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Pendellösung Interferometry Probes the Neutron Charge Radius, Lattice Dynamics, and Fifth Forces

Data from manuscript entitled: "Pendellosung Interferometry Probes the Neutron Charge Radius, Lattice Dynamics, and Fifth Forces"  arXiv:2103.05428

Stability analysis of roadside backfill body at gob-side entry retaining under combined static and dynamic loading

The applications of gob-side entry retaining (GER) techniques tends to increase over time as it can increase the minerals recovery rate and reduce the output of the waste. In the literature, only the performance of the roadside backfill body (RBB) at gob-side entry retaining under static loading has been investigated. However, failure mechanisms of the RBB under dynamic loading with various roof cutting angles have not been addressed. This study presented a numerical simulation of the fracture propagation and distribution in the roadside backfill body along the gob-side under combined static and dynamic loadings using the Trigon model built in UDEC (Discrete element methods) software. The influence of the roof cutting angles on the behavior of the RBB was also discussed. The input parameters were determined by back analysis with the field data. Results of the model show that static loading is a bigger contributor to the failure of the RBB compared to the dynamic loading. Several clear fractures were observed at top left and bottom right of the RBB and the fracture was more intensive at top left. In addition, it was found that if the roof cutting angle is 70°, the influence of the dynamic loading on the RBB is minimum, and the area and severity of the shearing failure in the RBB is minimum as well. As a result, it was determined the optimal roof cutting angle was 70° and a combined support measure of "roof cutting + roof support above RBBs + RBB reinforcement" is proposed. The application of roof cutting in gob-side entry retaining (RCGER) techniques in the Lingzhida coal mine indicates that deformation of the surrounding rocks can be effectively controlled.

Field-realistic antidepressant exposure disrupts group foraging dynamics in mosquitofish

Psychoactive pollutants, such as antidepressants, are increasingly detected in the environment. Mounting evidence suggests that such pollutants can disrupt the behaviour of non-target species. Despite this, few studies have considered how the response of exposed organisms might be mediated by social context. To redress this, we investigated the impacts of two environmentally realistic concentrations of a pervasive antidepressant pollutant, fluoxetine, on foraging behaviour in fish (Gambusia holbrooki), tested individually or in a group. Fluoxetine did not alter behaviour of solitary fish. However, in a group setting, fluoxetine exposure disrupted the frequency of aggressive interactions and food consumption, with observed effects being contingent on both the mean weight of group members and the level of within-group variation in weight. Our results suggest that behavioural tests in social isolation may not accurately predict the environmental risk of chemical pollutants for group-living species and highlight the potential for social context to mediate the effects of psychoactive pollutants in exposed wildlife.

Data from: Incorporating capture heterogeneity in the estimation of autoregressive coefficients of animal population dynamics using capture-recapture data

Population dynamics models combine density-dependence and environmental effects. Ignoring sampling uncertainty might lead to biased estimation of the strength of density-dependence. This is typically addressed using state-space model approaches, which integrate sampling error and population process estimates. Such models seldom include an explicit link between the sampling procedures and the true abundance, which is common in capture-recapture settings. However, many of the models proposed to estimate abundance in the presence of capture heterogeneity lead to incomplete likelihood functions and cannot be straightforwardly included in state-space models. We assessed the importance of estimating sampling error explicitly by taking an intermediate approach between ignoring uncertainty in abundance estimates and fully specified state-space models for density-dependence estimation based on autoregressive processes. First, we estimated individual capture probabilities based on a heterogeneity model, using a conditional multinomial likelihood, followed by a Horvitz-Thompson estimate for abundance. Second, we estimated coefficients of autoregressive models for the log abundance. Inference was performed using the methodology of integrated nested Laplace approximation (INLA). We performed an extensive simulation study to compare our approach with estimates disregarding capture history information, and using R-package VGAM, for different parameter specifications. The methods were then applied to a real dataset of gray-sided voles Myodes rufocanusfrom Northern Norway. We found that density-dependence estimation was improved when explicitly modelling sampling error in scenarios with low process variances, in which differences in coverage reached up to 8% in estimating the coefficients of the autoregressive processes. In this case, the bias also increased assuming a Poisson distribution in the observational model. For high process variances, the differences between methods were small and it appeared less important to model heterogeneity.

Mapping circuit dynamics during function and dysfunction

Contains reduced data for analysis. Most scripts that make figures will operate on these data.

Cryo-EM structure and dynamics of the green-light absorbing proteorhodopsin

Data underlying the figures in the publication “Cryo-EM structure and dynamics of the green-light absorbing proteorhodopsin”, published in Nat Commun, 2021, 12, 4107.  <a href="https://doi.org/10.1038/s41467-021-24429-6">https://doi.org/10.1038/s41467-021-24429-6</a> Table of contents: 1. Dataset; Excel file containing the numerical data for Figures S1A and 4C. 2. Methods; Word file containing the description of the methods. The cryo-EM map was deposited in the Electron Microscopy Data Bank (EMDB) under accession code <a href="https://www.ebi.ac.uk/pdbe/entry/emdb/EMD-11955">EMD-11955</a> and the protein coordinates were deposited in the Protein Data Bank (PDB) with the accession code <a href="https://doi.org/10.2210/pdb7B03/pdb">7B03</a>. EMDB: <a href="https://www.emdataresource.org/EMD-11955">https://www.emdataresource.org/EMD-11955</a> PDB: <a href="https://www.rcsb.org/structure/7B03">https://www.rcsb.org/structure/7B03</a> (DOI: <a href="http://doi.org/10.2210/pdb7B03/pdb">10.2210/pdb7B03/pdb</a>)

MD data for "Selective G protein signaling driven by Substance P-Neurokinin Receptor structural dynamics"

Molecular dynamics (MD) data for "Selective G protein signaling driven by Substance P-Neurokinin Receptor structural dynamics" (Harris et al., Nature Chemical Biology (2021), DOI: 10.1038/s41589-021-00890-8, URL: https://www.nature.com/articles/s41589-021-00890-8). See the included readme.txt for more details. Please cite the paper if you use these data.

Dynamics of HCN hexamers

Equilibrated trajectories of HCN hexamers in two states

Data set of the article "Comparative analysis of the unbinding pathways of antiviral drug Indinavir from HIV and HTLV1 proteases by supervised molecular dynamics simulation"

Data set of the article "Comparative analysis of the unbinding pathways of antiviral drug Indinavir from HIV and HTLV1 proteases by supervised molecular dynamics simulation"

opencc-zeroDec 2018View details →

Data from: Genomic reconstruction of 100 000-year grassland history in a forested country: population dynamics of specialist forbs

Grassland ecosystems worldwide have been extensively converted to other land uses and are globally imperiled. Because many grasslands have been maintained by human activities, understanding their origin and history is fundamentally important to better contemporary management. However, existing methods to reconstruct past vegetation can produce contrasting views on grassland history. Here, we inferred demographic histories of 40 populations of four grassland forb species throughout Japan using high-resolution genome sequences and model-flexible demographic simulation based on the site frequency spectrum. Although two species showed a slight decline in population size between 100 000–10 000 years ago, our results suggest that population sizes of studied species have been maintained within the range of 0.5–2.0 times the most recent estimates for at least 100 000 years across Japan. Our results suggest that greater than 90% declines in Japanese grasslands and subsequent losses of grassland species in the last 100 years are geologically and biologically important and will have substantial consequences for Japanese biota and culture. People have had critical roles in maintaining disturbance-dependent grassland ecosystems and biota in this warm and wet forested country. In these contexts, disturbances associated with forest harvesting and traditional extensive farming have the potential to maintain grassland ecosystems and can provide important opportunities to reconcile resource production and conservation of grassland biodiversity.

Source–sink dynamics assists the maintenance of a pollinating wasp

Dispersal that unites spatially subdivided populations into a metapopulation with source–sink dynamics is crucial for species persistence in fragmented landscapes. Understanding such dynamics for pollinators is particularly urgent owing to the ongoing global pollination crisis. Here, we investigated the population structure and source–sink dynamics of a pollinating wasp (Wiebesia sp. 3) of Ficus pumila in the Zhoushan Archipelago of China. We found significant asymmetry in the pairwise migrant numbers for 22 of 28 cases on the historical timescale, but only 2 on the contemporary timescale. Despite a small population size, the sole island not colonized by a superior competitor wasp (Wiebesia sp. 1) consistently behaved as a net exporter of migrants, supplying large sinks. Comparable levels of genetic diversity, with few private alleles and low genetic differentiation (total FST: 0.03; pairwise FST: 0.0005–0.0791), were revealed among all the islands. There was a significant isolation-by-distance pattern caused mainly by migration between the competition-free island and other islands, otherwise the pattern was negligible. The clustering analysis failed to detect multiple gene pools for the whole region. Thus, the sinks were most likely organized into a patchy population. Moreover, the estimates of effective population sizes were comparable between the two timescales. Thus the source–sink dynamics embedded within a well-connected population network may allow Wiebesia sp. 3 to persist at a competitive disadvantage. This study provides evidence that metapopulations in the real world may be complicated and changeable over time, highlighting the necessity to study such metapopulations in detail.

opencc-by-4.0May 2020View details →

Magnetic resonance imaging in the assessment of pancreatic cancer with quantitative parameter extraction by means of dynamic contrast-enhanced magnetic resonance imaging, diffusion kurtosis imaging and intravoxel incoherent motion diffusion-weighted imaging

We uploaded IVIM and DKI parameters values of included patients in the manuscript: Fusco, Roberta, Adele Piccirillo, Mario Sansone, Vincenza Granata, Paolo Vallone, Maria L. Barretta, Teresa Petrosino, Claudio Siani, Raimondo Di Giacomo, Maurizio Di Bonito, Gerardo Botti, and Antonella Petrillo. 2021. "Radiomic and Artificial Intelligence Analysis with Textural Metrics, Morphological and Dynamic Perfusion Features Extracted by Dynamic Contrast-Enhanced Magnetic Resonance Imaging in the Classification of Breast Lesions" Applied Sciences 11, no. 4: 1880. https://doi.org/10.3390/app11041880

opencc-by-4.0Feb 2021View details →

Radiomic and Artificial Intelligence Analysis with Textural Metrics, Morphological and Dynamic Perfusion Features Extracted by Dynamic Contrast-Enhanced Magnetic Resonance Imaging in the Classification of Breast Lesions

We uploaded the 15 morphological features of  91 samples of 85 patients analyzed in the manuscript: Fusco, Roberta, Adele Piccirillo, Mario Sansone, Vincenza Granata, Paolo Vallone, Maria L. Barretta, Teresa Petrosino, Claudio Siani, Raimondo Di Giacomo, Maurizio Di Bonito, Gerardo Botti, and Antonella Petrillo. 2021. "Radiomic and Artificial Intelligence Analysis with Textural Metrics, Morphological and Dynamic Perfusion Features Extracted by Dynamic Contrast-Enhanced Magnetic Resonance Imaging in the Classification of Breast Lesions" Applied Sciences 11, no. 4: 1880. https://doi.org/10.3390/app11041880

opencc-by-4.0Aug 2021View details →

Dataset of "Electron holography details the Tagish Lake parent body and implies early planetary dynamics of the Solar System"

Input files for iSALE-2D of the paper "Electron holography details the Tagish Lake parent body and implies early planetary dynamics of the Solar System" by Y. Kimura et al. Please note that usage of the iSALE-2D is not fully open source; it is distributed on a case-by-case basis to academic users in the impact community, strictly for noncommercial use. Scientists interested in using or developing iSALE code may apply at the iSALE Web page (http://www.isale-code.de).

Figure 7 in Population dynamics and phenology of two congeneric and sympatric lynx spiders Peucetia rubrolineata Keyserling, 1877 and Peucetia flava Keyserling, 1877 (Oxyopidae)

Figure 7. Circular histograms of the frequency of age structure established for the population of Peucetia rubrolineata (Oxyopidae) from July 2013 to December 2015 in Serra do Japi, SP, Brazil. The black line vector inside the circle indicates the angular mean or direction of the data. The transverse line in the sector outside the circle indicates the 95% confidence interval.

Figure 6 in Population dynamics and phenology of two congeneric and sympatric lynx spiders Peucetia rubrolineata Keyserling, 1877 and Peucetia flava Keyserling, 1877 (Oxyopidae)

Figure 6. Phenogram of the population of Peucetia flava (Oxyopidae) on plants of Trichogoniopsis adenantha (Asteraceae, n = 200) between July 2013 and December 2015, Serra do Japi, SP, Brazil.

Figure 5 in Population dynamics and phenology of two congeneric and sympatric lynx spiders Peucetia rubrolineata Keyserling, 1877 and Peucetia flava Keyserling, 1877 (Oxyopidae)

Figure 5. Phenogram of the population of Peucetia rubrolineata (Oxyopidae) on Trichogoniopsis adenantha (Asteraceae, n = 100) between July 2013 and December 2015, Serra do Japi, SP, Brazil.

Figure 2 in Population dynamics and phenology of two congeneric and sympatric lynx spiders Peucetia rubrolineata Keyserling, 1877 and Peucetia flava Keyserling, 1877 (Oxyopidae)

Figure 2. Instars of Peucetia rubrolineata (a–h) and Peucetia flava (i–o) (Oxyopidae) recorded in the Trichogoniopsis adenantha (Asteraceae) plant in the Serra do Japi, SP, Brazil. (a, i) second instar; (b, j) third instar; (c, k) fourth instar; (d, l) fifth instar; (e, m) sixth instar; (f, n) seventh instar (subadult); (g, h, n) eighth instar (adult).

Figure 1 in Population dynamics and phenology of two congeneric and sympatric lynx spiders Peucetia rubrolineata Keyserling, 1877 and Peucetia flava Keyserling, 1877 (Oxyopidae)

Figure 1. Climatic diagram of the Serra do Japi, SP, Brazil, based on the climatic data collected from the Jundiaí experimental station. Areas in black indicate very humid periods. Areas with vertical lines indicate humid periods. Dotted areas indicate dry periods.

Figure 4 in Population dynamics and phenology of two congeneric and sympatric lynx spiders Peucetia rubrolineata Keyserling, 1877 and Peucetia flava Keyserling, 1877 (Oxyopidae)

Figure 4. Circular histogram of the abundance of the two spider populations: right, Peucetia rubrolineata; left, Peucetia flava, from July 2013 to December 2015 in Serra do Japi, SP, Brazil. The black line outside the circle indicates the average angle or direction of the data. The transverse line on the outside of the circle indicates the 95% confidence interval.