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opencc-by-4.0Feb 2023View details →

Giant worm-shaped ESCRT-scaffolds surround actin-independent integrin clusters, data part 5

Part 5 of data for the article Giant worm-shaped ESCRT-scaffolds surround actin-independent integrin clusters.

opencc-zeroFeb 2023View details →

Intraspecific independent evolution of floral spur length in response to local flower visitor size in Japanese Aquilegia in different mountain regions

Geographic differences in floral traits may reflect geographic differences in effective pollinator assemblages. Independent local adaptation to pollinator assemblages in multiple regions would be expected to cause parallel floral trait evolution, although sufficient evidence for this is still lacking. In this study, we investigated the relationship between flower spur length and pollinator size in 16 populations of Aquilegia buergeriana var. buergeriana distributed in four mountain regions in the Japanese Alps. We also examined the genetic relationship between yellow- and red-flowered individuals, to see if color differences caused genetic differentiation by pollinator isolation. Genetic relationships among 16 populations were analyzed based on genome-wide single-nucleotide polymorphisms. Even among populations within the same mountain region, pollinator size varied widely, and the average spur length of A. buergeriana var. buergeriana in each population was strongly related to the average visitor size of that population. Genetic relatedness between populations was not related to the similarity of spur length between populations; rather, it was related to the geographic proximity of populations in each mountain region. Our results indicate that spur length in each population evolved independently of the population genetic structure but in parallel in different mountain regions. Further, yellow- and red-flowered individuals of A. buergeriana var. buergeriana were not genetically differentiated. Unlike other Aquilegia species in Europe and America visited by hummingbirds and hawkmoths, this species is consistently visited by bumblebees in Japan. As a result, genetic isolation by flower color has not occurred.

opencc-by-4.0Feb 2023View details →

Dataset of WiFi-based Environment-independent In-baggage Object Identification System

Description: The dataset of environment-independent in-baggage object identification system leveraging low-cost WiFi. The dataset contains the extracted CSI features from 14 representative in-baggage objects of 4 different materials. The experiments are conducted in 3 different office environments with different sizes. We hope this dataset will help researchers to reproduce the former work of in-baggage object identification through WiFi sensing.     Dataset Format:  .mat files   Section 1: Device Configuration:  <ul> <li> Transmitter: Aaronia HyperLOG 7060 direction antenna with a Dell Inspiron 3910 desktop for control.   </li> <li> Receiver: Hawking HD9DP orthogonal antennas with a Dell Inspiron 3910 desktop for control </li> <li> NIC: Atheros QCA9590. The configuration and installation guide of CSI tool can be found at <a href="https://wands.sg/research/wifi/AtherosCSI/">https://wands.sg/research/wifi/AtherosCSI/</a> </li> <li> WiFi Packet Rate: 1000 pkts/s  </li> </ul>   Section 2: Data Format We provide the CSI features through .mat files. The details are shown in the following: <ul> <li> 14 different objects made of 4 different materials are included in 3 different environments and 3 different days. </li> <li> Each object is tested for 60 seconds and repeated for 3 times.  </li> <li> The dataset file name is presented as "Object_Number". The detailed information are: <ul> <li> Object: The object we involved in the experiment (e.g., book, laptop) </li> <li> Number: The number of repeats.   </li> </ul> </li> </ul>   Section 3: Experimental Setups There are 3 different office experiment setups for our data collection. The detailed setups are shown in the paper. For the objects, we involve 14 types of objects made of 4 different materials.   <ul> <li> Environments:  <ul> <li> 3 different environments are involved, including 3 office environments with the size of 15 ft × 13 ft, 16 ft × 12 ft, 28 ft × 23 ft, respectively.  </li> <li> For each room environment, data is collected on different days and with different furniture settings (i.e., 2 desks and 2 chairs are moved at least 3 ft. ) </li> </ul> </li> <li> Representative objects:  <ul> <li> Data is collected using 14 representative objects of 4 different materials including fiber: book, magazine, newspaper; metal: thermal cup, laptop; cotton/polyester: cotton T-shirts (×2), cotton T-shirts (×4), hoodie, polyester T-shirts, polyester pants; water: 1L bottle with 1L water, 1L bottle with 500ml water, 500ml bottle with 500ml water.  </li> </ul> </li> </ul>   Section 4: Data Description For our data organization, we separate the data files into different folders based on different days and different environments. Under these folders, data are further distributed in terms of different objects and repeat times.  All the files are .mat files, which can be directly read for further applications.   <ul> <li> Features of CSI amplitude: We calculate 7 different types of statistical features, including mean, variance, median, skewness, kurtosis, interquartile range and range, and polarization feature from CSI amplitude. Particularly, we calculate the features for all 56 subcarriers with different operating frequencies and responses to the target object.   </li> <li> Features of CSI phase: For the features of CSI phase, the same features with CSI amplitude are extracted and stored in the dataset.   </li> </ul>   Section 6: Citations If your work is related to our work, please cite our papers as follows.  <a href="https://ieeexplore.ieee.org/document/9637801">https://ieeexplore.ieee.org/document/9637801</a> Shi, Cong, Tianming Zhao, Yucheng Xie, Tianfang Zhang, Yan Wang, Xiaonan Guo, and Yingying Chen. "Environment-independent in-baggage object identification using wifi signals." In 2021 IEEE 18th International Conference on Mobile Ad Hoc and Smart Systems (MASS), pp. 71-79. IEEE, 2021.

opencc-by-4.0Mar 2023View details →

Data for the manuscript "Electronic excitations of the charged nitrogen-vacancy center in diamond obtained using time-independent variational density functional calculations"

This folder contains all the input, output, and geometry files used to produce the results for the manuscript.  We included unprocessed data for LDA, PBE, TPSS, and r2SCAN functionals. We also provide a keynote file for figure 1 and a jupyter notebook which we used to make figures 2-4.

opencc-by-4.0Mar 2023View details →

Multiplex imaging of breast cancer lymph node metastases identifies prognostic single-cell populations independent of clinical classifiers

This repository contains the continuation of dataset 10.5281/zenodo.7494413 and 10.5281/zenodo.7494509. The file tiff_stacks_masks.zip contains the IMC image stacks and single-cell masks as tiff files. The IHC_TMAs.zip contains the scans of the IHC stains of ZTMA25 and the QuPATH projects used to extract the single-cell data (incl. the single-cell measurements as csv files).

opencc-zeroMar 2023View details →

Selection-driven trait loss in independently evolved cavefish populations

Laboratory studies have demonstrated that a single phenotype can be produced by many different genotypes; however, in natural systems, it is frequently found that phenotypic convergence is due to parallel genetic changes. This suggests a substantial role for constraint and determinism in evolution and indicates that certain mutations are more likely to contribute to phenotypic evolution. Here we use whole-genome resequencing in the Mexican tetra, Astyanax mexicanus, to investigate how selection has shaped the repeated evolution of both trait loss and enhancement across independent cavefish lineages. We show that selection on standing genetic variation and de novo mutations both contribute substantially to repeated adaptation. Our findings provide empirical support for the hypothesis that genes with larger mutational targets are more likely to be the substrate of repeated evolution and indicate that features of the cave environment may impact the rate at which mutations occur.

opencc-zeroApr 2023View details →

Warming and grazing independently and interactively impact plant defenses and palatability

The ecological impacts of multiple stressors are hard to predict but important to understand. When multiple stressors influence foundation species, the effects can cascade throughout the ecosystem. Gulf of Mexico seagrass ecosystems are currently experiencing a suite of novel stressors, including warmer water temperatures and increased herbivory due to tropicalization and conservation efforts. We investigated the impact of warming temperatures and grazing history on plant performance, morphology, and palatability by integrating a mesocosm study using the seagrass Thalassia testudinum with feeding trials using the sea urchin Lytechinus variegatus. Warming temperatures negatively impacted T. testudinum tolerance traits, reducing belowground biomass by 34%, productivity by 74%, shoot density by 10%, and the number of leaves per plant by 24%, and negatively impacted resistance traits through 13% lower toughness of young leaves and a trend for reduced leaf carbon:nitrogen. Lytechinus variegatus individuals preferred to consume plants grown under heated conditions, which supports findings of enhanced palatability. Simulated turtle grazing impacted more plant traits than grazing by other herbivores, potentially diminishing plant resilience to future disturbances through reduced rhizome non-structural carbohydrate concentrations and increasing palatability through reduced fiber content and 23% lower leaf carbon:phosphorus. Simulated turtle, simulated parrotfish, and urchin grazing reduced leaf carbon:nitrogen by 11%, also potentially increasing nutritive value. Interactions between warming temperatures and grazers on plant traits were additive for 16 out of 19 response variables. However, the stressors non-additively impacted the number of leaves per plant, fiber content, and epiphyte load. We suggest that the impacts of grazers on leaf turnover rate and leaf age may vary based on water temperature, potentially driving these interactions. Overall, increased temperatures and grazing pressure will likely reduce seagrass resilience, structure, and biomass, potentially impacting feedback systems and producing negative consequences for seagrass cover, associated species, and ecosystem services.

opencc-zeroMay 2023View details →

Stress induced TDP-43 mobility loss independent of stress granules

TAR DNA binding protein 43 (TDP-43) is closely related to the pathogenesis of amyotrophic lateral sclerosis (ALS) and translocates to stress granules (SGs). The role of SGs as aggregation-promoting "bioreactors" for TDP-43, however, is still under debate. We analyzed TDP-43 mobility and localization under different stress and recovery conditions using live cell single-molecule tracking and super-resolution microscopy. Besides reduced mobility within SGs, a stress induced decrease of TDP-43 mobility in the cytoplasm and the nucleus was observed. Stress removal led to a recovery of TDP-43 mobility, which strongly depended on the stress duration. 'Stimulated-emission depletion microscopy' (STED) and 'tracking and localization microscopy' (TALM) revealed not only TDP-43 substructures within stress granules but also numerous patches of slow TDP-43 species throughout the cytoplasm. The data provide new insights into the aggregation of TDP-43 in living cells and provide evidence suggesting that TDP-43 oligomerization takes place in the cytoplasm separate from SGs.

opencc-by-4.0Dec 2022View details →

CD4 T cell receptor hierarchies are stable and independent of HIV-mediated dysregulation of immune homeostasis

LT-ART and A5248 folders contain preprocessed CyTOF files (FCS format) from a 31-marker mass cytometry panel to examine all major PBMC lineages and specifically CD4 and CD8 T cell memory dynamics in people with HIV (PWH) who are durably ART suppressed for an average of 6.7 years (LT-ART, n = 10) and PWH in the first 500 days following ART initiation (A5248, n = 10). The panel also includes markers of activation (HLA-DR, CD38, CCR5), activation/exhaustion (PD-1), proliferation (Ki67), survival (Bcl-2) and long-lived memory (CD127). Preprocessed annotated data objects (A5248_subsample.h5ad, LT-ART_subsample.h5ad) for unsupervised analysis can be accessed using the 'read_h5ad' function in Scanpy. CD4_MSI and CD8_MSI folders contain the MSI data for the Gamma fixed-effects regression models.  All source code for reproduction of the results can be found in the GitHub repository: <a href="https://github.com/glab-hiv/immune-recovery">https://github.com/glab-hiv/immune-recovery</a>

openJul 2023View details →

Simulation outputs for the manuscript "Snowball Earth transitions from Last Glacial Maximum conditions provide an independent upper limit on Earth's climate sensitivity"

This dataset contains outputs for the simulations shown in the paper "Snowball Earth transitions from Last Glacial Maximum conditions provide an independent upper limit on Earth’s climate sensitivity" by Renoult et al. (submitted).  The outputs contain different 2D and 3D variables described in the paper and the file "README.txt".

opencc-zeroAug 2023View details →

The midnolin-proteasome pathway catches proteins for ubiquitination-independent degradation

Cells use ubiquitin to mark proteins for proteasomal degradation. While the proteasome also eliminates proteins that are not modified by ubiquitin, how this occurs mechanistically is unclear. We show here that midnolin promotes the destruction of many nuclear proteins including transcription factors encoded by the immediate-early-genes. Diverse environmental cues induce midnolin and its overexpression is sufficient to cause the degradation of its targets by a mechanism, which, remarkably, does not require ubiquitination. Instead, midnolin associates with the proteasome via an alpha-helix, employs its Catch-domain to bind a region within substrates that adopts a beta-strand conformation, and uses a ubiquitin-like-domain to promote substrate destruction. Thus, midnolin contains three regions that function in concert to target a large set of nuclear proteins to the proteasome for degradation.

FIGURE 1. A in A new species of Cyrtodactylus Gray, 1827 (Squamata: Gekkonidae) from the Thai-Malay Peninsula and the independent evolution of cave ecomorphology on opposite sides of the Gulf of Thailand

FIGURE 1. A. Distribution of the species of the Cyrtodactylus intermedius group after Murdoch et al. (2019). B. Location of Cyrtodactylus disjunctus sp. nov. (star) at the type locality of Meung Satun, Satun Province, Thailand.

FIGURE 4. A in A new species of Cyrtodactylus Gray, 1827 (Squamata: Gekkonidae) from the Thai-Malay Peninsula and the independent evolution of cave ecomorphology on opposite sides of the Gulf of Thailand

FIGURE 4. A MFA of the species of the Cyrtodactylus intermedius group. B Percent contributions of each data type to the inertia of dimensions 1–4 of the MFA. Percentage values on the bar graphs are the amounts of inertia for the respective dimensions. The red line represents the value if all contributions were equal. C The percent contribution of each character to dimensions 1–3. The red line represents the value if all contributions were equal.

FIGURE 9 in A new species of Cyrtodactylus Gray, 1827 (Squamata: Gekkonidae) from the Thai-Malay Peninsula and the independent evolution of cave ecomorphology on opposite sides of the Gulf of Thailand

FIGURE 9. Forest habitat at the type locality of Cyrotactylus disjunctus sp. nov. ISS 130 from Meung Satun, Satun Province, Thailand. Photograph by Parinya Pawangkhanan.

FIGURE 3 in A new species of Cyrtodactylus Gray, 1827 (Squamata: Gekkonidae) from the Thai-Malay Peninsula and the independent evolution of cave ecomorphology on opposite sides of the Gulf of Thailand

FIGURE 3. PCAs and DAPCs, respectively of A and D meristic, B and D morphometric, and C and E meristic-morphometric datasets. F Statistically significant variation based the permutation and bootstrap analyses conducted in the PCAtest. F PC 1of the meristic data set. G PCs 1 and 2 of the morphometric dataset. H PCs 1 and 2 of the meristic-morphometric dataset.

FIGURE 7 in A new species of Cyrtodactylus Gray, 1827 (Squamata: Gekkonidae) from the Thai-Malay Peninsula and the independent evolution of cave ecomorphology on opposite sides of the Gulf of Thailand

FIGURE 7. Holotype of Cyrtodactylus disjunctus sp. nov. ISS 130 ZMMU re-17674 from Meung Satun, Satun Province, Thailand. A Dorsal view of head. B right lateral view of head. C Gular region. D Ventral view of hand. E Ventral view of foot. F Ventral view of femora and precloacal region. G Subcaudal region. Photographs by Parinya Pawangkhanan.

FIGURE 2 in A new species of Cyrtodactylus Gray, 1827 (Squamata: Gekkonidae) from the Thai-Malay Peninsula and the independent evolution of cave ecomorphology on opposite sides of the Gulf of Thailand

FIGURE 2. Maximum clade credibility BEAST phylogeny of the Cyrtodactylus intermedius group highlighting the new species described herein. Bayesian posterior probabilities (BPP) are listed at the nodes. Photograph by Parinya Pawangkhanan.

FIGURE 6. A in A new species of Cyrtodactylus Gray, 1827 (Squamata: Gekkonidae) from the Thai-Malay Peninsula and the independent evolution of cave ecomorphology on opposite sides of the Gulf of Thailand

FIGURE 6. A Dorsal and ventral views of the holotype of Cyrtodactylus disjunctus sp. nov. ISS 130 ZMMU re-17674 from Meung Satun, Satun Province, Thailand. B Photo of the holotype in life. Photographs by Parinya Pawangkhanan.