Find research datasets worth reusing

opencc-byDec 2021View details →

Network pharmacology and UPLC-Q-TOF-MS-based method to explore the underlying mechanism of Shaoyao–Gancao decoction acting on atopic dermatitis

This study aimed to investigate the immunomodulation and anti-inflammatory effects of SGD and further explore its pharmacodynamics material basis and potential molecular mechanisms on atopic dermatitis (AD) disorder.

Mechanism of receptor assembly via the pleiotropic adipokine Leptin - single molecule tracking - raw data

This dataset contains the raw single-molecule image data that was analyzed in the manuscript "Mechanism of receptor assembly via the pleiotropic adipokine Leptin"

Data for: Reproductive isolating mechanisms contributing to asymmetric hybridization in Killifishes (Fundulus spp.)

When species hybridize, one F1 hybrid cross type often predominates. Such asymmetry can arise from differences in a variety of reproductive barriers, but the relative roles and concordance of pre-mating, post-mating prezygotic barriers, and post-zygotic barriers in producing these biases in natural animal populations have not been widely investigated. Here, we study a population of predominantly F1 hybrids between two killifish species (Fundulus heteroclitus and Fundulus diaphanus) in which >95% of F1 hybrids have F. diaphanus mothers and F. heteroclitus fathers (D♀×H♂). To determine why F. heteroclitus x F. diaphanus F1 hybrids (H♀×D♂) are so rare, we tested for asymmetry in pre-mating reproductive barriers (female preference, male aggression) at a common salinity (10 ppt) and post-mating, pre-zygotic (fertilization success) and post-zygotic (embryonic development time and hatching success) reproductive barriers at a range of ecologically relevant salinities (0, 5, 10, and 15 ppt). We found that F. heteroclitus females preferred conspecific males, while F. diaphanus females did not, matching the observed cross bias in the wild. Naturally rare H♀×D♂ crosses also had lower fertilization success than all other cross types, and a lower hatching success than the prevalent D♀×H♂ crosses at the salinity found in the hybrid zone centre (10 ppt). Furthermore, the naturally predominant D♀×H♂ crosses had a higher hatching success than F. diaphanus crosses at 10ppt, which may affect their relative abundance. The present study suggests that a combination of incomplete mating, post-mating pre-zygotic and post-zygotic reproductive isolating mechanisms act in concert to produce hybrid asymmetry in this system.

Code and data for: Nitrogen-induced hysteresis in grassland biodiversity: A theoretical test of litter-mediated mechanisms

The global rise in anthropogenic reactive nitrogen (N) and the negative impacts of N deposition on terrestrial plant diversity are well-documented. The R* theory of resource competition predicts reversible decreases in plant diversity in response to N loading. However, empirical evidence for the reversibility of N-induced biodiversity loss is mixed. In a long-term N-enrichment experiment in Minnesota, a low-diversity state that emerged during N addition has persisted for decades after additions ceased. Hypothesized mechanisms preventing recovery of biodiversity include nutrient recycling, insufficient external seed supply, and litter inhibition of plant growth. Here we present an ODE model that unifies these mechanisms, produces bistability at intermediate N inputs, and qualitatively matches the observed hysteresis at Cedar Creek. Key features of the model, including native species' growth advantage in low-N conditions and limitation by litter accumulation, generalize from Cedar Creek to North American grasslands. Our results suggest that effective biodiversity restoration in these systems may require management beyond reducing N inputs, such as burning, grazing, haying, and seed additions. By coupling resource competition with an additional inter-specific inhibitory process, the model also illustrates a general mechanism for bistability and hysteresis that may occur in multiple ecosystem types.

Cytoscape files - Systems-level analyses of protein-protein interaction network dysfunctions via epichaperomics identify cancer-specific mechanisms of stress adaptation

Cytoscape files of pathway enrichment analyses and PPI mapping associated with manuscript https://www.nature.com/articles/s41467-023-39241-7 Systems-level analyses of protein-protein interaction network dysfunctions via epichaperomics identify cancer-specific mechanisms of stress adaptation Anna Rodina1,11, Chao Xu1,11, Chander S. Digwal1,11, Suhasini Joshi1,11, Anand R. Santhaseela1, Sadik Bay1, Swathi Merugu1, Aftab Alam1, Pengrong Yan1, Chenghua Yang1,12, Tanaya Roychowdhury1, Palak Panchal1, Liza Shrestha1, Yanlong Kang1, Sahil Sharma1, Yogita Patel2, Justina Almadovar1, Adriana Corben3,13, Mary Alpaugh1,14, Shanu Modi4, Monica L. Guzman5, Teng Fei6, Tony Taldone1, Stephen D. Ginsberg7,8, Hediye Erdjument-Bromage9, Thomas A. Neubert9, Katia Manova-Todorova10, Jason C. Young2, Meng-Fu Bryan Tsou10, Tai Wang1,*, Gabriela Chiosis1,4,* Abstract Systems-level assessments of protein-protein interaction (PPI) network dysfunctions are currently out-of-reach because approaches enabling proteome-wide identification, analysis, and modulation of context-specific PPI changes in native (unengineered) cells and tissues are lacking. Herein, we take advantage of first-in-class chemical binders of maladaptive scaffolding structures termed epichaperomes and develop an epichaperome-based ‘omics platform, epichaperomics, to identify PPI alterations in disease. We provide multiple lines of evidence, at both biochemical and functional levels, demonstrating the importance of these probes to identify and study PPI network dysfunctions and provide mechanistically and therapeutically relevant proteome-wide insights. As proof-of-principle, we derive systems-level insight into PPI dysfunctions of cancer cells which enabled the discovery of a context-dependent mechanism by which cancer cells enhance the fitness of mitotic protein networks. Importantly, our systems levels analyses support the use of epichaperome chemical binders as therapeutic strategies aimed at normalizing PPI networks.

Hosts winnow symbionts with multiple layers of absolute and conditional discrimination mechanisms

In mutualism, hosts select symbionts via partner choice and preferentially direct more resources to symbionts that provide greater benefits via sanctions. At the initiation of symbiosis, prior to resource exchange, it is not known how the presence of multiple symbiont options (i.e., the symbiont social environment) impacts partner choice outcomes. Furthermore, little research addresses whether hosts primarily discriminate among symbionts via sanctions, partner choice or a combination. We inoculated the legume, Acmispon wrangelianus, with 28 pairs of fluorescently labeled Mesorhizobium strains that vary continuously in quality as nitrogen-fixing symbionts. We find that hosts exert robust partner choice, which enhances their fitness. This partner choice is conditional such that a strain's success in initiating nodules is impacted by other strains in the social environment. This social genetic effect is as important as a strain's own genotype in determining nodulation and has both transitive (consistent) and intransitive (idiosyncratic) effects on the probability that a symbiont will form a nodule. Furthermore, both absolute and conditional partner choice act in concert with sanctions, among and within nodules. Thus, multiple forms of host discrimination act as a series of sieves that optimize host benefits and select for costly symbiont cooperation in mixed symbiont populations.

Mechanical Parts Dataset 2022

Mechanical Parts Dataset The dataset consists of a total of 2250 images obtained by downloading from various internet platforms. Among the images in the dataset, there are 714 images with bearings, 632 images with bolts, 616 images with gears and 586 images with nuts. A total of 10597 manual labeling processes were carried out in the dataset, including 2099 labels belonging to the bearing class, 2734 labels belonging to the bolt class, 2662 labels belonging to the gear class and 3102 labels belonging to the nut class.    Folder Content The created dataset is divided into 3 as 80% train, 10% validation and 10% test. In the "Mechanical Parts Dataset" folder, there are three separate folders as "train", "test" and "val". In each of these three folders there are folders named "images" and "labels". Images are kept in the "images" folder and tag information is kept in the "labels" folder. Finally, inside the folder there is a yaml file named "mech_parts_data" for the Yolo algorithm. This file contains the number of classes and class names.   Images and Labels The dataset was prepared in accordance with the Yolov5 algorithm. For example, the tag information of the image named "2a0xhkr_jpg.rf.45a11bf63c40ad6e47da384fdf6bb7a1.jpg" is stored in the txt file with the same name. The tag information (coordinates) in the txt file are as follows: "class x_center y_center width height".   Update 05.01.2023 ***Pascal voc and coco json formats have been added.***   Related paper: doi.org/10.5281/zenodo.7496767

Mechanical behavior of C45 steel at high temperatures and high strain rates—experimental data set and numerical approach

In this publication we provide experimental data of dynamic compression tests of four microstructural variants of the C45 steel alloy performed at high temperatures and high strain rates. The presented data evidences the presence of Dynamic Strain Aging (DSA) in the material. Moreover, we provided the MATLAB codes of a calibration approach to estimate the material parameters of a plasticity model that accounts for DSA. The file "Mechanical behavior of C45" contains: 1) Folder EXP_DATA contains experimental data of dynamic compression tests of the C45 steel variants in .mat format. The data is organized in cell arrays, and every cell in the arrays contains the data of one experiment. The data of each experiment is arranged as four columns arrays, as: column 1: Plastic strain, column 2: Flow stress, column 3: absolute temperature, column 4: strain rate 2) Matlab code named CALIBRATION.m which executes a calibration approach of a modified Johnson-Cook that accounts for DSA. The form of the model is the following: \(\sigma(\varepsilon ,T,\dot{\varepsilon}) = (A+B\varepsilon^n)\left(1+Cln\left(\frac{\dot{\varepsilon}}{\dot{\varepsilon}^{ref}}\right)\right)\left( 1-\left(\frac{T-T^{ref}}{T^{melt}-T^{ref}}\right)^m\right) +\sigma^{dsa}(\varepsilon ,T,\dot{\varepsilon}) \) with, \(σ^{dsa} (ε,T,\dotε )=\frac{B_1}{ν} \left(\frac{ε^β}{ ε ̇T} exp⁡(-\frac{Q_m}{KT}) \right)^{\frac{2}{3}}\), \(\frac{B_1}{\nu} = \frac{\psi \dot{\varepsilon}}{exp(\eta \frac{T}{\dot{\varepsilon}^\alpha})} \)   The code CALIBRATION contains a data presentation section that can be used to generate plots to compare calibrated models with the experimental data. Further instructions are commented in the code CALIBRATION.m.

Pollen limitation and context-dependent alleviating mechanisms in a co-flowering alpine grassland community

1. The consequences of community metrics (e.g., co-flowering diversity and floral density) and plant traits (e.g., pollinator dependency and trait similarity) on pollen limitation may depend on pollinator-mediated competitive or facilitative interactions among plants in co-flowering communities, which could vary with community contexts (i.e. different altitude communities) and under human disturbances (e.g., livestock grazing). However, the mechanisms to alleviate pollen limitation under the different contexts, considering pollinator-mediated interactions among neighbor plants are unclear. 2. We investigated pollen limitation under grazing versus ungrazing conditions in low versus high altitude alpine meadows on the Tibetan Plateau to uncover the underlying mechanisms mediating pollen limitation associated with livestock grazing. 3. Pollen limitation is prevalent in alpine grasslands, irrespective of community contexts. Grazing exclusion decreased pollen limitation in the two sites but in different ways. In the high-altitude site, pollen limitation was reduced by the exclusion of grazers through increased trait similarity (suggesting facilitation). While pollen limitation was reduced by decreased trait similarity (suggesting competition avoidance) under grazing exclusion in the low-altitude site. 4. Synthesis and Applications: This study suggests that flower trait distribution patterns (i.e. trait similarity) influence pollen limitation through reducing competition in the low-altitude site or enhancing facilitation in the high-altitude site under grazing exclusion in alpine grasslands. Our results provide a mechanistic understanding of pollen limitation in co-flowering alpine grassland communities under distinct human disturbances at different altitudes, emphasizing the role of pollinator-mediated interactions among plants on plant reproductive success.

opencc-by-4.0Jan 2023View details →

Implications of large binding energies of massive stripped core collapse supernova progenitors on the explosion mechanism

Inlist files (r15140) used for the creation of the core-collapse progenitor models in the paper "The implications of large binding energies of massive, stripped, core-collapse supernova progenitors on the explosion mechanism". Based on the ‘20M pre ms to core collapse’ example from MESA r22.05, adapted for use in r15140, and include several variations as detailed in the paper appendix A. See README.txt for running details and example script. Also included are the full simulation list and the profiles of the 52 simulated cases, including the pre-collapse profiles at the point of termination for the 27 models that reached collapse. Profiles are at central oxygen depletion (5% abundance at center), central silicon depletion (5% abundance at center) and collapse, as defined in the paper.

opencc-zeroJan 2023View details →

Data for: Chloride-dependent mechanisms of multimodal sensory discrimination and nociceptive sensitization in Drosophila

Individual sensory neurons can be tuned to many stimuli, each driving unique, stimulus-relevant behaviors, and the ability of multimodal nociceptor neurons to discriminate between potentially harmful and innocuous stimuli is broadly important for organismal survival. Moreover, disruptions in the capacity to differentiate between noxious and innocuous stimuli can result in neuropathic pain. Drosophila larval Class III (CIII) neurons are peripheral noxious cold nociceptors and innocuous touch mechanosensors; high levels of activation drive cold-evoked contraction (CT) behavior, while low levels of activation result in a suite of touch-associated behaviors. However, it is unknown what molecular factors underlie CIII multimodality. Here, we show that the TMEM16/anoctamins subdued and white walker (wwk; CG15270) are required for cold-evoked CT, but not for touch-associated behavior, indicating a conserved role for anoctamins in nociception. We also evidence that CIII neurons make use of atypical depolarizing chloride currents to encode cold, and that overexpression of ncc69-a fly homologue of NKCC1-results in phenotypes consistent with neuropathic sensitization, including behavioral sensitization and neuronal hyperexcitability, making Drosophila CIII neurons a candidate system for future studies of the basic mechanisms underlying neuropathic pain

opencc-zeroJan 2023View details →

A mechanism of uncompetitive inhibition of the serotonin transporter

The serotonin transporter (SERT/SLC6A4) is arguably the most extensively studied solute carrier (SLC). During its eponymous action - i.e., the retrieval of serotonin from the extracellular space - SERT undergoes a conformational cycle. Typical inhibitors (antidepressant drugs and cocaine), partial and full substrates (amphetamines and their derivatives) and atypical inhibitors (ibogaine analogues) bind preferentially to different states in this cycle. This results in competitive or non-competitive transport inhibition. Here, we explored the action of N-formyl-1,3-bis (3,4-methylenedioxyphenyl)-prop-2-yl-amine (ECSI#6) on SERT: inhibition of serotonin uptake by ECSI#6 was enhanced with increasing serotonin concentration. Conversely, the KM for serotonin was lowered by augmenting ECSI#6. ECSI#6 bound with low affinity to the outward-facing state of SERT but with increased affinity to a potassium-bound state. Electrophysiological recordings showed that ECSI#6 preferentially interacted with the inward-facing state. Kinetic modeling recapitulated the experimental data and verified that uncompetitive inhibition arose from preferential binding of ECSI#6 to the K+-bound, inward-facing conformation of SERT. This binding mode predicted a pharmacochaperoning action of ECSI#6, which was confirmed by examining its effect on the folding-deficient mutant SERT-PG601,602AA: pre-incubation of HEK293 cells with ECSI#6 restored export of SERT-PG601,602AA from the endoplasmic reticulum and substrate transport. Similarly, in transgenic flies, administration of ECSI#6 promoted delivery of SERT-PG601,602AA to the presynaptic specialization of serotonergic neurons. To the best of our knowledge, ECSI#6 is the first example of an uncompetitive SLC inhibitor. Pharmacochaperones endowed with the binding mode of ECSI#6 are attractive because they can rescue misfolded transporters at concentrations, which cause modest transport inhibition.

opencc-by-4.0Feb 2023View details →

Data for "Structure and mechanism of oxalate transporter OxlT in an oxalate-degrading bacterium in the gut microbiota"

MD simulation data of OxlT. Trajectory data and NAMD input files are included. The first 500 ns trajectory that starts from the occluded conformation with a transition to the outward-open conformation is in the OxlT-occ directory. The 200 ns trajectories that start from the outward-open conformation with different protonation states of K355 are in the  OxlT-out directory.

Data for: Causal mechanisms for negative impacts of energy development inform management triggers for sagebrush birds

Estimated population trends can identify declining species to focus biological conservation, but monitoring may fail to illuminate causes of population change and strategies for reversing declines. Monitoring programs can relate trends with environmental attributes to test causal hypotheses, but typical analytical approaches do not explicitly support causal inference, diluting available data for informing conservation. The U.S. Bureau of Land Management (BLM) extended Integrated Monitoring in Bird Conservation Regions with a quasi-experimental sampling design over a 10-year period (2010–2019) to evaluate impacts of oil and gas development on sagebrush birds within the Atlantic Rim Natural Gas Development Project in southern Wyoming. We analyzed resulting data using a multi-scale community occupancy model to estimate trends in species occupancy and richness relevant to management triggers. Additionally, we employed path analysis to evaluate mechanisms underlying observed trends to inform potential management responses. Fine-scale occupancy for sage thrasher (Oreoscoptes montanus) declined within the high-development stratum at a rate sufficient to meet an a priori management trigger established by the BLM. Two additional sagebrush-associated species, Brewer's (Spizella breweri) and sagebrush sparrow (Artemisiospiza nevadensis), exhibited negative development relationships with trend, as did overall species richness, and richness of grassland, sagebrush, and generalist guilds. We identified well pad density and invasive plants associated with energy development as causal factors contributing to these negative development impacts. We demonstrate an analytical approach for both estimating occupancy trends and identifying underlying causes to inform conservation action. Reducing the development footprint, including well pad density and associated invasive plants, could help reduce or limit impacts on birds within this landscape.

Neural mechanism of experience-dependent sensory gain control in c. elegans

Animals' sensory systems adjust their responsiveness to environmental stimuli that vary greatly in their intensity. Here we report the neural mechanism of experience-dependent sensory adjustment, especially gain control, in the ASH nociceptive neurons in Caenorhabditis elegans. Using calcium imaging under gradual changes in stimulus intensity, we find that the ASH neurons of naive animals respond to concentration increases in a repulsive odor 2-nonanone regardless of the magnitude of the concentration increase. However, after preexposure to the odor, the ASH neurons exhibit significantly weak responses to a small gradual increase in odor concentration while their responses to a large gradual increase remain strong. Thus, preexposure changes the slope of stimulus-response relationships (i.e., gain control). Behavioral analysis suggests that this gain control contributes to the preexposure-dependent enhancement of odor avoidance behavior. Mathematical analysis reveals that the ASH response consists of fast and slow components, and that the fast component is specifically suppressed by preexposure for the gain control. In addition, genetic analysis suggests that G protein signaling is required for the fast component. Thus, our integrative study demonstrates how prior experience dynamically modulates stimulus-response relationships in sensory neurons, eventually leading to adaptive modulation of behavior.

Data for: Carbon-concentrating mechanisms are a key trait in lichen ecology and distribution

Carbon-concentrating mechanisms (CCMs) are a widespread phenomenon in photosynthetic organisms. In vascular plants, the evolution of CCMs (C4 and CAM) is associated with significant shifts, most often to hot, dry and bright or aquatic environments. If and how CCMs drive distributions of other terrestrial photosynthetic organisms, remains little studied. Lichens are ecologically important obligate symbioses between fungi and photosynthetic organisms. The primary photosynthetic partner in these symbioses can include CCM-presenting cyanobacteria (as carboxysomes), CCM-presenting green algae (as pyrenoids) or green algae lacking any CCM. We use an extensive dataset of lichen communities from eastern North America, spanning a wide climatic range, to test the importance of CCMs as predictors of lichen ecology and distribution. We show that presence or absence of CCMs leads to opposite responses to temperature and precipitation in green algal lichens, and with different responses in cyanobacterial lichens. These responses contrast with our understanding of lichen physiology, whereby CCMs mitigate carbon limitation by water saturation at the cost of efficient use of vapor hydration. This study demonstrates that CCM-status is a key functional trait in obligate lichen symbioses, equivalent in importance to its role in vascular plants, and central for studying present and future climate responses.

Different assembly mechanisms of leaf epiphytic and endophytic bacterial communities underlie their higher diversity in more diverse forests

Plant microbiomes are known to influence host fitness and ecosystem functioning, but mechanisms regulating their structure are poorly understood. Here, we explored the assembly mechanisms of leaf epiphytic and endophytic bacterial communities using a subtropical forest biodiversity experiment. Both epiphytic and endophytic bacterial diversity increased as host tree diversity increased. However, the increased epiphytic diversity in more diverse forests was driven by greater epiphytic diversity (i.e., greater α diversity) on individual trees, whereas the increased endophytic diversity in more diverse forests was driven by greater dissimilarity in endophytic composition (i.e., greater β diversity) among trees. Mechanistically, responses of epiphytes to changes in host diversity were consistent with mass effects, whereas responses of endophytes were consistent with species sorting. Synthesis: These results provided novel experimental evidence that biodiversity declines of plant species will lead to biodiversity declines of plant-associated microbiomes, but the underlying mechanism may differ between habitats on the plant host.

opencc-by-4.0Feb 2023View details →

Data of Energy mechanism of atmospheric boundary layer development over the Tibetan Plateau

Processed data of Energy mechanism of atmospheric boundary layer development over the Tibetan Plateau

Data for: A structure-based mechanism for displacement of the HEXIM adapter from 7SK small nuclear RNA

Productive transcriptional elongation of many cellular and viral mRNAs requires transcriptional factors to extract pTEFb from the 7SK snRNP by modulating the association between the HEXIM protein and the 7SK snRNA. Here we report the structure of the HEXIM arginine-rich motif in complex with the apical stemloop-1 of 7SK (7SK-SL1apical) and detail how the HIV transcriptional regulator Tat from various subtypes overcome the structural constraints required to displace HEXIM. While most interactions between 7SK and HEXIM and Tat are similar, critical differences exist that guide function. First, the conformational plasticity of 7SK enables the formation of three different base pair configurations at a critical remodeling site, which allows for the modulation required for HEXIM binding and its subsequent displacement by Tat. Furthermore, the specific sequence variations observed in various Tat subtypes all converge on remodeling 7SK at this region. Second, we show that HEXIM primes its own displacement by causing specific local destabilization upon binding — a feature that is then exploited by Tat to bind 7SK more efficiently. Overall, our study details the molecular environment presented by HEXIM and uncovers a destabilization-driven displacement strategy that increases the conformational sampling of 7SK-snRNP, which may allow diverse transcriptional factors to competitively regulate pTEFb.