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opencc-by-4.0Nov 2022View details →

RESONATE case study disturbance information

Disturbance information for the RESONATE case studies: <a href="https://efi.int/projects/resonate">https://efi.int/projects/resonate</a>. The data was compiled from existing disturbance and agent attribution data that was extended to the year 2020 within the RESONATE project. Folter 'agent classification': Raster layers with four values: 0=no disturbance, 1=harvest, 2=bark beetle/storm, 3=fire Folder 'disturbance_summaries': Rummary tables with year, agent, disturbance area (ha) and disturbance rate (percent of forest area) Folder 'disturbances': Raster layers with disturbance year (0=no disturbance) Folder 'forest_masks': Forest makes (1=no forest/2=forest) to calculate disturbance ratesF older 'outlines': Outlines of case studies as vector files  All spatial files are in EPSG:3035.

opencc-zeroNov 2022View details →

Data and code for: Uncovering commercial activity in informal cities

Knowledge of the spatial organisation of economic activity within a city is key to policy concerns. However, in developing cities with high levels of informality, this information is often unavailable. Recent progress in machine learning together with the availability of street imagery offers an affordable and easily automated solution. Here we propose an algorithm that can detect what we call visible firms using street view imagery. Using Medellín, Colombia as a case study, we illustrate how this approach can be used to uncover previously unseen economic activity. This dataset contains the data and code required to replicate our analysis for the manuscript: "Uncovering commercial activity in informal cities."

When should bees be flower constant? An agent-based model highlights the importance of social information and foraging conditions

1. Many bee species show flower constancy, i.e. a tendency to visit flowers of one type during a foraging trip. Flower constancy is important for plant reproduction, but the benefits of constancy to bees are unclear. Social bees, which often use communication about food sources, show particularly strong flower constancy. 2. We aimed to better understand the benefits of flower constancy in social bees and how these benefits depend on foraging conditions. We hypothesised that sharing social information increases the benefits of flower constancy because social foragers share information selectively about high-quality food sources, thereby reducing the need to sample alternatives. 3. We developed an agent-based model that allowed us to simulate bee colonies with and without communication and flower constancy in different foraging environments. By varying key environmental parameters, such as food source numbers and reward size, we explored how the costs and benefits of flower constancy depend on the foraging landscape. 4. Flower constancy alone performed poorly in all environments, while indiscriminate flower choice was often the most successful strategy. However, communication improved the performance of flower constant colonies considerably in most environments. This combination was particularly successful when high-quality food sources were abundant and competition was weak. 5. Our findings help explain why social bees tend to be more flower constant than solitary bees and suggest that flower constancy can be an adaptive strategy in social bees. Simulations suggest that anthropogenic changes of foraging landscapes will have different effects on the foraging performance of bees that vary in flower constancy.

Supplemental information and Data for: Colloidal physics modeling reveals how per-ribosome productivity increases with growth rate in E. coli

Faster growing cells must synthesize proteins more quickly. Increased ribosome abundance only partly accounts for increases in total protein synthesis rates. The productivity of individual ribosomes must increase too, almost doubling by an unknown mechanism. Prior models point to diffusive transport as a limiting factor but surface a paradox: faster growing cells are more crowded, yet crowding slows diffusion. We suspected physical crowding, transport, and stoichiometry, considered together, might reveal a more nuanced explanation. To investigate, we built a first-principles physics-based model of E. coli cytoplasm in which Brownian motion and diffusion arise directly from physical interactions between individual molecules of finite size, density, and physiological abundance. Using our microscopically-detailed model, we predict that physical transport of individual ternary complexes accounts for ~80% of translation elongation latency. We also find that volumetric crowding increases at faster growth even as cytoplasmic mass density remains relatively constant. Despite slowed diffusion, we predict that improved proximity between ternary complexes and ribosomes wins out, illustrating a simple physics-based mechanism for how individual elongating ribosomes become more productive. We speculate how crowding imposes a physical limit on growth rate and undergirds cellular behavior more broadly. Unfitted colloidal-scale modeling offers systems biology a complementary "physics engine" for exploring how cellular-scale behaviors arise from physical transport and reactions among individual molecules.

Supporting information for: Lagrange-NG: The Next Generation of Lagrange

Computing ancestral ranges via the Dispersion Extinction and Cladogensis (DEC) model of biogeography is characterized by an exponential number of states relative to the number of regions considered. This is because the DEC model requires computing a large matrix exponential, which typically accounts for up to 80% of overall runtime. Therefore, the kinds of biogeographical analyses that can be conducted under the DEC model are limited by the number of regions under consideration. In this work, we present a completely redesigned efficient version of the popular tool Lagrange which is up to 2.5 times faster, which we call Lagrange-NG (Next Generation). We further reduce time-to-completion by introducing a multi-grained parallelization approach, achieving a total parallel speedup of 8.5 over Lagrange on a machine with 8 cores. In order to validate the correctness of Lagrange-NG, we also introduce a novel metric on range distributions for trees in order to assess the difference between any two range inferences. Finally, Lagrange-NG exhibits substantially higher adherence to coding quality standards. It improves a respective software quality indicator as implemented in the SoftWipe tool from average (5.5; Lagrange) to high (7.8; Lagrange-NG). Lagrange-NG is freely available under GPL2.

Supplementary information for: NUMT PARSER: Automated identification and removal of nuclear mitochondrial pseudogenes (numts) for accurate mitochondrial genome reconstruction in Panthera

Nuclear mitochondrial pseudogenes (numts) may hinder the reconstruction of mtDNA genomes and affect the reliability of mtDNA datasets for phylogenetic and population genetic comparisons. Here, we present the program Numt Parser, which allows for the identification of DNA sequences that likely originate from numt pseudogene DNA. Sequencing reads are classified as originating from either numt or true cytoplasmic mitochondrial (cymt) DNA by direct comparison against cymt and numt reference sequences. Classified reads can then be parsed into cymt or numt datasets. We tested this program using whole genome shotgun-sequenced data from two ancient Cape lions (Panthera leo) because mtDNA is often the marker of choice for ancient DNA studies, and the genus Panthera is known to have numt pseudogenes. Numt Parser decreased sequence disagreements that were likely due to numt pseudogene contamination and equalized read coverage across the mitogenome by removing reads that likely originated from numts. We compared the efficacy of Numt Parser to two other bioinformatic approaches that can be used to account for numt contamination. We found that Numt Parser outperformed approaches that rely only on read alignment or Basic Local Alignment Search Tool (BLAST) properties, and was effective at identifying sequences that likely originated from numts while having minimal impacts on the recovery of cymt reads. Numt Parser therefore improves the reconstruction of true mitogenomes, allowing for more accurate and robust biological inferences.

Supplementary Information for "Modeling the circular economy in environmentally extended input–output: A web application"

Supplementary Information for "Modeling the circular economy in environmentally extended input–output: A web application" Annex I: This supporting information provides the software review for native and web-based tools that could be used for Circular Economy and environmental analysis. Annex II: This supporting information provides the use-case result analysis.

Dataset for paper: Perception of Software Quality Teaching from Information Technology Undergraduate Final-Year Students

Dataset mentioned in the paper "Perception of Software Quality Teaching from Information Technology Undergraduate Final-Year Students", submitted to XXVI Ibero-American Conference on Software Engineering (CIbSE 2023). There are two files available: one PDF file, where the survey presented as it was submitted to the participants of our study, in portuguese; and a .CSV one, with the answers of this survey.

Exercise training prior to manifestation of hypertrophic cardiomyopathy in mice attenuates expression of pro-fibrotic genes - supplementary information

Supplementary data for research article titled "Exercise training prior to manifestation of hypertrophic cardiomyopathy in mice attenuates expression of pro-fibrotic genes"

Supplemental Information in Support of "Moment tensor event identification for collapses"

Supplemental Information in support of manuscript "Moment tensor event identification for collapses". File 00_Collapse_MT_Table.csv is a summary of moment tensor solutions for all of the collapses in this manuscript. A Jupyter notebook (file 00_Collapse_MT_Table.ipynb) is provided which loads the information from the provided table and creates an example plot of one of the full moment tensor solutions and plots all the solutions on a global map. The notebook creates two PNG images mt.png and map.png which are also provided. Directories (e.g., 1980-06-12_Southern_Nevada) contain figures showing waveform fits for the collapses. For each event, the waveforms to the left show displacement data (black) and synthetics (red - used in inversion, blue - predicted only) for the vertical, radial, and transverse components.  Detailed information about the event and the moment tensor solution are provided on the right-hand side of the last figure.

Propagating spatio-temporal activity patterns across macaque motor cortex carry kinematic information

Propagating spatio-temporal neural patterns are widely evident across sensory, motor and association cortical areas. However, it remains unclear whether any characteristics of neural propagation carry information about specific behavioral details. Here, we provide the first evidence for a link between the direction of cortical propagation and specific behavioral features of an upcoming movement on a trial-by-trial basis. We recorded local field potentials (LFPs) from multi-electrode arrays implanted in the primary motor cortex of two rhesus macaque monkeys while they performed a 2-D reach task. Propagating patterns were extracted from the information-rich high-gamma band (200–400Hz) envelopes in the LFP amplitude. We found that the exact direction of propagating patterns varied systematically according to initial movement direction, enabling kinematic predictions. Furthermore, characteristics of these propagation patterns provided additional predictive capability beyond the LFP amplitude themselves, which suggests the value of including mesoscopic spatio-temporal characteristics in refining brain-machine interfaces.

data-informed calibration of WRF-Hydro data1

This is the first part of a dataset used to produce the results in a data-informed calibration study of WRF-Hydro.  1. It contains the simulated hourly soil moisture time series from 2016/10/1 to 2017/05/31 before and after calibration at seven in-situ stations. The 7 lines in the .txt files are for the 7 stations in the following order: stat1=['sld',36.461040, -121.381170] stat2=['lgs', 37.261590, -122.132870] stat3=['gry', 37.071800, -121.478800] stat4=['lwd', 35.937080, -121.108030] stat5=['blueoak',37.381667,-121.744722] stat6=['hastings',36.386389,-121.550278] stat7=['norris',35.534167,-121.083333] 2. It contains the hourly simulated streamflow simulations from 2016/10/1 to 2017/05/31 before and after calibration at 9 USGS stream gages. The lines in the txt files are in the following order: gageID=["11169500","11169800","11159200","11148900","11160000","11157500","11149900","11152050","11152000"] 3. It also contains the spatially-distributed soil parameters before and after calibration. The "smcmax", "dksat","bexp" parameters in the soil_properties.nc are for soil porosity, saturated hydraulic conductivity, and b coefficient, respectively.

National High-Resolution Cropland Classification of Japan with Agricultural Census Information and Multi-temporal Multi-modality datasets

Multi-modality datasets offer advantages for processing frameworks with complementary information, particularly for large-scale cropland mapping. Extensive training datasets are required to train machine learning algorithms, which can be challenging to obtain. To alleviate the limitations, we extract the training samples from the agricultural census information. We focus on Japan and demonstrate how agricultural census data in 2015 can map different crop types for the entire country. Due to the lack of Sentinel-2 datasets in 2015, this study utilized Sentinel-1 and Landsat-8 collected across Japan and combined observations into composites for different prefecture periods (monthly, bimonthly, seasonal). Recent deep learning techniques have been investigated the performance of the samples from agricultural census information. Finally, we obtain nine crop types on a countrywide scale (around 31 million parcels) and compare our results to those obtained from agricultural census testing samples as well as those obtained from recent land cover products in Japan. The generated map accurately represents the distribution of crop types across Japan and achieves an overall accuracy of 87% for nine classes in 47 prefectures.

Health versus environmental benefits: Does additional information influence consumer acceptance of pulse-based spreads?

Despite the known health benefits and the potential for substituting less environmentally sustainable consumed foods such as meat, the current intake of pulses in developed countries remains less than recommended. Barriers are related to sensory characteristics and lack of knowledge about preparation, while drivers of environmental benefits are intangible. The aim of this study was to investigate the effect of additional information about health or environmental benefits of pulses on the acceptance of novel pulse-based products from chickpeas, black beans, and faba beans. Perceptions of these pulse-based spreads in a blind and informed stage were assessed with 202 consumers in urban and sub-urban areas of Denmark. In general, the familiar chickpea spread followed by the relatively most unfamiliar black bean spread was liked the most. Only for these two products, additional information increased hedonic perception, regardless of the context (health or environmental benefits). If consumers did not like the spread, as found for the faba bean spread, providing additional information did not significantly alter this perception. Participants’ preferences and willingness-to-pay (WTP) in a discrete choice experiment (DCE) was corresponding with hedonic scores while providing additional information was found to increase the WTP. These findings suggest that extrinsic cues such as health or environmental benefits may only be useful in products with an acceptable baseline taste profile. Moreover, black beans might be investigated as a promising source for further product development due to their acceptance by consumers besides being the comparably most unfamiliar pulse type.

Informes de casos de estudio finales en hábitats humanos (anexo del libro: La visión sistémica del ambiente construido, 2024). [Data sets for the article: The Habitat Intervention Design Process -Part II]

From the book: Estos informes están escritos en español por los estudiantes que se mencionan en cada informe, quienes son los autores. Cada uno de estos seis documentos contiene casos de estudio y muestra la implementación de la metodología del 'Proceso de Diseño de Intervención del Hábitat' (IDP) en cada uno de los 6 casos mencionados en el libro (Capítulo 2.5 y Capítulo 3.2) (Libro: La visión sistémica del ambiente construido).  Estos hacen parte de la Fase 2 Fundamentos Prácticos del Modelo del proyecto de investigación "Modelo Pedagógico para la Enseñanza del Diseño de Intervención del Hábitat en Programas de Educación Superior".  From the article: These reports are Spanish-written. Each of these six documents contains one of the case studies and shows the implementation of the 'Habitat Intervention Design Process' (IDP) methodology in each of the 6 case studies mentioned in the article "The Habitat Intervention Design Process -Part II: A Transdisciplinary Model in the Pedagogy of the Design of the Built Environment" published in The International Journal of Design Education in its 2023 version. Find it here: <a href="https://doi.org/10.18848/2325-128X/CGP/v17i02/155-195">https://doi.org/10.18848/2325-128X/CGP/v17i02/155-195 </a>

Informing upper extremity rehabilitation through endpoint kinematics of the functional reaching movement after stroke

Background. Stroke is a leading contributor to upper limb disability. Current assessments of motor ability are at best subjective estimates. Rehabilitation could be more effective when informed by an individual's specific capacities rather than diagnostic observation. This study characterizes sub-movements of interest during functional reach-to-target tasks with endpoint analysis.\newline Methods. Using Fugl-Meyer (FM) scores and reach capacities, stroke survivors were placed in either mild or severe impairment groups. Individual completed sets of reach-to-target tasks over two visits. The averaged reach curve for each subject was analyzed for angular orientation and velocity profile. The Procrustes method of statistical shape analysis was modified to identify reaching sub-movements that were incongruous to control sub-movements.\newline Findings. Reach-to-target curves were investigated for 15 individuals with mild impairment (FM \(52 \pm 9\)) and 14 individuals with severe impairment (FM \(16 \pm 7\)). The endpoint kinematic analysis found that individuals with severe impairment demonstrate lower peak velocities (centimeters per second) [\(28.5 \pm 17.3 , 80.3 \pm 29.5\)] which occurred sooner in the movement (milliseconds) [\(36.81 \pm 27.0, 59.6 \pm 14.8\)]. The mild group demonstrated variability in orientation in the medial-lateral space, and movement initiation that was congruous to healthy movement. The severe impairment group demonstrated variability in orientation in every axis and showed incongruous initiation and completion behaviors, with some comparable movement in between. \newline Interpretation. Endpoint analysis is a valuable option for clinicians to inform physiotherapy. In addition to kinematic metrics such as orientation and velocity, sub-movements that are comparable to healthy movement can be identified in both mild and severe impairment.

opencc-by-4.0Sep 2022View details →

The Role of Spatial Information in an Approximate Cross-Modal Number Matching Task

Data for article: The Role of Spatial Information in an Approximate Cross-Modal Number Matching Task

opencc-zeroFeb 2023View details →

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.

opencc-by-4.0Oct 2022View details →

Supplementary Information Materials for the G-Cubed submission by Zakharov et al.

The supporting information is provided for the publication <a href="https://doi.org/10.1029/2022GC010741">https://doi.org/10.1029/2022GC010741</a>. The upload contains identification of MGL opal-CT as well as the results of the SIMS and EMPA measurements in cherts. This file also features δD values plotted against the triple O-isotope values of cherts. The Secondary Ion Probe Mass Spectrometry (SIMS) measurements are included as the .xslx table (Data Set S1) with analytical conditions, raw measurements and VSMOW-calibrated values. The Electron Microprobe (EMPA) analyses are provided in the .xslx file (Data Set S2). The Data Set S2 is separated by tabs for individual sample. Images feature the analyzed areas, including petrographic image, reflected light and the SIMS points.