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13,117 results for “Maps”
Data from: Scalability of asynchronous networks is limited by one-to-one mapping between effective connectivity and correlations
Network models are routinely downscaled compared to nature in terms of numbers of nodes or edges because of a lack of computational resources, often without explicit mention of the limitations this entails. While reliable methods have long existed to adjust parameters such that the first-order statistics of network dynamics are conserved, here we show that limitations already arise if also second-order statistics are to be maintained. The temporal structure of pairwise averaged correlations in the activity of recurrent networks is determined by the effective population-level connectivity. We first show that in general the converse is also true and explicitly mention degenerate cases when this one-to-one relationship does not hold. The one-to-one correspondence between effective connectivity and the temporal structure of pairwise averaged correlations implies that network scalings should preserve the effective connectivity if pairwise averaged correlations are to be held constant. Changes in effective connectivity can even push a network from a linearly stable to an unstable, oscillatory regime and vice versa. On this basis, we derive conditions for the preservation of both mean population-averaged activities and pairwise averaged correlations under a change in numbers of neurons or synapses in the asynchronous regime typical of cortical networks. We find that mean activities and correlation structure can be maintained by an appropriate scaling of the synaptic weights, but only over a range of numbers of synapses that is limited by the variance of external inputs to the network. Our results therefore show that the reducibility of asynchronous networks is fundamentally limited.
Data from: Fast and cost-effective genetic mapping in apple using next-generation sequencing
Next-generation DNA sequencing (NGS) produces vast amounts of DNA sequence data, but it is not specifically designed to generate data suitable for genetic mapping. Recently developed DNA library preparation methods for NGS have helped solve this problem, however, by combining the use of reduced representation libraries with DNA sample barcoding to generate genome-wide genotype data from a common set of genetic markers across a large number of samples. Here we use such a method, called genotyping-by-sequencing (GBS), to produce a data set for genetic mapping in an F1 population of apples (Malus x domestica) segregating for skin color. We show that GBS produces a relatively large, but extremely sparse, genotype matrix: over 270,000 SNPs were discovered, but most SNPs have too much missing data across samples to be useful for genetic mapping. After filtering for genotype quality and missing data, only 6% of the 85 million DNA sequence reads contributed to useful genotype calls. Despite this limitation, using existing software and a set of simple heuristics, we generated a final genotype matrix containing 3967 SNPs from 89 DNA samples from a single lane of Illumina HiSeq and used it to create a saturated genetic linkage map and to identify a known QTL underlying apple skin color. We therefore demonstrate that GBS is a cost effective method for generating genome-wide SNP data suitable for genetic mapping in a highly diverse and heterozygous agricultural species. We anticipate future improvements to the GBS analysis pipeline presented here that will enhance the utility of next-generation DNA sequence data for the purposes of genetic mapping across diverse species.
Data from: Genetic mapping of molar size relations identifies inhibitory locus for third molars in mice
Molar size in Mammals shows considerable disparity and exhibits variation similar to that predicted by the Inhibitory Cascade model. The importance of such developmental systems in favoring evolutionary trajectories is also underlined by the fact that this model can predict macroevolutionary patterns. Using backcross mice, we mapped QTL for molar sizes controlling for their sequential development. Genetic controls for upper and lower molars appear somewhat similar, and regions containing genes implied in dental defects drive this variation. We mapped three relationship QTLs (rQTL) modifying the control of the mesial molars on the focal third molar. These regions overlap Shh, Sostdc1 and Fst genes, which have pervasive roles in development and should be buffered against new variation. It has theoretically been shown that rQTL produces new variation channeled in the direction of adaptive changes. Our results provide evidence that evolutionary/disease patterns of tooth size variation could result from such a non-random generating process.
Data from: Using linkage maps as a tool to determine patterns of chromosome synteny in the genus Salvelinus
Next generation sequencing techniques have revolutionized the collection of genome and transcriptome data from non-model organisms. This manuscript details the application of restriction site associated DNA sequencing (RADseq) to generate a marker dense genetic map for Brook trout (Salvelinus fontinalis). The consensus map was constructed from three full-sib families totaling 176 F1 individuals. The map consisted of 42 linkage groups with a total female map size of 2502.5 cM, and a total male map size of 1863.8 cM. Synteny was confirmed with Atlantic salmon for 38 linkage groups, with Rainbow trout for 37 linkage groups, Arctic char for 36 linkage groups, and with a previously published Brook trout linkage map for 39 linkage groups. Comparative mapping confirmed the presence of eight metacentric and 34 acrocentric chromosomes in Brook trout. Six metacentric chromosomes seem to be conserved with Arctic char suggesting there have been at least two species specific fusion and fission events within the genus Salvelinus. In addition, the sex marker (sdY; sexually dimorphic on the Y chromosome) was mapped to Brook trout BC35, which is homologous with Atlantic salmon Ssa09qa, Rainbow trout Omy25, and Arctic char AC04q. Ultimately, this linkage map will be a useful resource for studies on the genome organization of Salvelinus, and facilitates comparisons of the Salvelinus genome with Salmo and Oncorhynchus.
MAP 1 in Chuanicosmetura gen. nov. of the tribe Meconematini (Orthoptera: Tettigoniidae) from southwest China and Chuanicosmetura emarginata (Liu, 2000) comb. nov.
MAP 1. The distribution of Chuanicosmetura emarginata (Liu, 2020) comb. nov. (green points)
Distribution of large carnivores in Europe 2012 - 2016: Distribution maps for Brown bear, Eurasian lynx, Grey wolf, and Wolverine
<p>Regular assessments of species' status are an essential component of conservation planning and adaptive management. They allow the progress of past or ongoing conservation actions to be evaluated and can be used to redirect and prioritise future conservation actions. Most countries perform periodic assessments for their own national adaptive management procedures or national red lists. Furthermore, the countries of the European Union have to report on the status of all species listed on the directives of the Habitats Directive every 6 years as part of their obligations under Article 17. However, these national level assessments are often made using non-standardised procedures and do not always adequately reflect the biological units (i.e. the populations) which are needed for ecologically meaningful assessments.</p> <p>Since the early 2000's the Large Carnivore Initiative for Europe (a Specialist Group of the IUCN's Species Survival Commission) has been coordinating periodic surveys of the status of large carnivores across Europe (e.g. von Arx et al. 2004; Salvatori & Linnell 2005, Kaczensky et al. 2013). These have covered the Eurasian lynx (Lynx lynx), the wolf (Canis lupus), the brown bear (Ursus arctos) and the wolverine (Gulo gulo). These surveys involve the contributions of the best available experts and sources of information. While the underlying data quality and field methodology varies widely across Europe, these coordinated assessments do their best to integrate the diverse data in a comparable manner and make the differences transparent. They also endeavour to conduct the assessments on the most important scales. This includes the continental scale (all countries except for Russia, Belarus, Moldova and the parts of Ukraine outside the Carpathian mountain range), the scale of the EU 28 (where the Habitats Directive operates) and of the biological populations which reflect the scale at which ecological processes occur (Linnell et al. 2008). In this way, the independent LCIE assessments provide a valuable complement to the ongoing national processes.</p> <p>Our last assessments covered the period 2006-2011 (Kaczensky et al. 2013; Chapron et al. 2014). The current assessment is mainly based on the period 2012-2016 and broadly follows the same methodology. The population definitions used in this report broadly follow those proposed in Linnell et al. (2008) and described in Kaczensky et al. (2013). However, as these were always intended to be dynamic definitions there have been a few small changes, namely the upgrading of the lynx in the Harz mountains to being a population (formerly they were viewed as an "occurrence"), and the exclusion of the wolves in the Sierra Morena mountains of southern Spain because of their regional extinction. </p> <p>Additional information on issues related to large carnivore status assessment is available in other reports. For example, Linnell & Cretois (2018) summarise data on large carnivore depredation on livestock, Linnell (2013) summarises data on social conflicts associated with large carnivore recovery, and Boitani et al. (2015) summarises key actions required to address the main threats facing large carnivores in Europe.</p> <p><strong>References</strong></p> <ul> <li><span>Boitani, L., F. Alvarez, O. Anders, H. Andren, E. Avanzinelli, V. Balys, J. C. Blanco, U. Breitenmoser, G. Chapron, P. Ciucci, A. Dutsov, C. Groff, D. Huber, O. Ionescu, F. Knauer, I. Kojola, J. Kubala, M. Kutal, J. Linnell, A. Majic, P. Mannil, R. Manz, F. Marucco, D. Melovski, A. Molinari, H. Norberg, S. Nowak, J. Ozolins, S. Palazon, H. Potocnik, P.-Y. Quenette, I. Reinhardt, R. Rigg, N. Selva, A. Sergiel, M. Shkvyria, J. Swenson, A. Trajce, M. Von Arx, M. Wolfl, U. Wotschikowsky, D. Zlatanova, 2015. Key actions for Large Carnivore populations in Europe. Institute of Applied Ecology (Rome, Italy). Report to DG Environment, European Commission, Bruxelles. Contract no. 07.0307/2013/654446/SER/B3</span></li> <li><span>Chapron, G., Kaczensky, P., Linnell, J.D.C., von Arx, M., Huber, D., Andrén, H., López-Bao, J.V., Adamec, M., Álvares, F., Anders, O., Balčiauskas, L., Balys, V., Bedő, P., Bego, F., Blanco, J.C., Breitenmoser, U., Brøseth, H., Bufka, L., Bunikyte, R., Ciucci, P., Dutsov, A., Engleder, T., Fuxjäger, C., Groff, C., Holmala, K., Hoxha, B., Iliopoulos, Y., Ionescu, O., Jeremić, J., Jerina, K., Kluth, G., Knauer, F., Kojola, I., Kos, I., Krofel, M., Kubala, J., Kunovac, S., Kusak, J., Kutal, M., Liberg, O., Majić, A., Männil, P., Manz, R., Marboutin, E., Marucco, F., Melovski, D., Mersini, K., Mertzanis, Y., Mysłajek, R.W., Nowak, S., Odden, J., Ozolins, J., Palomero, G., Paunović, M., Persson, J., Potočnik, H., Quenette, P.-Y., Rauer, G., Reinhardt, I., Rigg, R., Ryser, A., Salvatori, V., Skrbinšek, T., Stojanov, A., Swenson, J.E., Szemethy, L., Trajçe, A., Tsingarska[1]Sedefcheva, E., Váňa, M., Veeroja, R., Wabakken, P., Wölfl, M., Wölfl, S., Zimmermann, F., Zlatanova, D. & Boitani, L. 2014. Recovery of large carnivores in Europe's modern human-dominated landscapes. Science 346(6216): 1517-1519.</span></li> <li><span>Kaczensky, P., Chapron, G., Von Arx, M., Huber, D., Andrén, H. & Linnell, J. 2013. Status, management and distribution of large carnivores - bear, lynx, wolf and wolverine - in Europe. Istituto di Ecologia Applicata, Rome, Italy.</span></li> <li><span>Linnell, J.D.C., Cretois, B., 2018. Research for AGRI Committee – The revival of wolves and other large predators and its impact on farmers and their livelihood in rural regions of Europe. Research for AGRI Committee – The revival of wolves and other large predators and its impact on farmers and their livelihood in rural regions of Europe, European Parliament, Policy Department for Structural and Cohesion Policies, Brussels.</span></li> <li>Linnell, J.D.C. 2013. From conflict to coexistence: insights from multi-disciplinary research into the relationships between people, large carnivores and institutions. Istituto di Ecologia Applicata, Rome.</li> <li>Linnell, J.D.C., Salvatori, V. & Boitani, L. 2008. Guidelines for population level management plans for large carnivores in Europe. A Large Carnivore Initiative for Europe report prepared for the European Commission (contract 070501/2005/424162/MAR/B2).</li> <li>Salvatori, V. & Linnell, J.D.C. 2005. Report on the conservation status and threats for wolf (Canis lupus) in Europe. Council of Europe Report T-PVS/Inf (2005) 16.</li> <li>von Arx, M., Breitenmoser-Würsten, C., Zimmermann, F. & Breitenmoser, U. 2004. Status and conservation of the Eurasian lynx (Lynx lynx) in Europe in 2001. KORA Report 19e: 1- 330.</li> </ul>
Supplementary material 1 from: Seijo C, Calado H, McClintock WJ, Gil A, Fonseca C (2021) Mapping recreational ecosystem services from stakeholders' perspective in the Azores. One Ecosystem 6: e65751. https://doi.org/10.3897/oneeco.6.e65751
Summary of data registered in SeaSketch
FIGURE 8. Distribution map for Oressinoma sorina n in A new species of the enigmatic genus Oressinoma Doubleday from the Andes of central Peru (Lepidoptera: Nymphalidae, Satyrinae)
FIGURE 8. Distribution map for Oressinoma sorina n. sp. and Oressinoma sorata.
Data from: Brain-wide cellular resolution imaging of Cre transgenic zebrafish lines for functional circuit-mapping
Decoding the functional connectivity of the nervous system is facilitated by transgenic methods that express a genetically encoded reporter or effector in specific neurons; however, most transgenic lines show broad spatiotemporal and cell-type expression. Increased specificity can be achieved using intersectional genetic methods which restrict reporter expression to cells that co-express multiple drivers, such as Gal4 and Cre. To facilitate intersectional targeting in zebrafish, we have generated more than 50 new Cre lines, and co-registered brain expression images with the Zebrafish Brain Browser, a cellular resolution atlas of 264 transgenic lines. Lines labeling neurons of interest can be identified using a web-browser to perform a 3D spatial search (zbbrowser.com). This resource facilitates the design of intersectional genetic experiments and will advance a wide range of precision circuit-mapping studies.
Data from: Immunoreactive peptide maps of SARS-CoV-2
<p>Serodiagnosis of SARS-CoV-2 infection is impeded by immunological cross-reactivity among the human coronaviruses (HCoVs) SARS-CoV-2, SARS-CoV-1, MERS-CoV, OC43, 229E, HKU1, and NL63. To study humoral immune responses specific to SARS-CoV-2, it is imperative to identify peptides that may enable discrimination between exposure to SARS-CoV-2 and other HCoVs. We used a high-density peptide microarray and plasma samples collected at two time points from 50 subjects with SARS-CoV-2 infection confirmed by qPCR, samples collected in 2004-2005 from 11 subjects with IgG antibodies to SARS-CoV-1, 11 subjects with IgG antibodies to other seasonal human coronaviruses (HCoV), and 10 healthy human subjects. The peptide microarrays consist of ~172000 12-mer peptide probes spanning whole viral genomes. This dataset consists of reactivity values for individual peptides from all 132 plasma samples for both IgG and IgM. Also made available is the correspondence key that provides a reference for all viral genome sequences that a peptide originated from.</p>
MAP 1 in Remarks on the genus Dolicholobosa Bian, Zhu & Shi, 2017 (Orthoptera Tettigoniidae: Meconematinae) with one new species from Guizhou, China
MAP 1. Distribution of the Dolicholobosa species.
Data from: Systems analysis of adaptive responses to MAP Kinase pathway blockade in BRAF mutant melanoma
Fifty percent of cutaneous melanomas are driven by activated BRAFV600E, but tumors treated with RAF inhibitors, even when they respond dramatically, rapidly adapt and develop resistance. Thus, there is a pressing need to identify the major mechanisms of intrinsic and adaptive resistance and develop drug combinations that target these resistance mechanisms. In a combinatorial drug screen on a panel of 12 treatment-naïve BRAFV600E mutant melanoma cell lines of varying levels of resistance to mitogen-activated protein kinase (MAPK) pathway inhibition, we identified the combination of PLX4720, a targeted inhibitor of mutated BRaf, and lapatinib, an inhibitor of the ErbB family of receptor tyrosine kinases, as synergistically cytotoxic in the subset of cell lines that displayed the most resistance to PLX4720. To identify potential mechanisms of resistance to PLX4720 treatment and synergy with lapatinib treatment, we performed a multi-platform functional genomics analysis to profile the genome as well as the transcriptional and proteomic responses of these cell lines to treatment with PLX4720. We found modest levels of resistance correlated with the zygosity of the BRAF V600E allele and receptor tyrosine kinase (RTK) mutational status. Layered over base-line resistance was substantial upregulation of many ErbB pathway genes in response to BRaf inhibition, thus generating the vulnerability to combination with lapatinib. The transcriptional responses of ErbB pathway genes are associated with a number of transcription factors, including ETS2 and its associated cofactors that represent a convergent regulatory mechanism conferring synergistic drug susceptibility in the context of diverse mutational landscapes.
Map 1 in Notes on the genus Pseudokuzicus Gorochov, 1993 (Orthoptera: Tettigoniidae: Meconematinae: Meconematini) from China
Map 1. Distribution of the genus Pseudokuzicus from P. R. China
pogo model for thickness mapping
<p>These are pogo models for reconstruction of thickness variation.</p>
Data from: Mapping QTL contributing to variation in posterior lobe morphology between strains of Drosophila melanogaster
Closely-related, and otherwise morphologically similar insect species frequently show striking divergence in the shape and/or size of male genital structures, a phenomenon thought to be driven by sexual selection. Comparative interspecific studies can help elucidate the evolutionary forces acting on genital structures to drive this rapid differentiation. However, genetic dissection of sexual trait divergence between species is frequently hampered by the difficulty generating interspecific recombinants. Intraspecific variation can be leveraged to investigate the genetics of rapidly-evolving sexual traits, and here we carry out a genetic analysis of variation in the posterior lobe within D. melanogaster. The lobe is a male-specific process emerging from the genital arch of D. melanogaster and three closely-related species, is essential for copulation, and shows radical divergence in form across species. There is also abundant variation within species in the shape and size of the lobe, and while this variation is considerably more subtle than that seen among species, it nonetheless provides the raw material for QTL mapping. We created an advanced intercross population from a pair of phenotypically-different inbred strains, and after phenotyping and genotyping-by-sequencing the recombinants, mapped several QTL contributing to various measures of lobe morphology. The additional generations of crossing over in our mapping population led to QTL intervals that are smaller than is typical for an F2 mapping design. The intervals we map overlap with a pair of lobe QTL we previously identified in an independent mapping cross, potentially suggesting a level of shared genetic control of trait variation. Our QTL additionally implicate a suite of genes that have been shown to contribute to the development of the posterior lobe. These loci are strong candidates to harbor naturally-segregating sites contributing to phenotypic variation within D. melanogaster, and may also be those contributing to divergence in lobe morphology between species.
Figure 1-2. Maps. 1 in The milliped family Tingupidae (Chordeumatida) on Kodiak Island, Alaska, USA, a geographically remote record of indigenous Diplopoda
Figure 1-2. Maps. 1) Occurrences of Tingupidae in far northwestern North America; the arrow denotes the location of Yakutat. Dots, Tingupa spp.; star, T. tlingitorum; triangle, undetermined genus and species. 2) Distance of Kodiak Island locality from most proximate milliped records in northern Pacific area, miles and kilometers (in parentheses) shown.
Figures 300-305. Distribution maps. 300 in Notes on the tiger beetles (Coleoptera: Carabidae: Cicindelinae) of Vietnam. 135. Contribution towards the knowledge of Cicindelinae
Figures 300-305. Distribution maps. 300) Therates kaliakini Matalin and Wiesner, 2006. 301) Therates dalatensis Matalin, Wiesner and Udovichenko, 2012. 302) Therates angustatus angustatus Horn, 1902. 303) Therates angustatus pseudotuberosus Wiesner, 1988. 304) Therates rugosoangustatus Horn, 1929. 305) Therates fruhstorferi fruhstorferi Horn, 1902.
Figures 366-368. Distribution maps. 366 in Notes on the tiger beetles (Coleoptera: Carabidae: Cicindelinae) of Vietnam. 135. Contribution towards the knowledge of Cicindelinae
Figures 366-368. Distribution maps. 366) Callytron nivicinctum (Chevrolat, 1845). 367) Callytron andersonii (Gestro, 1889). 368) Enantiola hewittii (Horn, 1908).
Figure 2. Map showing sites for Acacia drepanolobium and A in The Lepidoptera of Acacia domatia in Kenya, with description of two new genera and six new species
Figure 2. Map showing sites for Acacia drepanolobium and A. seyal var. fistula.
Map 6 in Revision of the Anaulacaspis species of the Palaearctic region (Coleoptera: Staphylinidae: Aleocharinae)
Map 6: Distributions of Anaulacaspis convexa (white circles), A. seclusa (black circles), and A. gilva (white diamonds) in the West Palaearctic and Middle Asia, based on revised records.
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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.