scholarly journals Lidar reveals activity anomaly of malaria vectors during pan-African eclipse

2020 ◽  
Vol 6 (20) ◽  
pp. eaay5487 ◽  
Author(s):  
Mikkel Brydegaard ◽  
Samuel Jansson ◽  
Elin Malmqvist ◽  
Yeromin P. Mlacha ◽  
Alem Gebru ◽  
...  
Keyword(s):  
High Resolution ◽  
Activity Patterns ◽  
Malaria Vectors ◽  
Fine Scale ◽  
Vector Ecology ◽  
Pan African ◽  
Insect Activity ◽  
Annular Solar Eclipse

Yearly, a quarter billion people are infected and a half a million killed by the mosquito-borne disease malaria. Lack of real-time observational tools for continuously assessing the unperturbed mosquito flight activity in situ limits progress toward improved vector control. We deployed a high-resolution entomological lidar to monitor a half-kilometer static transect adjacent to a Tanzanian village. We evaluated one-third million insect observations during five nights, four days, and one annular solar eclipse. We demonstrate in situ lidar classification of several insect families and their sexes based on their modulation signatures. We were able to compare the fine-scale spatiotemporal activity patterns of malaria vectors during ordinary days and an eclipse to disentangle phototactic activity patterns from the circadian mechanism. We observed an increased insect activity during the eclipse attributable to mosquitoes. These unprecedented findings demonstrate how lidar-based monitoring of distinct mosquito activities could advance our understanding of vector ecology.

scholarly journals Augmenting biologging with supervised machine learning to studyin situbehavior of the medusaChrysaora fuscescens

2019 ◽  
Author(s):  
Clara Fannjiang ◽  
T. Aran Mooney ◽  
Seth Cones ◽  
David Mann ◽  
K. Alex Shorter ◽  
...  
Keyword(s):  
Machine Learning ◽  
High Resolution ◽  
Laboratory Data ◽  
Supervised Machine Learning ◽  
Motion Sensors ◽  
Fine Scale ◽  
Video Footage ◽  
Research Findings ◽  
Summary Statement

AbstractZooplankton occupy critical roles in marine ecosystems, yet their fine-scale behavior remains poorly understood due to the difficulty of studying individualsin situ. Here we combine biologging with supervised machine learning (ML) to demonstrate a pipeline for studyingin situbehavior of larger zooplankton such as jellyfish. We deployed the ITAG, a biologging package with high-resolution motion sensors designed for soft-bodied invertebrates, on 8Chrysaora fuscescensin Monterey Bay, using the tether method for retrieval. Using simultaneous video footage of the tagged jellyfish, we develop ML methods to 1) identify periods of tag data corrupted by the tether method, which may have compromised prior research findings, and 2) classify jellyfish behaviors. Our tools yield characterizations of fine-scale jellyfish activity and orientation over long durations, and provide evidence that developing behavioral classifiers onin siturather than laboratory data is essential.Summary StatementHigh-resolution motion sensors paired with supervised machine learning can be used to infer fine-scalein situbehavior of zooplankton for long durations.

scholarly journals Coupling physics and biogeochemistry thanks to high resolution observations of the phytoplankton community structure in the North-Western Mediterranean Sea

2017 ◽  
Author(s):  
Pierre Marrec ◽  
Andrea M. Doglioli ◽  
Gérald Grégori ◽  
Mathilde Dugenne ◽  
Alice Della Penna ◽  
...  
Keyword(s):  
High Resolution ◽  
Surface Waters ◽  
Phytoplankton Community ◽  
Western Mediterranean ◽  
Fine Scale ◽  
Phytoplankton Community Structure ◽  
The North ◽  
Cold Core ◽  
North Western

Abstract. Fine-scale physical structures and ocean dynamics strongly influence and regulate biogeochemical and ecological processes. These processes are particularly challenging to describe and understand because of their ephemeral nature. The OSCAHR (Observing Submesoscale Coupling At High Resolution) campaign has been conducted in fall 2015 in which, a fine-scale structure in the North Western Mediterranean Ligurian subbasin was pre-identified using both satellite and numerical modeling data. Along the ship track, various variables were measured at the surface (temperature, salinity, chlorophyll-a and nutrients concentrations) with ADCP current velocity. We also deployed a new model of CytoSense automated flow cytometer (AFCM) optimized for small and dim cells, for near real-time characterization of surface phytoplankton community structure of surface waters with a spatial resolution of few km and a hourly temporal resolution. For the first time with this type of AFCM we were able to resolve Prochlorococcus and Synechococcus picocyanobacteria. The vertical physical dynamics and biogeochemical properties of the studied area were investigated by continuous high resolution CTD profiles thanks to a moving vessel profiler (MVP) during the vessel underway associated to a 1-m vertical resolution pumping system deployed during fixed stations. The observed fine-scale feature presented a cyclonic structure with a relatively cold core surrounded by warmer waters. Surface waters were totally depleted in nitrate and phosphate. In addition to the doming of the isopycnals by the cyclonic circulation, an intense wind event induced Ekman pumping. The upwelled subsurface cold nutrient-rich water fertilized surface waters, characterized by an increase in Chl-a concentration. Prochlorococcus, pico- and nano-eukaryotes were more abundant in cold core waters while Synechococcus dominated in warm boundary waters. Nanoeukaryote were the main contributors (> 50 %) in terms of pigment content (FLR) and biomass. Biological observations based on the mean cell's red fluorescence recorded by AFCM combined with physical properties of surface waters suggest a distinct origin for two warm boundary waters. Finally, the application of a matrix growth population model based on high-frequency AFCM measurements in warm boundary surface waters provides estimates of in-situ growth rate and apparent net primary production for Prochlorococcus (μ = 0.21 d−1, NPP = 0.11 mgC m−3 d−1) and Synechococcus (μ = 0.72 d−1, NPP = 2.68 mgC m−3 d−1), which corroborate their opposite surface distribution pattern. The innovative adaptive strategy applied during OSCAHR with a combination of several multidisciplinary and complementary approaches involving high-resolution in-situ observations and sampling, remote-sensing and model simulations provided a deeper understanding of the marine biogeochemical dynamics through the first trophic levels.

scholarly journals Portraying Gradients of Structural Complexity in Coral Reefs Using Fine-Scale Depth Profiles

2021 ◽  
Vol 8 ◽  
Author(s):  
Lauriane Ribas-Deulofeu ◽  
Pierre-Alexandre Château ◽  
Vianney Denis ◽  
Chaolun Allen Chen
Keyword(s):  
High Resolution ◽  
Surface Profile ◽  
Structural Complexity ◽  
Mean Square ◽  
Fine Scale ◽  
Coarse Scale ◽  
Predator Prey ◽  
Depth Profiles ◽  
Multiple Levels

Structural complexity is an important feature to understand reef resilience abilities, through its role in mediating predator-prey interactions, regulating competition, and promoting recruitment. Most of the current methods used to measure reef structural complexity fail to quantify the contributions of fine and coarse scales of rugosity simultaneously, while other methods require heavy data computation. In this study, we propose estimating reef structural complexity based on high-resolution depth profiles to quantify the contributions of both fine and coarse rugosities. We adapted the root mean square of the deviation from the assessed surface profile (Rq) with polynomials. The efficiency of the proposed method was tested on nine theoretical cases and 50 in situ transects from South Taiwan, and compared to both the chain method and the visual rugosity index commonly employed to characterize reef structural complexity. The Rq indices proposed as rugosity estimators in this study consider multiple levels of reef rugosity, which the chain method and the visual rugosity index fail to apprehend. Furthermore, relationships were found between Rq scores and specific functional groups in the benthic community. Indeed, the fine scale rugosity of the South Taiwan reefs mainly comes from biotic components such as hard corals, while their coarse scale rugosity is essentially provided by the topographic variations that reflect the geological context of the reefs. This approach allows identifying the component of the rugosity that could be managed and which could, ultimately, improve strategies designed for conservation.

scholarly journals A critical assessment of data quality and venous effects in ultra-high-resolution fMRI

2018 ◽  
Author(s):  
Kendrick Kay ◽  
Keith W. Jamison ◽  
Luca Vizioli ◽  
Ruyuan Zhang ◽  
Eshed Margalit ◽  
...  
Keyword(s):  
High Resolution ◽  
Signal To Noise Ratio ◽  
Activity Patterns ◽  
Sampling Rate ◽  
Pulse Sequences ◽  
Blood Oxygenation ◽  
Fine Scale ◽  
Cortical Folding ◽  
Neuroscience Research ◽  
Spatial Coverage

AbstractAdvances in hardware, pulse sequences, and reconstruction techniques have made it possible to perform functional magnetic resonance imaging (fMRI) at sub-millimeter resolution while maintaining high spatial coverage and acceptable signal-to-noise ratio. Here, we examine whether ultra-high-resolution fMRI can be exploited for routine use in neuroscience research. We conducted fMRI in human visual cortex during a simple event-related visual experiment (7T, gradient-echo EPI, 0.8-mm isotropic voxels, 2.2-s sampling rate, 84 slices), and developed analysis and visualization tools to assess the quality of the data. We make three main observations. First, we find that the acquired fMRI images, combined with appropriate surface-based processing, provide reliable and accurate measurements of fine-scale blood oxygenation level dependent (BOLD) activity patterns. Second, we show that the highly folded structure of cortex causes substantial biases on spatial resolution and data visualization. Third, we examine the well-recognized issue of venous contributions to fMRI signals. In a systematic assessment of large sections of cortex measured at a fine scale, we show that time-averaged T2*-weighted EPI intensity is a simple, robust marker of venous effects. These venous effects are unevenly distributed across cortex, are more pronounced in gyri and outer cortical depths, and are, to a certain degree, in consistent locations across subjects relative to cortical folding. Furthermore, we show that these venous effects are strongly correlated with BOLD responses evoked by the experiment. We conclude that ultra-high-resolution fMRI can provide robust information about fine-scale BOLD activity patterns, but special care must be exercised in visualizing and interpreting these patterns, especially with regards to the confounding influence of the brain’s vasculature. To help translate these methodological findings to neuroscience research, we provide practical suggestions for both high-resolution and standard-resolution fMRI studies.

scholarly journals Real-time dispersal of malaria vectors in rural Africa monitored with lidar

PLoS ONE ◽  
2021 ◽  
Vol 16 (3) ◽  
pp. e0247803
Author(s):  
Samuel Jansson ◽  
Elin Malmqvist ◽  
Yeromin Mlacha ◽  
Rickard Ignell ◽  
Fredros Okumu ◽  
...  
Keyword(s):  
Real Time ◽  
Malaria Vector ◽  
Malaria Vectors ◽  
Malaria Vector Control ◽  
Vector Ecology ◽  
Spatio Temporal ◽  
Time Observation ◽  
And Control ◽  
The Village

Lack of tools for detailed, real-time observation of mosquito behavior with high spatio-temporal resolution limits progress towards improved malaria vector control. We deployed a high-resolution entomological lidar to monitor a half-kilometer static transect positioned over rice fields outside a Tanzanian village. A quarter of a million in situ insect observations were classified, and several insect taxa were identified based on their modulation signatures. We observed distinct range distributions of male and female mosquitoes in relation to the village periphery, and spatio-temporal behavioral features, such as swarming. Furthermore, we observed that the spatial distributions of males and females change independently of each other during the day, and were able to estimate the daily dispersal of mosquitoes towards and away from the village. The findings of this study demonstrate how lidar-based monitoring could dramatically improve our understanding of malaria vector ecology and control options.

scholarly journals HIPPIE2: a method for fine-scale identification of physically interacting chromatin regions

2020 ◽  
Vol 2 (2) ◽  
Author(s):  
Pavel P Kuksa ◽  
Alexandre Amlie-Wolf ◽  
Yih-Chii Hwang ◽  
Otto Valladares ◽  
Brian D Gregory ◽  
...  
Keyword(s):  
High Resolution ◽  
Dna Looping ◽  
Open Chromatin ◽  
The Novel ◽  
Fine Scale ◽  
Chromosome Conformation ◽  
Chromatin Interactions ◽  
Restriction Sites

Abstract Most regulatory chromatin interactions are mediated by various transcription factors (TFs) and involve physically interacting elements such as enhancers, insulators or promoters. To map these elements and interactions at a fine scale, we developed HIPPIE2 that analyzes raw reads from high-throughput chromosome conformation (Hi-C) experiments to identify precise loci of DNA physically interacting regions (PIRs). Unlike standard genome binning approaches (e.g. 10-kb to 1-Mb bins), HIPPIE2 dynamically infers the physical locations of PIRs using the distribution of restriction sites to increase analysis precision and resolution. We applied HIPPIE2 to in situ Hi-C datasets across six human cell lines (GM12878, IMR90, K562, HMEC, HUVEC, NHEK) with matched ENCODE/Roadmap functional genomic data. HIPPIE2 detected 1042 738 distinct PIRs, with high resolution (average PIR length of 1006 bp) and high reproducibility (92.3% in GM12878). PIRs are enriched for epigenetic marks (H3K27ac, H3K4me1) and open chromatin, suggesting active regulatory roles. HIPPIE2 identified 2.8 million significant PIR–PIR interactions, 27.2% of which were enriched for TF binding sites. 50 608 interactions were enhancer–promoter interactions and were enriched for 33 TFs, including known DNA looping/long-range mediators. These findings demonstrate that the novel dynamic approach of HIPPIE2 (https://bitbucket.com/wanglab-upenn/HIPPIE2) enables the characterization of chromatin and regulatory interactions with high resolution and reproducibility.

scholarly journals CAPACITY BUILDING FOR HIGH-RESOLUTION LAND COVER INTERCOMPARISON AND VALIDATION: WHAT IS AVAILABLE AND WHAT IS NEEDED

2018 ◽  
Vol XLII-4/W8 ◽  
pp. 15-22
Author(s):  
M. A. Brovelli ◽  
M. Minghini ◽  
M. E. Molinari ◽  
H. Wu ◽  
X. Zheng ◽  
...  
Keyword(s):  
High Resolution ◽  
Land Cover ◽  
Capacity Building ◽  
Ad Hoc ◽  
Educational Material ◽  
Reference Dataset ◽  
Training Material ◽  
In Situ Observations

<p><strong>Abstract.</strong> Land Cover (LC) maps are fundamental products for a wide variety of applications. The workflow for their production is composed of classification of satellite imagery and validation against a reference dataset. Different LC maps as well as multiple versions in time of the same LC map can be also compared with one another to assess LC changes. Since the current richness of both space and in-situ observations makes it quite easy to produce LC maps, it is fundamental to assess their accuracy before using them for real applications. This paper focuses on education and capacity building on the intercomparison and validation of global (i.e. covering the whole world) and high-resolution (i.e. with a spatial resolution of at least 30<span class="thinspace"></span>m) LC maps. The availability of Free and Open Source for Geospatial (FOSS4G) technology capable to process LC maps, as well as the existence of ad hoc educational material, is carefully assessed. In parallel, an ad hoc survey has showed that users, especially in developing countries, often lack awareness about the need to validate them and are not aware about the existence of training material. With this premise, a new project presented in the paper aims to produce new, openly licensed and FOSS4G-based training material on the intercomparison and validation of global high-resolution LC maps.</p>

scholarly journals Coupling physics and biogeochemistry thanks to high-resolution observations of the phytoplankton community structure in the northwestern Mediterranean Sea

2018 ◽  
Vol 15 (5) ◽  
pp. 1579-1606 ◽  
Author(s):  
Pierre Marrec ◽  
Gérald Grégori ◽  
Andrea M. Doglioli ◽  
Mathilde Dugenne ◽  
Alice Della Penna ◽  
...  
Keyword(s):  
Community Structure ◽  
High Resolution ◽  
Surface Waters ◽  
Phytoplankton Community ◽  
Fine Scale ◽  
Phytoplankton Community Structure ◽  
Red Fluorescence ◽  
Cold Core ◽  
Northwestern Mediterranean

Abstract. Fine-scale physical structures and ocean dynamics strongly influence and regulate biogeochemical and ecological processes. These processes are particularly challenging to describe and understand because of their ephemeral nature. The OSCAHR (Observing Submesoscale Coupling At High Resolution) campaign was conducted in fall 2015 in which a fine-scale structure (1–10 km∕1–10 days) in the northwestern Mediterranean Ligurian subbasin was pre-identified using both satellite and numerical modeling data. Along the ship track, various variables were measured at the surface (temperature, salinity, chlorophyll a and nutrient concentrations) with ADCP current velocity. We also deployed a new model of the CytoSense automated flow cytometer (AFCM) optimized for small and dim cells, for near real-time characterization of the surface phytoplankton community structure of surface waters with a spatial resolution of a few kilometers and an hourly temporal resolution. For the first time with this optimized version of the AFCM, we were able to fully resolve Prochlorococcus picocyanobacteria in addition to the easily distinguishable Synechococcus. The vertical physical dynamics and biogeochemical properties of the studied area were investigated by continuous high-resolution CTD profiles thanks to a moving vessel profiler (MVP) during the vessel underway associated with a high-resolution pumping system deployed during fixed stations allowing sampling of the water column at a fine resolution (below 1 m). The observed fine-scale feature presented a cyclonic structure with a relatively cold core surrounded by warmer waters. Surface waters were totally depleted in nitrate and phosphate. In addition to the doming of the isopycnals by the cyclonic circulation, an intense wind event induced Ekman pumping. The upwelled subsurface cold nutrient-rich water fertilized surface waters and was marked by an increase in Chl a concentration. Prochlorococcus and pico- and nano-eukaryotes were more abundant in cold core waters, while Synechococcus dominated in warm boundary waters. Nanoeukaryotes were the main contributors (>50 %) in terms of pigment content (red fluorescence) and biomass. Biological observations based on the mean cell's red fluorescence recorded by AFCM combined with physical properties of surface waters suggest a distinct origin for two warm boundary waters. Finally, the application of a matrix growth population model based on high-frequency AFCM measurements in warm boundary surface waters provides estimates of in situ growth rate and apparent net primary production for Prochlorococcus (μ=0.21 d−1, NPP =0.11 mgCm-3d-1) and Synechococcus (μ=0.72 d−1, NPP =2.68 mgCm-3d-1), which corroborate their opposite surface distribution pattern. The innovative adaptive strategy applied during OSCAHR with a combination of several multidisciplinary and complementary approaches involving high-resolution in situ observations and sampling, remote-sensing and model simulations provided a deeper understanding of the marine biogeochemical dynamics through the first trophic levels.

High Resolution Stereography of Complementary Freeze-Fracture Replicas Reveals the Presence of Depressions Opposite Membrane Associated Particles of Split Membranes

1971 ◽  
Vol 29 ◽  
pp. 442-443
Author(s):  
Russell L. Steere
Keyword(s):  
High Resolution ◽  
Cardiac Muscle ◽  
Electron Micrographs ◽  
Chromic Acid ◽  
Freeze Fracture ◽  
Distilled Water ◽  
Fine Scale ◽  
Acid Cleaning ◽  
Cleaning Solution

Complementary replicas have revealed the fact that the two common faces observed in electron micrographs of freeze-fracture and freeze-etch specimens are complementary to each other and are thus the new faces of a split membrane rather than the original inner and outer surfaces (1, 2 and personal observations). The big question raised by published electron micrographs is why do we not see depressions in the complementary face opposite membrane-associated particles? Reports have appeared indicating that some depressions do appear but complementarity on such a fine scale has yet to be shown.Dog cardiac muscle was perfused with glutaraldehyde, washed in distilled water, then transferred to 30% glycerol (material furnished by Dr. Joaquim Sommer, Duke Univ., and VA Hospital, Durham, N.C.). Small strips were freeze-fractured in a Denton Vacuum DFE-2 Freeze-Etch Unit with complementary replica tooling. Replicas were cleaned in chromic acid cleaning solution, then washed in 4 changes of distilled water and mounted on opposite sides of the center wire of a Formvar-coated grid.

mRNA localization by Electron microscopic in situ hybridization

1991 ◽  
Vol 49 ◽  
pp. 430-431
Author(s):  
J. A. Pollock ◽  
M. Martone ◽  
T. Deerinck ◽  
M. H. Ellisman
Keyword(s):  
Electron Microscopy ◽  
High Resolution ◽  
Nucleic Acids ◽  
Recombinant Dna ◽  
Light And Electron Microscopy ◽  
Electron Microscopic ◽  
High Voltage Electron Microscopy ◽  
Functional Sites ◽  
Voltage Electron

Localization of specific proteins in cells by both light and electron microscopy has been facilitate by the availability of antibodies that recognize unique features of these proteins. High resolution localization studies conducted over the last 25 years have allowed biologists to study the synthesis, translocation and ultimate functional sites for many important classes of proteins. Recently, recombinant DNA techniques in molecular biology have allowed the production of specific probes for localization of nucleic acids by “in situ” hybridization. The availability of these probes potentially opens a new set of questions to experimental investigation regarding the subcellular distribution of specific DNA's and RNA's. Nucleic acids have a much lower “copy number” per cell than a typical protein, ranging from one copy to perhaps several thousand. Therefore, sensitive, high resolution techniques are required. There are several reasons why Intermediate Voltage Electron Microscopy (IVEM) and High Voltage Electron Microscopy (HVEM) are most useful for localization of nucleic acids in situ.

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