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849 results for “linear”
Data and code to replicate: Diet analysis using generalized linear models derived from foraging processes using R package mvtweedie
<p>Diet analysis integrates a wide variety of visual, chemical and biological identification of prey. Samples are often treated as compositional data, where each prey is analyzed as a continuous percentage of the total. However, analyzing compositional data results in analytical challenges, e.g., highly parameterized models or prior transformation of data. Here, we present a novel approximation involving a Tweedie generalized linear model (GLM). We first review how this approximation emerges from considering predator foraging as a thinned and marked point process (with marks representing prey species and individual prey size). This derivation can motivate future theoretical and applied developments. We then provide a practical tutorial for the Tweedie GLM using new package <i>mvtweedie</i> that extends capabilities of widely used packages in R (<i>mgcv</i> and <i>ggplot2</i>) by transforming output to calculate prey compositions. We demonstrate this approach and software using two examples. Tufted puffins (<i>Fratercula cirrhata</i>) provisioning their chicks on a colony in the northern Gulf of Alaska show decadal prey switching among sand lance and prowfish (1980-2000) and then Pacific herring and capelin (2000-2020), while wolves (<i>Canis lupus ligoni</i>) in Southeast Alaska forage on mountain goats and marmots in northern uplands and marine mammals in seaward island coastlines. </p>
A multi-uncertainty-set-based robust transmission expansion planning model using an efficient linear AC network
<p>The file uploaded provides input data for the paper "A multi-uncertainty-set-based robust transmission expansion planning model using an efficient linear AC network".</p>
DLOFTBs - Deformable Linear Objects Tracking with B-splines - dataset
<p>A dataset associated with the paper "DLOFTBs - Fast Tracking of Deformable Linear Objects with B-splines".</p> <p>Contains 2D images and ROS bags with 3D videos of deformable linear objects manipulated by humans and robots.</p>
Linearity Data Set
<p>Data behind Linearity Fig 1, Fig 2, and Fig 3, and the full data set for 175 SPARC galaxies</p>
Neighboring edges: interacting edge effects of linear disturbances on vegetation in treed fens
<p>The influence of edges on forest biodiversity is an important environmental effect associated with habitat fragmentation, as edge effects can further reduce the remaining 'interior' habitat. However, extrapolating the influence of edges across the broader landscape has been difficult, especially regarding how to treat multiple edges in close proximity, where edge effects might interact. In this study, we examined the interaction of edge effects for multiple edges from a dense network of narrow (3-8 m wide) and low-severity linear disturbances called 'seismic lines'. Seismic lines are created during oil and gas exploration and are responsible for severe dissection of boreal forests in western Canada. Specifically, our objectives were to: (1) to compare the edge influence of "wide" (~8 m) and "narrow" (~3 m) seismic lines; and (2) to determine whether edges in close proximity show interaction of edge influences, i.e. do multiple narrow seismic lines have a stronger or weaker edge influence than a single narrow seismic line. We sampled vegetation along transects perpendicular to seismic lines in treed moderate-rich and poor fens. We used randomization tests of edge influence to calculate the magnitude and distance of edge effects. In moderate-rich fens, we found a positive edge influence on understory diversity from both wide and narrow seismic lines. We also found a weakening edge interaction on diversity, i.e., single narrow seismic lines had a stronger edge influence on diversity than multiple narrow seismic lines. In treed poor fens, multiple narrow seismic lines had a negative edge effect on tree density, understory abundance, richness, and composition. In addition, we found strengthening edge interactions in treed poor fens on tree density, graminoid cover, and understory composition. Our results show how assessing the edge influence of multiple disturbances can provide a better understanding of the cumulative effects of habitat fragmentation.</p>
Non-linear susceptibility to interferences in declarative memory formation
<p>After encoding, memories go through a labile state followed by a stabilization process known as consolidation. Once consolidated they can enter a new labile state after the presentation of a reminder of the original memory, followed by a period of re-stabilization (reconsolidation). During these periods of lability the memory traces can be modified. Currently, some studies show a rapid stabilization after 30 min, while others show that stabilization occurs after longer periods (e.g. > 6 h). Here we investigate the effect of an interference treatment on declarative memory consolidation, comparing distinct time intervals after acquisition. On day 1, participants learned a list of non- syllable pairs (List 1). 5 min, 30 min, 3 h or 8 h later, they received an interference list (List 2) that acted as an amnesic agent. On day 2 (48 h after training) participants had to recall List 1 first, followed by List 2. We found that the List 1 memory was susceptible to interference when List 2 was administered 5 min or 3 h after learning but not when it was administered 30 min or 8 h after. We propose the possibility that this rapid memory protection could be induced by a fast and transient neocortical integration. Our results open a discussion about the contribution of molecular and systemic aspects to memory consolidation.</p>
Dynamic data of body weight and feed intake in fattening pigs and the determination of energetic allocation factors using a dynamic linear model
<p>This is the R script (DLM_script.R) to characterize the evolution of the energetic allocation factor (α<sub>t</sub>) which represents the link between the cumulative net energy available (estimated from feed intake) and cumulative weight gain during fattening period. The data for the 100 fattening pigs are stored in the csv file (DataAxiom.csv) and structured as follows:</p> <ul> <li>ID: pig identification number;</li> <li>Fattening_group.Pen : fattening group and pen number for a given ID;</li> <li>t (day): time in days since the transfer to fattening room;</li> <li>Wt (kg) : median weight in kg at day t for a given ID;</li> <li>FIt (kg day-1) : total feed intake in kg at day t for a given ID.</li> </ul> <p>For detail description of the procedure please see article.</p>
Generating spatiotemporal patterns of linearly polarised light at high frame rates for insect vision research
<p><strong>Electrophysiology dataset for the work presented in:</strong></p> <p>Supple et al., (2022) Generating spatiotemporal patterns of linearly polarised light at high frame rates for insect vision research. J. Exp. Biol. 225, jeb244087. doi:10.1242/jeb.244087</p> <p><strong>Analysis code available at:</strong> https://github.com/jacksupple/Supple22_JEB_PolDevice_DataAnalysisScripts</p> <p>Download, select all, and extract files. Navigate to the assembled folder to re-run the analysis code.</p> <p><em>Argynnis paphia</em> butterfly intracellular photoreceptor traces are located in "\Photoreceptor_data". Results of the analysed data are found in "\photoreceptor_results"</p> <p><em>Calliphora vicina</em> blowfly extracellular lobula plate tangential cell (LPTC) recordings are located in "\LPTC_data". Results of the analysed data are found in "\LPTC_results".</p> <p>"\DualDLP_Stim" contains parameter files for the rotating dot stimuli, which are used during analysis.</p>
Consensus nucleotide sequences for env and gag for paper: Insights to HIV-1 coreceptor usage by estimating HLA adaptation with Bayesian generalized linear mixed models
<p>This is the consensus sequence repository to the manuscript "Insights to HIV-1 coreceptor usage by estimating HLA adaptation with Bayesian generalized linear mixed models".<br> It contains the 10% consensus nucleotide sequences of the env and gag (only p24) protein of HIV-1 used for the training and leftout data set. The NGS sequences are available under BioProject ID PRJNA810303 and the corresponding BioSample Accession IDs are SAMN26241863:26242168 and SAMN28728524:SAMN28728529</p> <ul> <li>env_leftout.fasta <ul> <li>A fasta file that contains the consensus nucleotide sequences for the env protein for the leftout data set</li> </ul> </li> <li>env_nt_274.fasta <ul> <li>A fasta file that contains the consensus nucleotide sequences for the env protein for the training data set</li> </ul> </li> <li>gag_leftout.fasta <ul> <li>A fasta file that contains the consensus nucleotide sequences for the gag protein for the leftout data set</li> </ul> </li> <li>gag_nt_274.fasta <ul> <li>A fasta file that contains the consensus nucleotide sequences for the gag protein for the training data set</li> </ul> </li> </ul>
Electron-phonon coupling and vibrational properties of size-selected linear carbon chains by resonance Raman scattering
<p>Data repository for the paper "Electron-phonon coupling and vibrational properties of size-selected linear carbon chains by resonance Raman scattering"</p>
Floral visitation to alien plants is non-linearly related to their phylogenetic and floral similarity to native plants
<p>Biological invasions are key to understanding ecological processes that determine the formation of novel interactions. Alien species can negatively impact floral visitation to native species, but native species may also facilitate early establishment of closely related alien species by providing a preadapted pollinator community. We tested whether floral visitation to alien species depended on phylogenetic relatedness and floral similarity to native species. In a field experiment, we simulated the early stages of an invasion by adding potted alien plants into co-flowering native communities. We paired each alien plant with a host native plant, and recorded floral visitation to them for 3,068 hours (totalling 84,814 visits). We used 34 alien and 20 native species in 151 species combinations. We tested whether the number of floral visits to alien plants, the proportion of visits to alien plant relative to visits to both alien and native plants, and the similarity in flower visitor compositions of alien and native plants depended on phylogenetic and floral trait distances between alien and native species. Floral visitation to alien species was highest when they had intermediate floral trait distances to native species, and either low or high phylogenetic distances. Alien species received more similar flower-visitor groups to natives when they had low phylogenetic and either low or high floral trait distances to native species. Co-flowering native species may facilitate floral visitation to closely related alien species, and distantly related alien plants seem to avoid competition for flower visitors with native plants. Alien species with similar floral traits to natives compete with them for flower visitors, and alien species with dissimilar floral traits may not share flower visitors with native species. Alien species with intermediate floral trait distances to natives are most likely to receive flower visitors, as they are not too dissimilar and may still share flower visitors with native species, but not too similar to compete for flower visitors with them. The non-linear patterns between floral visitation and similarity of the alien and native species suggest that an interplay of facilitation and competition simultaneously drives the formation of novel plant-pollinator interactions.</p>
alfa-synuclein spectra for the paper "Linear discriminant analysis reveals hidden patterns in NMR chemical shifts of intrinsically disordered proteins"
<p>The experimental data for the paper "Linear discriminant analysis<br> reveals hidden patterns in NMR chemical shifts of intrinsically<br> disordered proteins" - four spectra of an intrinsically disordered<br> protein alfa-synuclein:</p> <p>3D HNCO</p> <p>4D HabCab(CO)NH</p> <p>4D (H)N(CA)CONH</p> <p>4D HNCACO</p> <p>All spectra were acquired using non-uniform sampling (schedules included<br> as 'schedule.txt' files in a format of 'Kozminski' method in VnmrJ). 3D<br> spectrum (HNCO_nuFT.ucsf) was processed using multidimensional Fourier transform<br> (http://nmr.cent3.uw.edu.pl/software, program 'toastd'). Additionally, we provide a spectrum cleaned of NUS artifacts (HNCO_artifacts_cleaned.ucsf) using program handy (http://nmr.cent3.uw.edu.pl/software, program 'handy').</p> <p>4D spectra were processed using sparse multidimensional Fourier transform<br> (http://nmr.cent3.uw.edu.pl/software, program 'reduced'), based on a<br> HNCO peak list ('peak.list' file). Files with processing parameters are<br> included as 'parameters.txt' files.</p> <p>The resulting spectra are included as Sparky .ucsf files. The files for<br> 4D spectra are the collections of 2D cross-sections with the<br> cross-section number corresponding to the numbering of HNCO peaks in the<br> 'peak.list' file.</p> <p>The folder 'Application2_assignment_transfer' contains Sparky 'ucsf' and 'save' files of the two-dimensional NH projection of the HNCO spectrum with the experimental (HSQC_exp.list) and BMRB (HSQC_bmrb.list) peak lists read into the spectrum. The experimental peaks are marked with arbitrary numbers and BMRB peaks - with names of the preceding aa-residues. The correct assignment is shown in the file 'assignment.txt'.</p>
Bumble bee demographic data for functional linear models
<p>1. Behavior and organization of social groups is thought to be vital to the functioning of societies, yet the contributions of various roles within social groups towards population growth and dynamics have been difficult to quantify. A common approach to quantifying these role-based contributions is evaluating the number of individuals conducting certain roles, which ignores how behavior might scale up to effects at the population-level. Manipulative experiments are another common approach to determine population-level effects, but they often ignore potential feedbacks associated with these various roles.<br> 2. Here, we evaluate the effects of worker size distribution in bumblebee colonies on worker production in 24 observational colonies across three environments, using functional linear models. Functional linear models are an underused correlative technique that has been used to assess lag effects of environmental drivers on plant performance. We demonstrate potential applications of this technique for exploring high-dimensional ecological systems, such as the contributions of individuals with different traits to colony dynamics.<br> 3. We found that more larger workers had mostly positive effects and more smaller workers had negative effects on worker production. Most of these effects were only detected under low or fluctuating resource environments suggesting that the advantage of colonies with larger-bodied workers becomes more apparent under stressful conditions.<br> 4. We also demonstrate the wider ecological application of functional linear models. We highlight the advantages and limitations when considering these models, and how they are a valuable complement to many of these performance-based and manipulative experiments.</p>
Normalized linear counts from NanoString autoimmune profiling panel and summary of statistical analyses
<p>Though dependent on genetic anomalies, clinical manifestations of the human autoimmune disease systemic lupus erythematosus (lupus) can be triggered by environmental exposures including inhalation toxicants such as crystalline silica dust (cSiO<sub>2</sub>), tobacco smoke, and ambient air particles. Prednisone, a glucocorticoid (GC), is a keystone therapy for managing lupus flaring and progression, however, long-term use is associated with many adverse side effects. Here, we characterized the dose-dependent immunomodulation and toxicity of prednisone in a preclinical model that emulates onset and progression of cSiO<sub>2</sub>-triggered lupus. Two cohorts of 6-wk-old female NZBWF1 mice were fed either control AIN-93G diet or one of three AIN-93G diets containing prednisone at 5, 15, or 50 mg/kg diet which span human equivalent oral doses (HED) currently considered to be low (PL; 5 mg/d HED), moderate (PM; 14 mg/d HED), or high (PH; 46 mg/d HED), respectively. At 8 wk of age, mice were intranasally instilled with either saline vehicle or 1 mg cSiO<sub>2</sub> once weekly for 4 wk. The experimental plan was to 1) terminate one cohort of mice (n=8/group) 14 wk after the last cSiO<sub>2</sub> instillation for pathology and autoimmunity assessment and 2) to maintain a second cohort (n=9/group) to monitor glomerulonephritis development and survival. Mean blood concentrations of prednisone's chief active metabolite, prednisolone, in mice fed PL, PM, and PH diets were 27, 105, 151 ng/ml, respectively, which are consistent with levels observed in human blood ≤ 12 h after single bolus treatments with equivalent prednisone doses. Results from the first cohort revealed that consumption of PM but not PL diet significantly reduced cSiO<sub>2</sub>-induced pulmonary ectopic lymphoid structure formation, nuclear-specific AAb production, and inflammation/autoimmune gene expression in the lung, splenomegaly, and glomerulonephritis in the kidney. Relative to GC-associated toxicity, PM but not PL diet elicited muscle wasting, but these diets did not affect bone density or cause glucosuria. Importantly, neither PM nor PL diet influenced latency of cSiO<sub>2</sub>-accelerated death. PH-fed mice in both cohorts displayed robust GC-associated toxicity including body weight loss, reduced muscle mass, and hyperglycemia 7 wk after the final cSiO<sub>2</sub> instillation requiring their early removal from the study. Taken together, our results demonstrate that while moderate doses of prednisone can reduce certain pathological endpoints of cSiO<sub>2</sub>-induced autoimmunity in lupus-prone mice, these ameliorative effects come with unwanted GC toxicity and, crucially, none of these three doses extended survival time.</p>
Figure 6 in The linear stem egg-sac of a Cocalus C. L. Koch 1846 (Araneae: Salticidae: Spartaeini) in Karnataka, India
Figure 6. Four views of emergent (second instar) Cocalus spiderlings resting on the surface of a stem egg-sac, attended by the female (visible beneath stem in 2), in Puttur, Karnataka. Photographs copyright © Ms. Vasanthi Sametadka, used with permission.
Figure 5 in The linear stem egg-sac of a Cocalus C. L. Koch 1846 (Araneae: Salticidae: Spartaeini) in Karnataka, India
Figure 5. Three views of the Siam Weed in the Turahalli forest of southwestern Bengaluru where this brooding Cocalus was found. 1, Siam Weed identified in inset rectangle. 2-3, Note the dry stem at the top of this plant where the egg-sac was located. Photographs copyright © Naveen Iyer.
Figure 2 in The linear stem egg-sac of a Cocalus C. L. Koch 1846 (Araneae: Salticidae: Spartaeini) in Karnataka, India
Figure 2. Cocalus sp. from Singapore and Malaysia. 1-4, Adult male from Lim Chu Kang mangrove, Singapore (1.44N 103.70E, SGM05-3088, record 12 in Figure 1). 5-6, Adult female from Ulu Gombak Field Station, Selangor, Malaysia (3.325N 101.753E, SGM05-4675, record 13 in Figure 1). All photos (1-6) copyright © Wayne P. Maddison (Maddison 2015), used under a CC-BY 3.0 license.
Figure 3 in The linear stem egg-sac of a Cocalus C. L. Koch 1846 (Araneae: Salticidae: Spartaeini) in Karnataka, India
Figure 3. Adult female Cocalus concolor Sai Kung, Hong Kong, 16 JUL 2018. This corresponds to record 2 in Figure 1. Photos copyright © wklegend (wklegend 2018), used under a CC-BY-NC 4.0 license.
Figure 4 in The linear stem egg-sac of a Cocalus C. L. Koch 1846 (Araneae: Salticidae: Spartaeini) in Karnataka, India
Figure 4. Adult female Cocalus sp. guarding her egg sac along a dry stem of Chromolaena odorata in Bengaluru (10:30-11:00 IST, 30 MAY 2020). 6, The two regular rows of eggs within the sac are evident in this view. 12-13, Detailed views showing tightly wrapped rows of eggs within this sac. Photographs copyright © Naveen Iyer.
Figure 5 in Statistical analysis on the cnidome of genus Hydra using Generalized Linear Models
Figure 5. Relative abundances of each type of cnidocyst for each species. (A) stenotele, (B) desmoneme, (C) atrichous isorhiza and (D) holotrichous isorhiza.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.