Scale ◽  
Principal Component ◽  
Farm Income ◽  
Purchase Decisions ◽  
Wealth Status ◽  
Feed Formulation ◽  
Alternative Protein ◽  
Livestock Products ◽  
The Impact

The utilization of insect-based feeds (IBF) as an alternative protein source is increasingly gaining momentum worldwide owing to recent concerns over the impact of food systems on the environment. However, its large-scale adoption will depend on farmers’ acceptance of its key qualities. This study evaluates farmer’s perceptions of commercial IBF products and assesses the factors that would influence its adoption. It employs principal component analysis (PCA) to develop perception indices that are subsequently used in multiple regression analysis of survey data collected from a sample of 310 farmers. Over 90% of the farmers were ready and willing to use IBF. The PCA identified feed performance, social acceptability of the use of insects in feed formulation, feed versatility and marketability of livestock products reared on IBF as the key attributes that would inform farmers’ purchase decisions. Awareness of IBF attributes, group membership, off-farm income, wealth status and education significantly influenced farmers’ perceptions of IBF. Interventions such as experimental demonstrations that increase farmers’ technical knowledge on the productivity of livestock fed on IBF are crucial to reducing farmers’ uncertainties towards acceptability of IBF. Public partnerships with resource-endowed farmers and farmer groups are recommended to improve knowledge sharing on IBF.

Production, crystallization and preliminary X-ray analysis of the human integrin \alpha_1 I domain

1999 ◽  
Vol 55 (7) ◽  
pp. 1365-1367 ◽  
Author(s):  
Tiina A. Salminen ◽  
Yvonne Nymalm ◽  
Jussi Kankare ◽  
Jarmo Käpylä ◽  
Jyrki Heino ◽  
...  
Keyword(s):  
Large Scale ◽  
Cell Types ◽  
Diffusion Method ◽  
Scale Production ◽  
Data Set ◽  
Cell Parameters ◽  
Collagen Receptors ◽  
Large Scale Production ◽  
Peg 4000 ◽  
Reservoir Solution

Integrin α1β1 is one of the main collagen receptors in many cell types. A fast large-scale production, purification and crystallization method for the integrin α1 I domain is reported here. The α1 I domain was crystallized using the vapour-diffusion method with a reservoir solution containing a mixture of PEG 4000, sodium acetate, glycerol and Tris–HCl buffer. The crystals beong to the C2 space group, with unit-cell parameters a = 74.5, b = 81.9, c = 37.3 Å, α = γ = 90.0, β = 90.8°. The crystals diffract to 2.0 Å and a 94.2% complete data set to 2.2 Å has been collected from a single crystal with an R merge of 5.8%.

scholarly journals The Midlatitude Continental Convective Clouds Experiment (MC3E) sounding network: operations, processing and analysis

2015 ◽  
Vol 8 (1) ◽  
pp. 421-434 ◽  
Author(s):  
M. P. Jensen ◽  
T. Toto ◽  
D. Troyan ◽  
P. E. Ciesielski ◽  
D. Holdridge ◽  
...  
Keyword(s):  
Large Scale ◽  
Scale Model ◽  
Data Sets ◽  
Central Plains ◽  
Data Set ◽  
Convective Systems ◽  
Convective Clouds ◽  
Quality Checks ◽  
Network Operations ◽  
The Impact

Abstract. The Midlatitude Continental Convective Clouds Experiment (MC3E) took place during the spring of 2011 centered in north-central Oklahoma, USA. The main goal of this field campaign was to capture the dynamical and microphysical characteristics of precipitating convective systems in the US Central Plains. A major component of the campaign was a six-site radiosonde array designed to capture the large-scale variability of the atmospheric state with the intent of deriving model forcing data sets. Over the course of the 46-day MC3E campaign, a total of 1362 radiosondes were launched from the enhanced sonde network. This manuscript provides details on the instrumentation used as part of the sounding array, the data processing activities including quality checks and humidity bias corrections and an analysis of the impacts of bias correction and algorithm assumptions on the determination of convective levels and indices. It is found that corrections for known radiosonde humidity biases and assumptions regarding the characteristics of the surface convective parcel result in significant differences in the derived values of convective levels and indices in many soundings. In addition, the impact of including the humidity corrections and quality controls on the thermodynamic profiles that are used in the derivation of a large-scale model forcing data set are investigated. The results show a significant impact on the derived large-scale vertical velocity field illustrating the importance of addressing these humidity biases.

scholarly journals Continuous high-resolution midlatitude-belt simulations for July–August 2013 with WRF

2017 ◽  
Vol 10 (5) ◽  
pp. 2031-2055 ◽  
Author(s):  
Thomas Schwitalla ◽  
Hans-Stefan Bauer ◽  
Volker Wulfmeyer ◽  
Kirsten Warrach-Sagi
Keyword(s):  
High Resolution ◽  
Land Surface ◽  
Large Scale ◽  
Temperature Fields ◽  
Surface Model ◽  
Limited Area ◽  
Data Set ◽  
Latitude Belt ◽  
Simulated Precipitation ◽  
The Impact

Abstract. Increasing computational resources and the demands of impact modelers, stake holders, and society envision seasonal and climate simulations with the convection-permitting resolution. So far such a resolution is only achieved with a limited-area model whose results are impacted by zonal and meridional boundaries. Here, we present the setup of a latitude-belt domain that reduces disturbances originating from the western and eastern boundaries and therefore allows for studying the impact of model resolution and physical parameterization. The Weather Research and Forecasting (WRF) model coupled to the NOAH land–surface model was operated during July and August 2013 at two different horizontal resolutions, namely 0.03 (HIRES) and 0.12° (LOWRES). Both simulations were forced by the European Centre for Medium-Range Weather Forecasts (ECMWF) operational analysis data at the northern and southern domain boundaries, and the high-resolution Operational Sea Surface Temperature and Sea Ice Analysis (OSTIA) data at the sea surface.The simulations are compared to the operational ECMWF analysis for the representation of large-scale features. To analyze the simulated precipitation, the operational ECMWF forecast, the CPC MORPHing (CMORPH), and the ENSEMBLES gridded observation precipitation data set (E-OBS) were used as references.Analyzing pressure, geopotential height, wind, and temperature fields as well as precipitation revealed (1) a benefit from the higher resolution concerning the reduction of monthly biases, root mean square error, and an improved Pearson skill score, and (2) deficiencies in the physical parameterizations leading to notable biases in distinct regions like the polar Atlantic for the LOWRES simulation, the North Pacific, and Inner Mongolia for both resolutions.In summary, the application of a latitude belt on a convection-permitting resolution shows promising results that are beneficial for future seasonal forecasting.

Toward functional proteomics of alveolar macrophages

2005 ◽  
Vol 288 (4) ◽  
pp. L585-L595 ◽  
Author(s):  
Haifeng M. Wu ◽  
Ming Jin ◽  
Clay B. Marsh
Keyword(s):  
Alveolar Macrophages ◽  
Large Scale ◽  
Cell Types ◽  
Mononuclear Phagocyte ◽  
Detection Sensitivity ◽  
Current Status ◽  
Blood Monocytes ◽  
Protein Patterns ◽  
Additional Information ◽  
The Impact

Alveolar macrophages (AM) belong to a phenotype of macrophages with distinct biological functions and important pathophysiological roles in lung health and disease. The molecular details determining AM differentiation from blood monocytes and AM roles in lung homeostasis are largely unknown. With the use of different technological platforms, advances in the field of proteomics have made it possible to search for differences in protein expression between AM and their precursor monocytes. Proteome features of each cell type provide new clues into understanding mononuclear phagocyte biology. In-depth analyses using subproteomics and subcellular proteomics offer additional information by providing greater protein resolution and detection sensitivity. With the use of proteomic techniques, large-scale mapping of phosphorylation differences between the cell types have become possible. Furthermore, two-dimensional gel proteomics can detect germline protein variants and evaluate the impact of protein polymorphisms on an individual's susceptibility to disease. Finally, surface-enhanced laser desorption and ionization (SELDI) time-of-flight mass spectrometry offers an alternative method to recognizing differences in protein patterns between AM and monocytes or between AM under different pathological conditions. This review details the current status of this field and outlines future directions in functional proteomic analyses of AM and monocytes. Furthermore, this review presents viewpoints of integrating proteomics with translational topics in lung diseases to define the mechanisms of disease and to uncover new diagnostic and therapeutic targets.

scholarly journals Six years of total ozone column measurements from SCIAMACHY nadir observations

2009 ◽  
Vol 2 (1) ◽  
pp. 87-98 ◽  
Author(s):  
C. Lerot ◽  
M. Van Roozendael ◽  
J. van Geffen ◽  
J. van Gent ◽  
C. Fayt ◽  
...  
Keyword(s):  
Cross Sections ◽  
Total Ozone ◽  
Large Scale ◽  
European Space Agency ◽  
Data Sets ◽  
Data Set ◽  
Ozone Data ◽  
Space Agency ◽  
German Aerospace ◽  
The Impact

Abstract. Total O3 columns have been retrieved from six years of SCIAMACHY nadir UV radiance measurements using SDOAS, an adaptation of the GDOAS algorithm previously developed at BIRA-IASB for the GOME instrument. GDOAS and SDOAS have been implemented by the German Aerospace Center (DLR) in the version 4 of the GOME Data Processor (GDP) and in version 3 of the SCIAMACHY Ground Processor (SGP), respectively. The processors are being run at the DLR processing centre on behalf of the European Space Agency (ESA). We first focus on the description of the SDOAS algorithm with particular attention to the impact of uncertainties on the reference O3 absorption cross-sections. Second, the resulting SCIAMACHY total ozone data set is globally evaluated through large-scale comparisons with results from GOME and OMI as well as with ground-based correlative measurements. The various total ozone data sets are found to agree within 2% on average. However, a negative trend of 0.2–0.4%/year has been identified in the SCIAMACHY O3 columns; this probably originates from instrumental degradation effects that have not yet been fully characterized.

scholarly journals Tropical troposphere to stratosphere transport of carbon monoxide and long-lived trace species in the Chemical Lagrangian Model of the Stratosphere (CLaMS)

2014 ◽  
Vol 7 (4) ◽  
pp. 5087-5139 ◽  
Author(s):  
R. Pommrich ◽  
R. Müller ◽  
J.-U. Grooß ◽  
P. Konopka ◽  
F. Ploeger ◽  
...  
Keyword(s):  
Carbon Monoxide ◽  
Large Scale ◽  
Lower Stratosphere ◽  
Lagrangian Model ◽  
Quasi Biennial Oscillation ◽  
Data Set ◽  
Model Version ◽  
The Tropics ◽  
The Impact ◽  
Good Agreement

Abstract. Variations in the mixing ratio of trace gases of tropospheric origin entering the stratosphere in the tropics are of interest for assessing both troposphere to stratosphere transport fluxes in the tropics and the impact of these transport fluxes on the composition of the tropical lower stratosphere. Anomaly patterns of carbon monoxide (CO) and long-lived tracers in the lower tropical stratosphere allow conclusions about the rate and the variability of tropical upwelling to be drawn. Here, we present a simplified chemistry scheme for the Chemical Lagrangian Model of the Stratosphere (CLaMS) for the simulation, at comparatively low numerical cost, of CO, ozone, and long-lived trace substances (CH4, N2O, CCl3F (CFC-11), CCl2F2 (CFC-12), and CO2) in the lower tropical stratosphere. For the long-lived trace substances, the boundary conditions at the surface are prescribed based on ground-based measurements in the lowest model level. The boundary condition for CO in the free troposphere is deduced from MOPITT measurements (at ≈ 700–200 hPa). Due to the lack of a specific representation of mixing and convective uplift in the troposphere in this model version, enhanced CO values, in particular those resulting from convective outflow are underestimated. However, in the tropical tropopause layer and the lower tropical stratosphere, there is relatively good agreement of simulated CO with in-situ measurements (with the exception of the TROCCINOX campaign, where CO in the simulation is biased low ≈ 10–20 ppbv). Further, the model results are of sufficient quality to describe large scale anomaly patterns of CO in the lower stratosphere. In particular, the zonally averaged tropical CO anomaly patterns (the so called "tape recorder" patterns) simulated by this model version of CLaMS are in good agreement with observations. The simulations show a too rapid upwelling compared to observations as a consequence of the overestimated vertical velocities in the ERA-interim reanalysis data set. Moreover, the simulated tropical anomaly patterns of N2O are in good agreement with observations. In the simulations, anomaly patterns for CH4 and CFC-11 were found to be consistent with those of N2O; for all long-lived tracers, positive anomalies are simulated because of the enhanced tropical upwelling in the easterly phase of the quasi-biennial oscillation.

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