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opencc-zeroJan 2023View details →

Data for: The conserved centrosomin motif, γTuNA, forms a dimer that directly activates microtubule nucleation by the γ-tubulin ring complex (γTuRC)

To establish the microtubule cytoskeleton, the cell must tightly regulate when and where microtubules are nucleated. This regulation involves controlling the initial nucleation template, the γ-tubulin ring complex (γTuRC). Although γTuRC is present throughout the cytoplasm, its activity is restricted to specific sites including the centrosome and Golgi. The well-conserved γ-tubulin nucleation activator (γTuNA) domain has been reported to increase the number of microtubules (MTs) generated by γTuRCs. However, previously we and others observed that γTuNA had a minimal effect on the activity of antibody-purified Xenopus γTuRCs in vitro (Thawani et al., eLife, 2020; Liu et al., 2020). Here we instead report, based on improved versions of γTuRC, γTuNA, and our TIRF assay, the first real-time observation that γTuNA directly increases γTuRC activity in vitro, which is thus a bona fide γTuRC activator. We further validate this effect in Xenopus egg extract. Via mutation analysis, we find that γTuNA is an obligate dimer. Moreover, efficient dimerization as well as γTuNA's L70, F75, and L77 residues are required for binding to and activation of γTuRC. Finally, we find that γTuNA's activating effect opposes inhibitory regulation by stathmin. In sum, our improved assays prove that direct γTuNA binding strongly activates γTuRCs, explaining previously observed effects of γTuNA expression in cells and illuminating how γTuRC-mediated microtubule nucleation is regulated.

opencc-by-4.0Jan 2023View details →

A potential biomarker of brain activity in ASD: a pilot fNIRS study in female preschoolers

Looking for visual cortical activity as putative brain biomarker: a pilot fNIR study on autistic female preschoolers. We performed an observational prospective monocentric study in a tertiary care University hospital (IRCCS Stella Maris Foundation, Pisa, IT). We recruited 12 females with idiopathic ASD and 13 sex/age-matched control typically developed peers. Established inclusion criteria were: 1) diagnosis of ASD according to the DSM-5 criteria (APA, 2013); 2) age range: between 3 and 6 years; 3) female gender; 4) negative genetic testing for Fragile X and MECP2; 5) negative history of premature birth or neurologic complications possibly related to delivery and 6) non-verbal IQ &gt; 70. ASD diagnosis has been performed by a multidisciplinary team including a senior child psychiatrist, an experienced clinically trained research child psychologist and a speech-language pathologist during 5-7 days of extensive evaluation. Demographic characteristics and clinical features of experimental cohorts are listed in Tables 1 and 2. Clinical measures such as Autism Diagnostic Observation Schedule (ADOS) (Lord et al., 2012), Autism Questionnaire (AQ) – children’s version, cognitive and adaptive profile were systematically collected for each subject using internationally validated scales/interviews, such as Wechsler Preschool and Primary Scale of Intelligence (Wechsler, 2002) and Vineland Adaptive Behavior Scales-II –VABS- (Sparrow et al., 2005). All participants reported normal or corrected-to-normal vision.

opencc-zeroJan 2023View details →

Data from: Assessing the deep carbon release in an active volcanic field using hydrochemistry, δ13CDIC and Δ14CDIC

Volcanic activities have great implications on geological carbon cycle, and ascertaining the deep carbon contribution in earth surface that run along the volcanic edifices is important to understand the relationship between earth degassing and global climate change. This study reports analytical results of major dissolved ions, stable carbon isotope (δ13CDIC) and radiocarbon (Δ14CDIC) of dissolved inorganic carbon (DIC) of rivers, cold springs and hot springs from Changbaishan volcanic area, Northeast China.

opencc-by-4.0Jan 2023View details →

Effects of grip position on forearm muscle surface electromyography activity during maximal isometric finger dead-hangs in rock climbers

Dataset from the study titled: "Effects of grip position on forearm muscle surface electromyography activity during maximal isometric finger dead-hangs in rock climbers" The dataset includes data from: participant's characteristics, maximal absolute and BW relative loads used during dead-hangs, EMG RMS data for each of the registered muscles and grip positions, and neuromuscular efficiency data for each muscle and grip position.

STRA6 promotes thyroid carcinoma progression via activation of the ILK/AKT/mTOR axis in cells and female nude mice

Background: Metastasis has emerged to be an important cause for poor prognosis of thyroid carcinoma (TC) and its molecular mechanisms are not fully understood. STRA6 is a multifunctional membrane protein widely expressed in embryonic and adult tissues. The function and mechanism of STRA6 in TC remain elusive. Objective: We aimed to explore the role of STRA6 in TC progression and provide a therapeutic target for TC. Methods: The expression and clinicopathological relevance of STRA6 were explored in TC. Stable STRA6-knockdown TC cells were established and used to determine the biological function of STRA6 in vitro and in vivo. RNA-sequencing and Co-immunoprecipitation were performed to unveil the molecular mechanism of STRA6 in TC progression. The potential of STRA6 as a therapeutic target was evaluated by lipid nanoparticles (LNPs) containing siRNA. Results: STRA6 was upregulated in TC and correlated with aggressive clinicopathological features including extrathyroidal extension and lymph node metastasis, which contributed to the poor prognosis of TC. STRA6 facilitated TC progression by enhancing proliferation and metastasis in vitro and in vivo. Mechanistically, STRA6 could interact with ILK and subsequently activate the AKT/mTOR signaling pathway. We further unveiled that STRA6 reprogrammed lipid metabolism through SREBP1, which was crucial for the metastasis of TC. Moreover, STRA6 siRNA delivered by LNP significantly inhibited cell growth in xenograft tumor models. Conclusions: Our study demonstrates the critical roles of STRA6 contributing to TC progression via the ILK/AKT/mTOR axis, which may provide a novel prognostic marker as well as a promising therapeutic target for aggressive TC.

Numerical data from: Gasotransmitter modulation of hypoglossal motoneuron activity

Using the rhythmic brainstem slice preparation, which contains the preBötzinger complex (preBötC) and the hypoglossal nucleus, we tested the hypothesis that central HO-2 dysregulation weakens hypoglossal motoneuron output. Disrupting HO-2 activity increased transmission failure as determined by the intermittent inability of the preBötC rhythm to trigger output from the hypoglossal nucleus. Failed transmission was associated with a reduced input-output relationship between the preBötC and the motor nucleus. These network phenomena were related to smaller inspiratory drive currents and reduced intrinsic excitability among hypoglossal neurons. In addition to HO-2, hypoglossal neurons also expressed the CO-regulated H2S producing enzyme cystathionine ϒ-lyase (CSE). H2S abundance was higher in hypoglossal neurons of HO-2 null mice than wild-type controls. Disrupting CSE function normalized transmission in HO-2 null mice and an H2S donor mimicked the effects of HO-2 dysregulation. These findings demonstrate a hitherto uncharacterized modulation of hypoglossal activity through the interaction of HO‑2 and CSE-derived H2S, and supports the perspective that centrally derived HO-2 activity plays an important role regulating upper airway control. This archived dataset contains the numerical data used to generate the figures in the preprint titled: Gasotransmitter Modulation of Hypoglossal Motoneuron Activity by Brigitte Browe, Ying-Jie Peng, Jayasri Nanduri, Nanduri R. Prabhakar, and Alfredo J. Garcia III. This report can be found at <a href="https://www.biorxiv.org/content/10.1101/2022.03.23.485481">https://www.biorxiv.org/content/10.1101/2022.03.23.485481</a>.

Chiral Active Rods Simulation Data II

Simulation data of agent-based simulations of active point particles following the following overdamped Langevin dynamics: d/dt x_i= v* cos(phi_i) d/dt y_i= v* sin(phi_i) d/dt phi_i= omega + gamma*\sum_{j is neighbor of i} sin[2*(phi_j-phi_i)] + sigma*xi_i with independent Gaussian white noise xi_i. i and j are considered to be neighbors if their distance is less than R. Parameters: sigma=sqrt(2), R=1, v=1, simulation box size: Lx=Ly=sqrt(N/10), N, gamma, omega are given in the data base. Periodic boundary conditions are used. Euler-Maruyama scheme was used to integrate the equations of motion.

Chiral Active Rods Simulation Data I

Simulation data of agent-based simulations of active point particles following the following overdamped Langevin dynamics: d/dt x_i= v* cos(phi_i) d/dt y_i= v* sin(phi_i) d/dt phi_i= omega + gamma*\sum_{j is neighbor of i} sin[2*(phi_j-phi_i)] + sigma*xi_i with independent Gaussian white noise xi_i. i and j are considered to be neighbors if their distance is less than R. Parameters: sigma=sqrt(2), R=1, v=1, simulation box size: Lx=Ly=sqrt(N/10), N, gamma, omega are given in the data base. Periodic boundary conditions are used. A second order discretization scheme was used to integrate the equation of motion.

Aerosol activation from E3SM and cloud parcel model

This dataset contains maximum supersaturation, activation fraction, temperature, pressure, relative humidity, updraft velocity, and size, number, standard deviation, and hygroscopicity of aerosol from the 4-mode version of Modal Aerosol Module (MAM4) in U.S. Department of Energy's Energy Exascale Earth System Model (E3SM) and from a cloud parcel model.

Symbiotic nitrogen fixation does not stimulate soil phosphatase activity under temperate and tropical trees

Symbiotic nitrogen (N)-fixing plants can enrich ecosystems with N, which can alter the cycling and demand for other nutrients. Researchers have hypothesized that fixed N could be used by plants and soil microbes to produce extracellular phosphatase enzymes, which release P from organic matter. Consistent with this speculation, the presence of N-fixing plants is often associated with high phosphatase activity, either in the soil or on root surfaces, although other studies have not found this association, and the connection between phosphatase and rates of N fixation—the mechanistic part of the argument—is tenuous. Here, we measured soil phosphatase activity under N-fixing trees and non-fixing trees transplanted and grown in tropical and temperate sites in the USA: two sites in Hawaii, and one each in New York and Oregon. This provides a rare example of phosphatase activity measured in a multi-site field experiment with rigorously quantified rates of N fixation. We found no difference in soil phosphatase activity under N-fixing vs. non-fixing trees nor across rates of N fixation, though we note that no sites were P limited and only one was N limited. Our results add to the literature showing no connection between N fixation rates and phosphatase activity.

Raw Data for the article: Cigarette smoke promotes inflammasome-independent activation of caspase-1 and -4 leading to gasdermin D cleavage in human macrophages

Mechanisms and consequences of gasdermin D (GSDMD) activation in cigarette smoke (CS)-associated inflammation and lung disease are unknown. GSDMD is a downstream effector of caspase-1, -8, and -4. Upon cleavage, GSDMD generates pores into cell membranes. Different degrees of GSDMD activation are associated with a range of physiological outputs ranging from cell hyperactivation to pyroptosis. We have previously reported that in human monocyte-derived macrophages CS extract (CSE) inhibits the NLRP3 inflammasome and shifts the response to lipopolysaccharide (LPS) towards the TLR4-TRIF axis leading to activation of caspase-8, which, in turn, activates caspase-1. In the present work, we investigated whether other ASC-dependent inflammasomes could be involved in caspase activation by CSE and whether caspase activation led to GSDMD cleavage and other downstream effects. Presented results demonstrate that CSE promoted ASC-independent activation of caspase-1 leading to GSDMD cleavage and increased cell permeability, in the absence of cell death. GSDMD cleavage was strongly enhanced upon stimulation with LPS+CSE, suggesting a synergistic effect between the two stimuli. Noteworthy, CSE promoted LPS internalization leading to caspase-4 activation, thus contributing to increased GSDMD cleavage. Caspase-dependent GSDMD cleavage was associated with mitochondrial superoxide generation. Increased cleaved GSDMD was found in lung macrophages of smokers compared to ex-smokers and non-smoking controls. Our findings revealed that ASC-independent activation of caspase-1, -4, and -8 and GSDMD cleavage upon exposure to CS may contribute to macrophage dysfunction and feed the chronic inflammation observed in the smokers' lung.

D-Glu hydrolysis in the active site of the AmicoTA, a transaminase from the Gram-negative mesophilic bacterium Aminobacterium colombiense

500 frames from the QM(PBE0-D3/6-31G**)/MM molecular dynamic trajectory in the transition state region. The external potential is centered at 3.9 Å of the collective variable (a sum of the distances between the hydrogen atom of the protonated amino group and an oxygen atom the α-carboxylate group of the substrate and between the nitrogen atom of the substrate and a C4´ atom of PLP). In the PDB file the QM atoms have  beta=1 and MM beta=0.

New_Korespondensi The Role of Moderation Activities The Influence of The Audit Committee And The Board Of Directors on The Planning of The Sustainability Report

Abstract: In order to show the consistency of agency theory as a theory to explain the influence of the Audit Committee and the Board of Directors on Sustainability, this study will explore the role of moderating actions of the Audit Committee and the Board of Directors on Sustainability. The firms that make up the demographic and research sample for this study, which uses a quantitative technique, are those that are included in the Jakarta Islamic Index for the years 2017 through 2021. the study's yearly financial report panel data. The data analysis methods employed in this study were robust, fixed effects, random effects, and ordinary least square regression. These methods are one of the regression solution approaches that may be used with a lot of flexibility in research that combines thoughts, ideas, and facts. The first study found that the audit committee had an effect on sustainability, whereas the second found that the board of directors has no effect. Due to the third and fourth conclusions of the role of activities, the audit committee and board of directors are less strong on sustainability. Keywords : Activity; Board of Directors; Sustainability; Audit Committee; Stata JEL Classification: G32, G02, M1, G34, Z1

Cortical oscillations and interareal synchronization as a preparatory activity for postural response

The EEG data of each participant is composed by three subset: Condition1(Perturbation), Condition2(No Perturbation), and Time. The analysis was performed  by MATLAB software (.mat).

Data for: Endogenous DAF-16 spatiotemporal activity quantitatively predicts lifespan extension induced by dietary restriction

In many organisms, dietary restriction (DR) leads to lifespan extension through the activation of cell protection and pro-longevity gene expression programs. In the nematode C. elegans, the DAF-16 transcription factor is a key aging regulator that governs the Insulin/IGF-1 signaling pathway and undergoes translocation from the cytoplasm to the nucleus of cells when animals are exposed to food limitation. However, how large is the influence of DR on DAF-16 activity, and its subsequent impact on lifespan has not been quantitatively determined. In this work, we assess the endogenous activity of DAF-16 under various DR regimes by coupling CRISPR/Cas9-enabled fluorescent tagging of DAF-16 with quantitative image analysis and machine learning. Our results indicate that DR regimes induce strong endogenous DAF-16 activity, although DAF-16 is less responsive in aged individuals. DAF-16 activity is in turn a robust predictor of mean lifespan in C. elegans, accounting for 78% of its variability under DR. Analysis of tissue-specific expression aided by a machine learning tissue classifier reveals that, under DR, the DAF-16 influence on lifespan extension mainly originates from the intestine and neurons. DR also drives DAF-16 activity in unexpected locations such as the germline and intestinal nucleoli.

Acoustic activity of bats at power lines correlates with relative humidity: A potential role for corona discharges

With the ever-increasing dependency on electric power, electrical grid networks are expanding worldwide. Bats exhibit a wide diversity of foraging and flight behaviours, and their sensitivity to anthropogenic stressors suggests this group is very likely to be affected by power lines in a myriad of ways. Yet the effects of power lines on bats remain unknown. Here we assessed the responses of insectivorous bats to very-high-voltage power lines (>220 kV, VHVPL). We implemented a paired sampling design and monitored bats acoustically at 25 pairs, one pair consisting of one forest edge near to VHVPL matched with one control forest edge. Relative humidity mediates the effects of power lines on bats: we detected bat attraction to VHVPL at high relative humidity levels and avoidance of VHVPL by bats at low relative humidity levels. We argue that the former could be explained by insect attraction to the light emitted by VHVPL due to corona discharges while the latter may be due to the physical presence of pylons/cables at foraging height and/or because of electromagnetic fields. Our work highlights the response of bats to power lines at foraging habitats, providing new insight into the interactions between power lines and biodiversity.

Imprint of tree species mycorrhizal association on microbial-mediated enzyme activity and stoichiometry

1. Understanding the effects of tree species and their mycorrhizal association on soil processes is critical for predicting the ecosystem consequences of species shifts owing to global change and forest management decisions. While it is well established that forests dominated by different mycorrhizal types can vary in how they cycle carbon (C), nitrogen (N) and phosphorus (P), the degree to which these patterns are driven by microbial-mediated enzyme activity (EA) and ecoenzymatic stoichiometry (ES) remain elusive. 2. Here, we synthesized the effects of mycorrhizal association on seven soil enzymes involved in microbial C, N and P acquisition and ES using data from 56 peer-reviewed papers. 3. We found that relative to soil in ectomycorrhizal (EcM) trees, soil in arbuscular mycorrhizal (AM) trees exhibited greater activity of some C acquisition enzymes (e.g., beta-glucosidase; BG) and higher ecoenzymatic ratios of BG/NAG (N-acetyl-glucosaminidase) and BG/AP (acid phosphatase). These results supported that AM trees had rapid C and nutrient turnover rates, inorganic nutrient economics and high soil microbial C limitation. We also found evidence for an organic nutrient economy and greater soil microbial demand for nutrients in EcM trees compared to AM trees. In addition, the effect of mycorrhizal association on the activity of certain soil enzymes and enzymatic stoichiometry (i.e., BG and BG/NAG ratio) appeared to be associated with the differences in soil pH, phylogenetic group (i.e., conifers and broadleaves) and leaf habit (i.e., evergreen and deciduous) between AM and EcM trees. 4. The results from the global meta-analysis suggested that soil EA and ES appear to play critical roles in shaping the differences in the nutrient economy between AM and EcM tree species, but leaf morphology and soil conditions should be considered in evaluations of soil processes in forests of different mycorrhizal associations. Given that most of the studies in the database were from the temperate and subtropical regions, further research in other biomes is needed to elucidate the underlying mechanisms driving the mycorrhizal effect at the global scale.

opencc-by-4.0Mar 2023View details →

Data for: The Neonicotinoid Imidacloprid Impairs Sucrose Solution Consumption, Learning and Locomotor Activity Levels In Bumblebees (Bombus Terrestris)

# README The following files are for creating the figures from the paper:  ## `plot_flowervisits_nectar.ipynb` Jupyter notebook that creates the figures concerning flower visits, nectar consumption and the proportion of empty honeypots. ## `plot_activity.py` Python script that takes trajectory fragments from video analysis and computes the locomotor activity level through making histograms of bumblebee speeds. Makes two figures that are equivalent to the figure on locomotor activity in the paper. ## `statistical analysis.py` R markdown notebook that performs all the hypothesis testing for the paper. ## Data These files contain the data, and are located in the folder called `data`.  `activity/activityproportions.csv` contains the computed locomotor activity level for easy plotting. `boldata/boldata.csv` contains data about the nectar bag weight before and after experiment and the counted number of empty and full honeypots. Used by `plot_flowervisits_nectar.ipynb` `flower_data/flowerData.csv` contains the computed number of visits to blue and yellow flowers per hive for easy plotting. `humlevideo_production/*/traj*_trajectories*.csv` contains constructed trajectories from all experiments seen from both cameras. These are being used by the script `plot_activity`. `humlevideo_production/*/traj*.json` contains data about the occurence of bees on flowers in each frame in each experiment. `landinger_csv` contains data about landings, that have been extracted from the `humlevideo_production/*/traj*.json` files. Used by `plot_flowervisits_nectar.ipynb`.

opencc-by-4.0Mar 2023View details →

T-cell activity - Imaging flow cytometry experiment data

Raw image data from the imaging flow cytometry experiments for correlating receptor localization and cytokine production.

Data supplement for PhD thesis "Pattern Formation with Mass Conservation - From Passive to Active Models"

Here, we provide Mathematica files that provide the details of the weakly nonlinear analysis employed in the PhD thesis "Pattern Formation with Mass Conservation - From Passive to Active Models" submitted by Tobias Frohoff-Hülsmann.