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opencc-zeroNov 2023View details →

Data for: The pace of mitochondrial molecular evolution varies with seasonal migration distance

This repository contains data associated with "The pace of mitochondrial molecular evolution varies with seasonal migration distance." This study demonstrates relationships between traits (migration distance, mass, population genetic parameters representing genetic diversity) and molecular evolutionary rates (dS and dN/dS). The main conclusions are based on models from the program Coevol. The files included here are input files necessary to run models with Coevol, as well as selected Coevol output files used for figure generation associated with the manuscript. We also include a copy of a GitHub repository of manuscript code. Other necessary data for replicating analyses in the manuscript are included in the manuscript supplement.

opencc-by-4.0Dec 2023View details →

Questionnaire and Data of Neck Pain and Distance learning among university Students During COVID-19

The shift to online learning during COVID-19 led to increased musculoskeletal discomforts and impacted students' quality of life. Neck pain, once a minor issue, has become more prevalent due to prolonged electronic device use in new learning methods. This study aims to measure the prevalence of neck pain among University of Sharjah (UOS) students during the COVID-19 online learning period and to investigate the factors that provoked it. This cross-sectional study used an online survey distributed to UOS students via social media from February 16 to March 12, 2021. Demographic data, Neck Disability Index (NDI) assessments, and pain management information were gathered and analyzed using SPSS 24 through univariate and bivariate methods.The prevalence of neck pain during COVID-19, among 325 UOS students was found to be 62.7%, 64.41% of which had neck pain at the time of doing the survey. The mean NDI percentage point was 19.19%. The most common location of pain was the back of the neck 38.77%). Participants reported prolonged sitting (81.23%) while leaning forward as the most prevalent cause of their neck pain. Bivariate analysis showed that the most significant factors affecting the NDI were lifting, personal care, headaches, concentration, sleeping, recreational activities, reading, anxiousness, depression, and work. Moreover, subjects who did not seek medical attention treatment had significantly higher NDI scores as compared to those who did (83.89 vs 125.80, p=0.002).By determining the prevalence of neck pain among UOS students, this research can attract attention to the importance of postural changes and time spent in e-learning on neck pain, and the gaps of previously published articles can be filled. Future studies about neck pain and additional preventative measures should be catalyzed in the UAE.

Long-distance electron transfer along redox gradients in the subsurface

Electron transfer (ET) is the fundamental process of life and element cycling. In the subsurface, the distance of ET determines its influencing area, normally as short as nanometers or micrometers. Here we provide direct evidence from column experiments that ET can last over 10 cm along the redox gradient in sediment columns, through a long-distance ET chain constituted by a series of short-distance electron hopping reactions involving with microbes and redox-active species like iron ions (and/or minerals) and natural organic matters. Microbial processes contribute largely under biologically active conditions, while chemical processes are important under extremely acidic/alkaline and cold conditions. Microbial and chemical processes synergistically mediate the long-distance ET process, with an estimated electron flux of 6.73 μmol e-/cm2 per day. This long-distance ET represents an overlooked but important background process influencing subsurface biogeochemical processes and remediation activities.

Data from: Plant-soil microbe feedbacks depend on distance and ploidy in a mixed cytotype population of Larrea tridentata

Premise of the study Theory predicts that mixed ploidy populations should be short-lived due to strong fitness disadvantages for the rare ploidy. However, mixed ploidy populations are common, suggesting that the fitness costs for rare ploidies are counterbalanced by ecological benefits that emerge when rare. We investigated whether differences in ecological interactions with soil microbes help to maintain a tetraploid-hexaploid population of Larrea tridentata (creosote bush) in the Sonoran Desert, California, USA, where prior work documented ploidy-specific root-associated microbes. Methods We used a plant-soil feedback (PSF) experiment to test whether host-specific soil microbes can alter the outcomes of intra-ploidy vs. inter-ploidy competition. Host-specific soil microbes can build up over time; thus, distance from a host plant can affect the fitness of nearby plants. Key results Seedlings grown in soils from near plants of a different ploidy produced greater biomass relative to seedlings grown in soils from near plants of the same ploidy. Moreover, seedlings grown in soils from near plants of a different ploidy produced greater biomass than those grown in soils from further away from plants of a different ploidy. This suggests the ecological consequences of PSF may facilitate the persistence of mixed ploidy populations. Conclusions This is the first evidence, to our knowledge, consistent with plant-soil microbe feedback as a viable mechanism to maintain the coexistence of multiple ploidy levels in a single population.

Data from: Distances and their visualization in studies of spatial-temporal genetic variation using single nucleotide polymorphisms (SNPs)

Distance measures are widely used for examining genetic structure in datasets that comprise many individuals scored for a very large number of attributes. Genotype datasets composed of single nucleotide polymorphisms (SNPs) typically contain bi-allelic scores for tens of thousands if not hundreds of thousands of loci. We examine the application of distance measures to SNP genotypes and sequence tag presence-absences (SilicoDArT) and use real datasets and simulated data to illustrate pitfalls in the application of genetic distances and their visualization. The datasets used to illustrate points in the associated review are provided here together with the R script used to analyse the data. Data are either simulated internal to this script or are SNP data generated as part of other studies and included as compressed binary files readily accessable by reading into R using R base function readRDS(). Refer to the analysis script for examples.

opencc-zeroMar 2024View details →

Data from: Odor source distance is predictable from time-histories of odor statistics for large scale outdoor plumes

Odor plumes in turbulent environments are intermittent and sparse. Lab-scaled experiments suggest that information about the source distance may be encoded in odor signal statistics, yet it is unclear whether useful and continuous distance estimates can be made under real-world flow conditions. Here we analyze odor signals from outdoor experiments with a sensor moving across large spatial scales in desert and forest environments to show that odor signal statistics can yield useful estimates of distance. We show that achieving accurate estimates of distance requires integrating statistics from 5-10 seconds, with a high temporal encoding of the olfactory signal of at least 20 Hz. By combining distance estimates from a linear model with wind-relative motion dynamics, we achieved source distance estimates in a 60x60 m2 search area with median errors of 3-8 meters, a distance at which point odor sources are often within visual range for animals such as mosquitoes.

opencc-zeroMar 2024View details →

Distance-dependence seed set of Vasconcellea chilensis

Plant reproductive failure is a critical concern for conserving rare and endangered species that typically have low-density and sparse populations. One important factor contributing to reproductive failure is the spatial arrangement of plants within a population, which can lead to isolation and negatively affect seed output, particularly in obligate outcrosses. Additionally, this effect can be compounded by plant size. Here, we investigate how plants' spatial distribution and size influence the reproductive success of Vasconcellea chilensis, a threatened papaya species from northern Chile. Using flower exclusion experiments, we first examined whether V. chilensis can produce seeds via apomixis. We then used Spatial Point Pattern Analysis (SPPA) in three populations to examine the spatial arrangement of plants in three populations, and, finally, we assessed whether plant size and mate distance influence the reproductive success of this plant species. V. chilensis is a dioecious shrub unable to produce fruits through apomixis. The SPPA revealed significant clustering of female and male plants at different spatial scales, indicating a non-random distribution. Moreover, a significant attraction between the sexes suggested a preference for proximity. In two populations, closer proximity to male plants was linked to higher seed production. Our study revealed that the absence of apomixis in V. chilensis makes it prone to experiencing distance-dependent reproductive failure. In particular, the seed set was compromised in female plants isolated from male neighbors. This link between isolation and seed production was especially significant in the driest site, and we discussed how environmental factors can exacerbate this effect.

opencc-zeroMar 2024View details →

Data from: Range-wide genetic analysis of an endangered bumble bee (Bombus affinis) reveals population structure, isolation by distance, and low colony abundance

Declines in bumblebee species ranges and abundances are documented across multiple continents and have prompted the need for research to aid species recovery and conservation. The rusty patched bumblebee (Bombus affinis) is the first federally-listed bumblebee species in North America. We conducted a range-wide population genetics study of B. affinis from across all extant conservation units to inform conservation efforts. To understand the species' vulnerability and help establish recovery targets, we examined population structure, patterns of genetic diversity, and population differentiation. Additionally, we conducted site-level analysis of colony abundance to inform prioritizing areas for conservation, translocation, and other recovery actions. We find substantial evidence of population structuring along an east-to-west gradient. Putative populations show evidence of isolation by distance, high inbreeding coefficients, and a range wide male diploidy rate of ~15%. Our results suggest the Appalachians represents a genetically distinct cluster with high levels of private alleles and substantial differentiation from the rest of the extant range. Site-level analyses suggest low colony abundance estimates for B. affinis compared to similar datasets of stable, co-occurring species. These results lend genetic support to trends from observational studies suggesting B. affinis has undergone a recent decline and exhibits substantial spatial structure. The low colony abundances observed here suggest caution in overinterpreting the stability of populations even where B. affinis is reliably detected interannually. These results help delineate informed management units, provide context for the potential risks of translocation programs, and can help set clear recovery targets for this and other threatened bumblebee species.

opencc-by-4.0Mar 2024View details →

Distances between Brazilian Social Housing and Urban Services

This database presents the results of a survey conducted through research using the Google Maps Platform API for grocery stores, drugstores, bank branches, lottery agencies, public schools, health centers, and parks services in a sample of 2241 social housing developments built under Brazilian government programs. It was developed to evaluate the quality of urban insertion of social housing by the HabLabEEE project. Esta base de dados apresenta os resultados de um levantamento realizado por meio de pesquisa com API do Google Maps Platform por serviços de mercado, farmácia, banco, lotérica, escola pública, posto de saúde e parque em uma amostra de 2241 conjuntos habitacionais construídos no âmbito de programas governamentais brasileiros. Foi desenvolvida para avaliar a qualidade da inserção urbana das HIS brasileiras pelo projeto HabLabEEE.

opencc-zeroApr 2024View details →

Data from: Time or distance: flexible coding of Hippocampal cells

Analysis of neuronal activity in the hippocampus of behaving animals has revealed cells acting as "Time Cells," which exhibit selective spiking patterns at specific time intervals since a triggering event, and "Distance Cells," which encode the traversal of specific distances. Other neurons exhibit a combination of these features, alongside place selectivity. This study aims to investigate how the task performed by animals during recording sessions influences the formation of these representations. The data used here was originally curated in a treadmill running study conducted by Kraus et al. (2013) in which rats were trained to run at different velocities. The rats were recorded in two trial contexts: a "fixed time" condition, where the animal ran on the treadmill for a predetermined duration before proceeding, and a "fixed distance" condition, where the animal ran a specific distance on the treadmill. Our findings indicate that the type of experimental condition significantly influenced the encoding of hippocampal cells. Specifically, distance-encoding cells dominated in fixed-distance experiments, whereas time-encoding cells dominated in fixed-time experiments. These results underscore the flexible coding capabilities of the hippocampus, which are shaped by over-representation of salient variables associated with reward conditions. Data used in Absramson et al., 2023, "Time or distance: flexible coding of Hippocampal cells", originally curated by Kraus et al., Neuron, 78(6), 1090-1101, 2013.

opencc-by-4.0Nov 2024View details →

Distance Explainer experiment gallery

This is a gallery of experiments carried out during the creation of the <a href="https://zenodo.org/records/10637098">distance_explainer Python module.</a>

opencc-by-4.0Nov 2024View details →

Simplified Trigonometric Method for Distance Measurements

This research paper introduces a simplified trigonometric method for measuring the distance to celestial objects using angular measurements and basic geometry. The methodology involves capturing the angular size of an object from two distinct positions along a known baseline, utilizing trigonometric relationships to derive a precise formula. The approach was validated by calculating the Moon's distance from Earth using angular measurements, yielding a result closely matching the Moon's average distance. This accessible method has potential applications for amateur astronomers, educators, and anyone interested in celestial distance measurement without relying on advanced equipment.

opencc-by-4.0Dec 2024View details →

Data from: "Distance decay effects predominantly shape spider but not carabid community composition in crop fields in north-western Europe"

Open the record for dataset details and reuse information.

Data and Software for: Resolved Near-infrared Stellar Photometry from the Magellan Telescope for 13 Nearby Galaxies: JAGB Method Distances

12/17/24 Update: I was made aware that the MRT files had the J-band and H-band column header labels incorrectly switched (this occured when converting the CSV files to MRT). I have fixed this mistake. The CSV files were correct the entire time. No data have been changed. Apologies for any inconvinence this may have caused.    Data for Resolved Near-infrared Stellar Photometry from the Magellan Telescope for 13 Nearby Galaxies: JAGB Method Distances The files are provided in two formats. A CSV format with a single line header, and a MRT files (zipped) written in the machine-readable format used by AAS & CDS: <a href="https://journals.aas.org/mrt-overview/" target="_blank" rel="noopener noreferrer">https://journals.aas.org/mrt-overview/</a> Column descriptions in photometry catalogs: X/Y: Image coordinates from Fourstar camera J, J_err: J-band magnitudes and photometric errors returned from DAOPHOT/ALLFRAME H, H_er: H-band magnitudes and photometric errors returned from DAOPHOT/ALLFRAME K, K_err: K-band magnitudes and photometric errors returned from DAOPHOT/ALLFRAME chi: chi value returned from DAOPHOT/ALLFRAME sharp: sharpness value returned from DAOPHOT/ALLFRAME ra/dec: RA/Decl  RGC: semi-major axis distance   Notes on versions: all catalogs from all versions contain the same information, style was just adjusted to adhere to AAS standards.

opencc-by-4.0Nov 2023View details →

Data set of axle loads and distances for operating passenger and freight trains for development of load models

Train data for moving load models of operating trains (5,007 passenger trains and 139,182 freight trains). <ul> <li>axle distances [m] and axle loads [kN] for all trains included in zip-files as txt-files</li> <li>information on line categories (DIN EN 15528), loadcases and maximum speeds for passenger trains (and assignment to passenger train numbers in previous version of publication (used for development of load model)) in xlsx-file</li> </ul>

opencc-by-4.0Nov 2024View details →

Modeling Protein Conformations by Guiding AlphaFold2 with Distance Distributions. Application to Double Electron Electron Resonance (DEER) Spectroscopy.

We describe a modified version of AlphaFold2 that incorporates experiential distance distributions into the network architecture for protein structure prediction.  Harnessing the OpenFold platform, we fine-tuned AlphaFold2 on a small number of structurally dissimilar proteins to explicitly model distance distributions between spin labels determined from Double Electron-Electron Resonance (DEER) spectroscopy. We demonstrate the performance of the modified AlphaFold2, referred to as DEERFold, in switching the predicted conformations guided by experimental or simulated distance distributions. Remarkably, the intrinsic performance of AlphaFold2 substantially reduces the number and the accuracy of the widths of the distributions needed to drive conformational selection thereby increasing the experimental throughput. The blueprint of DEERFold can be generalized to other experimental methods where distance constraints can be represented by distributions.

opencc-zeroDec 2021View details →

Age-dependent timing and routes demonstrate developmental plasticity in a long-distance migratory bird

1. Longitudinal tracking studies have revealed consistent differences in the migration patterns of individuals from the same populations. The sources or processes causing this individual variation are largely unresolved. As a result, it is mostly unknown how much, how fast, and when animals can adjust their migrations to changing environments. 2. We studied the ontogeny of migration in a long-distance migratory shorebird, the black-tailed godwit (Limosa limosa limosa), a species known to exhibit marked individuality in the migratory routines of adults. By observing how and when these individual differences arise, we aimed to elucidate whether individual differences in migratory behaviour are inherited or emerge as a result of developmental plasticity. 3. We simultaneously tracked juvenile and adult godwits from the same breeding area on their south- and northward migrations. To determine how and when individual differences begin to arise, we related juvenile migration routes, timing, and mortality rates to hatch date and year of birth. Then, we compared adult and juvenile migration patterns to identify potential age-dependent differences. 4. In juveniles, the timing of their first southward departure was related to hatch date. However, their subsequent migration routes, orientation, destination, migratory duration, and likelihood of mortality were unrelated to the year or timing of migration, or their sex. Juveniles left the Netherlands after all tracked adults. They then flew non-stop to West Africa more often and incurred higher mortality rates than adults. Some juveniles also took routes and visited stopover sites far outside the well-documented adult migratory corridor. Such juveniles, however, were not more likely to die. 5. We found that juveniles exhibited different migratory patterns than adults, but no evidence that these behaviours are under natural selection. We thus eliminate the possibility that the individual differences observed among adult godwits are present at birth or during their first migration. This adds to the mounting evidence that animals possess the developmental plasticity to change their migration later in life in response to environmental conditions as those conditions are experienced.

opencc-zeroDec 2021View details →

Data to support publication figures and animation scripts at GitHub: Modeling weather-driven long-distance dispersal of spruce budworm moths (Choristoneura fumiferana)

Long-term studies of insect populations in the North American boreal forest have shown the vital importance of long-distance dispersal to the maintenance and expansion of insect outbreaks. In this work, we extend several concepts established previously in an empirically-based dispersal flight model with recent work on the physiology and behavior of the adult eastern spruce budworm (SBW) moth, Choristoneura fumiferana (Clem.). An outbreak of defoliating SBW in Quebec, ongoing since the mid-2000s, already covers millions of hectares of forests in eastern Canada and threatens to spread into neighboring areas through annual summertime episodes of long-distance dispersal. Such flight events in favorable conditions frequently include billions of SBW moths dispersing in the warm atmospheric boundary layer, typically starting around sunset and often lasting through several hours of wind-driven transport over hundreds of kilometers. Successful SBW dispersal to possibly distant host forest areas depends acutely on the weather. Here we describe the components and results of SBW–pyATM, an open-source individual-based modeling framework developed in Python for the simulation of these weather-driven SBW dispersal events. Using seasonal SBW phenology results from BioSIM at known outbreak locations and high-resolution Weather Research and Forecasting (WRF) model output, we focus on modeling dispersal flights over two successive nights in July 2013 in southern Quebec. Our flight model closely reproduces the SBW spatial patterns and motions observed by weather surveillance radar over the St. Lawrence estuary. With SBW–pyATM we can estimate landing locations for both male and female SBW and the resulting spatial patterns of egg distribution, allowing us eventually to forecast future larval defoliation activity in new locations where immigration could help overcome local limitations on SBW populations. This information could then support forest management decisions where SBW outbreaks threaten valuable resources.

opencc-zeroDec 2021View details →

Soil nitrogen mediates the effect of distance from climatic center on herbivory rates in a tropical herb

The center-periphery hypothesis predicts that species are most abundant at the center of their range. Differential herbivory rates between center and periphery populations can explain this variation in species abundance. However, if the geographic center of a species distribution coincides with its ecological optimum, the resource availability hypothesis predicts higher herbivory rates and tolerances at the center compared to the periphery. Biogeographic studies on herbivory have treated these two mechanisms separately, limiting our mechanistic understanding of the role of herbivory in shaping species range limits. We analyzed the role of resource availability on herbivory variation from center to periphery using data collected across the distribution of Thunberbia atacorensis, a range limited species of West Africa. We used two types of distances: geographic distance (the distance from each plot to the geographic center of all populations) and climatic distance (the distance from each plot to the preferendum of the species). We found no increase in herbivory toward the periphery of the climatic and geographic ranges. However, herbivory rates increased with soil nitrogen. Nitrogen in soil decrease from center to periphery of climatic range. Phylogenetic diversity and surrounding plants' competition did not affect herbivory rates. Our study provides insights into how nutrient limitation can shape species center-periphery distribution by altering spatial variation in herbivory rates.