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Figure 6 in Population dynamics and reproductive biology of the sandhopper Atlantorchestoidea brasiliensis (Amphipoda: Talitridae) of a sandy beach in Southwestern Atlantic Coast

Figure 6. Atlantorchestoidea brasiliensis: relationship of length to number of eggs per marsupium at Sossego Beach, Rio de Janeiro State, Brazil.

Figure 5 in Population dynamics and reproductive biology of the sandhopper Atlantorchestoidea brasiliensis (Amphipoda: Talitridae) of a sandy beach in Southwestern Atlantic Coast

Figure 5. Fecundity of Atlantorchestoidea brasiliensis from Sossego Beach, Rio de Janeiro State, Brazil.

Figure 4 in Population dynamics and reproductive biology of the sandhopper Atlantorchestoidea brasiliensis (Amphipoda: Talitridae) of a sandy beach in Southwestern Atlantic Coast

Figure 4. Sexual maturity (L50%) of Atlantorchestoidea brasiliensis males and females from Sossego Beach, Rio de Janeiro State, Brazil.

Figure 3 in Population dynamics and reproductive biology of the sandhopper Atlantorchestoidea brasiliensis (Amphipoda: Talitridae) of a sandy beach in Southwestern Atlantic Coast

Figure 3. Modal progression analysis of Atlantorchestoidea brasiliensis from Sossego Beach (a) females, (b) males.

Figure 2 in Population dynamics and reproductive biology of the sandhopper Atlantorchestoidea brasiliensis (Amphipoda: Talitridae) of a sandy beach in Southwestern Atlantic Coast

Figure 2. Atlantorchestoidea brasiliensis: (a) male, (b) female, and (c) ovigerous female. Scale bar: 5 mm.

opencc-zeroAug 2022View details →

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Improvements in airflow characteristics and effect on the NOSE score after septoturbinoplasty: A computational fluid dynamics analysis

Septoturbinoplasty is a surgical procedure that can improve nasal congestion symptoms in patients with nasal septal deviation and inferior turbinate hypertrophy. However, it is unclear which physical domains of nasal airflow after septoturbinoplasty are related to symptomatic improvement. This work employs computational fluid dynamics modeling to identify the physical variables and domains associated with symptomatic improvement. Sixteen numerical models were generated using eight patients' pre- and postoperative computed tomography scans. Changes in unilateral nasal resistance, surface heat flux, relative humidity, and air temperature and their correlations with improvement in the Nasal Obstruction Symptom Evaluation (NOSE) score were analyzed. The NOSE score significantly improved after septoturbinoplasty, from 14.4 ± 3.6 to 4.0 ± 4.2 (p < 0.001). The surgery not only increased the airflow partition on the more obstructed side (MOS) from 31.6 ± 9.6 to 41.9 ± 4.7% (p = 0.043), but also reduced the unilateral nasal resistance in the MOS from 0.200 ± 0.095 to 0.066 ± 0.055 Pa/(mL×s) (p = 0.004). Improvement in the NOSE score correlated significantly with the reduction in unilateral nasal resistance in the preoperative MOS (r=0.81). Also, improvement in the NOSE score correlated better with the increase in surface heat flux in the preoperative MOS region from the nasal valve to the choanae (r=0.87) than in the vestibule area (r=0.63). Therefore, unilateral nasal resistance and mucous cooling in the preoperative MOS can explain the perceived improvement in symptoms after septoturbinoplasty. Moreover, the physical domain between the nasal valve and the choanae might be more relevant to patient-reported patency than the vestibule area.

Prediction of ternary complex structures using molecular dynamics and proteomics

Source code and structural PDBs that went into the Prediction of ternary complex structures using molecular dynamics and proteomics paper.

Raw data on dynamic light scattering assessment of small cellular particles isolated from conditioned culture media of Dunaliella tertiolecta and Phaeodactylum tricornutum. Effect of Triton X-100 and temperature

Raw data on dynamic light scattering assessment of small cellular particles isolated from conditioned culture media of microalgae Dunaliella tertiolecta (D. tertiolecta) and Phaeodactylum tricurnutum (P. tricornutum) by dynamic light scattering are presented. The project contains spreadsheet files with the measured dependencies of g2 function on time. We collected several g2 functions for each setting (3 for D. tertiolecta samples, 5 for D. tertiolecta with added TX100, 3 for P. tricornutum samples, 3 for P. tricornutum with added TX100). Curves were analyzed independently and compared with the respective averaged curve fitted by the inverse Laplace transform program CONTIN (freely available at: <a href="http://s-provencher.com/index.shtml">http://s-provencher.com/index.shtml</a>, the code was accessed 25. 1. 2011). The correlation curves were fitted with up to 50 exponents. For analysis of stability of small cellular particles with respect to temperature change, we have overall reports for each microalgae type and reports on the size distribution function, data for the g2 function and dependence of scattered light intensity on time for each temperature measured. There were 14 temperatures chosen for each type of microalgae. The files are marked with respective temperatures. The samples were prepared as described below: Cultivation of the algae: Cultures of D. tertiolecta CCAP 19/22 and P. tricornutum CCAP 1052/1A from the Culture Collection of Algae and Protozoa (CCAP) of SAMS (Oban, Scotland) were grown in artificial seawater (Reef Crystals, Aquarium Systems, France). 22 g of salt was dissolved in one litre of distilled water, sterile filtered (0.2-micron cellulose filters, ref. 11107-47-CAN, Sartorius Stedim Biotech GmbH, Germany), autoclaved, and supplemented with Guillard’s (F/2) Marine Water Enrichment Solution (ref. G0154, Sigma Aldrich, USA). Cultures were grown in a respirometer (Echo, Slovenia) in 0.5-L borosilicate bottles, at 20 °C and 20 % illumination (approximately 250 μmol/m2s) with a 14-hour light / 10-hour dark cycle, with aeration of 0.2 L/min. Isolation of small cellular nanoparticles: Small cellular particles were isolated by differential centrifugation, using a protocol widely used for the isolation of extracellular vesicles (Théry C, Amigorena S, Raposo G, Clayton A. Isolation and Characterization of Exosomes from Cell Culture Supernatants and Biological Fluids. Current Protocols in Cell Biology. 2006;30(1). doi:10.1002/0471143030.cb0322s30). Microalgal cells were removed by low-speed centrifugation (300 g, 10 min, 4°C, centrifuge Centric 260R with rotor RA 6/50 (Domel, Slovenia)), using 50 mL conical centrifuge tubes (ref. S.078.02.008.050, Isolab Laborgeräte GmbH, Germany); and 2000 g, 10 min, 4°C (Centric 400R centrifuge with rotor RS4/100 (Domel, Slovenia)), using 15 mL conical centrifuge tubes (ref. S.078.02.001.050, Isolab Laborgeräte GmbH, Germany). Each step was repeated twice. Then, the cell-depleted medium was centrifuged twice at 10 000g and 4°C for 30 min (Beckman L8-70M ultracentrifuge, rotor SW55Ti (Beckman Coulter, USA)), using thin-wall polypropylene centrifuge tubes (ref. 326819, Beckman Coulter, USA) to remove larger cell debris. Finally, small cellular particles were pelleted by centrifugation at 118 000 g and 4°C, for 70 min in the same type of ultracentrifuge and ultracentrifuge tubes. The isolate obtained from about 30 mL of conditioned media was not visible to the eye. For treatment with Triton X-100, the sample was incubated with Triton X-100 at concentration of 0.1%. Dynamic light scattering (DLS): The average hydrodynamic radius (Rh) of NPs and the average intensity of scattered light (I) were assessed for characterization of small cellular particles by DLS. The value of I was interpreted as a measure of small cellular particles concentration (in the case of preserved particle size distribution) or as a topological change (in the case of altered particle size distribution)(Paterna A, Rao E, Adamo G, et al. Isolation of Extracellular Vesicles From Microalgae: A Renewable and Scalable Bioprocess. Front Bioeng Biotechnol. 2022;10:836747. doi:10.3389/fbioe.2022.836747; Brown W, ed. Dynamic Light Scattering: The Method and Some Applications. Clarendon Press ; Oxford University Press; 1993). For analysis of the samples we used Instrument 3D-DLS-SLS cross-correlation spectrometer from LS Instruments GmbH (Fribourg, Switzerla nd) with a 100 mW DPSS laser (Cobolt Flamenco, Cobolt AB, Sweden) having a wavelength λ0 = 660 nm. Before measurements, samples were equilibrated in a decalin bath at 25 °C for 15 min. The scattered light was measured at an angle θ = 90° for 120 s. The correlation functions and integral time-averaged intensities I(θ)&equiv; I(q) (where q is the scattering vector, defined as q =(4πn0/λ0)sin(θ/2), with n0  the refractive index of the medium, in our case estimated by the corresponding value for water, i.e. n0 = 1.33 at 25°C), were recorded simultaneously. The Rh values of small cellular particles were obtained from the diffusion coefficients (D) that were assessed from the correlation function of the scattered electric field (g1(t)). The g1(t) function was calculated from the measured correlation function of the scattered light intensity g2(t) by applying Siegert’s relation (Schärtl W. Light Scattering from Polymer Solutions and Nanoparticle Dispersions. Springer; 2007; Shurer CR, Kuo JCH, Roberts LM, et al. Physical Principles of Membrane Shape Regulation by the Glycocalyx. Cell. 2019;177(7):1757-1770.e21. doi:10.1016/j.cell.2019.04.017). To convert D to Rh, the Stokes-Einstein equation was used (Rh = kT6πηD, where k is the Boltzmann constant, T is the absolute temperature, and η is the viscosity of the medium in which the particles diffuse). It was assumed that particles have a spherical shape. The viscosity of the medium was not known. We approximated the viscosity value to that of of water at 25°C.To test the effect of Triton X-100 on the samples, 0.1% (V/V) of Triton X-100 was added to the sample before the measurement. The change in Rh distribution and the change of scattered light intensity (ΔI = Isample - Isample+0.1%.TX100) was determined. The analysis was made with an in-house created software based on the inverse Laplace transform program CONTIN (freely available at: <a href="http://s-provencher.com/index.shtml">http://s-provencher.com/index.shtml</a>, the code was accessed 25. 1. 2011). We collected several intensity correlation functions for each setting. Curves were analyzed independently and compared with the averaged curve. The correlation curves were fitted with up to 50 exponents. To test the effect of Triton X-100 on NPs, 0.1% (V/V) of Triton X-100 was added to the sample before the measurement. The change in Rh distribution and the change of scattered light intensity (ΔI = Isample - Isample+0.1%.TritonX-100) was determined. Thermal stability analysis was performed using the LitesizerTM 500 instrument (Anton Paar GmbH). Samples were heated from 15 °C to 80 °C in 5 °C steps. When the target temperature was reached, the samples were equilibrated for another 5 minutes before 10 measurements of 20 s duration were performed. The size distributions were determined from the mean correlation function using the Anton Paar Kalliope Professional; Version 2.16.0. (Anton Paar GmbH), <a href="https://www.anton-paar.com/corp-en/products/details/software-for-particle-analysis-kalliopetm/">https://www.anton-paar.com/corp-en/products/details/software-for-particle-analysis-kalliopetm/</a>,  applying the CONTIN approach. A new version of KalliopeTM 4.12.0 <a href="https://www.kalliope.com/2021/05/03/versione-firmware-4-12-0/?lang=en">https://www.kalliope.com/2021/05/03/versione-firmware-4-12-0/?lang=en</a> is freely available online.

Mapping global lake dynamics reveals the emerging roles of small lakes: code and data

This repository contains the relevant code and data for the paper Mapping global lake dynamics reveals the emerging roles of small lakes (<a href="http://dx.doi.org/10.1038/s41467-022-33239-3">https://www.nature.com/articles/s41467-022-33239-3</a>). Specifically, the U-Net.zip file includes the associated codes for segmenting global lakes by using the U-Net model, and the labels used in this process. The GLAKES.zip file includes the GLAKES lake polygon product (.gdb & .shp) and the corresponding water probability-weighted area of GLAKES lakes during the three periods (1984-1999, 2000-2009, 2010-2019). Please refer to the README file in both the U-Net.zip and the GLAKES.zip file for more detailed information.

opencc-by-4.0Aug 2021View details →

NanoString dataset for study: Dynamic changes in the NK-, Neutrophil-, and B-cell immunophenotypes relevant in high metastatic risk post neoadjuvant chemotherapy–resistant early breast cancers

Pre-processed DSP and mRNA abundance datasets used in this study.

The oscillatory motion of Jupiter's polar cyclones results from vorticity dynamics - Movies S1, S2

Movie S1: An animation of the observed trajectories of the south polar cyclones, as illustrated in Fig. 2a, along the 45-months of observations. The blue arrows represent the estimated net forces on the cyclones, as presented in Fig. 4. Movie S2: An animation of the simulated trajectories of the south polar cyclones, as illustrated in Fig. 5a, along 45-months. The blue arrows represent the net forces on the cyclones.

Numerical data for dynamic rupture simulations of coseismic slickenlines on non-planar and rough faults

Numerical data used to make Figures in the manuscript entitled "Dynamic simulations of coseismic slickenlines on non-planar and rough faults (Aoki et al., GJI)"

Population Dynamics of the date palm mite, Oligonychus afrasiaticus over 4 years data

The data uploaded in MS Excel is related to the population dynamics of the date palm mite, Oligonychus afrasiaticus. This field study was conducted in 02 regions of Saudi Arabia. The duty was collected over 04 years.

opencc-by-4.0May 2022View details →

Dynamic rupture simulation of Wenchuan-Maoxian and Lixian Fault

The Video shows the slip rates of 4 earthquake cases on the LMS fault system. The ruptures started from different hypocenters and results in different earthquake magnitudes.

Experimental data for: Long-term memory and synapse-like dynamics in two-dimensional nanofluidic channels

Experimental data set for: Long-term memory and synapse-like dynamics in two-dimensional nanofluidic channels. Provides all raw data needed to reproduce experimental graphs presented within the paper.

opencc-zeroSep 2022View details →

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Competition dynamics in long-term propagations of Schizosaccharomyces pombe strain communities

Experimental evolution studies with microorganisms such as bacteria and yeast have been an increasingly important and powerful tool to draw long-term inferences of how microbes interact. However, while several strains of the same species often exist in natural environments, many ecology and evolution studies in microbes are typically performed with isogenic populations of bacteria or yeast. In the present study, we firstly perform a genotypic and phenotypic characterization of two lab and eight natural strains of the yeast Schizosaccharomyces pombe. We then propagated, in a rich resource environment, yeast communities of 2-, 3-, 4- and 5-strains for hundreds of generations and asked which fitness related phenotypes – maximum growth rate or relative competitive fitness – would better predict the outcome of a focal strain during the propagations. While the strain's growth rates would wrongly predict long-term co-existence, pairwise competitive fitness with a focal strain qualitatively predicted the success or extinction of the focal strain by a simple multi-genotype population genetics model, given the initial community composition. Interestingly, we have also measured the competitive fitness of the ancestral and evolved communities by the end of the experiment (≈370 generations) and observed frequent maladaptation to the abiotic environment in communities with more than three members. Overall, our results aid establishing pairwise competitive fitness as good qualitative measurement of long-term community composition but also reveal a complex adaptive scenario when trying to predict the evolutionary outcome of those communities.

Appendix for "Is JavaScript Call Graph Extraction Solved Yet? A Comparative Study of Static and Dynamic Tools"

Abstract The popularity and wide adoption of JavaScript both at the client and server-side makes its code analysis more essential than ever before. Most of the algorithms for vulnerability analysis, coding issue detection, or type inference rely on the call graph representation of the underlying program. Luckily, there are quite a few tools to get this job done already. However, their performance in vitro and especially in vivo has not yet been extensively compared and evaluated. In this paper, we systematically compare five static and two dynamic approaches for building JavaScript call graphs on 26 WebKit SunSpider benchmark programs and two static and two dynamic methods on 12 real-world Node.js modules. The tools under examination using static techniques were npm call graph, IBM WALA, Google Closure Compiler, Approximate Call Graph, and Type Analyzer for JavaScript. We performed dynamic analyzes relying on the nodejs-cg tool (a customized Node.js runtime) and the NodeProf instrumentation and profiling framework. We provide a quantitative evaluation of the results, and a result quality analysis based on 941 manually validated call edges. On the SunSpider programs, which do not take any inputs, so dynamic extraction could be complete, all the static tools also performed well. For example, TAJS found 93% of all edges while having a 97% precision compared to the precise dynamic call graph. When it comes to real-world Node.js modules, our evaluation shows that static tools struggle with parsing the code and fail to detect a significant amount of call edges that dynamic approaches can capture. Nonetheless, a significant number of edges not detected by dynamic approaches are also reported. Among these, however, there are also edges that are real, but for some reason the unit tests did not execute the branches in which these calls were included.

opencc-by-4.0Feb 2022View details →

A comparative study of the dynamics and diversity of Bdel-lovibrio and like organisms in Lakes Annecy and Geneva

Specific run : Raw files R1 and R2 Tags lists OTUs tables filtered and unfiltered

dryad32/100

Experimental evidence that host species composition alters host-pathogen dynamics in a ranavirus-amphibian assemblage

Losses in biodiversity can alter disease risk through changes in host species composition. Host species vary in pathogen susceptibility and competence. Yet how changes in diversity alter host-pathogen dynamics remains unclear in many systems, particularly with respect to generalist pathogens. Amphibians are experiencing worldwide population declines linked to generalist pathogens, such as ranavirus, and thus represent an ideal group to investigate how host species composition affects disease risk. We conducted experiments where individuals in the laboratory and assemblages of three amphibian species (Pacific tree frogs, Pseudacris regilla; Cascades frogs, Rana cascadae; and Western toads, Anaxyrus boreas) or just A. boreas alone in outdoor mesocosms were exposed to ranavirus as larvae. In laboratory experiment, we observed low survival and high viral loads in P. regilla compared to the other species suggesting that this species was highly susceptible to the pathogen. In the mesocosm experiment, we observed 41% A. boreas mortality when alone and 98% mortality when maintained with P. regilla and R. cascadae. Our results suggest that the presence of highly susceptible species can alter disease dynamics across multiple species, potentially increasing infection risk and mortality in co-occurring species.

opencc-zeroSep 2022View details →

Code and data for results and figures of the manuscript "Multi-million year cycles in modelled δ13C as a response to astronomical forcing of organic matter fluxes." submitted to Earth System Dynamics

This dataset contains the code of the model used in the manuscript submitted to Earth System Dynamics "Multi-million year cycles in modelled δ13C as a response to astronomical forcing of organic matter fluxes.". It also contains some model outputs and code to draw the figures.