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116 results for “Bottlenecks”
Pairwise Learning using Unsupervised Bottleneck Features for Zero-Resource Speech Challenge 2017 (System 2)
<p>The system is for track1 alone. We trained an antoencoder using unsupervised bottleneck features with word-pair information from unsupervised term detection (UTD) only on the give ENGLISH corpus. The unsupervised bottleneck features was extracted from an extractor of multi-task learning deep neural networks (MTL-DNN). The word-pair was found by UTD. The UTD process was built on ZRTools. The final features are obtained from the third layer in our pairwise trained autoencoder.</p>
Data and Scripts for Publication: Information Bottleneck in Peptide Conformation Determination by X-ray Absorption Spectroscopy
<p>Data and scripts for the publication titled Information Bottleneck in Peptide Conformation Determination by X-ray Absorption Spectroscopy.</p> <p>Article available at <a href="https://doi.org/10.1088/2399-6528/ad1f73">10.1088/2399-6528/ad1f73</a></p>
Data from: Pre-domestication bottlenecks of the cultivated seaweed Gracilaria chilensis
<p><em><span>Gracilaria</span></em><span><em> chilensis</em> is the main cultivated seaweed in Chile.</span> <span>The low genetic diversity observed in the Chilean population has been associated with the over-exploitation of natural beds and/or the founder effect that occurred during the post-glacial colonization from New Zealand. How these processes have affected its evolutionary trajectory before farming and incipient domestication is poorly understood. </span><span>In this study, we used 2,232 SNPs to assess how the species' evolutionary history in New Zealand (its region of origin), the founder effect linked to transoceanic dispersion and colonization of South America, and the recent over-exploitation of natural populations have influenced the genetic architecture of <em>G</em>. <em>chilensis</em> in Chile. The contrasting patterns of genetic diversity and structure observed between the two main islands in New Zealand attest to the important effects of Quaternary glacial cycles on <em>G</em>. <em>chilensis</em>. ABC analyses indicated that Chatham Island and South America were colonized independently near the end of the Last Glacial Maximum and emphasized the importance of coastal and oceanic currents during that period. Furthermore, ABC analyses inferred the existence of a recent and strong genetic bottleneck in Chile, matching the period of over-exploitation of the natural beds during the 1970s, followed by rapid demographic expansion linked to active clonal propagation used in farming. Recurrent genetic bottlenecks strongly eroded the genetic diversity of <em>G</em>. <em>chilensis</em> prior to its cultivation, raising important challenges for the management of genetic resources in this incipiently domesticated species. </span></p>
Figure 2 in A Lessepsian invader round herring (Etrumeus golanii) with high genetic diversity without bottlenecking in the northeastern Mediterranean Sea
Figure 2. Neighbor-joining tree of E. golanii populations.
Figure 1 in A Lessepsian invader round herring (Etrumeus golanii) with high genetic diversity without bottlenecking in the northeastern Mediterranean Sea
Figure 1. Sampling localities (1. İskenderun, 2. Antalya, 3. Marmaris).
Metapopulation connectivity retains genetic diversity following historical bottleneck in a federally endangered seabird
<p>Despite intensive management since the 1970s, recovery of the endangered northwestern Atlantic population of the Roseate Tern (<i>Sterna dougallii dougallii</i>) has not offset low productivity from a female-biased sex ratio, low adult survival, and habitat constriction. Now, >90% of individuals breed at three sites within 200 km from Long Island, NY to Buzzards Bay, MA (warm-water subregion). To characterize the impact of historical bottlenecks, metapopulation structure, and demographic fluctuations on genetic variation, Roseate Terns from the warm-water (1870s, 1970s, 1997, 2016) and cold-water (Nova Scotia, Canada; 2018) subregions were genotyped at 8-16 microsatellites and two-three mitochondrial regions. Diversity declined in the warm-water subregion from the 1870s (H<sub>E</sub>= 0.44, A<sub>R</sub>= 2.86) and 1970s (H<sub>E</sub> = 0.53, A<sub>R </sub>= 3.25) to 1997 (H<sub>E</sub> = 0.38, A<sub>R </sub>= 2.58). Genetic signatures of bottlenecks persisted in 1997 (<i>P</i> = 0.001 – 0.003) and 2016 (<i>P</i> = <0.001 – 0.005), but an increase in variation occurred by 2016 (H<sub>E</sub>= 0.50, A<sub>R</sub>= 2.85). Weak structure was detected between contemporary warm- and cold-water subregions (θ = 0.06) and within the warm-water subregion (θ = 0.04). Both demographic (<span><span></span></span>= 3439-3821) and genetic (<span><span></span></span>= 3040) estimates suggested effective population size stability over the last 100 years, despite large fluctuations in census size (4000 – 8662). Results suggest that 50 years of management (restoring habitat, preventing gull encroachment, controlling predators) at colony sites supported a small, stable <i>N<sub>e</sub></i> and maintained a hierarchical metapopulation that allowed gene flow to redistribute genetic variation throughout the NW Atlantic. The metapopulation remains highly vulnerable to stochastic events but harbors resiliency and redundancy through gene flow and a stable <i>Ne</i>. For long-term persistence from a genetic perspective, managers must maintain the major source colonies, increase availability of high-quality peripheral breeding sites, and protect concentrated non-breeding sites that facilitate gene flow.</p>
Experimental data for Pseudomonas aeruginosa from experimental evolution under different bottleneck sizes and antibiotic selection pressures
<p>We here combined evolution experiments with genomic and genetic analyses to assess whether bottleneck size and antibiotic-induced selection influences the evolutionary path to resistance in pathogenic<i> Pseudomonas aeruginosa</i>, one of the most problematic opportunistic human pathogens. Two sets of evolution experiments were performed across 16 transfers, in which either the aminoglycoside gentamicin or the fluoroquinolone ciprofloxacin were used as antibiotic. The evolutionary response was studied using counts of bacterial cells at the end of each transfer period (i.e., yield) or by calculating the growth rate from regular optical density measurement during the respective transfer periods. For the populations at the end of the evolution experiments, we also determined their antibiotic resistance with the help of standardized dose response curves. Moreover, we performed whole genome sequencing to assess the frequency of variants, which emerged and spread during the evolution experiments. We further focused on variants in two specific genes, which were selectively favoured in the gentamicin evolution experiments, and assessed their relative fitness using competition experiments. We found that antibiotic resistance is favoured under high antibiotic selection and weak bottlenecks, but also under low antibiotic selection and severe bottlenecks. We found that the absence of high resistance under low selection and weak bottlenecks is caused by the spread of low-resistance variants with high competitive fitness under these conditions. We conclude that bottlenecks in combination with drug-induced selection are currently neglected key determinants of pathogen evolution and antibiotic treatment outcome.</p>
Fig. 1 in Selectivity of fish ladders: a bottleneck in Neotropical fish movement
Fig. 1. Overview of the fish ladder and details of the weirs. SWR = Still Water Rest.
Population bottleneck associated with but likely preceded the recent evolution of self-fertilization in a coastal dune plant
<p>Evolution of self-fertilization may be initiated by a historical population bottleneck, which should diagnostically reduce lineage-wide genetic variation. However, selfing can also strongly reduce genetic variation after it evolves. Distinguishing process from pattern is less problematic if mating system divergence is recent and geographically simple. Dramatically reduced diversity is associated with the transition from outcrossing to selfing in the Pacific coastal endemic Abronia umbellata that includes large-flowered, self-incompatible populations (var. umbellata) south of San Francisco Bay and small-flowered, autogamous populations (var. breviflora) to the north. Compared to umbellata, synonymous nucleotide diversity across 10 single-copy nuclear genes was reduced by 94% within individual populations and 90% across the whole selfing breviflora lineage, which contained no unique polymorphisms. The geographic pattern of genetic variation is consistent with a single origin of selfing that occurred recently (7–28 kya). These results are best explained by a historical bottleneck, but the two most northerly umbellata populations also contained little variation and clustered with selfing populations, suggesting that substantial diversity loss preceded the origin of selfing. A bottleneck may have set the stage for the eventual evolution of selfing by purging genetic load that prevents the spread of selfing.</p>
Runs of homozygosity reveal past bottlenecks and contemporary inbreeding across diverging populations of an island-colonizing bird
<p>Genomes retain evidence of the demographic history and evolutionary forces that have shaped populations. Across island systems, contemporary patterns of genetic diversity reflect complex population demography, including colonisation events, bottlenecks, gene flow and genetic drift. Here, we investigate whether island founder events have prolonged effects on genome-wide diversity and runs of homozygosity (ROH) distributions, using whole genome resequencing from six populations across three archipelagos of Berthelot's pipit (<em>Anthus</em> <em>berthelotii</em>) – a passerine which has undergone island speciation relatively recently. Pairwise sequential Markovian coalescent (PSMC) analyses estimated divergence from its sister species approximately two million years ago. Results indicate that all Berthelot's pipit populations had shared ancestry until approximately 50,000 years ago, when the Madeiran archipelago populations were founded, while the Selvagens were colonised within the last 8,000 years. We identify extensive long ROH (>1 Mb) in genomes in the most recently colonised populations of Madeira and Selvagens which have experienced sequential island founder events and population crashes. Population expansion within the last 100 years may have eroded long ROH in the Madeiran archipelago, resulting in a prevalence of short ROH (<1 Mb). Extensive long and short ROH in the Selvagens reflects strong recent inbreeding, small contemporary effective population size and past bottleneck effects, with as much as 37.7% of the autosomes comprised of ROH >250 kb in length. These findings highlight the importance of demographic history, as well as selection and genetic drift, in shaping contemporary patterns of genomic diversity across diverging populations. </p>
Rethinking pose estimation in crowds: overcoming the detection information bottleneck and ambiguity
<p>#############</p><p>Rethinking pose estimation in crowds: overcoming the detection information-bottleneck and ambiguity, ICCV 2023</p><p>#############</p><p> </p><p>Authors: Zhou, Mu and Stoffl, Lucas and Mathis, Mackenzie Weygandt and Mathis, Alexander</p><p>Affiliation: EPFL</p><p>Date: October, 2023</p><p> </p><p>Here we provide neural networks weights for the best models in our article "Rethinking pose estimation in crowds: overcoming the detection information-bottleneck and ambiguity", ICCV 2023. Each model has the naming convention "dataset"-"modeltype".pth</p><p>These pth files can be loaded with PyTorch. The code to load and use the models is available at The code to load and use the models is available at: <a href="https://github.com/amathislab/BUCTD">https://github.com/amathislab/BUCTD</a></p><p><strong>Note: The weights for OCHuman</strong>, are called COCO-* as one only trains on COCO. So OCHuman-X := COCO-X</p><p>We also share the predictions from various bottom-up models to reproduce the training stored in *.json format (compressed as zip files). See our repository for more details.</p><p> </p><p>Link to the ICCV article: </p><p><a href="https://openaccess.thecvf.com/content/ICCV2023/papers/Zhou_Rethinking_Pose_Estimation_in_Crowds_Overcoming_the_Detection_Information_Bottleneck_ICCV_2023_paper.pdf">https://openaccess.thecvf.com/content/ICCV2023/papers/Zhou_Rethinking_Pose_Estimation_in_Crowds_Overcoming_the_Detection_Information_Bottleneck_ICCV_2023_paper.pdf</a></p><p> </p><p>The weights and predictions are released with Creative Commons Attribution 4.0 license. The code is released under the Apache 2.0 license, see https://github.com/amathislab/BUCTD </p><p><i>If you find our weights, code or ideas useful, please cite:</i></p><p> </p><p>@InProceedings{Zhou_2023_ICCV,</p><p> author = {Zhou, Mu and Stoffl, Lucas and Mathis, Mackenzie Weygandt and Mathis, Alexander},</p><p> title = {Rethinking Pose Estimation in Crowds: Overcoming the Detection Information Bottleneck and Ambiguity},</p><p> booktitle = {Proceedings of the IEEE/CVF International Conference on Computer Vision (ICCV)},</p><p> month = {October},</p><p> year = {2023},</p><p> pages = {14689-14699}</p><p>}</p><p> </p>
Population bottleneck associated with but likely preceded the recent evolution of self-fertilization in a coastal dune plant
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A physiological crisis drives the coral recruitment bottleneck
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Data from: Did Late Pleistocene climate change result in parallel genetic structure and demographic bottlenecks in sympatric Central African crocodiles, Mecistops and Osteolaemus?
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Data from: Genetic diagnosis of a rare myrmecochorous species, Plagiorhegma dubium (Berberidaceae): historical genetic bottlenecks and strong spatial structures among populations
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Experimental data for Pseudomonas aeruginosa from experimental evolution under different bottleneck sizes and antibiotic selection pressures
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Data from: Genomic signatures of population bottleneck and recovery in Northwest Atlantic pinnipeds
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Data from: Bottlenecks and inbreeding depression in autotetraploids
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Caught in a bottleneck: Habitat loss for woolly mammoths in central North America and the ice-free corridor during the last deglaciation
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Runs of homozygosity reveal past bottlenecks and contemporary inbreeding across diverging populations of an island-colonizing bird
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Allen Brain Atlas
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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.