Nappe oscillations on free-overfall structures, data from laboratory experiments.
Ontology highlight
ABSTRACT:
SUBMITTER: Lodomez M
PROVIDER: S-EPMC7299961 | biostudies-literature | 2020 Jun
REPOSITORIES: biostudies-literature
Publications
Nappe oscillations on free-overfall structures, data from laboratory experiments.
Lodomez Maurine M Tullis Blake B Archambeau Pierre P Kitsikoudis Vasileios V Pirotton Michel M Dewals Benjamin B Erpicum Sébastien S
Scientific data 20200617 1
This paper presents a dataset obtained from fifty-two laboratory experiments of nappe oscillations on free overfall structures. Data were collected on two complementary experimental setups, each consisting of a linear weir model. The dataset covers test configurations involving varied geometric parameters (i.e. weir crest shape, weir width, fall height and nappe confinement) and inflow discharges. The following experimental data were produced: assessment of nappe oscillation occurrence and assoc ...[more]
Similar Datasets
Project description:Several ocean Western Boundary Currents (WBCs) encounter a lateral gap along their path. Examples are the Kuroshio Current penetrating into the South China Sea through the Luzon Strait and the Gulf of Mexico Loop Current leaping from the Yucatan peninsula to Florida as part of the Gulf Stream system. Here, we present results on WBC relevant flows, generated in the world's largest rotating platform, where the Earth's sphericity necessary to support WBCs is realized by an equivalent topographic effect. The fluid is put in motion by a pump system, which produces a current that is stationary far from the gap. When the jet reaches the gap entrance, time-dependent patterns with complex spatial structures appear, with the jet leaking, leaping or looping through the gap. The occurrence of these intrinsic self-sustained periodic or aperiodic oscillations depending on current intensity is well known in nonlinear dynamical systems theory and occurs in many real systems. It has been observed here for the first time in real rotating fluid flows and is thought to be highly relevant to explain low-frequency variability in ocean WBCs.
| S-EPMC8792033 | biostudies-literature
Project description:BACKGROUND:QT interval-prolonging drug-drug interactions (QT-DDIs) may increase the risk of life-threatening arrhythmia. Despite guidelines for testing from regulatory agencies, these interactions are usually discovered after drugs are marketed and may go undiscovered for years. OBJECTIVES:Using a combination of adverse event reports, electronic health records (EHR), and laboratory experiments, the goal of this study was to develop a data-driven pipeline for discovering QT-DDIs. METHODS:1.8 million adverse event reports were mined for signals indicating a QT-DDI. Using 1.6 million electrocardiogram results from 380,000 patients in our institutional EHR, these putative interactions were either refuted or corroborated. In the laboratory, we used patch-clamp electrophysiology to measure the human ether-à-go-go-related gene (hERG) channel block (the primary mechanism by which drugs prolong the QT interval) to evaluate our top candidate. RESULTS:Both direct and indirect signals in the adverse event reports provided evidence that the combination of ceftriaxone (a cephalosporin antibiotic) and lansoprazole (a proton-pump inhibitor) will prolong the QT interval. In the EHR, we found that patients taking both ceftriaxone and lansoprazole had significantly longer QTc intervals (up to 12 ms in white men) and were 1.4 times more likely to have a QTc interval above 500 ms. In the laboratory, we found that, in combination and at clinically relevant concentrations, these drugs blocked the hERG channel. As a negative control, we evaluated the combination of lansoprazole and cefuroxime (another cephalosporin), which lacked evidence of an interaction in the adverse event reports. We found no significant effect of this pair in either the EHR or in the electrophysiology experiments. Class effect analyses suggested this interaction was specific to lansoprazole combined with ceftriaxone but not with other cephalosporins. CONCLUSIONS:Coupling data mining and laboratory experiments is an efficient method for identifying QT-DDIs. Combination therapy of ceftriaxone and lansoprazole is associated with increased risk of acquired long QT syndrome.
| S-EPMC5082283 | biostudies-literature
Project description:This paper presents a dataset obtained from fifty four laboratory experiments of the breaching of fluvial dikes due to flow overtopping. Data were collected on two complementary experimental setups, each consisting of a main channel representing the river, an erodible lateral dike and a floodplain. The dataset covers seven test series, involving varying hydraulic boundary conditions (e.g. inflow discharge, downstream boundary conditions), main channel dimensions, as well as bottom and dike material. The following experimental data were produced: time series of water levels in the main channel, time series of flow discharges in the main channel and through the breach, as well as high resolution 3D reconstructions of the breach geometry during its expansion. The latter measurements were performed using a novel non-intrusive laser profilometry technique developed for this research. Reuse of the collected data will support efforts to improve our understanding of the physical processes underpinning fluvial dike breaching. It will also enable benchmarking the accuracy of conceptual or detailed numerical models for the prediction of dike breaching, which is central to flood risk management.
| S-EPMC6514018 | biostudies-literature
Project description:Some studies have ascribed a protective effect against neurodegenerative diseases to the β-carbolines harman (H) and norharman (NH), which occur mostly in coffee and coffee substitutes. We determined the concentrations of β-carbolines and undesirable compounds (such as acrylamide) in roasted coffee substitute ingredients and found that chicory coffee was optimal. Two in vivo experiments were conducted with seventeen-month-old male Sprague Dawley rats fed a diet with the addition of pure carboline standards in the first stage, and chicory in the second. We observed an increase in the level of H and NH in blood plasma, as well as higher activity of animals in the battery behavioral test, particularly in the second stage. The results of in vitro studies-particularly the level of the expression in brain tissue of genes associated with aging processes and neurodegenerative diseases-clearly show the benefits of a diet rich in β-carbolines.
| S-EPMC7432475 | biostudies-literature
Project description:Successful eutrophication control strategies need to address the limiting nutrient. We conducted a battery of laboratory and in situ nutrient-limitation tests with waters collected from 9 streams in an agricultural region of the upper Snake River basin, Idaho, USA. Laboratory tests used the green alga Raphidocelis subcapitata, the macrophyte Lemna minor (duckweed) with native epiphytes, and in situ nutrient-limitation tests of periphyton were conducted with nutrient-diffusing substrates (NDS). In the duckweed/epiphyte test, P saturation occurred when concentrations reached about 100 μg/L. Chlorophyll a in epiphytic periphyton was stimulated at low P additions and by about 100 μg/L P, epiphytic periphyton chlorophyll a appeared to be P saturated. Both duckweed and epiphyte response patterns with total N were weaker but suggested a growth stimulation threshold for duckweed when total N concentrations exceeded about 300 μg/L and approached saturation at the highest N concentration tested, 1300 μg/L. Nutrient uptake by epiphytes and macrophytes removed up to 70 and 90% of the N and P, respectively. The green algae and the NDS nutrient-limitation test results were mostly congruent; N and P co-limitation was the most frequent result for both test series. Across all tests, when N:P molar ratios >30 (mass ratios >14), algae or macrophyte growth was P limited; N limitation was observed at N:P molar ratios up to 23 (mass ratios up to 10). A comparison of ambient periphyton chlorophyll a concentrations with chlorophyll a accrued on control artificial substrates in N-limited streams, suggests that total N concentrations associated with a periphyton chlorophyll a benchmark for desirable or undesirable conditions for recreation would be about 600 to 1000 μg/L total N, respectively. For P-limited streams, the corresponding benchmark concentrations were about 50 to 90 μg/L total P, respectively. Our approach of integrating controlled experiments and matched biomonitoring field surveys was cost effective and more informative than either approach alone.
| S-EPMC8213151 | biostudies-literature
Project description:An idealized version of a label-free discovery mass spectrometry proteomics experiment would provide absolute abundance measurements for a whole proteome, across varying conditions. Unfortunately, this ideal is not realized. Measurements are made on peptides requiring an inferential step to obtain protein level estimates. The inference is complicated by experimental factors that necessitate relative abundance estimation and result in widespread non-ignorable missing data. Relative abundance on the log scale takes the form of parameter contrasts. In a complete-case analysis, contrast estimates may be biased by missing data and a substantial amount of useful information will often go unused. To avoid problems with missing data, many analysts have turned to single imputation solutions. Unfortunately, these methods often create further difficulties by hiding inestimable contrasts, preventing the recovery of interblock information and failing to account for imputation uncertainty. To mitigate many of the problems caused by missing values, we propose the use of a Bayesian selection model. Our model is tested on simulated data, real data with simulated missing values, and on a ground truth dilution experiment where all of the true relative changes are known. The analysis suggests that our model, compared with various imputation strategies and complete-case analyses, can increase accuracy and provide substantial improvements to interval coverage.
| S-EPMC6249692 | biostudies-literature
Project description:The occurrence of mutations is a cornerstone of the evolutionary theory of adaptation, capitalizing on the rare chance that a mutation confers a fitness benefit. Natural selection is increasingly being leveraged in laboratory settings for industrial and basic science applications. Despite increasing deployment, there are no standardized procedures available for designing and performing adaptive laboratory evolution (ALE) experiments. Thus, there is a need to optimize the experimental design, specifically for determining when to consider an experiment complete and for balancing outcomes with available resources (i.e., laboratory supplies, personnel, and time). To design and to better understand ALE experiments, a simulator, ALEsim, was developed, validated, and applied to the optimization of ALE experiments. The effects of various passage sizes were experimentally determined and subsequently evaluated with ALEsim, to explain differences in experimental outcomes. Furthermore, a beneficial mutation rate of 10-6.9 to 10-8.4 mutations per cell division was derived. A retrospective analysis of ALE experiments revealed that passage sizes typically employed in serial passage batch culture ALE experiments led to inefficient production and fixation of beneficial mutations. ALEsim and the results described here will aid in the design of ALE experiments to fit the exact needs of a project while taking into account the resources required and will lower the barriers to entry for this experimental technique.IMPORTANCE ALE is a widely used scientific technique to increase scientific understanding, as well as to create industrially relevant organisms. The manner in which ALE experiments are conducted is highly manual and uniform, with little optimization for efficiency. Such inefficiencies result in suboptimal experiments that can take multiple months to complete. With the availability of automation and computer simulations, we can now perform these experiments in an optimized fashion and can design experiments to generate greater fitness in an accelerated time frame, thereby pushing the limits of what adaptive laboratory evolution can achieve.
| S-EPMC5377496 | biostudies-literature
Project description:The observation of heterothermy in a single suborder (Strepsirrhini) only within the primates is puzzling. Given that the placental-mammal ancestor was likely a heterotherm, we explored the potential for heterothermy in a primate closely related to the Strepsirrhini. Based upon phylogeny, body size and habitat stability since the Late Eocene, we selected western tarsiers (Cephalopachus bancanus) from the island of Borneo. Being the sister clade to Strepsirrhini and basal in Haplorrhini (monkeys and apes), we hypothesized that C. bancanus might have retained the heterothermic capacity observed in several small strepsirrhines. We measured resting metabolic rate, subcutaneous temperature, evaporative water loss and the percentage of heat dissipated through evaporation, at ambient temperatures between 22 and 35°C in fresh-caught wild animals (126.1 ± 2.4 g). We also measured core body temperatures in free-ranging animals. The thermoneutral zone was 25-30°C and the basal metabolic rate was 3.52 ± 0.06 W.kg-1 (0.65 ± 0.01 ml O2.g-1.h-1). There was no evidence of adaptive heterothermy in either the laboratory data or the free-ranging data. Instead, animals appeared to be cold sensitive (Tb ~ 31°C) at the lowest temperatures. We discuss possible reasons for the apparent lack of heterothermy in tarsiers, and identify putative heterotherms within Platyrrhini. We also document our concern for the vulnerability of C. bancanus to future temperature increases associated with global warming.
| S-EPMC5623056 | biostudies-literature
Project description:In order to understand gene function in bacterial life cycles, time lapse bioimaging is applied in combination with different marker protocols in so called microfluidics chambers (i.e., a multi-well plate). In one experiment, a series of T images is recorded for one visual field, with a pixel resolution of 60 nm/px. Any (semi-)automatic analysis of the data is hampered by a strong image noise, low contrast and, last but not least, considerable irregular shifts during the acquisition. Image registration corrects such shifts enabling next steps of the analysis (e.g., feature extraction or tracking). Image alignment faces two obstacles in this microscopic context: (a) highly dynamic structural changes in the sample (i.e., colony growth) and (b) an individual data set-specific sample environment which makes the application of landmarks-based alignments almost impossible. We present a computational image registration solution, we refer to as ViCAR: (Vi)sual (C)ues based (A)daptive (R)egistration, for such microfluidics experiments, consisting of (1) the detection of particular polygons (outlined and segmented ones, referred to as visual cues), (2) the adaptive retrieval of three coordinates throughout different sets of frames, and finally (3) an image registration based on the relation of these points correcting both rotation and translation. We tested ViCAR with different data sets and have found that it provides an effective spatial alignment thereby paving the way to extract temporal features pertinent to each resulting bacterial colony. By using ViCAR, we achieved an image registration with 99.9% of image closeness, based on the average rmsd of 4.10-2 pixels, and superior results compared to a state of the art algorithm.
| S-EPMC5449445 | biostudies-literature
Project description:Microtubules (MTs) are unique components of the cytoskeleton formed by hollow cylindrical structures of αβ tubulin dimeric units. The structural wall of the MT is interspersed by nanopores formed by the lateral arrangement of its subunits. MTs are also highly charged polar polyelectrolytes, capable of amplifying electrical signals. The actual nature of these electrodynamic capabilities remains largely unknown. Herein we applied the patch clamp technique to two-dimensional MT sheets, to characterize their electrical properties. Voltage-clamped MT sheets generated cation-selective oscillatory electrical currents whose magnitude depended on both the holding potential, and ionic strength and composition. The oscillations progressed through various modes including single and double periodic regimes and more complex behaviours, being prominent a fundamental frequency at 29 Hz. In physiological K(+) (140 mM), oscillations represented in average a 640% change in conductance that was also affected by the prevalent anion. Current injection induced voltage oscillations, thus showing excitability akin with action potentials. The electrical oscillations were entirely blocked by taxol, with pseudo Michaelis-Menten kinetics and a KD of ~1.29 μM. The findings suggest a functional role of the nanopores in the MT wall on the genesis of electrical oscillations that offer new insights into the nonlinear behaviour of the cytoskeleton.
| S-EPMC4891677 | biostudies-other