Four dimensional material movies: High speed phase-contrast tomography by backprojection along dynamically curved paths.
Ontology highlight
ABSTRACT:
SUBMITTER: Ruhlandt A
PROVIDER: S-EPMC5529574 | biostudies-literature | 2017 Jul
REPOSITORIES: biostudies-literature
Publications
Four dimensional material movies: High speed phase-contrast tomography by backprojection along dynamically curved paths.
Ruhlandt A A Töpperwien M M Krenkel M M Mokso R R Salditt T T
Scientific reports 20170726 1
We present an approach towards four dimensional (4d) movies of materials, showing dynamic processes within the entire 3d structure. The method is based on tomographic reconstruction on dynamically curved paths using a motion model estimated by optical flow techniques, considerably reducing the typical motion artefacts of dynamic tomography. At the same time we exploit x-ray phase contrast based on free propagation to enhance the signal from micron scale structure recorded with illumination times ...[more]
Similar Datasets
Project description:Accurate perception of motion depends critically on accurate estimation of retinal motion speed. Here we first analyse natural image movies to determine the optimal space-time receptive fields (RFs) for encoding local motion speed in a particular direction, given the constraints of the early visual system. Next, from the RF responses to natural stimuli, we determine the neural computations that are optimal for combining and decoding the responses into estimates of speed. The computations show how selective, invariant speed-tuned units might be constructed by the nervous system. Then, in a psychophysical experiment using matched stimuli, we show that human performance is nearly optimal. Indeed, a single efficiency parameter accurately predicts the detailed shapes of a large set of human psychometric functions. We conclude that many properties of speed-selective neurons and human speed discrimination performance are predicted by the optimal computations, and that natural stimulus variation affects optimal and human observers almost identically.
| S-EPMC4532855 | biostudies-literature
Project description:Antibiotic resistance can evolve through the sequential accumulation of multiple mutations. To study such gradual evolution, we developed a selection device, the 'morbidostat', that continuously monitors bacterial growth and dynamically regulates drug concentrations, such that the evolving population is constantly challenged. We analyzed the evolution of resistance in Escherichia coli under selection with single drugs, including chloramphenicol, doxycycline and trimethoprim. Over a period of ?20 days, resistance levels increased dramatically, with parallel populations showing similar phenotypic trajectories. Whole-genome sequencing of the evolved strains identified mutations both specific to resistance to a particular drug and shared in resistance to multiple drugs. Chloramphenicol and doxycycline resistance evolved smoothly through diverse combinations of mutations in genes involved in translation, transcription and transport. In contrast, trimethoprim resistance evolved in a stepwise manner, through mutations restricted to the gene encoding the enzyme dihydrofolate reductase (DHFR). Sequencing of DHFR over the time course of the experiment showed that parallel populations evolved similar mutations and acquired them in a similar order.
| S-EPMC3534735 | biostudies-literature
Project description:Brain-computer interfaces (BCIs) are being developed to assist paralyzed people and amputees by translating neural activity into movements of a computer cursor or prosthetic limb. Here we introduce a novel BCI task paradigm, intended to help accelerate improvements to BCI systems. Through this task, we can push the performance limits of BCI systems, we can quantify more accurately how well a BCI system captures the user's intent, and we can increase the richness of the BCI movement repertoire.We have implemented an instructed path task, wherein the user must drive a cursor along a visible path. The instructed path task provides a versatile framework to increase the difficulty of the task and thereby push the limits of performance. Relative to traditional point-to-point tasks, the instructed path task allows more thorough analysis of decoding performance and greater richness of movement kinematics.We demonstrate that monkeys are able to perform the instructed path task in a closed-loop BCI setting. We further investigate how the performance under BCI control compares to native arm control, whether users can decrease their movement variability in the face of a more demanding task, and how the kinematic richness is enhanced in this task.The use of the instructed path task has the potential to accelerate the development of BCI systems and their clinical translation.
| S-EPMC4330471 | biostudies-literature
Project description:Using a generalized Brownian ratchet model that accounts for the interactions of actin filaments with the surface of Listeria mediated by proteins like ActA and Arp2/3, we have developed a microscopic model for the movement of Listeria. Specifically, we show that a net torque can be generated within the comet tail, causing the bacteria to spin about its long axis, which in conjunction with spatially varying polymerization at the surface leads to motions of bacteria in curved paths that include circles, sinusoidal-like curves, translating figure eights, and serpentine shapes, as observed in recent experiments. A key ingredient in our formulation is the coupling between the motion of Listeria and the force-dependent rate of filament growth. For this reason, a numerical scheme was developed to determine the kinematic parameters of motion and stress distribution among filaments in a self-consistent manner. We find that a 5-15% variation in polymerization rates can lead to radii of curvatures of the order of 4-20 microm, measured in experiments. In a similar way, our results also show that most of the observed trajectories can be produced by a very low degree of correlation, <10%, among filament orientations. Since small fluctuations in polymerization rate, as well as filament orientation, can easily be induced by various factors, our findings here provide a reasonable explanation for why Listeria can travel along totally different paths under seemingly identical experimental conditions. Besides trajectories, stress distributions corresponding to different polymerization profiles are also presented. We have found that although some actin filaments generate propelling forces that push the bacteria forward, others can exert forces opposing the movement of Listeria, consistent with recent experimental observations.
| S-EPMC2920721 | biostudies-literature
Project description:This paper examines tongue movements between the two vowels in sequences of vowel-labial consonant-vowel, addressing the question whether the movement is a straight line or a curved path. Native speakers of Japanese and Italian served as subjects. The linguistic material consisted of words where the bilabial consonant was either long or short. The inclusion of words with different consonant lengths was motivated by earlier findings that the tongue movement is often longer when the consonant is long, which may be due to a more curved movement path. Tongue movements were recorded using a three-transmitter magnetometer system. To assess the movement path, the movement magnitude was calculated in two ways, as a straight line, the Euclidean distance, and as the actual path, obtained by summing the individual Euclidean distances between successive samples from movement onset to offset. The ratio between the path and the Euclidean distance is 1 when the movement is a straight line and greater than 1 when the path is curved. Results show that in virtually all 21 cases examined the ratio was very close to 1 and in most cases 1.2 or less. There was no reliable influence of consonant length on the ratio.
| S-EPMC3078025 | biostudies-other
Project description:To determine whether intravenous low-osmolality iodinated contrast material is associated with post-computed tomography (CT) acute kidney injury (AKI).Institutional review board approval was obtained and patient consent waived for this HIPAA-compliant retrospective study. CT examinations performed over a 10-year period in adult inpatients with sufficient serum creatinine (SCr) data were identified. A one-to-one propensity-matched matched cohort analysis with multivariate analysis of effects was performed with post-CT AKI as the primary outcome measure (10,121 unenhanced and 10,121 intravenous contrast-enhanced CT examinations in 20,242 patients). Propensity matching was performed with respect to likelihood of patient receiving intravenous contrast material (36 tested covariates). The primary endpoint was post-CT AKI by using Acute Kidney Injury Network SCr criteria; the secondary endpoint was post-CT AKI by using traditional SCr criteria for contrast material-induced nephrotoxicity (CIN; SCr increase ≥0.5 mg/dL [44.20 μmol/L] or ≥25%). Multivariate subgroup threshold analysis was performed (SCr <1.5 [<132.60 μmol/L]; ≥1.5 to ≥2.0 mg/dL [≥132.60 to ≥176.80 μmol/L]) and adjusted for assigned propensity scores.Intravenous low-osmolality iodinated contrast material had a significant effect on the development of post-CT AKI for patients with pre-CT SCr levels of 1.6 mg/dL (141.44 μmol/L) or greater (odds ratio, 1.45; 95% confidence interval [CI]: 1.11, 1.89;P = .007). This effect strengthened as pre-CT SCr increased. Patients with stable SCr less than 1.5 mg/dL (132.60 μmol/L) were not at risk for developing CIN (P = .25, power > 95%). Both endpoints demonstrated similar results (eg, SCr ≥1.6 mg/dL [141.44 μmol/L] by using traditional CIN criteria: odds ratio, 1.64; 95% CI: 1.18, 2.28; P = .003). Post-CT AKI was prevalent in both the unenhanced and contrast-enhanced CT subgroups, and it increased with increases in pre-CT SCr. Many risk factors contributed to development of post-CT AKI, regardless of iodinated contrast material.Intravenous low-osmolality iodinated contrast material is a nephrotoxic risk factor, but not in patients with a stable SCr level less than 1.5 mg/dL. Many factors other than contrast material can affect post-CT AKI rates.
| S-EPMC3606541 | biostudies-other
Project description:For more than a century, transplantation of tissues and organs from animals into man, xenotransplantation, has been viewed as a potential way to treat disease. Ironically, interest in xenotransplantation was fueled especially by successful application of allotransplantation, that is, transplantation of human tissue and organs, as a treatment for a variety of diseases, especially organ failure because scarcity of human tissues limited allotransplantation to a fraction of those who could benefit. In principle, use of animals such as pigs as a source of transplants would allow transplantation to exert a vastly greater impact than allotransplantation on medicine and public health. However, biological barriers to xenotransplantation, including immunity of the recipient, incompatibility of biological systems, and transmission of novel infectious agents, are believed to exceed the barriers to allotransplantation and presently to hinder clinical applications. One way potentially to address the barriers to xenotransplantation is by genetic engineering animal sources. The last 2 decades have brought progressive advances in approaches that can be applied to genetic modification of large animals. Application of these approaches to genetic engineering of pigs has contributed to dramatic improvement in the outcome of experimental xenografts in nonhuman primates and have encouraged the development of a new type of xenograft, a reverse xenograft, in which human stem cells are introduced into pigs under conditions that support differentiation and expansion into functional tissues and potentially organs. These advances make it appropriate to consider the potential limitation of genetic engineering and of current models for advancing the clinical applications of xenotransplantation and reverse xenotransplantation.
| S-EPMC6808066 | biostudies-literature
Project description:Sperm require a sense of direction to locate the egg for fertilization. They follow gradients of chemical and physical cues provided by the egg or the oviduct. However, the principles underlying three-dimensional (3D) navigation in chemical landscapes are unknown. Here using holographic microscopy and optochemical techniques, we track sea urchin sperm navigating in 3D chemoattractant gradients. Sperm sense gradients on two timescales, which produces two different steering responses. A periodic component, resulting from the helical swimming, gradually aligns the helix towards the gradient. When incremental path corrections fail and sperm get off course, a sharp turning manoeuvre puts sperm back on track. Turning results from an 'off' Ca(2+) response signifying a chemoattractant stimulation decrease and, thereby, a drop in cyclic GMP concentration and membrane voltage. These findings highlight the computational sophistication by which sperm sample gradients for deterministic klinotaxis. We provide a conceptual and technical framework for studying microswimmers in 3D chemical landscapes.
| S-EPMC4557273 | biostudies-literature
Project description:Follicular lymphoma (FL) is an indolent disease, characterized by a median life expectancy of 18-20 years and by intermittent periods of relapse and remission. FL frequently transforms into the more aggressive diffuse large B cell lymphoma (t-FL). In previous studies, the analysis of immunoglobulin heavy chain variable region (IgHV) genes in sequential biopsies from the same patient revealed two different patterns of tumor clonal evolution: direct evolution, through acquisition of additional IgHV mutations over time, or divergent evolution, in which lymphoma clones from serial biopsies independently develop from a less-mutated common progenitor cell (CPC). Our goal in this study was to characterize the somatic hypermutation (SHM) patterns of IgHV genes in sequential FL samples from the same patients, and address the question of whether the mutation mechanisms (SHM targeting, DNA repair or both), or selection forces acting on the tumor clones, were different in FL samples compared to healthy control samples, or in late relapsed/transformed FL samples compared to earlier ones. Our analysis revealed differences in the distribution of mutations from each of the nucleotides when tumor and non-tumor clones were compared, while FL and transformed FL (t-FL) tumor clones displayed similar mutation distributions. Lineage tree measurements suggested that either initial clone affinity or selection thresholds were lower in FL samples compared to controls, but similar between FL and t-FL samples. Finally, we observed that both FL and t-FL tumor clones tend to accumulate larger numbers of potential N-glycosylation sites due to the introduction of new SHM. Taken together, these results suggest that transformation into t-FL, in contrast to initial FL development, is not associated with any major changes in DNA targeting or repair, or the selection threshold of the tumor clone.
| S-EPMC9686334 | biostudies-literature
Project description:High-speed atomic force microscopy (HS-AFM) is becoming a reference tool for the study of dynamic biological processes. The spatial and time resolutions of HS-AFM are on the order of nanometers and milliseconds, respectively, and allow structural and functional characterization of biological processes at the single-molecule level. In this work we present contact-mode HS-AFM movies of purple membranes containing two-dimensional arrays of bacteriorhodopsin (bR). In high-resolution movies acquired at a 100 ms frame acquisition time, the substructure on individual bR trimers was visualized. In regions in between different bR arrays, dynamic topographies were observed and interpreted as motion of the bR trimers. Similarly, motion of bR monomers in the vicinity of lattice defects in the purple membrane was observed. Our findings indicate that the bR arrays are in a mobile association-dissociation equilibrium. HS-AFM on membranes provides novel perspectives for analyzing the membrane diffusion processes of nonlabeled molecules.
| S-EPMC2749746 | biostudies-literature