Improving LC-MS sensitivity through increases in chromatographic performance: comparisons of UPLC-ES/MS/MS to HPLC-ES/MS/MS

Recent technological advances have made available reverse phase chromatographic media with a 1.7 microm particle size along with a liquid handling system that can operate such columns at much higher pressures. This technology, termed ultra performance liquid chromatography (UPLC), offers significant theoretical advantages in resolution, speed, and sensitivity for analytical determinations, particularly when coupled with mass spectrometers capable of high-speed acquisitions. This paper explores the differences in LC-MS performance by conducting a side-by-side comparison of UPLC for several methods previously optimized for HPLC-based separation and quantification of multiple analytes with maximum throughput. In general, UPLC produced significant improvements in method sensitivity, speed, and resolution. Sensitivity increases with UPLC, which were found to be analyte-dependent, were as large as 10-fold and improvements in method speed were as large as 5-fold under conditions of comparable peak separations. Improvements in chromatographic resolution with UPLC were apparent from generally narrower peak widths and from a separation of diastereomers not possible using HPLC. Overall, the improvements in LC-MS method sensitivity, speed, and resolution provided by UPLC show that further advances can be made in analytical methodology to add significant value to hypothesis-driven research.     

High-resolution profiles of temperature and dissolved oxygen in a river

Longitudinal profiles of water quality along a well-mixed tidal river are, ideally, based on simultaneous measurements at fixed stations distributed along the river. The resolution of the profiles is limited by the density of the stations. However, for a given number of stations the resolution is greatly increased if water quality date can be extrapolated upstream and downstream of the stations, making use of velocity data; the resolution is then determined by the density of the extrapolated data points, which may be an order of magnitude higher than the density of the stations. A 15-km length of river was investigated using 5 current meters equipped to measure depth, temperature, conductivity and dissolved oxygen. Data were recorded simultaneously every 10 minutes. When the average cross-sectional speed was 0.25 ms⁻¹ (typical of tidal conditions), the extrapolated data points were 150 m apart, so the resolution of the resulting profiles (7 per kilometre) was much higher than that of the stations alone (0.3 per kilometre). The extrapolation process required a means of deducing the average cross-sectional speed from the speed measured at a given station. The key to this was provided by temperature data recorded during the onset of a spate, when tidal flow was suspended and the average cross-sectional speed was uniformly about 0.75 ms ⁻¹ at four of the stations. Profiles of temperature and dissolved oxygen were generated by this method; the resolution was about 2 data points km⁻¹ during the onset of the spate, and 6 points km⁻¹ during tidal flow.     

Chromatographic techniques for the isolation and purification of lipoproteins

Various modes of chromatography are available for lipoprotein separation. Gel permeation and affinity chromatography are used for preparative purposes and to separate lipoproteins according to size and apolipoprotein content, respectively. Development of rigid supports for gel permeation has led to large improvements in speed and resolution. Reversed-phase high-performance liquid chromatography (HPLC) of apolipoproteins offers the best performance in terms of speed and resolution of structural variants. Due to its high speed and superior resolving power, the recently developed technique of capillary electrophoresis should emerge as an important method for lipoprotein analysis.     

Acoustic resolution photoacoustic microscopy based on microelectromechanical systems scanner

Photoacoustic microscopy (PAM) can be classified as optical resolution (OR)‐PAM and acoustic resolution (AR)‐PAM depending on the type of resolution achieved. Using microelectromechanical systems (MEMS) scanner, high‐speed OR‐PAM system was developed earlier. Depth of imaging limits the use of OR‐PAM technology for many preclinical and clinical imaging applications. Here, we demonstrate the use of a high‐speed MEMS scanner for AR‐PAM imaging. Lateral resolution of 84 μm and an axial resolution of 27 μm with ~2.7 mm imaging depth was achieved using a 50 MHz transducer‐based AR‐PAM system. Use of a higher frequency transducer at 75 MHz has further improved the resolution characteristics of the system with a reduction in imaging depth and a lateral resolution of 53 μm and an axial resolution of 18 μm with ~1.8 mm imaging depth was achieved. Using the two‐axis MEMS scanner a 2 × 2 .5 mm² area was imaged in 3 seconds. The capability of achieving acoustic resolution images using the MEMS scanner makes it beneficial for the development of high‐speed miniaturized systems for deeper tissue imaging.      

Factors affecting flow karyotype resolution.

BACKGROUND: One of the major factors which influences the chromosome purity achievable particularly during high speed sorting is the analytical resolution of individual chromosome peaks in the flow karyotype, as well as the amount of debris and fragmented chromosomes. We have investigated the factors involved in the preparation of chromosome suspensions that influence karyotype resolution. METHODS: Chromosomes were isolated from various human and animal cell types using a series of polyamine buffer isolation protocols modified with respect to pH, salt concentration, and chromosome staining time. Each preparation was analyzed on a MoFlo sorter (DAKO) configured for high speed sorting and the resolution of the flow karyotypes compared. RESULTS: High resolution flow cytometric data was obtained with chromosomes optimally isolated using hypotonic solution buffered at pH 8.0 and polyamine isolation buffer (with NaCl excluded) between pH 7.50 and 8.0. Extending staining time to more than 8 h with chromosome suspensions isolated from cell lines subjected to sufficient metaphase arrest times gave the best result with the lowest percentage of debris generated, tighter chromosome peaks with overall lower coefficients of variation, and a 1- to 5-fold increase in the yield of isolated chromosomes. CONCLUSIONS: Optimization of buffer pH and the length of staining improved karyotype resolution particularly for larger chromosomes and reduced the presence of chromosome fragments (debris). However, the most interesting and surprising finding was that the exclusion of NaCl in PAB buffer improved the yield and resolution of larger chromosomes.     

Quantifying and Optimizing Single-Molecule Switching Nanoscopy at High Speeds

Single-molecule switching nanoscopy overcomes the diffraction limit of light by stochastically switching single fluorescent molecules on and off, and then localizing their positions individually. Recent advances in this technique have greatly accelerated the data acquisition speed and improved the temporal resolution of super-resolution imaging. However, it has not been quantified whether this speed increase comes at the cost of compromised image quality. The spatial and temporal resolution depends on many factors, among which laser intensity and camera speed are the two most critical parameters. Here we quantitatively compare the image quality achieved when imaging Alexa Fluor 647-immunolabeled microtubules over an extended range of laser intensities and camera speeds using three criteria – localization precision, density of localized molecules, and resolution of reconstructed images based on Fourier Ring Correlation. We found that, with optimized parameters, single-molecule switching nanoscopy at high speeds can achieve the same image quality as imaging at conventional speeds in a 5–25 times shorter time period. Furthermore, we measured the photoswitching kinetics of Alexa Fluor 647 from single-molecule experiments, and, based on this kinetic data, we developed algorithms to simulate single-molecule switching nanoscopy images. We used this software tool to demonstrate how laser intensity and camera speed affect the density of active fluorophores and influence the achievable resolution. Our study provides guidelines for choosing appropriate laser intensities for imaging Alexa Fluor 647 at different speeds and a quantification protocol for future evaluations of other probes and imaging parameters.     

Design of High Speed and Low Offset Dynamic Latch Comparator in 0.18 μm CMOS Process

The cross-coupled circuit mechanism based dynamic latch comparator is presented in this research. The comparator is designed using differential input stages with regenerative S-R latch to achieve lower offset, lower power, higher speed and higher resolution. In order to decrease circuit complexity, a comparator should maintain power, speed, resolution and offset-voltage properly. Simulations show that this novel dynamic latch comparator designed in 0.18 µm CMOS technology achieves 3.44 mV resolution with 8 bit precision at a frequency of 50 MHz while dissipating 158.5 µW from 1.8 V supply and 88.05 µA average current. Moreover, the proposed design propagates as fast as 4.2 nS with energy efficiency of 0.7 fJ/conversion-step. Additionally, the core circuit layout only occupies 0.008 mm².     

A Review of the Deep Learning Methods for Medical Images Super Resolution Problems

Super resolution problems are widely discussed in medical imaging. Spatial resolution of medical images are not sufficient due to the constraints such as image acquisition time, low irradiation dose or hardware limits. To address these problems, different super resolution methods have been proposed, such as optimization or learning-based approaches. Recently, deep learning methods become a thriving technology and are developing at an exponential speed. We think it is necessary to write a review to present the current situation of deep learning in medical imaging super resolution. In this paper, we first briefly introduce deep learning methods, then present a number of important deep learning approaches to solve super resolution problems, different architectures as well as up-sampling operations will be introduced. Afterwards, we focus on the applications of deep learning methods in medical imaging super resolution problems, the challenges to overcome will be presented as well.     

Fluorescence microscopy below the diffraction limit

Fluorescence imaging with conventional microscopy has experienced numerous advances in almost every limiting factor from sensitivity to speed. But improved resolution beyond the fundamental limitation of light diffraction has been elusive until recent years. Now, techniques are available that surpass this barrier and improve resolution up to 10 times over that of conventional microscopy. This chapter provides an overview of these new “super-resolution” imaging methods.     

Rapid separation of seed gliadins by reversed-phase ultra performance liquid chromatography (RP-UPLC) and its application in wheat cultivar and germplasm identification

To separate gliadin from wheat flour, a novel and stability-indicating reversed-phase ultra performance liquid chromatography (RP-UPLC) method is established and optimized. A comparative analysis of routine capillary electrophoresis (CE), reversed-phase high-performance liquid chromatography (RP-HPLC), and RP-UPLC was performed and the results showed that the resolution and efficiency of RP-UPLC were significantly higher than those of CE and RP-HPLC. Characteristic RP-UPLC patterns of different bread wheat variety and related species were readily identified. These results demonstrated that our RP-UPLC procedure resulted in significant improvements in sensitivity, speed, and resolution, and thus is highly useful in wheat cultivar and germplasm identification.     

Analysis of polyacrylamide gel electrophoresis through the PIQUANT image recognition system

Polyacrylamide gels, with separated components which can be made visible by fluorescent or colored dyes and thereafter photographed, can be analyzed at high speed and resolution by a computerized image-recognition device (PIQUANT). The system provides relative mobilities and relative distributions of separated components of multiple samples at the rate of about 1 sec/sample and with greater resolution than can be attained by conventional methods.     

The locomotory function of the fins in the squid Loligo pealei

Kinematic data of high spatial and temporal resolution, acquired from image sequences of adult long-finned squid, Loligo pealei, during steady swimming in a flume, were used to examine the role of fins and the coordination between fin and jet propulsion in squid locomotion. Fin shape and body outlines were digitized and used to calculate fin wave speed, amplitude, frequency, angle of attack, body deformation, speed, and acceleration. L. pealei were observed to have two fin gait patterns with a transition at 1.4-1.8 mantle lengths per second (Lm s-1) marked by alternation between the two patterns. Fin motion in L. pealei exhibited characteristics of both traveling waves and flapping wings. At low speeds, fin motion was more wave-like; at high speeds, fin motion was more flap-like and was marked by regular periods during which the fins were wrapped tightly against the mantle. Fin cycle frequencies were dependent on swimming speed and gait, and obvious coordination between the fins and jet were observed. Fin wave speed, angle of attack, and body acceleration confirmed the role of fins in thrust production and revealed a role of fins at all swimming speeds by a transition from drag-based to lift-based thrust when fin wave speed dropped below swimming speed. Estimates of peak fin thrust were as high as 0.44-0.96 times peak jet thrust in steady swimming over the range of swimming speeds observed. Fin downstrokes generally contributed more to thrust than did upstrokes, especially at high speeds.     

A flexible multiple sequence alignment program

The 'regions' method for multisequence alignment used in the previously reported program MALIGN has been generalized to include recursive refinement so that unaligned portions between two regions at the current level of resolution can be handled with increased resolution. Additionally, there is incorporated a limiting of the number of regions to be used at any level of resolution from which to abstract an alignment. This provides a significant increase in speed over the unlimited version. The program GENALIGN uses this improved regions method to execute fast pairwise alignments in the framework of Taylor's multisequence alignment procedure using clustered pairwise alignments. Pairwise alignments by dynamic programming are also provided in the program.     

Issues for application of virtual microscopy to cytoscreening,perspectives based on questionnaire to Japanese cytotechnologists

To clarify the issues associated with the applications of virtual microscopy to the daily cytology slide screening, we conducted a survey at a slide conference of cytology. The survey was conducted specifically to the Japanese cytology technologists who use microscopes on a routine basis. Virtual slides (VS) were prepared from cytology slides using NanoZoomer (Hamamatsu Photonics, Japan), which is capable of adjusting focus on any part of the slide. A total of ten layers were scanned from the same slides, with 2 micrometer intervals. To simulate the cytology slide screening, no marker points were created. The total data volume of six slides was approximately 25 Giga Bytes. The slides were stored on the Windows 2003 Server, and were made accessible on the web to the cytology technologists. Most cytotechnologists answered "Satisfied" or "Acceptable" to the VS resolution and drawing speed, and "Dissatisfied" to the operation speed. To the ten layered focus, an answer "insufficient" was slightly more frequent than the answer "sufficient", while no one answered "fewer is acceptable" or "no need for depth". As for the use of cytology slide screening, answers "usable, but requires effort" and "not usable" were about equal in number. In a Japanese cytology meeting, a unique VS system has been used in slide conferences with markings to the discussion point for years. Therefore, Japanese cytotechnologists are relatively well accustomed to the use of VS, and the survey results showed that they regarded VS more positively than we expected. Currently, VS has the acceptable resolution and drawing speed even on the web. Most cytotechnologists regard the focusing capability crucial for cytology slide screening, but the consequential enlargement of data size, longer scanning time, and slower drawing speed are the issues that are yet to be resolved.     

Environmental and seasonal correlates of capercaillie movement traits in a Swedish wind farm

Animals continuously interact with their environment through behavioral decisions, rendering the appropriate choice of movement speed and directionality an important phenotypic trait. Anthropogenic activities may alter animal behavior, including movement. A detailed understanding of movement decisions is therefore of great relevance for science and conservation alike. The study of movement decisions in relation to environmental and seasonal cues requires continuous observation of movement behavior, recently made possible by high‐resolution telemetry. We studied movement traits of 13 capercaillie (Tetrao urogallus), a mainly ground‐moving forest bird species of conservation interest, over two summer seasons in a Swedish windfarm using high‐resolution GPS tracking data (5‐min sampling interval). We filtered and removed unreliable movement steps using accelerometer data and step characteristics. We explored variation in movement speed and directionality in relation to environmental and seasonal covariates using generalized additive mixed models (GAMMs). We found evidence for clear daily and seasonal variation in speed and directionality of movement that reflected behavioral adjustments to biological and environmental seasonality. Capercaillie moved slower when more turbines were visible and faster close to turbine access roads. Movement speed and directionality were highest on open bogs, lowest on recent clear‐cuts (<5 y.o.), and intermediate in all types of forest. Our results provide novel insights into the seasonal and environmental correlates of capercaillie movement patterns and supplement previous behavioral observations on lekking behavior and wind turbine avoidance with a more mechanistic understanding.     

Fluorescence Microscopy Gets Faster and Clearer: Roles of Photochemistry and Selective Illumination

Significant advances in fluorescence microscopy tend be a balance between two competing qualities wherein improvements in resolution and low light detection are typically accompanied by losses in acquisition rate and signal-to-noise, respectively. These trade-offs are becoming less of a barrier to biomedical research as recent advances in optoelectronic microscopy and developments in fluorophore chemistry have enabled scientists to see beyond the diffraction barrier, image deeper into live specimens, and acquire images at unprecedented speed. Selective plane illumination microscopy has provided significant gains in the spatial and temporal acquisition of fluorescence specimens several mm in thickness. With commercial systems now available, this method promises to expand on recent advances in 2-photon deep-tissue imaging with improved speed and reduced photobleaching compared to laser scanning confocal microscopy. Superresolution microscopes are also available in several modalities and can be coupled with selective plane illumination techniques. The combination of methods to increase resolution, acquisition speed, and depth of collection are now being married to common microscope systems, enabling scientists to make significant advances in live cell and in situ imaging in real time. We show that light sheet microscopy provides significant advantages for imaging live zebrafish embryos compared to laser scanning confocal microscopy.     

Making sense of ultrahigh‐resolution movement data: A new algorithm for inferring sites of interest

Decomposing the life track of an animal into behavioral segments is a fundamental challenge for movement ecology. The proliferation of high‐resolution data, often collected many times per second, offers much opportunity for understanding animal movement. However, the sheer size of modern data sets means there is an increasing need for rapid, novel computational techniques to make sense of these data. Most existing methods were designed with smaller data sets in mind and can thus be prohibitively slow. Here, we introduce a method for segmenting high‐resolution movement trajectories into sites of interest and transitions between these sites. This builds on a previous algorithm of Benhamou and Riotte‐Lambert (2012). Adapting it for use with high‐resolution data. The data’s resolution removed the need to interpolate between successive locations, allowing us to increase the algorithm’s speed by approximately two orders of magnitude with essentially no drop in accuracy. Furthermore, we incorporate a color scheme for testing the level of confidence in the algorithm's inference (high = green, medium = amber, low = red). We demonstrate the speed and accuracy of our algorithm with application to both simulated and real data (Alpine cattle at 1 Hz resolution). On simulated data, our algorithm correctly identified the sites of interest for 99% of “high confidence” paths. For the cattle data, the algorithm identified the two known sites of interest: a watering hole and a milking station. It also identified several other sites which can be related to hypothesized environmental drivers (e.g., food). Our algorithm gives an efficient method for turning a long, high‐resolution movement path into a schematic representation of broadscale decisions, allowing a direct link to existing point‐to‐point analysis techniques such as optimal foraging theory. It is encoded into an R package called SitesInterest , so should serve as a valuable tool for making sense of these increasingly large data streams.     

Three-dimensional sub-100 nm resolution fluorescence microscopy of thick samples

Imaging volumes as thick as whole cells at three-dimensional (3D) super-resolution is required to reveal unknown features of cellular organization. We report a light microscope that generates images with translationally invariant 30 x 30 x 75 nm resolution over a depth of several micrometers. This method, named biplane (BP) FPALM, combines a double-plane detection scheme with fluorescence photoactivation localization microscopy (FPALM) enabling 3D sub-diffraction resolution without compromising speed or sensitivity.     

The locomotory function of the fins in the squid Loligo pealei

Kinematic data of high spatial and temporal resolution, acquired from image sequences of adult long-finned squid, Loligo pealei, during steady swimming in a flume, were used to examine the role of fins and the coordination between fin and jet propulsion in squid locomotion. Fin shape and body outlines were digitized and used to calculate fin wave speed, amplitude, frequency, angle of attack, body deformation, speed, and acceleration. L. pealei were observed to have two fin gait patterns with a transition at 1.4-1.8 mantle lengths per second (L_m s^-1) marked by alternation between the two patterns. Fin motion in L. pealei exhibited characteristics of both traveling waves and flapping wings. At low speeds, fin motion was more wave-like; at high speeds, fin motion was more flap-like and was marked by regular periods during which the fins were wrapped tightly against the mantle. Fin cycle frequencies were dependent on swimming speed and gait, and obvious coordination between the fins and jet were observed. Fin wave speed, angle of attack, and body acceleration confirmed the role of fins in thrust production and revealed a role of fins at all swimming speeds by a transition from drag-based to lift-based thrust when fin wave speed dropped below swimming speed. Estimates of peak fin thrust were as high as 0.44-0.96 times peak jet thrust in steady swimming over the range of swimming speeds observed. Fin downstrokes generally contributed more to thrust than did upstrokes, especially at high speeds.     

The mechanics of stridulation of the cricketGryllus campestris

Summary Details in the stridulatory movement ofGryllus campestris were investigated using an improved high resolution miniature angle measurement system. The following results were obtained: During the closing (sound producing) stroke, the speed of the plectrum always has the same value (within measuring accuracy) at a given position. Plectrum speed is directly proportional to tooth spacing, which is known to vary along the file. The only exception to this rule were occasions when closing velocities of precisely 2 times the standard value were found. In between values were never recorded. While temperature has a large effect on the opening speed and duration, the closing speed has a very smallQ ₁₀ (0.07) which is equal to theQ ₁₀ of the resonance frequency of the harp. When the harps are removed, the proportionality between tooth spacing and scraper velocity is lost; the velocity is much increased (up to 3-fold) and the variance of the speed is enhanced 5-fold.These results are discussed with respect to 3 hypothetical models explaining the function of the sound generator system. The model describing the cricket sound generator as a clockwork with an escapement system is capable of accommodating all experimental data without any extra assumptions.