The effect of integration time on fluctuation measurements: calibrating an optical trap in the presence of motion blur

Dynamical instrument limitations, such as finite detection bandwidth, do not simply add statistical errors to fluctuation measurements, but can create significant systematic biases that affect the measurement of steady-state properties. Such effects must be considered when calibrating ultra-sensitive force probes by analyzing the observed Brownian fluctuations. In this article, we present a novel method for extracting the true spring constant and diffusion coefficient of a harmonically confined Brownian particle that extends the standard equipartition and power spectrum techniques to account for video-image motion blur. These results are confirmed both numerically with a Brownian dynamics simulation, and experimentally with laser optical tweezers.Comment: 12 pages, 6 figures, revtex4; published in Optics Express. http://www.opticsinfobase.org/abstract.cfm?URI=oe-14-25-1251

Massively parallel single-molecule manipulation using centrifugal force

Precise manipulation of single molecules has already led to remarkable insights in physics, chemistry, biology and medicine. However, widespread adoption of single-molecule techniques has been impeded by equipment cost and the laborious nature of making measurements one molecule at a time. We have solved these issues with a new approach: massively parallel single-molecule force measurements using centrifugal force. This approach is realized in a novel instrument that we call the Centrifuge Force Microscope (CFM), in which objects in an orbiting sample are subjected to a calibration-free, macroscopically uniform force-field while their micro-to-nanoscopic motions are observed. We demonstrate high-throughput single-molecule force spectroscopy with this technique by performing thousands of rupture experiments in parallel, characterizing force-dependent unbinding kinetics of an antibody-antigen pair in minutes rather than days. Additionally, we verify the force accuracy of the instrument by measuring the well-established DNA overstretching transition at 66 $\pm$ 3 pN. With significant benefits in efficiency, cost, simplicity, and versatility, "single-molecule centrifugation" has the potential to revolutionize single-molecule experimentation, and open access to a wider range of researchers and experimental systems.Comment: 5 pages, 3 figure

Beyond the frame rate: Measuring high-frequency fluctuations with light intensity modulation

Power spectral density measurements of any sampled signal are typically restricted by both acquisition rate and frequency response limitations of instruments, which can be particularly prohibitive for video-based measurements. We have developed a new method called Intensity Modulation Spectral Analysis (IMSA) that circumvents these limitations, dramatically extending the effective detection bandwidth. We demonstrate this by video-tracking an optically-trapped microsphere while oscillating an LED illumination source. This approach allows us to quantify fluctuations of the microsphere at frequencies over 10 times higher than the Nyquist frequency, mimicking a significantly higher frame rate.Comment: 4 pages, 2 figure

Phadiatop Infant in the Diagnosis of Atopy in Children with Allergy-Like Symptoms

Background and Objective. Allergy-like symptoms such as wheezing and eczema are common in young children and an early diagnosis is important to initiate correct management. The objective of this study was to evaluate the diagnostic performance of Phadiatop Infant, an in vitro test for determination of early sensitisation to food and inhalant allergens. Patients and Methods. The study was conducted, retrospectively, using frozen sera from 122 children (median age 2.7 years) admitted to the hospital with suspected allergic symptoms. The doctor's diagnosis atopic/nonatopic was based on routinely used procedures such as clinical evaluation, SPT, total and allergen-specific IgE antibodies. The performance of Phadiatop Infant was evaluated in a blinded manner against this diagnosis. Results. Eighty-four of the 86 children classified as atopic showed a positive Phadiatop Infant test. Thirty-six were classified as nonatopic, 32 of who had a negative test. With a prevalence of atopy of 70% in this population, this gives a sensitivity of 98%, a specificity of 89%, and a positive and negative predictive value of 95% and 94%, respectively. Conclusion. The results from the present study suggest that Phadiatop Infant could be recommended as a complement to the clinical information in the differential diagnosis on IgE-mediated disease in young children with allergy-like symptoms

Biometric Fish Classification of Temperate Species Using Convolutional Neural Network with Squeeze-and-Excitation

submittedVersio

Massively parallel singlemolecule manipulation using centrifugal force

ABSTRACT Precise manipulation of single molecules has already led to remarkable insights in physics, chemistry, biology, and medicine. However, widespread adoption of single-molecule techniques has been impeded by equipment cost and the laborious nature of making measurements one molecule at a time. We have solved these issues by developing an approach that enables massively parallel single-molecule force measurements using centrifugal force. This approach is realized in an instrument that we call the centrifuge force microscope in which objects in an orbiting sample are subjected to a calibration-free, macroscopically uniform force-field while their micro-to-nanoscopic motions are observed. We demonstrate high-throughput singlemolecule force spectroscopy with this technique by performing thousands of rupture experiments in parallel, characterizing force-dependent unbinding kinetics of an antibody-antigen pair in minutes rather than days. Additionally, we verify the force accuracy of the instrument by measuring the well-established DNA overstretching transition at 66 5 3 pN. With significant benefits in efficiency, cost, simplicity, and versatility, single-molecule centrifugation has the potential to expand single-molecule experimentation to a wider range of researchers and experimental systems. Received for publication 8 January 2010 and in final form 10 March 2010. Single-molecule research has advanced greatly in the last decade, fueled in part by the development of technologies such as the atomic force microscope (AFM) and optical and magnetic tweezers, which enable precise physical manipulation of single molecular constructs (1). Remarkable studies with these instruments have already yielded new insight into such diverse areas as protein folding and unfolding dynamics, motor proteins, dynamic strength of receptor ligand interactions, enzymatic activity, and DNA mechanics (1-5). Widespread use of these powerful techniques, however, has been impeded by the laborious nature of making measurements one molecule at a time, the typically costly equipment, and the requisite technical expertise to perform these measurements. Recently these issues have received some attention with innovations such as multiplexed magnetic tweezer systems (6,7) to increase efficiency and more cost-effective designs for optical tweezers systems (8). We have developed an approach to solve these problems: massively parallel single-molecule force measurements using centrifugal force. The basic concept is that by rapidly rotating a high-resolution detection system, a centrifugal force field can be applied to an ensemble of objects while simultaneously observing their micro-to-nanoscopic motions. This is implemented in a new instrument that we call the centrifuge force microscope (CFM) The centrifugal force applied to each molecular tether can be easily determined using F ¼ mu 2 R, where m is the mass of the bead (minus the mass of the medium displaced to account for buoyancy), u is the magnitude of its angular velocity, and R is its distance from the axis of rotation. Since R is a macroscopic length much larger than the motion of the particles and the region of observation, the force field is conveniently uniform over the sample and as stable as the constancy of u. For monodisperse beads of known size and density (available commercially or by processing (11)) the centrifugal force on each particle is identical and can be calculated directly without calibration. Detection of molecular transitions, such as bond rupture or tether extension, is also straightforward. Since the force is normal to the coverslip and the whole system rotates, the beads appear relatively stationary in the field of view, but are pulled out of focus as a molecular tether stretches or detaches. Although a variety of bead detection schemes are possible, image focus provides the simplest way to determine if a bead is connected to the surface or not. For example, when measuring bond dissociation kinetics under constant force, one simply needs to measure the times at which singly tethered beads abruptly detach from the coverslip and disappear from view. We demonstrate this method by performing thousands of single-molecule measurements in parallel to characterize the force-dependent unbinding kinetics of digoxigenin and its antibody By applying various force clamps, we determined the force-dependent off-rate k off (f) ¼ k 0 exp(f/f b ) (12,13) for the interaction of digoxigenin and its antibody. We found a stress-free off-rate of k 0 ¼ 0.015 5 0.002 s À1 and a force scale of f b ¼ 4.6 5 1.3 p

EEG reinvestigations of visual statistical learning for faces, scenes, and objects

The objective of this ongoing, replication study is to understand temporal and spatial patterns in our environment by using the technique of electroencephalography (EEG). Visual statistical learning (VSL) helps us to understand conditional probabilities from our environments. This concept is why we know that chairs are located under tables, not above. The goal of this study is to understand whether participants can unconsciously associate pairs of items (faces, scenes, and objects) from their short-term memory. Strong pairs become more similar to each other, as compared to weak pairs, which become less similar. In the main task, participants saw items appear on the screen, on at a time, for 100ms each. Items directly followed each other without transitions. In the post-task, participants were asked to rate how familiar pairs of items were, using a sliding scale. There were three types of pairs presented: strong pairs where item B followed item A 100% of the time; weak pairs where item B followed item A 11% of the time; and foil pairs where item B followed item A 0% of the time. In conclusion, results are similar to the current study (n = 10) in that there are behavioral differences between strong vs. foil and strong vs. weak pairs

A simplicial gauge theory

We provide an action for gauge theories discretized on simplicial meshes, inspired by finite element methods. The action is discretely gauge invariant and we give a proof of consistency. A discrete Noether's theorem that can be applied to our setting, is also proved.Comment: 24 pages. v2: New version includes a longer introduction and a discrete Noether's theorem. v3: Section 4 on Noether's theorem has been expanded with Proposition 8, section 2 has been expanded with a paragraph on standard LGT. v4: Thorough revision with new introduction and more background materia

Elevated reactive oxygen species and antioxidant enzyme activities in animal and cellular models of Parkinson's disease

AbstractThe dopaminergic neurotoxin N-methyl,4-phenyl-1,2,3,6 tetrahydropyridine (MPTP) causes a syndrome in primates and humans which mimics Parkinson's disease (PD) in clinical, pathological, and biochemical findings, including diminished activity of complex I in the mitochondrial electron transport chain. Reduced complex I activity is found in sporadic PD and can be transferred through mitochondrial DNA, suggesting a mitochondrial genetic etiology. We now show that MPTP treatment of mice and N-methylpyridinium (MPP+) exposure of human SH-SY5Y neuroblastoma cells increases oxygen free radical production and antioxidant enzyme activities. Cybrid cells created by transfer of PD mitochondria exhibit similar characteristics; however, PD cybrids' antioxidant enzyme activities are not further increased by MPP+ exposure, as are the activities in control cybrids. PD mitochondrial cybrids are subject to metabolic and oxidative stresses similar to MPTP parkinsonism and provide a model to determine mechanisms of oxidative damage and cell death in PD