soft-matter/trackpy: Trackpy v0.4.2

Allan, Dan; Wel, Casper van der; Keim, Nathan C.; Caswell, Thomas A; Wieker, Devin; Verweij, Ruben W.; Reid, Chaz; Thierry,; Grueter, Lars; Ramos, K.; apiszcz,; zoeith,; Perry, Rebecca W.; Boulogne, François; Sinha, Prashant R.; pfigliozzi,; Bruot, Nicolas; Uieda, Leonardo; Katins, Jan; Mary, Hadrien; Ahmadia, Aron

doi:10.5281/zenodo.3492186

Cited by 71 publications

(46 citation statements)

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“…The particle suspension, with 50% ethanol as a spreading agent, is handled using pipette tips and Eppendorf tubes that are free of surface treatments (Axygen "Maxymum Recovery"). The typical spacing between particle centers is a = 8.8 µm, corresponding to the first peak of the radial pair correlation function g(r) (62). In some movies we observe voids and small aggregates that are presumably due to trace contaminants, but in experiments these act as rigid inclusions and have no special role in rearrangements or memory (see Supplemental Information).…”

Section: Methodsmentioning

confidence: 93%

Mechanical annealing and memories in a disordered solid

Keim¹,

Medina²

2021

Preprint

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Shearing a disordered or amorphous solid for many cycles with a constant strain amplitude can anneal it, relaxing a sample to a steady state that encodes a memory of that amplitude. This steady state also features a remarkable stability to amplitude variations that allows one to read the memory. Here we shed new light on both annealing and memory, by considering how to mechanically anneal a sample to have as little memory content as possible. In experiments, we show that a "ring-down" protocol reaches a comparable steady state, but with no discernible memories and minimal structural anisotropy. We introduce a method to characterize the population of rearrangements within a sample, and show how it connects with the response to amplitude variation and the size of annealing steps. These techniques can be generalized to other forms of glassy matter and a wide array of disordered solids, especially those that yield by flowing homogeneously.

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Section: Methodsmentioning

confidence: 93%

Mechanical annealing and memories in a disordered solid

Keim¹,

Medina²

2021

Preprint

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“…The HTS system utilized a Yokogawa CV7000 Cell Voyager high-throughput microscope to record time-lapse images from two positions in each well. An adaptation of a tracking algorithm, Trackpy v0.4.1 ( Allan et al , 2018 ), was utilized to track individual spermatozoa within each well and obtain kinematic parameters. Within the compound-test plates, dimethylsulphoxide (DMSO) was used as the vehicle control.…”

Section: Methodsmentioning

confidence: 99%

Compounds enhancing human sperm motility identified using a high-throughput phenotypic screening platform

et al. 2022

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STUDY QUESTION Can a high-throughput screening (HTS) platform facilitate male fertility drug discovery? SUMMARY ANSWER An HTS platform identified a large number of compounds that enhanced sperm motility. WHAT IS KNOWN ALREADY Several efforts to find small molecules modulating sperm function have been performed but none have used high-throughput technology. STUDY DESIGN, SIZE, DURATION Healthy donor semen samples were used and samples were pooled (3–5 donors per pool). Primary screening was performed singly; dose–response screening was performed in duplicate (using independent donor pools). PARTICIPANTS/MATERIALS, SETTING, METHODS Spermatozoa isolated from healthy donors were prepared by density gradient centrifugation and incubated in 384-well plates with compounds (6.25 μM) to identify those compounds with enhancing effects on motility. Approximately 17 000 compounds from the libraries, ReFRAME, Prestwick, Tocris, LOPAC, CLOUD and MMV Pathogen Box, were screened. Dose–response experiments of screening hits were performed to confirm the enhancing effect on sperm motility. Experiments were performed in a university setting. MAIN RESULTS AND THE ROLE OF CHANCE From our primary single concentration screening, 105 compounds elicited an enhancing effect on sperm motility compared to dimethylsulphoxide-treated wells. Confirmed enhancing compounds were grouped based on their annotated targets/target classes. A major target class, phosphodiesterase inhibitors, were identified, in particular PDE10A inhibitors as well as number of compounds not previously known to enhance human sperm motility, such as those related to GABA signalling. LARGE SCALE DATA N/A. LIMITATIONS, REASONS FOR CAUTION Although this approach provides data about the activity of the compound, it is only a starting point. For example, further substantive experiments are necessary to provide a more comprehensive picture of each compound’s activity, the effect on the kinetics of the cell populations and subpopulations, and their potential mechanisms of action. Compounds have been tested with prepared donor spermatozoa, incubated under non-capacitating conditions, and only incubated with compounds for a relatively short period of time. Therefore, the effect of compounds under different conditions, for example in whole semen, for longer incubation times, or using samples from patient groups, may be different and require further study. All experiments were performed in vitro. WIDER IMPLICATIONS OF THE FINDINGS This phenotypic screening assay identified a large number of compounds that increased sperm motility. In addition to furthering our understanding of human sperm function, for example identifying new avenues for discovery, we highlight potential compounds as promising start-point for a medicinal chemistry programme for potential enhancement of male fertility. Moreover, with disclosure of the results of screening, we present a substantial resource to inform further work in the field. STUDY FUNDING/COMPETING INTEREST(S) This study was supported by the Bill and Melinda Gates Foundation, Scottish Funding Council and Scottish Universities Life Science Alliance. C.L.R.B. is Editor for RBMO. C.L.R.B. receives funding from Chief Scientists Office (Scotland), ESHRE and Genus PLC, consulting fees from Exscientia and lecture fees from Cooper Surgical and Ferring. S.M.d.S. is an Associate Editor of Human Reproduction, and an Associate Editor of Reproduction and Fertility. S.M.d.S. receives funding from Cooper Surgical and British Dietetic Society. No other authors declared a COI.

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“…As in our previous work, the fluids were prepared with glass microspheres, and a laser (with wavelength of 532 nm) and a high speed camera (Phantom Miro 310) were used to image the flow plane. Particle trajectories were obtained from short clips of the video of the flow (much shorter than the time scales of flow evolution) using a Python script based on the TrackPy library 34 and (in the same script) averaged over small intervals along the radial axis to obtain spatially resolved velocity data with quantified uncertainty. In a modified version of the script, the above analysis was repeated for many consecutive intervals throughout longer videos to obtain a spatiotemporal map of either start-up or quasi-steady flow velocity.…”

Section: Rheo-optical Measurementsmentioning

confidence: 99%

Role of Micellar Entanglement Density on Kinetics of Shear Banding Flow Formation

Rassolov¹,

Hadi²

2022

Preprint

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We investigate the effects of micellar entanglement density on the kinetics of shear banding flow formation in a Taylor-Couette flow via a combination of experiments and simulations of the Vasquez-Cook-McKinley (VCM) model. In experiments, three sets of wormlike micellar solutions, each set with a similar fluid elasticity and zero-shearrate viscosity, but with varying entanglement densities, are studied under start-up of steady shear. Our experiments indicate that in the set with the low fluid elasticity, the transient shear banding flow is characterized by the formation of a transient flow reversal in a range of entanglement densities. Outside of this range, the transient flow reversal is not observed. For the sets of medium and high elasticities, the transient flow reversals exist for relatively small entanglement densities, and disappear for large entanglement densities. Our analysis shows that wall slip and elastic instabilities do not affect this transient flow feature. Consistent with experiments, simulations of the VCM model predict that as the micellar entanglement density increases, the strength of the transient flow reversal first increases, then, at a higher entanglement density, the transient flow reversal weakens. We identify a correlation between micellar entanglement density, the width of the stress plateau, and the extent of the transient flow reversal. As the micellar entanglement density increases, the width of the stress plateau first increases, then, at a higher micellar entanglement density, plateau width decreases. Therefore, we hypothesize that the transient flow reversal is connected to the micellar entanglement density through the width of the stress plateau.

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soft-matter/trackpy: Trackpy v0.4.2

Cited by 71 publications

References 0 publications

Mechanical annealing and memories in a disordered solid

Mechanical annealing and memories in a disordered solid

Compounds enhancing human sperm motility identified using a high-throughput phenotypic screening platform

Role of Micellar Entanglement Density on Kinetics of Shear Banding Flow Formation

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