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opencc-zeroJul 2023View details →

Dataset for: Biomimetic models of fish gill rakers as lateral displacement arrays for particle separation

Ram suspension-feeding fish such as herring use gill rakers to separate small food particles from large water volumes while swimming forward with an open mouth. Fish gill raker function was tested using 3D-printed conical models and computational fluid dynamics (CFD) simulations over a range of slot aspect ratios. (See CFD simulation output in Dryad dataset: case and data files for ANSYS Fluent 19.1 CFD simulations.) Our hypothesis predicting the exit of particles based on mass flow rates, dividing streamlines (i.e., stagnation streamlines) at the slots between gill rakers, and particle size was supported by the results of experiments with physical models in a recirculating flume. (See R code with embedded comments in Dryad dataset to test Hypotheses 1 and 2 for particle exit/trapping.) Particle movement in suspension-feeding fish gill raker models was consistent with the physical principles of lateral displacement arrays ("bump arrays") for microfluidic and mesofluidic separation of particles by size. Although particles were smaller than the slots between rakers, particles skipped over the vortical region that was generated downstream from each raker. Particles "bumped" on anterior raker surfaces during posterior transport. (See particle movement data in Dryad dataset: three files for particle contact, exit, and retention in the physical models.) Experiments in a recirculating flume demonstrated that the shortest distance between the dividing streamline and the raker surface preceding the slot predicts the maximum radius of a particle that will exit from the model by passing through the slot. This theoretical maximum radius is analogous to the critical separation radius identified with reference to the stagnation streamlines in microfluidic and mesofluidic devices that use deterministic lateral displacement and sieve-based lateral displacement. These conclusions provide new perspectives and metrics for analyzing crossflow and cross-step filtration in fish with applications to filtration engineering.

opencc-zeroJul 2023View details →

Elevated CO2 does not alter behavioural lateralization in free‐swimming juvenile European sea bass ( Dicentrarchus labrax) tested in groups

Rising concentrations of atmospheric carbon dioxide (CO2) equilibrate with oceanic CO2, contributing to ocean acidification (OA). OA can induce changes in fish behavioural lateralization (an expression of brain functional asymmetries) manifested in a left or right turning preference in detour tests. However, recent works find no such effects, and other work demonstrates assessment of turning preferences by detour tests to be a flawed methodology. Behavioural lateralization and OA effects on lateralization therefore need to be assessed with alternative paradigms. Here, we investigate left-right turning preferences of N=260 free-swimming juvenile European sea bass (Dicentrarchus labrax) reared in either: ambient conditions; OA conditions; or reared in ambient conditions but tested in OA water. Fish were observed free-swimming in groups of 10 individuals in a circular tank, and individuals' turning preferences were quantified using trajectory data from video. In contrast to early studies, and in support of recent comprehensive work on coral reef fishes, we show that near future OA levels have no effect on behavioural lateralization (left–right turning preference) in juvenile European sea bass.

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Lateral interactions govern self-assembly of the bacterial biofilm matrix protein BslA (experimental and simulation data)

The soil bacterium Bacillus subtilis is a model organism to investigate the formation of biofilms, the predominant form of microbial life. The secreted protein BslA self-assembles at the surface of the biofilm to give the B. subtilis biofilm its characteristic hydrophobicity. To understand the mechanism of BslA self-assembly at interfaces, here we built a molecular model based on the previous BslA crystal structure and the newly determined crystal structure of the BslA paralogue YweA. Our analysis revealed two conserved protein-protein interaction interfaces supporting BslA self-assembly into an infinite 2d lattice that fits previously determined transmission microscopy images. Molecular dynamics simulations and in vitro protein assays further support our model of BslA elastic film formation, while mutagenesis experiments highlight the importance of the identified interactions for biofilm structure. Based on this knowledge, YweA was engineered to form more stable elastic films and rescue biofilm structure in bslA deficient strains. These findings shed new light on protein film assembly and will inform the development of BslA technologies which range from surface coatings to emulsions in fast-moving consumer goods.

opencc-by-4.0Aug 2023View details →

opencc-zeroSep 2023View details →

Lateral gene transfer generates accessory genes that accumulate at different rates within a grass lineage

Lateral gene transfer (LGT) is the movement of DNA between organism without sexual reproduction. The acquired genes represent genetic novelties that have independently evolved in the donor's genome. Phylogenetic methods have shown that LGT is widespread across the entire grass family, although we know little about the underlying dynamics. We identify laterally acquired genes in five de novo reference genomes from the same grass genus (four Alloteropsis semialata and one Alloteropsis angusta). Using additional resequencing data for a further 40 Alloteropsis individuals, we place the acquisition of each gene onto a phylogeny using stochastic character mapping, and then infer rates of gains and losses. We detect 168 laterally acquired genes in the five reference genomes [32-100 per genome]. Exponential decay models indicate that the rate of LGT acquisitions [6-28 per Ma] and subsequent losses [11-24% per Ma] varied significantly among lineages. Laterally acquired genes were lost at a higher rate than vertically inherited loci [0.02-0.8% per Ma]. This high turnover creates intraspecific gene content variation, with a preponderance of them occurring as accessory genes in the Alloteropsis pangenome. This rapid turnover generates standing variation that can ultimately fuel local adaptation.

opencc-zeroSep 2023View details →

Experiencing short heat waves early in development changes thermal responsiveness of turtle embryos to later heat waves

Although physiological responses to the thermal environment are most frequently investigated using constant temperatures, the incorporation of thermal variability can allow for a more accurate prediction of how thermally sensitive species respond to a rapidly changing climate. In species with temperature-dependent sex determination (TSD), developmental responses to incubation temperature are mediated by several genes involved in gonadal differentiation. Kdm6b and Dmrt1 respond to cool incubation temperatures and are associated with testis development, while Foxl2 and Cyp19A1 respond to warm incubation temperatures and are associated with ovary development. Using fluctuating incubation temperatures, we designed two studies, one investigating how conflicting thermal cues affect the timing of commitment to gonadal development, and another investigating the rapid molecular responses to conflicting thermal cues in the red-eared slider turtle (Trachemys scripta). Using gene expression as a proxy of timing of commitment to gonadal fate, results from the first study show that exposure to high amounts of conflicting thermal cues during development delays commitment to gonadal fate. Results from the second study show that Kdm6b splice variants exhibit differential responses to early heat wave exposure, but rapidly (within 2 days) recover to pre-exposure levels after the heat wave. Despite changes in the expression of Kdm6b splice variants, there was no effect on Dmrt1 expression. Collectively, these findings demonstrate how short exposures to heat early in development can change how embryos respond to heat later in development.

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Datasets and code for "Multi-site transfer function approach for real-time modeling of the ground electric field induced by laterally-nonuniform ionospheric source" by Kruglyakov et al. (2023)

<ol> <li>Archive calculate_weights_for_rt.tgz contains the code for calculation of weights used for computation of electric fields based on multi-site transfer function approach following Kruglyakov et al. (2023). The code is written in Fortran 2003 and the only external dependency is LAPACK/BLAS -compatible library, for example OpenBLAS from https://www.openblas.net. See READ.ME for details.</li> <li>Files GICs*.dat contain observed and modelled geomagnetically induced currents (GICs) at Mäntsälä compressor station in southern Finland (60.6 N, 25.2 E) (https://space.fmi.fi/gic/) for three events (in 2000, 2001, and 2003).</li> <li>Files E_x*. E_y* contain corresponding components of measured (detrended and downsampled from 1s to 10s) and modeled electric fields at sites M02 and M05 from 05:15 to 06:15 UT, 11 Sep 2005.</li> <li>Files MS_TF*.dat contain multi-site transfer functions for different sets of IMAGE magnetometers (based on the data availability during the simulated events) in the frequency domain and the corresponding weights for calculation of electric field in the time domain.</li> <li>File E_to_GICs_W.dat contains coefficients for computation of GICs at Mäntsälä station from electric fields at 18 sites used in the simulation. See Equation (15) of Kruglyakov et al. (2023) for details.</li> </ol>

opencc-by-4.0Oct 2023View details →

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Fig. 44. Character 64. Uncal lateral lobes, states 0 and 1 in An Appraisal of the Higher Classification of Cicadas (Hemiptera: Cicadoidea) with Special Reference to the Australian Fauna

Fig. 44. Character 64. Uncal lateral lobes, states 0 and 1: (0) absent; (1) present.

opencc-by-4.0Nov 2005View details →

Effects of Oral Levosimendan on Respiratory Function in Patients With Amyotrophic Lateral Sclerosis (ALS): Open-Label Extension

ClinicalTrials.gov study NCT03948178. IPD Sharing: Not stated. Countries: 14. Publications: 1.

The LAVA (Lateral Flow Antigen Validation and Applicability) Study for COVID-19

ClinicalTrials.gov study NCT04629157. IPD Sharing: NO. Countries: 1. Publications: 1.

HERV-K Suppression Using Antiretroviral Therapy in Volunteers With Amyotrophic Lateral Sclerosis (ALS)

ClinicalTrials.gov study NCT02437110. IPD Sharing: UNDECIDED. Countries: 1. Publications: 3.

Study of Ozanezumab (GSK1223249) Versus Placebo in the Treatment of Amyotrophic Lateral Sclerosis

ClinicalTrials.gov study NCT01753076. IPD Sharing: Not stated. Countries: 11. Publications: 1.

Arimoclomol in Amyotropic Lateral Sclerosis

ClinicalTrials.gov study NCT03491462. IPD Sharing: Not stated. Countries: 12. Publications: 1.

Antero-posterior Versus Antero-lateral Electrode Position for Electrical Cardioversion of Typical Atrial Flutter

ClinicalTrials.gov study NCT00860314. IPD Sharing: Not stated. Countries: 1. Publications: 10.

Kinesiotaping in Lateral Epicondylitis

ClinicalTrials.gov study NCT03074500. IPD Sharing: NO. Countries: 1. Publications: 6.

A Randomized Control Trial to Evaluate the Efficacy of Autologous Blood Injection Versus Local Corticosteroid Injection for Treatment of Lateral Epicondylitis

ClinicalTrials.gov study NCT00947765. IPD Sharing: Not stated. Countries: 1. Publications: 1.

Safety and Efficacy Study of Autologous Bone Marrow Derived Stem Cell Treatment in Amyotrophic Lateral Sclerosis

ClinicalTrials.gov study NCT01363401. IPD Sharing: NO. Countries: 1. Publications: 5.

Effectiveness of Laparoscopic Lateral Suspension With or Without Hysterectomy in Pelvic Organ Prolapse

ClinicalTrials.gov study NCT07094815. IPD Sharing: NO. Countries: 1. Publications: 1.

Safety Extension Study of Oral Edaravone Administered in Subjects With Amyotrophic Lateral Sclerosis (ALS)

ClinicalTrials.gov study NCT04577404. IPD Sharing: UNDECIDED. Countries: 6. Publications: 1.

controlledIPD-YESFeb 2026View details →

FUSION: A Study to Evaluate the Efficacy, Safety, Pharmacokinetics and Pharmacodynamics of ION363 in Amyotrophic Lateral Sclerosis Participants With Fused in Sarcoma Mutations (FUS-ALS)

ClinicalTrials.gov study NCT04768972. IPD Sharing: YES. Countries: 16. Publications: 1.