Spatial Probes Research Articles

An Integrated Hydrogeophysical Approach for Unsaturated Zone Monitoring Using Time Domain Reflectometry, Electrical Resistivity Tomography and Ground Penetrating Radar

Continuous measurements of soil moisture in the deeper parts of the unsaturated zone remain an important challenge. This study examines the development of an integrated system for the continuous and 3-D monitoring of the vadose zone processes in a cost- and energy-efficient way. This system comprises TDR, ERT and GPR geophysical techniques. Their capacities to adequately image subsurface moisture changes with continuous and time-lapse measurements are assessed during an artificial infiltration experiment conducted in a characteristic urban site with anthropogenic fills and much compaction. A 3-D array was designed for each method to expand the information of a single TDR probe and obtain a broader image of the subsurface. Custom spatial TDR probes installed in boreholes made with a percussion drilling instrument were used for soil moisture measurements. Moisture profiles along the probes were estimated with a numerical one-dimensional inversion model and a standard calibration equation. High conductivity water used during all infiltration tests led to the detection of the flow by all techniques. Preferential flow was present throughout the experiment and imaged sufficiently by all methods. Overall, the integrated approach conceals each method’s weaknesses and provides a reliable 3-D view of the subsurface. The results suggest that this approach can be used to monitor the unsaturated zone at even greater depths.

Full-length target sequences of GeoMx digital spatial profiling probes reveal that gene-promiscuity predicts probe sensitivity to EDTA tissue decalcification

GeoMx Digital Spatial Profiling (Nanostring) is a commercial spatial transcriptomics method to selectively analyze regions of interest within intact tissue sections. We show that decalcification with ethylene-diamine-tetra-acetic (EDTA) variably attenuates probe counts, while probes that are more resistant to this effect consequently appear overexpressed after quantile normalization. By determining the undisclosed full-length target sequences of probes used in the human whole transcriptome panel, hereby updating target transcripts and genes, we find that the gene-promiscuity of probes is an important factor that determines sensitivity to EDTA incubation.

Evaluation of Spatio-Temporal Soil Moisture Variability in Semi-Arid Rangeland Ecosystem, Maasai Mara National Reserve, Kenya

Aim: To evaluate the spatio-temporal soil moisture storage and retention capacities in semi-arid rangeland ecosystem, Maasai Mara National Reserve (MMNR), Kenya
 Study Design: Randomized complete block design (RCBD) of reference Cosmic Ray Neutron Sensor (CRNS) station, ten-(10) spatially distributed (soil moisture and temperature capacitance) probes (5TM-ECH20) sites.
 Place and Duration of Study: Kenya, MMNR, the oldest natural semi-arid rangeland ecosystem and globally unique for the great wildebeest migration, between May 2017 and April 2019.
 Methodology: Soil moisture (SM) variation data was collected using (CRNS) at spatial and point-scale 5TM-ECH2O probes, and gravimetric water content from (10) spatially distributed stations. Both CRNS and 5TM-ECH2O probes were used to monitor near-real time moisture levels at different soil layers ranging between 0-5cm, 5-10cm, 15-20cm, 35-40cm, and 75-80cm. Soil physical and chemical properties were laboratory analyzed. Calibration and validation datasets were obtained from 5TM-ECH2O probe and gravimetric soil samples extracted from respective layers and sites.
 Results: The pedological characteristics of the investigated ecosystem soil profile indicate decreased bulk density by 2.1% to 11.12% from upper layers (0-5cm) to deeper layers at (75–80 cm). Across the rangeland, 70% of soil textural classes were sandy clay loam (SCL) with higher clay percent and 30% sandy clay (SC) and soil porosity varied between 30.1% and 51% in the ecosystem. Moreover, volumetric
 
 
 
 
 
 
 
 
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 water content (VWC) of spatially distributed 5TM-ECH2O probes ranged between 0.11m3m-3 and 0.32m3m-3 during wet season with mean VWC of 0.16m3m-3, however, the VWC ranged between 0.04 m3m-3 and 0.17m3m-3 during the dry season with a mean volume of 0.11m3m-3 across the rangeland ecosystem.
 Conclusion: In this study, SM exhibited an annual periodicity of seasonal variation of spatial and temporal moisture partitioned as moisture gaining, losing, and a moisture stable period. This probably could be a consequence of increased movement of water to deeper layers caused by high precipitation and less evaporative demand caused by lower temperatures. The calibrated CRNS probe provided good estimates of spatial soil moisture variation when calibrated with 5TM-ECH20 and gravimetric sampling in relation to precipitation events and that deeper soil layers showed higher amount of soil moisture than shallow layers. The findings of the study will provide better formulation of the ecosystem vegetation management policies, conservation and planning for sustainable wildlife tourism industry.

Two-Color Visualization of Cholesterol Fluctuation in Plasma Membranes by Spatial Distribution-Controllable Single Fluorescent Probes.

Visualizing cholesterol (CL) fluctuation in plasma membranes is a crucially important yet challenging task in cell biology. Here, we proposed a new imaging strategy based on permeability changes of plasma membranes triggered by different CL contents to result in controllable spatial distribution of single fluorescent probes (SF-probes) in subcellular organelles. Three spatial distribution-controllable SF-probes (PMM-Me, PMM-Et, and PMM-Bu) for imaging CL fluctuation in plasma membranes were rationally developed. These SF-probes target plasma membranes and mitochondria at normal CL levels, while they display solely staining in plasma membranes and mitochondria at increased and decreased CL levels, respectively. These polarity-sensitive probes also show distinct emission colors with fluorescence peaks of 575 and 620 nm in plasma membranes and mitochondria, respectively. Thus, the CL fluctuation in plasma membranes can be clearly visualized by means of the spatially distributed and two-color emissive SF-probes.

From statistical room acoustics and acoustic intensity to spatial audio

Jiri Tichy was my graduate student advisor at Penn State. Jiri introduced me to statistical room acoustics and sound power measurements using a single pressure microphone in a reverberation room. From there we moved on to the measurement of sound power using acoustic intensity. We developed spatial microphone array probes with 2–4 microphones that measured the complex vector acoustic intensity in one to three dimensions. After graduation, the fundamentals developed analyzing the estimation of the complex acoustic intensity were applied to the development of a spherical microphone array that realized any first-order superdirectional directivity pattern pointing in any direction. It later became clear that higher-order arrays were needed to achieve higher directional gain. This led to the development of the Eigenmike® spherical microphone array with 32 pressure microphones and capable of 4th order spherical harmonic decomposition of the sound field. This array is finding application into AR/VR and statistical room acoustic analysis … bringing the technology full circle. I am incredibly lucky and grateful to have had Jiri as my mentor. He showed me how to look at acoustics problems and set the foundations of the many acoustic signal processing areas I have worked on in my career.

Hybrid 99mTc-magnetite tracer for dual modality sentinel lymph node mapping.

Accuracy of sentinel lymph node identification using radioactive tracers in non-superficial cancers can be limited by radiation shine through and low spatial resolution of detection systems such as intraoperative gamma probes. By utilising a dual radioactive/magnetic tracer, sensitive lymphoscintigraphy can be paired with high spatial resolution intraoperative magnetometer probes to improve the accuracy of sentinel node detection in cancers with complex multidirectional lymphatic drainage. Dextran-coated magnetite nanoparticles (33 nm mean hydrodynamic diameter) were labelled with 99mTc and applied as a lymphotropic tracer in small and large animal models. The dual tracer could be radiolabelled with 98 ± 2% efficiency after 10 min of incubation at room temperature. Biodistribution studies of the tracer were conducted in normal rats (subdermal and intravenous tail delivery, n = 3) and swine (subdermal hind limb delivery, n = 5). In rats the dual tracer migrated through four tiers of lymph node, 20 min after subdermal injection. Results from intravenous biodistribution test for radiocolloids demonstrated no aggregation in vivo, however indicated the presence of some lower-molecular weight radioactive impurities (99mTc-dextran). In swine, the dual tracer could be effectively used to map lymphatic drainage from hind hoof to popliteal and inguinal basins using intraoperative gamma and magnetometer probes. Of the eight primary nodes excised, eight were positively identified by gamma probe and seven by magnetometer probe. The high-purity dual tracer shows early promise for sentinel node identification in complex lymphatic environments by combining sensitive preoperative lymphoscintigraphy with a high-resolution intraoperative magnetometer probe.

Controlled Synthesis of Gold Nanoparticles on Fluorescent Nanodiamond via Electron-Beam-Induced Reduction Method for Dual-Modal Optical and Electron Bioimaging

Hybrid nanoparticles are emergent nanomaterials that combine particles with different characteristic properties to enhance their original functions or modulate their original physical or chemical properties for application in catalysis, sensing, and imaging. Fluorescent nanodiamonds (fNDs) have recently become more attractive for bioimaging because of their characteristic physicochemical properties and biocompatibility. Their wide applicability in bioimaging has been utilized in the single-particle tracking of biomolecules, local environmental sensors in cells, and stem cell tracking in tissues. However, the use of fNDs as multiscale spatial mapping probes for multiple biomolecules and cells in optical and electron microscopy techniques has been limited because of their broad fluorescence spectrum and composition of mainly light elements (C, O, H, N, etc.). On the other hand, metal nanoparticles (metal NPs) with unique photonic properties have been employed as functional labeling probes in bioimaging. The...

High-sensitivity and spatial resolution transient magnetic and electric field probes for transcranial magnetic stimulator characterizations

ABSTRACTTranscranial magnetic stimulation (TMS) is widely used for noninvasive brain stimulation. However, existing TMS tools cannot deliver targeted neural stimulation to deep brain regions, even though many important neurological disorders originate from there. To design TMS tools capable of delivering deep and focused stimulation, we have developed both electric and magnetic field probes to evaluate and improve new designs and calibrate products. Previous works related to magnetic field measurement had no detailed description of probe design or optimization. In this work, we demonstrated a magnetic field probe made of a cylindrical inductor and an electrical field probe modified from Rogowski coil structure. Both have much smaller size and higher directivity than commercial dipole probes. Using probe, we can calibrate and monitor any new types of TMS coil or array design and verify measured results with the other probe. We mathematically analyze their characteristics and performance and obtained a two-dimensional vector plot of the induced electric field, which matched the measured results from the second type of probe. A commercial circular coil and a figure-8 coil, with relatively complex vector field distribution, were used as examples to demonstrate the high-resolution and accurate measurement capability of our probes.

Casimir-Polder force fluctuations as spatial probes of dissipation in metals

We study the spatial fluctuations of the Casimir-Polder force experienced by an atom or a small sphere moved above a metallic plate at fixed separation distance. We demonstrate that unlike the mean force, the magnitude of these fluctuations crucially relies on the relaxation of conduction electron in the metallic bulk, and even achieves values that differ by orders of magnitude depending on the amount of dissipation. We also discover that fluctuations suffer a spectacular decrease at large distances in the case of nonzero temperature.

Continuous Manufacturing of High Quality Pharmaceutical Cocrystals Integrated with Process Analytical Tools for In-Line Process Control

A continuous manufacturing process for pharmaceutical indomethacin–saccharine cocrystals was achieved by extrusion processing with high throughput. Down-stream milling and blending of the extrudates was followed by feeding the formulated cocrystals in a capsule-filling machine. By applying a quality by design approach, the process was optimized and scaled up to produce 3000 capsules/h of pharmaceutical cocrystals. Process analytical tools such as near infrared reflectance and spatial filter velocimetry probes were coupled at various process stages for in-line monitoring and quality control. Further physicochemical characterization of extruded batches confirmed the manufacturing of high quality cocrystals. A fully integrated continuous process starting from raw materials to produce a finished product was assembled with only six unit operations and a small footprint. The study is a paradigm of continuous manufacturing of pharmaceutical cocrystals.

Concurrent cognitive processes in rat serial pattern learning: II. Discrimination learning, rule learning, chunk length, and multiple-item memories.

The current experiment examined the factors that determine acquisition for elements of highly structured serial patterns. Three groups of rats were trained on three patterns with parallel rule-based hierarchical structure, but with 3-, 4-, or 5-element chunks, each with a final violation element. Once rats mastered their patterns, probe patterns were introduced to answer several questions. To assess the extent to which the learned response pattern depended on intrachamber location cues for anticipating different element types, Spatial Shift Probes shifted the starting lever of patterns to locations that positioned chunk boundaries where they had never been experienced during training. To assess the extent to which a phrasing cue is necessary for rats to perform a chunk-boundary response, a Cue Removal Probe tested whether rats would produce a chunk-boundary response in the correct serial position if the phrasing cue was omitted. To assess the extent to which cues from multiple trials leading up to the violation element are required to anticipate the violation element, Multiple-Item Memory Probes required rats to make an unexpected response on one of the elements in the last two chunks of the pattern prior to the violation element. The results indicated that rats used multiple concurrent learning and memory processes to master serial patterns, including discrimination learning, rule learning, encoding of chunk length, and multiple-item memories.

Study of Earth and Jupiter-like plasmas for atmospheric entries using a non-transferred arc torch

This paper presents the results obtained by a 100 kW non-transferred arc plasma torch dedicated to the studies of plasmas characteristics of atmospheric entries of spatial probes, especially Earth and Jupiter entries. Spectra acquisition of the produced plasmas is achieved using optical emission spectroscopy. For Earth entry conditions, air plasma was obtained with a maximal temperature around 6800 K with a good agreement using atomic lines of oxygen and nitrogen (and also copper coming from electrode’s ablation) and molecular bands of N2, CN and , testifying to a good thermal equilibrium. As the first step in the study of Jupiter atmospheric entry, pure helium plasma was produced with the same maximal temperature of about 7500 K. Helium plasma was achieved for the first time using the plasma torch. Recorded spectra show a continuum, He I lines as well as copper. He II lines are not detected.

Confocal stereology: an efficient tool for measurement of microscopic structures.

Quantitative measurements of geometric forms or counting of objects in microscopic specimens is an essential tool in studies of microstructure. Confocal stereology represents a contemporary approach to the evaluation of microscopic structures by using a combination of stereological methods and confocal microscopy. 3-D images acquired by confocal microscopy can be used for the estimation of geometrical characteristics of microscopic structures by stereological methods, based on the evaluation of optical sections within a thick slice and using computer-generated virtual test probes. Such methods can be used for estimating volume, number, surface area and length using relevant spatial probes, which are generated by specific software. The interactions of the probes with the structure under study are interactively evaluated. An overview of the methods of confocal stereology developed during the past 30years is presented. Their advantages and pitfalls in comparison with other methods for measurement of geometrical characteristics of microscopic structures are discussed.

Photoactive Spatial Proximity Probes for Binding Pairs with Epigenetic Marks.

A new strategy for encoding polypeptide libraries with photolabile tags is developed. The photoassisted assay, based on conditional release of encoding tags only from bound pairs, can differentiate between peptides which have minor differences in a form of post-translational modifications with epigenetic marks. The encoding strategy is fully compatible with automated peptide synthesis. The encoding pendants are compact and do not perturb potential binding interactions.

When the sunny side is down: Re-mapping the relationship between direction and valence

Lakoff & Johnson (1999) argue that the understanding of positive or negative concepts is structured around our sensorimotor experience whereby “Happy is up” and “Sad is down”. Consistent with this, Meier and Robinson (2004) found that positive evaluations of words gave faster responses to spatial probes in an upper region of space compared to lower regions of space, and vice versa for negative evaluations. However, “She blew her top” or “He dropped his grudge” are both common metaphors despite reversing the basic mapping. Using Meier and Robinson’s (2004) paradigm, we generated “negative-up” and “positive-down” phrases. Results showed a probe position x valence interaction in the opposite direction to that found by Meier and Robinson (2004). This suggests the relationship between direction and valence is not necessarily a single mapping, as envisaged by Lakoff & Johnson (1999).

PLASTICITY OF SKELETAL MUSCLE STUDIED BY STEREOLOGY

The present contribution provides an overview of stereological methods applied in the skeletal muscle research at the Institute of Anatomy of the Medical Faculty in Ljubljana. Interested in skeletal muscle plasticity we studied three different topics: (i) expression of myosin heavy chain isoforms in slow and fast muscles under experimental conditions, (ii) frequency of satellite cells in young and old human and rat muscles and (iii) capillary supply of rat fast and slow muscles. We analysed the expression of myosin heavy chain isoforms within slow rat soleus and fast extensor digitorum longus muscles after (i) homotopic and heterotopic transplantation of both muscles, (ii) low frequency electrical stimulation of the fast muscle and (iii) transposition of the fast nerve to the slow muscle. The models applied were able to turn the fast muscle into a completely slow muscle, but not vice versa. One of the indicators for the regenerative potential of skeletal muscles is its satellite cell pool. The estimated parameters, number of satellite cells per unit fibre length, corrected to the reference sarcomere length (Nsc/Lfib) and number of satellite cells per number of nuclei (myonuclei and satellite cell nuclei) (Nsc/Nnucl) indicated that the frequency of M-cadherin stained satellite cells declines in healthy old human and rat muscles compared to young muscles. To access differences in capillary densities among slow and fast muscles and slow and fast muscle fibres, we have introduced Slicer and Fakir methods, and tested them on predominantly slow and fast rat muscles. Discussing three different topics that require different approach, the present paper reflects the three decades of the development of stereological methods: 2D analysis by simple point counting in the 70's, the disector in the 80's and virtual spatial probes in the 90's. In all methods the interactive computer assisted approach was utilised.

Radiation microbeams as spatial and temporal probes of subcellular and tissue response

Understanding the effects of ionizing radiations are key to determining their optimal use in therapy and assessing risks from exposure. The development of microbeams where radiations can be delivered in a highly temporal and spatially constrained manner has been a major advance. Several different types of radiation microbeams have been developed using X-rays, charged particles and electrons. For charged particles, beams can be targeted with sub-micron accuracy into biological samples and the lowest possible dose of a single particle track can be delivered with high reproducibility. Microbeams have provided powerful tools for understanding the kinetics of DNA damage and formation under conditions of physiological relevance and have significant advantages over other approaches for producing localized DNA damage, such as variable wavelength laser beam approaches. Recent studies have extended their use to probing for radiosensitive sites outside the cell nucleus, and testing for mechanisms underpinning bystander responses where irradiated and non-irradiated cells communicate with each other. Ongoing developments include the ability to locally target regions of 3D tissue models and ultimately to target localized regions in vivo. With future advances in radiation delivery and imaging microbeams will continue to be applied in a range of biological studies.

Light-Mediated Spatial Control via Photolabile Fluorescently Quenched Peptide Cassettes

Light-regulatable compounds are finding increasing utility as spatial and temporal probes of biological behavior. An independent measure of successful light-induced structural change is possible when alteration (e.g., activation, deactivation, etc.) of the bioprobe can be directly linked to a fluorescent readout. We have identified a series of photolabile fluorescently quenched cassettes that display extraordinarily large fluorescence enhancements upon photolysis. A pair of cassettes has been inserted into mitochondrial localization sequences to assess an organelle-targeted light-mediated release strategy for controlling biological activity. The peptide constructs are readily absorbed by mitochondria and subsequently can be cleaved in a light-dependent fashion as assessed by the predicted changes in absorbance and fluorescence.

Mislocalization of Flashed and Stationary Visual Stimuli after Adaptation of Reactive and Scanning Saccades

When we look around and register the location of visual objects, our oculomotor system continuously prepares targets for saccadic eye movements. The preparation of saccade targets may be directly involved in the perception of object location because modification of saccade amplitude by saccade adaptation leads to a distortion of the visual localization of briefly flashed spatial probes. Here, we investigated effects of adaptation on the localization of continuously visible objects. We compared adaptation-induced mislocalization of probes that were present for 20 ms during the saccade preparation period and of probes that were present for >1 s before saccade initiation. We studied the mislocalization of these probes for two different saccade types, reactive saccades to a suddenly appearing target and scanning saccades in the self-paced viewing of a stationary scene. Adaptation of reactive saccades induced mislocalization of flashed probes. Adaptation of scanning saccades induced in addition also mislocalization of stationary objects. The mislocalization occurred in the absence of visual landmarks and must therefore originate from the change in saccade motor parameters. After adaptation of one type of saccade, the saccade amplitude change and the mislocalization transferred only weakly to the other saccade type. Mislocalization of flashed and stationary probes thus followed the selectivity of saccade adaptation. Since the generation and adaptation of reactive and scanning saccades are known to involve partially different brain mechanisms, our results suggest that visual localization of objects in space is linked to saccade targeting at multiple sites in the brain.

MFM studies of interlayer exchange coupling in Co/Ru/Co films: Effect of Ru layer thickness

Antiferromagnetically coupled magnetic thin films are promising candidates for the design of new magnetic storage and logic devices. The ability to control the interlayer thickness, therefore the magnetic reversal response, of exchange-coupled magnetic layers is of paramount importance in nanotechnology, especially in magnetic sensing element design and applications. In this work, magnetic force microscopy (MFM) with improved sensitivity and high spatial resolution probes was used to obtain a more detailed view of magnetization reversal behavior and domain evolution in the indirect exchange-coupled trilayer system: Co/Ru/Co. The effect of the variable Ru interlayer thickness on the exchange coupling and thus the magnetic domain structure during the ferromagnetic (FM)/antiferromagnetic (AF) coupling transition in Co/Ru/Co films is well demonstrated. The MFM images display a distinct signature of AF coupling for the films with Ru thickness of 0.4 nm. MFM has proven to be an effective tool for detecting FM/AF interlayer coupling and exploring magnetic domain structures in exchange-coupled layered thin films.