Find research datasets worth reusing

openbsd-3-clauseFeb 2019View details →

Enhanced proximity effect in zigzag-shaped Majorana Josephson junctions

Dataset and source code for the paper "Enhanced proximity effect in zigzag-shaped Majorana Josephson junctions".

opencc-zeroNov 2019View details →

Fiber-tract localized diffusion coefficients highlight patterns of white matter disruption induced by proximity to glioma

Gliomas account for 26.5% of all primary central nervous system tumors. Recent studies have used diffusion tensor imaging (DTI) to extract white matter fibers and the diffusion coefficients derived from MR processing to provide useful, non-invasive insights into the extent of tumor invasion, axonal integrity, and gross differentiation of glioma from metastasis. Here, we extend this work by examining whether a tract-based analysis can improve non-invasive localization of tumor impact on white matter integrity. This study retrospectively analyzed preoperative magnetic resonance sequences highlighting contrast enhancement and DTI scans of 13 subjects that were biopsy confirmed to have either high or low-grade glioma. We reconstructed the corticospinal tract and superior longitudinal fasciculus by applying atlas-based regions of interest to fibers derived from whole-brain deterministic streamline tractography. Within-subject comparison of hemispheric diffusion coefficients (e.g., fractional anisotropy and mean diffusivity) indicated higher levels of white matter degradation in the ipsilesional hemisphere. Novel application of along-tract analyses revealed that tracts traversing the tumor region showed significant white matter degradation compared to the contralesional hemisphere and ipsilesional tracts displaced by the tumor.

opencc-zeroDec 2015View details →

Data from: Residue proximity information and protein model discrimination using saturation-suppressor mutagenesis

Identification of residue-residue contacts from primary sequence can be used to guide protein structure prediction. Using Escherichia coli CcdB as the test case, we describe an experimental method termed saturation-suppressor mutagenesis to acquire residue contact information. In this methodology, for each of five inactive CcdB mutants, exhaustive screens for suppressors were performed. Proximal suppressors were accurately discriminated from distal suppressors based on their phenotypes when present as single mutants. Experimentally identified putative proximal pairs formed spatial constraints to recover >98% of native-like models of CcdB from a decoy dataset. Suppressor methodology was also applied to the integral membrane protein, diacylglycerol kinase A where the structures determined by X-ray crystallography and NMR were significantly different. Suppressor as well as sequence co-variation data clearly point to the X-ray structure being the functional one adopted in vivo. The methodology is applicable to any macromolecular system for which a convenient phenotypic assay exists.

opencc-zeroJul 2019View details →

Data from: Proximity labeling reveals novel interactomes in live Drosophila tissue

Gametogenesis is dependent on intercellular communication facilitated by stable intercellular bridges connecting developing germ cells. During Drosophila oogenesis, intercellular bridges (referred to as ring canals) have a dynamic actin cytoskeleton that drives their expansion to a diameter of 10μm. While multiple proteins have been identified as components of ring canals (RCs), we lack a basic understanding of how RC proteins interact together to form and regulate the RC cytoskeleton. We optimized a procedure for proximity-dependent biotinylation in live tissue using the APEX enzyme to interrogate the RC interactome. APEX was fused to four different RC components (RC-APEX baits) and 55 unique high-confidence preys were identified. The RC-APEX baits produced almost entirely distinct interactomes that included both known RC proteins as well as uncharacterized proteins. The proximity ligation assay was used to validate close-proximity interactions between the RC-APEX baits and their respective preys. Further, an RNAi screen revealed functional roles for several high-confidence prey genes in RC biology. These findings highlight the utility of enzyme-catalyzed proximity labeling for protein interactome analysis in live tissue and expand our understanding of RC biology.

opencc-zeroDec 2018View details →

Data from: Ectomycorrhizas and tree seedling establishment are strongly influenced by forest edge proximity but not soil inoculum

Reforestation is challenging when timber harvested areas have been degraded, invaded by non-native species, or are of marginal suitability to begin with. Conifers form mutualistic partnerships with ectomycorrhizal fungi (EMF) to obtain greater access to soil resources, and these partnerships may be especially important in degraded areas. However, timber harvest can impact mycorrhizal fungi by removing or compacting topsoil, removing host plants, and warming and drying the soil. We used a field experiment to evaluate the role of EMF in Douglas-fir reforestation in clearcuts invaded by Cytisus scoparius (Scotch broom) where traditional reforestation approaches have repeatedly failed. We tested how planting distance from intact Douglas-fir forest edges influenced reforestation success and whether inoculation with forest soils can be used to restore EMF relationships. We used an Illumina DNA sequencing approach to measure the abundance, richness and composition of ectomycorrhizal fungi on Douglas-fir roots, and assessed differences in Douglas-fir seedling survival and growth near to and far from forest edges with and without forest soil inoculum. Planting Douglas-fir seedlings near forest edges increased seedling survival, growth and EMF root colonization. Edge proximity had no effect on EMF richness but did change fungal community composition. Inoculations with forest soil did not increase EMF abundance or richness or change community composition, nor did it improve seedling establishment. With Illumina sequencing we identified two to three times greater species richness than described in previous edge effects studies. Of the 95 EMF species we identified, 40% of the species occurred on less than 5% of the seedlings. The ability to detect fungi at low abundance may explain why we did not detect differences in EMF richness with distance to hosts as previous studies. Our findings suggest that forest edges are suitable for reforestation, even when the interiors of deforested areas are not. We advocate for timber harvest designs that maximize edge habitat where ectomycorrhizal fungi contribute to tree establishment. However, this study does not support the use of inoculation with forest soil as a simple method to enhance EMF and seedling survival.

opencc-zeroDec 2014View details →

Data from: Pardon the interruption: goal proximity, perceived spare time, and impatience

There is no worse time to be interrupted than right now. Being close to attaining a goal to complete a focal task increases the attractiveness of that task compared to an interrupting task (study 1), makes people less willing to take on some otherwise attractive interruption than if they were farther away from completion (studies 2, 3, and 4), and causes them to perceive that in that moment they have little spare time (studies 3 and 4). Consumers immersed in goal pursuit are affected by local progress on an individual subgoal that supports an overarching goal even if this has no effect on the timing of attaining the overarching goal. Observers do not appreciate the motivating power of proximity to completing subgoals, and this leads them to mispredict the behavior of others (study 5).

opencc-zeroDec 2015View details →

Data from: Synergism and antagonism of proximate mechanisms enable and constrain the response to simultaneous selection on body size and development time: an empirical test using experimental evolution

Natural selection acts on multiple traits simultaneously. How mechanisms underlying such traits enable or constrain their response to simultaneous selection is poorly understood. We show how antagonism and synergism among three traits at the developmental level enable or constrain evolutionary change in response to simultaneous selection on two focal traits at the phenotypic level. After 10 generations of 25% simultaneous directional selection on all four combinations of body size and development time in Manduca sexta (Sphingidae), the changes in the three developmental traits predict 93% of the response of development time and 100% of the response of body size. When the two focal traits were under synergistic selection, the response to simultaneous selection was enabled by juvenile hormone and ecdysteroids and constrained by growth rate. When the two focal traits were under antagonistic selection, the response to selection was due primarily to change in growth rate and constrained by the two hormonal traits. The approach used here reduces the complexity of the developmental and endocrine mechanisms to three proxy traits. This generates explicit predictions for the evolutionary response to selection that are based on biologically informed mechanisms. This approach has broad applicability to a diverse range of taxa, including algae, plants, amphibians, mammals, and insects.

opencc-zeroDec 2014View details →

Data from: The kinetochore prevents centromere-proximal crossover recombination during meiosis

During meiosis, crossover recombination is essential to link homologous chromosomes and drive 22 faithful chromosome segregation. Crossover recombination is non-random across the genome, 23 and centromere-proximal crossovers are associated with an increased risk of aneuploidy, 24 including Trisomy 21 in humans. Here, we identify the conserved Ctf19/CCAN kinetochore sub- 25 complex as a major factor that minimizes potentially deleterious centromere-proximal crossovers 26 in budding yeast. We uncover multi-layered suppression of pericentromeric recombination by the 27 Ctf19 complex, operating across distinct chromosomal distances. The Ctf19 complex prevents 28 meiotic DNA break formation, the initiating event of recombination, proximal to the centromere. 29 The Ctf19 complex independently drives the enrichment of cohesin throughout the broader 30 pericentromere to suppress crossovers, but not DNA breaks. This non-canonical role of the 31 kinetochore in defining a chromosome domain that is refractory to crossovers adds a new layer 32 of functionality by which the kinetochore prevents the incidence of chromosome segregation 33 errors that generate aneuploid gametes.

opencc-zeroDec 2016View details →

Data from: Proximate controls on semiarid soil greenhouse gas fluxes across 3 million years of soil development

Soils are important sources and sinks of three greenhouse gases (GHGs): carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O). However, it is unknown whether semiarid landscapes are important contributors to global fluxes of these gases, partly because our mechanistic understanding of soil GHG fluxes is largely derived from more humid ecosystems. We designed this study with the objective of identifying the important soil physical and biogeochemical controls on soil GHG fluxes in semiarid soils by observing seasonal changes in soil GHG fluxes across a three million year substrate age gradient in northern Arizona. We also manipulated soil nitrogen (N) and phosphorus availability with 7 years of fertilization and used regression tree analysis to identify drivers of unfertilized and fertilized soil GHG fluxes. Similar to humid ecosystems, soil N2O flux was correlated with changes in N and water availability and soil CO2 efflux was correlated with changes in water availability and temperature. Soil CH4 uptake was greatest in relatively colder and wetter soils. While fertilization had few direct effects on soil CH4 flux, soil nitrate was an important predictor of soil CH4 uptake in unfertilized soils and soil ammonium was an important predictor of soil CH4 uptake in fertilized soil. Like in humid ecosystems, N gas loss via nitrification or denitrification appears to increase with increases in N and water availability during ecosystem development. Our results suggest that, with some exceptions, the drivers of soil GHG fluxes in semiarid ecosystems are often similar to those observed in more humid ecosystems.

opencc-by-4.0Jul 2023View details →

Data and Code for: Proximal microclimate: moving beyond spatiotemporal resolution improves ecological predictions

Data and code corresponding to analyses and figures for the paper in review.

opencc-by-4.0Nov 2024View details →

Scripts and Datasets for Photocatalytic Nanoscale Metal-Organic Framework for Proximity Labeling in Living Cells

Please read data_process.ipynb for more details.

opencc-by-4.0Aug 2022View details →

FIG. 1 in Relations between metatarsal proximal extremity parameters and weight and height at the withers of the dromedary (Camelus dromedarius Linnaeus, 1758) in the Sahraoui and Targui "breeds".

FIG. 1. — Proximal view of a left metatarsal bone of a dromedary. Surface measurements (cm²): surface for the great cuneiform bone (GC); great cranial articular surface for the cuboid bone (NC 1); little caudal articular surface for the cuboid bone (NC 2); surface for the small cuneiform bone (PC). Linear measurements (cm): proximal width with T at the extremity (BpT); proximal depth with T at the extremity (DpT). Scale bar: 1 cm.

Supplementary material 3 from: Ren J, Bai M, Yang X-K, Zhang R-Z, Ge S-Q (2017) Geometric morphometrics analysis of the hind wing of leaf beetles: proximal and distal parts are separate modules. ZooKeys 685: 131-149. https://doi.org/10.3897/zookeys.685.13084

Coordinates data of landmarks. :

Figure 4 from: Ren J, Bai M, Yang X-K, Zhang R-Z, Ge S-Q (2017) Geometric morphometrics analysis of the hind wing of leaf beetles: proximal and distal parts are separate modules. ZooKeys 685: 131-149. https://doi.org/10.3897/zookeys.685.13084

Figure 4 - Modularity test results. A The hypothesized partition: proximal part landmarks 1-6, 23, 24, and 26–36 and distal part landmarks 7–22, 25; different colour presents different modules B The partition with minimal covariance in all evaluated 104 partitions by RV coefficient C The partition with minimal covariance in all evaluated 106 partitions by RV coefficient.

Figure 2 from: Ren J, Bai M, Yang X-K, Zhang R-Z, Ge S-Q (2017) Geometric morphometrics analysis of the hind wing of leaf beetles: proximal and distal parts are separate modules. ZooKeys 685: 131-149. https://doi.org/10.3897/zookeys.685.13084

Figure 2 - PCA and CVA results. A Centroid size graph of hind wing landmarks (Procrustes fit) B PCA results, the shape changes associated with the first three PCs: the relative size of the apical area which could be considered the main feature (variance contribution ratio was 45.01%) to influence of the overall variance of the hind wing, the changes of cross vein cv in the middle area (variance contribution ratio was 12.39%), and relative size of the anal area size (variance contribution ratio was 10.56%) C CVA results, the axis of CV1 and CV2 presented the first two large shape variance of all variance; points with different colours indicated different subtribes' specimens; the ellipse is presented as an equal-frequency ellipse with a given probability level of 90%, which contains approximately 90% of the data points.

Figure 1 from: Ren J, Bai M, Yang X-K, Zhang R-Z, Ge S-Q (2017) Geometric morphometrics analysis of the hind wing of leaf beetles: proximal and distal parts are separate modules. ZooKeys 685: 131-149. https://doi.org/10.3897/zookeys.685.13084

Figure 1 - Leaf beetle hind wing (Chrysomela populi Linnaeus), with landmark locations (the dot with number), vein nomenclature and regional division. The nomenclature of the wing venation follows that of Kukalová-Peck & Lawrence (1993, 2004). Radial area: green, central area: blue, medial area: purple, anal area: yellow, apical (folding) area: red. Proximal part landmarks 1–6, 23, 24, and 26–36 mainly include radial, medial, and anal areas; distal part landmarks 7–22 and 25 include the central area, radial cell, and apical area. Abbreviations: Costa (C), Subcosta (Sc), Subcosta Anterior (ScA), Subcosta Posterior (ScP), Radius Anterior (RA), Radius Posterior (RP), Radial cross veins (r3, r4), Media Posterior (MP), Radio-medial cross veins (rp-mp1, rp-mp2), medial cross vein (cv), Cubitus Anterior (CuA), Medio-cubital Cross-vein or Arculus (mp-cua), Anal Anterior (AA), Anal posterior (AP). "+" indicates fused veins. The sub-number of veins reflects vein branches.

Figure 3 from: Ren J, Bai M, Yang X-K, Zhang R-Z, Ge S-Q (2017) Geometric morphometrics analysis of the hind wing of leaf beetles: proximal and distal parts are separate modules. ZooKeys 685: 131-149. https://doi.org/10.3897/zookeys.685.13084

Figure 3 - PLS analysis results. A Scatter plot of the PLS1 of two blocks B Shape changes associated with the first PLS axes of two blocks: each diagram shows the block change along the PLS1 in the positive or negative direction, corresponding to Figure 3A.