Rapid Alignment Research Articles

A novel thin section preparation and staining protocol to increase contrast and resolution of cell details for light microscopy

ABSTRACTWe developed a novel sectioning and staining method to make high contrast, high resolution sections of plant tissue for light microscopy. Specimens of teosinte (Zea mays L., ssp. mexicana) root tips were fixed and embedded in Technovit 7100™ plastic resin. Thin sections, 1−2.5 μm, were cut and mounted on glass slides. The sections were either treated with RNase or not, then stained with 0.1% toluidine blue O and observed through ∞/0 objective lenses. For light microscopy, the enzyme staining procedure increased resolution and contrast. High magnification ∞/0 objective lenses produced high quality images for digital photography without using a coverslip or immersion oil. Our slide preparation and microscopic analysis were less labor intensive and more rapid than previous methods and enabled rapid and precise alignment of serial transverse sections for both tracking cell lineages and tissue measurements.

Rapid SINS Two-Position Ground Alignment Scheme Based on Piecewise Combined Kalman Filter and Azimuth Constraint Information.

The accuracy and rate of convergence are two important performance factors for initial ground alignment of a strapdown inertial navigation system (SINS). For navigation-grade SINS, gyro biases and accelerometer offsets can be modeled as constant values during the alignment period, and they can be calibrated through two-position ground alignment schemes. In many situations for SINS ground alignment, the azimuth of the vehicle remains nearly constant. This quasi-stationary alignment information can be used as an augmented measurement. In this paper, a piecewise combined Kalman filter utilizing relative azimuth constraint (RATP) is proposed to improve the alignment precision and to reduce the time consumption for error convergence. It is presented that a piecewise time-invariant linear system can be combined into a whole extended time-invariant linear system so that a piecewise combined Kalman filter can be designed for state estimation. A two-position ground alignment algorithm for SINS is designed based on the proposed piecewise combined Kalman filter. Numerical simulations and experimental results show its superiority to the conventional algorithms in terms of accuracy and the rate of convergence.

Marginal Reduced High-degree CKF and its Application in Nonlinear Rapid Transfer Alignment

The error model is not perfect when the nonlinear transfer alignment is applied to the inertial navigation system of shipborne aircraft. In this paper, a new model incorporating acceleration error of lever-arm is proposed. Considering the influence of flexure deformation and dynamic lever-arm, it is suitable for the case of large azimuth misalignment The state filtering estimation selects the High-degree Cubature Kalman filter (HCKF). A reduced HCKF algorithm with marginalized-sampling-based cubature transformation is designed according to the state equation and measurement equation structure of the transfer alignment model, and it is proved. This algorithm simplifies the measurement update process, and applies the marginal sampling algorithm to the time update process, achieving the purpose of reducing the calculation amount of HCKF. In the simulation, the velocity plus attitude matching method is used. The experimental results show that compared with the transfer alignment model without considering the dynamic lever-arm, this model has a higher accuracy, and the alignment precision and time also meet the requirements.

Digital frequency domain approach for fluorescence lifetime spectroscopy of the cornea using an enhanced confocal scanning microfluorometer

We report on enhancement to a confocal scanning microfluorometer (CSMF) for depth-resolved frequency domain lifetime spectroscopy across the cornea. Fluorescence was detected by a photomultiplier tube (PMT; R928P, Hamamatsu) and coupled to computer-controlled data acquisition module (K520, Digital Frequency Domain, ISS Inc.).The digital frequency domain (DFD) module performed acquisition of PMT pulses for further calculation of phase (ϕ) and modulation (M) in the emission of the sample, relative to excitation pulses, at 30 harmonics. As per the DFD approach, fluorescence lifetime (τ) was calculated by tanϕ =ωτ, where ω= 2πf with f being the excitation harmonic in Hz. The modulation depth can be calculated byM=1/√(1+ω2τ2). The DFD module was also used to pulse the excitation laser (450 nm; ISS Model N742) with the repetition rate of up to 10 MHz (fundamental frequency). Apart from coupling to DFD module, two other modifications were incorporated to enhance the CSMF: first, a sighting optic was constructed and placed before the PMT for rapid and precise confocal alignment of the excitation and emission slits, and second, a stepper motor was interfaced to the vertical nanostage for rapid depth scanning. These enhancements have enabled the CSMF to consistently produce a depth resolution of 7 µm during transcorneal scans with a 40x water immersion objective (Zeiss; WD = 1.2 mm, NA= 0.75). Overall, the CSMF is now capable of measuring transcorneal fluorescence lifetime with a wide array of fluorophores exhibiting lifetimes in the range of µs to nanoseconds.

Backtracking scheme for single-point self-calibration and rapid in-motion alignment with application to a position and azimuth determining system

The position and azimuth determining system (PADS) chiefly consists of an inertial navigation system and odometer. In order to improve the performance of the PADS, a backtracking scheme is proposed for odometer calibration and odometer-aided rapid alignment of PADS with a single pre-known landmark. Based on a backtracking scheme, a newly derived backward filter is presented to accomplish odometer calibration, fine alignment and positioning simultaneously by using the recorded forward data. Compared with normal methods, the proposed method can calibrate the odometer with only one pre-known landmark and lessens the environment restraints. Both the simulation and the experiment results show that the proposed method can calibrate the odometer with only one landmark and achieve good alignment and positioning accuracy in a short period of time.

Protein Palmitoylation Plays an Important Role in Trichomonas vaginalis Adherence

The flagellated protozoan parasite Trichomonas vaginalis is the etiologic agent of trichomoniasis, the most common non-viral sexually transmitted infection worldwide. As an obligate extracellular pathogen, adherence to epithelial cells is critical for parasite survival within the human host and a better understanding of this process is a prerequisite for the development of therapies to combat infection. In this sense, recent work has shown S-acylation as a key modification that regulates pathogenesis in different protozoan parasites. However, there are no reports indicating whether this post-translational modification is a mechanism operating in T. vaginalis In order to study the extent and function of S-acylation in T. vaginalis biology, we undertook a proteomic study to profile the full scope of S-acylated proteins in this parasite and reported the identification of 363 proteins involved in a variety of biological processes such as protein transport, pathogenesis related and signaling, among others. Importantly, treatment of parasites with the palmitoylation inhibitor 2-bromopalmitate causes a significant decrease in parasite: parasite aggregation as well as adherence to host cells suggesting that palmitoylation could be modifying proteins that are key regulators of Trichomonas vaginalis pathogenesis.

Bacterial chromosome organization by collective dynamics of SMC condensins.

A prominent organizational feature of bacterial chromosomes was revealed by Hi-C experiments, indicating anomalously high contacts between the left and right chromosomal arms. These long-range contacts have been attributed to various nucleoid-associated proteins, including the ATPase Structural Maintenance of Chromosomes (SMC) condensin. Although the molecular structure of these ATPases has been mapped in detail, it still remains unclear by which physical mechanisms they collectively generate long-range chromosomal contacts. Here, we develop a computational model that captures the subtle interplay between molecular-scale activity of slip-links and large-scale chromosome organization. We first consider a scenario in which the ATPase activity of slip-links regulates their DNA-recruitment near the origin of replication, while the slip-link dynamics is assumed to be diffusive. We find that such diffusive slip-links can collectively organize the entire chromosome into a state with aligned arms, but not within physiological constraints. However, slip-links that include motor activity are far more effective at organizing the entire chromosome over all length-scales. The persistence of motor slip-links at physiological densities can generate large, nested loops and drive them into the bulk of the DNA. Finally, our model with motor slip-links can quantitatively account for the rapid arm-arm alignment of chromosomal arms observed in vivo.

Simple retinal imaging system using a MEMS scanning mirror

We have fabricated a simple and compact scanning laser optical system using microelectromechanical system (MEMS) scanner that can be incorporated into portable health monitoring devices. The two-dimensional (2-D) MEMS scanner used in this system is much smaller and light in weight compared to galvanometer scanners and polygon scanners used in the commercially available ophthalmic devices. MEMS scanners have many advantages and also limitations compared to galvanometer and polygon scanners. An easy to use and compact device is more useful for rapid alignment for measurement and data acquisition. Sensitivity of the system was quantified by measuring signal-to-noise ratio (SNR) for both high and low reflectivity materials. SNR was 10 for the high reflectance materials and about 4 for low reflectance materials, which is sufficient for biological imaging. Distortion generated using large scanning angle of 2-D MEMS scanner was corrected in real time by custom made LabVIEW program. Ocular safety is important to consider when using a laser for ophthalmic devices. We calculated the maximum permissible beam power for thermal damage and photochemical damage considering the specification of our system such as visual angle and wavelength of the laser beam. The measured laser intensity in the front of model eye was 6 μW, which is much smaller than the maximum permissible beam power recommended by the American National Standards Institute.

Biodegradable and elastomeric vascular grafts enable vascular remodeling

Implanted grafts, including vascular substitutes, inevitably experience remodeling by host cells. The design of grafts capable of promoting constructive remodeling remains a challenge within regenerative medicine. Here, we used a biodegradable elastic polymer, poly (l-lactide-co-ε-caprolactone) (PLCL), to develop a vascular graft with circumferentially aligned microfibers. The grafts exhibited excellent handling properties and resistance to deformation. Upon implantation in rat abdominal aorta, graft-guided neoartery regeneration was achieved in a short period (4 weeks) as evidenced by rapid cell infiltration and alignment, and complete endothelialization. During vascular remodeling, a high ratio of M2/M1 macrophage was detected, and the expression of pro-inflammatory and anti-inflammatory cytokines first increased and then decreased to normal level for the follow-up period. By 12 months, the PLCL grafts were almost completely degraded and a well-integrated neoartery was formed with characteristics comparable to native arteries, such as transparent appearance, synchronous pulsation, dense and orderly extracellular matrix (ECM) arrangement, strong and compliant mechanical properties, and vasomotor response to pharmacologic agents. Taken together, our strategy represents a new avenue for guided tissue regeneration by designing the grafts to promote tissue remodeling via controlling structure, degradation and mechanical properties of the scaffolds.

Rapid and precise alignment of raw reads against redundant databases with KMA

BackgroundAs the cost of sequencing has declined, clinical diagnostics based on next generation sequencing (NGS) have become reality. Diagnostics based on sequencing will require rapid and precise mapping against redundant databases because some of the most important determinants, such as antimicrobial resistance and core genome multilocus sequence typing (MLST) alleles, are highly similar to one another.In order to facilitate this, a novel mapping method, KMA (k-mer alignment), was designed. KMA is able to map raw reads directly against redundant databases, it also scales well for large redundant databases. KMA uses k-mer seeding to speed up mapping and the Needleman-Wunsch algorithm to accurately align extensions from k-mer seeds. Multi-mapping reads are resolved using a novel sorting scheme (ConClave scheme), ensuring an accurate selection of templates.ResultsThe functionality of KMA was compared with SRST2, MGmapper, BWA-MEM, Bowtie2, Minimap2 and Salmon, using both simulated data and a dataset of Escherichia coli mapped against resistance genes and core genome MLST alleles. KMA outperforms current methods with respect to both accuracy and speed, while using a comparable amount of memory.ConclusionWith KMA, it was possible map raw reads directly against redundant databases with high accuracy, speed and memory efficiency.

Rapid alignment of functional trait variation with locality across the invaded range of Sahara mustard (Brassica tournefortii).

Mechanisms by which invasive species succeed across multiple novel environmental contexts are poorly understood. Functional traits show promise for identifying such mechanisms, yet we lack knowledge of which functional traits are critical for success and how they vary across invaded ranges and with environmental features. We evaluated the widespread recent invasion of Sahara mustard (Brassica tournefortii) in the southwestern United States to understand the extent of functional trait variation across the invaded range and how such variation is related to spatial and climatic gradients. We used a common garden approach, growing two generations of plants in controlled conditions sourced from 10 locations across the invaded range. We measured variation within and among populations in phenological, morphological, and physiological traits, as well as performance. We found nine key traits that varied among populations. These traits were related to phenology and early growth strategies, such as the timing of germination and flowering, as well as relative allocation of biomass to reproduction and individual seed mass. Trait variation was related most strongly to variation in winter precipitation patterns across localities, though variations in temperature and latitude also had significant contributions. Our results identify key functional traits of this invasive species that showed significant variation among introduced populations across a broad geographic and climatic range. Further, trait variation among populations was strongly related to key climatic variables, which suggests that population divergence in these traits may explain the successful colonization of Sahara mustard across its invaded US range.

Rapid Alignment of Resources and Capabilities in Time-Bound Networks: A Theoretical Proposition

Researchers studying the alignment of business resources usually focus on business cases that inherently have continuous interactions built on long-term relationships at the firm level, dyadic level, or broader network level. While contractual limitations can be applied to resource alignment, resource engagement holds the notion of a persistent value-adding relationship. This paper proposes a theoretical framework based on previous theories and empirical studies on resource alignment ranging from resource-based views to more complex network views of social organizational interactions and their implications for business performance activities. The main challenge comes from time-bound transactions built around the longevity of interorganizational relations. Thus, the key strategic management problem is how resources and capabilities can be rapidly aligned and managed in a time-bound network to achieve sustainable competitive advantages at the network level.

Effect of Photobiomodulation on Maxillary Decrowding and Root Resorption: A Randomized Clinical Trial

Purpose The effects of low-level laser therapy (LLLT) with light-emitting diode (LED) delivery (Biolux OrthoPulse® device) were tested for no differences from sham-controlled conventional orthodontics in maxillary anterior alignment treatment efficiency and maxillary central incisor root resorption after 6 months of treatment. Materials and Methods Two prospective clinical trial samples were matched for pretreatment irregularity index with (n = 14) and without (n = 12) photobiomodulation therapy (850 nm wavelength, 0.065 J/cm2, 5 min per-arch-per-day) and examined every 2 weeks for reduction of irregularity index to <1 mm. The sham control sample was provided with LED devices that did not deliver infrared light. Standardized periapical radiographs of maxillary central incisors were compared at initial and 6 months of treatment. Results Photobiomodulation resolved maxillary anterior crowding with 35.2% greater efficiency (41.0 vs. 63.3 days, P = 0.028) at nearly double the tooth movement rate-per-week (1.02 vs. 62 mm/week, P = 0.045). Mean maxillary central incisor root lengths were significantly shorter at the 6-month treatment interval after LLLT (19.63 vs. 20.85 mm, P = 0.021). Conclusions LED photobiomodulation therapy at 850 nm wavelength resulted in 1.7X more rapid maxillary anterior alignment.

Laminar shear stress modulates endothelial luminal surface stiffness in a tissue-specific manner.

Endothelial cells form vascular beds in all organs and are exposed to a range of mechanical forces that regulate cellular phenotype. We sought to determine the role of endothelial luminal surface stiffness in tissue-specific mechanotransduction of laminar shear stress in microvascular mouse cells and the role of arachidonic acid in mediating this response. Microvascular mouse endothelial cells were subjected to laminar shear stress at 4 dynes/cm2 for 12hours in parallel plate flow chambers that enabled real-time optical microscopy and atomic force microscopy measurements of cell stiffness. Lung endothelial cells aligned parallel to flow, while cardiac endothelial cells did not. This rapid alignment was accompanied by increased cell stiffness. The addition of arachidonic acid to cardiac endothelial cells increased alignment and stiffness in response to shear stress. Inhibition of arachidonic acid in lung endothelial cells and embryonic stem cell-derived endothelial cells prevented cellular alignment and decreased cell stiffness. Our findings suggest that increased endothelial luminal surface stiffness in microvascular cells may facilitate mechanotransduction and alignment in response to laminar shear stress. Furthermore, the arachidonic acid pathway may mediate this tissue-specific process. An improved understanding of this response will aid in the treatment of organ-specific vascular disease.

A modified rapid alignment method of SINS based on measurement augmentation

The precision and convergence time of initial alignment are two most important indicators for inertial navigation system, but they are usually contradictory. It is necessary to achieve considerable accuracy in a very short period for the launching of weapons such as artillery, torpedo and so on. However, the conventional methods need several minutes to complete the initial alignment. In this case, a Kalman filter method based on measurement augmentation (MAKF) is proposed to speed up convergence, and theoretical analysis of observability verifies the feasibility of the proposed method. Furthermore, a large misalignment angle model and a dimensionality reduction Cubature Kalman Filter using measurement augmentation (MACKF) are also employed to solve the invalidity of the linear model under the large misalignment angle. Finally, simulations and turntable experiment results show that the proposed method can speed up the convergence substantially. Even with initial misalignment angle of 70°, the azimuth error angle can be reduced within 1° in 5 s and 0.5° in 10 s. It has important engineering application value.

Laser beam alignment for a petawatt picosecond diagnostic system in SG-II laser facility

To satisfy the beam pointing and centering requirements of a sophisticated sampling beam path for petawatt picosecond diagnostic systems, a laser-beam alignment system is applied to this diagnostic platform. A mathematical model of a 4D linear matrix is applied to achieve rapid and accurate beam alignment. This alignment system can also switch quickly between two channels sampling beams without disturbing the beam’s pointing and centering. Experimental results indicate that the near-field centering accuracy is 0.3 mm and the far-field pointing accuracy is 0.16 mrad. With this alignment system, the picosecond diagnostic system can realize stable and reliable pulse width diagnostic between 1 and 10 ps, and obtains high dynamic range signal-to-noise ratio diagnostic results.

Theoretical Analysis of Liquid–Ice Interaction in the Unsaturated Environment with Application to the Problem of Homogeneous Mixing

Abstract The process of ice–liquid water interaction in the unsaturated environment is explored both analytically and with the help of a numerical simulation. Ice–liquid water interaction via the condensation–evaporation mechanism is considered in relation to the problem of homogeneous mixing in an unmovable air volume. The process is separated into three stages: the homogenization stage, during which the rapid alignment of thermodynamic and microphysical parameters in the mixing volume takes place; the glaciation stage, during which the liquid droplets evaporate; and the ice stage, which leads to attaining a thermodynamic equilibrium. Depending on the initial temperature, humidity, and mixing ratios of liquid water and of ice water, the third stage may result in two outcomes: existence of ice particles under zero supersaturation with respect to ice or a complete disappearance of ice particles. Three characteristic times are associated with the microphysical stages: the phase relaxation time associated with droplets, the glaciation time determined by the Wegener–Bergeron–Findeisen process, and the phase relaxation time associated with ice. Since the duration of the second and third microphysical stages may be of the same order as the homogenization time or even longer, the homogeneous mixing scenario is more probable in mixed-phase clouds than in liquid clouds. It is shown that mixing of a mixed-phase cloud with a dry environment accelerates cloud glaciation, leading to a decrease in the glaciation time by more than 2 times. The conditions of fast ice particles’ disappearance due to sublimation are analyzed as well.

SECAPR - A bioinformatics pipeline for the rapid and user-friendly alignment of hybrid enrichment sequences, from raw reads to alignments

SECAPR - A bioinformatics pipeline for the rapid and user-friendly alignment of hybrid enrichment sequences, from raw reads to alignments

A DDF-based IMM-TFS Approach for the Accuracy Evaluation Problem of Rapid Transfer Alignment

This study aims to address the accuracy evaluation problem for rapid transfer alignment with the coexistence of large misalignment angles and uncertain observation noises. For the requirement of accuracy evaluation, complete information in terms of misalignment angles should be estimated during the alignment process. Thus, a fixed-interval smoothing approach is the core of solving this problem. In this paper, a new Divided Difference Filter (DDF)-based an Interacting Multiple Model Two-Filter Smoother (IMM-TFS) is developed to estimate the misalignment angles. The proposed DDF-based IMM-TFS releases the restriction of inverse nonlinearity by using the weighted statistical linearization regression method, and the resulting pseudo-linear model can be used for backward-time IMM filtering. The smoothing step takes into account the merging of estimations and the interaction of multiple models simultaneously. The new smoother is compared with the previous well-known methodologies in simulations. The results show that the DDF-based IMM-TFS can achieve better accuracy for misalignment angles estimation, and has a high efficiency for detecting the changes in a model.

Rapid Initial Alignment Method of Inertial Navigation System Using Adaptive Time Delay Compensation

Rapid Initial Alignment Method of Inertial Navigation System Using Adaptive Time Delay Compensation