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67 results for “Relational values”
Relate-estimated coalescence rates, allele ages, and selection p-values for the 1000 Genomes Project
<p><strong>Overview</strong></p> <p>Coalescence rates, allele ages, and p-values for evidence of positive selection calculated for 2478 samples of the 1000 Genomes Project using Relate.</p> <p>We estimated the joint genealogy of all 1000 GP populations and then extracted the embedded genealogy for each population.<br> For the genealogy of each population, we jointly estimated the population size history and branch lengths. <br> Variants segregating in more than one population therefore have correlated but different allele ages in each population.</p> <p>Please refer to <a href="https://www.nature.com/articles/s41588-019-0484-x">Speidel et al. Nature Genetics (2019)</a> for more details or email leo.speidel@outlook.com for any queries.</p> <p><strong>Coalescence rates</strong></p> <p>The zipped directory coalescence_rates.zip contains coalescence rates for 26 populations in the 1000 Genomes Project data set.</p> <ul> <li>The .coal files show the haploid coalescence rates, please refer to the <a href="https://myersgroup.github.io/relate/modules.html#PopulationSizeScript_FileFormats">Relate documentation</a> for the file format.</li> <li>The popsize.RData file is an R data frame storing the diploid population sizes (0.5/coalescence rate) calculated using the .coal files. The columns of this data frame, named "pop_size", are <ul> <li>gens_ago: Time in generations at which epoch starts. (To get years from generations, we multiply by 28.)</li> <li>population_size: Diploid population size in this epoch.</li> <li>population: Name of population </li> <li>region: Name of region (AFR, AMR, EAS, EUR, SAS)</li> </ul> </li> </ul> <p><strong>Allele ages and selection p-values</strong></p> <p>The zipped directories allele_ages_*.zip contain R data frames for each 1000GP population storing allele ages and selection p-values.<br> Please note that only mutations that segregate in the population and map to a unique branch in the Relate-estimated marginal trees are included. Selection p-values are only provided for mutations of DAF > 2 that pass quality filters (see Speidel et al., 2019). </p> <p>To get an age estimate for a neutral mutation, use 0.5*(lower_age + upper_age). To get years from generations, we multiply by 28.</p> <p>The columns of these data frames, named "allele_ages", are</p> <ul> <li>CHR: chromosome index</li> <li>BP: base-pair position (GRCh37)</li> <li>ID: id of SNP</li> <li>lower_age: Age in generations of coalescence event at the lower end of the branch onto which the mutation maps</li> <li>upper_age: Age in generations of coalescence event at the upper end of the branch onto which the mutation maps</li> <li>ancestral/derived: Ancestral/derived allele</li> <li>upstream: Upstream (5') allele</li> <li>downstream: Downstream (3') allele</li> <li>DAF: Derived-allele frequency</li> <li>pvalue: log10 p-value for selection evidence</li> </ul>
Text-fig. 4. Graphical visualization of Phytogeographic Reference Regions Assessment (PRRA) of nearest living relative genera of fossil-taxa from late Early Miocene Wiesa assemblage in eastern Germany. Analysis yields only NLRs which have modern distribution area (partly) in E and SE Asia. For relationships of fossil-taxa to nearest living relatives or ecological equivalents, see Tab. 6; taxa used for analysis marked with asterisks. Three geographic resolutions conducted: a – grid with 1.5° latitude/longitude resolution, b – grid with 2°, c – grid with 3°; similarity column indicates cooccurrences of genera of nearest living relatives in single grid box. Maximum value in our analysis: grid box marked with arrow in map a, located in western Yunnan Province, P. R. China and southern Kachin Province, NE Myanmar (east of Myitkyina city), area with 97.371 7–98.874 2° longitude and 24.586 7–25.837 5° latitude, yields 23 co-occurring species of 13 genera (Tab. 7). in Assessment Of Phytogeographic Reference Regions For Cenozoic Vegetation: A Case Study On The Miocene Flora Of Wiesa (Germany)
Text-fig. 4. Graphical visualization of Phytogeographic Reference Regions Assessment (PRRA) of nearest living relative genera of fossil-taxa from late Early Miocene Wiesa assemblage in eastern Germany. Analysis yields only NLRs which have modern distribution area (partly) in E and SE Asia. For relationships of fossil-taxa to nearest living relatives or ecological equivalents, see Tab. 6; taxa used for analysis marked with asterisks. Three geographic resolutions conducted: a – grid with 1.5° latitude/longitude resolution, b – grid with 2°, c – grid with 3°; similarity column indicates cooccurrences of genera of nearest living relatives in single grid box. Maximum value in our analysis: grid box marked with arrow in map a, located in western Yunnan Province, P. R. China and southern Kachin Province, NE Myanmar (east of Myitkyina city), area with 97.371 7–98.874 2° longitude and 24.586 7–25.837 5° latitude, yields 23 co-occurring species of 13 genera (Tab. 7).
Figure. The proportion of benthic abundance for different invertebrate orders relative to the total benthic abundance [%] of the Munzur and Pülümür rivers, representing the mean value of the 2 sites per river. in Macroinvertebrate composition in the metarhithral zones of the Munzur and Pülümür rivers: a preliminary study
Figure. The proportion of benthic abundance for different invertebrate orders relative to the total benthic abundance [%] of the Munzur and Pülümür rivers, representing the mean value of the 2 sites per river.
Data and Code for "Value dissonance in research(er) assessment: Individual and institutional priorities in review, promotion and tenure criteria related to research quality, quantity, openness and responsibility"
<p>This snapshot contains code and data for the preprint "Value dissonance in research(er) assessment: Individual and institutional priorities in review, promotion and tenure criteria related to research quality, quantity, openness and responsibility".</p> <p>Instructions on re-using the data and running the code can be found in the README.md.</p> <p>Changes:</p> <ul> <li>Added survey instrument and informed consent.</li> </ul>
Time and matrix quality increase the relative habitat value of smaller patches in fragmented landscapes
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Data from: Value-related learning in the olfactory bulb occurs through pathway-dependent peri-somatic inhibition of mitral cells
<p>Associating values to environmental cues is a critical aspect of learning from experiences, allowing animals to predict and maximise future rewards. Value-related signals in the brain were once considered a property of higher sensory regions, but their wide distribution across many brain regions is increasingly recognised. Here, we investigate how reward-related signals begin to be incorporated, mechanistically, at the earliest stage of olfactory processing, namely, in the olfactory bulb. In head-fixed mice performing Go/No-Go discrimination of closely related olfactory mixtures, rewarded odours evoke widespread inhibition in one class of output neurons, that is, in mitral cells but not tufted cells. The temporal characteristics of this reward-related inhibition suggest it is odour-driven, but it is also context-dependent since it is absent during pseudo-conditioning and pharmacological silencing of the piriform cortex. Further, the reward-related modulation is present in the somata but not in the apical dendritic tuft of mitral cells, suggesting an involvement of circuit component located deep in the olfactory bulb. Depth-resolved imaging from granule cell dendritic gemmules suggests that granule cells that target mitral cells receive a reward-related extrinsic drive. Thus, our study supports the notion that value-related modulation of olfactory signals is a characteristic of olfactory processing in the primary olfactory area and narrows down the possible underlying mechanisms to deeper circuit components that contact mitral cells peri-somatically.</p>
Understanding relational values in cultural landscapes in Romania and Germany
<p>Relational values recently emerged as a concept to comprehensively understand and communicate the many values of nature. Relational values can be defined as preferences and principles about human-nature relationships and focus both on human-nature connections, as well as human-human connections.</p> <p>Here, drawing on 819 face-to-face questionnaires, we analysed relational, intrinsic and instrumental values across a total of six agricultural landscapes in Transylvania (Romania) and Lower Saxony (Germany). The landscapes described a gradient of land use intensity, within and across the countries.</p> <p>Our results suggest a bundling of values into four groups: those concerned with individual cognition (including intrinsic values), those that focus on nature as a place for social interaction and relaxation, those that capture cultural identity and spiritual values and one bundle that only includes instrumental values.</p> <p>These different values, in turn, were strongly related to (i) respondents' attitudes towards environmental conservation and the (ii) frequency with which respondents used nature as a resource. </p> <p>Instrumental values have the tendency to be inversely related with relational values and were found to increase with the land use intensity of the focal landscapes.</p>
B-value, Slip and Stress related to the Antakya 2023 earthquake
<p>On-fault b map for the Antakya 2023 earthquake sequence using the Godano et al. 2021 method plotted with the slip and shear-stress calcolated for the two main earthquakes.</p> <p> </p> <p>C. Godano, V. Convertito, N. A. Pino, and A. Tramelli. An automated method for mapping independent spatial b values. Earth and Space Science, 9(6):e2021EA002205, 2022. e2021EA002205 2021EA002205.</p>
Data from: Relational values of nature in empirical research: A systematic review
<p>In the past five years, scholarly and policy attention to relational values, a concept that articulates plural values of nature, has grown steadily. To date, there are no published syntheses of empirical research that explicitly address relational values. We perform a systematic literature review of n = 72 empirical studies of relational values to summarize the state of current research and to identify opportunities for future research and conceptual development. In our analysis, we categorize what authors identify as relational values and summarize study characteristics (e.g., study location, methods approach.) Authors collectively report n = 312 unique relational values. Categories of <em>identity, social cohesion, livelihoods, connection to place/human-nature connection</em>, and <em>religion</em> are most common. Scholarship that explicitly addresses relational values has increased since 2017 and exhibits substantial diversity: in how relational values are conceptualized (or not); in disciplinary associations; in geographical location; and in data collection methods. We find that most empirical research on relational values does not justify how its results reflect characteristics that establish the relational values concept as unique from other environmental values concepts. As a result, diverse interpretations of the relational values concept pose the risk of the relational values concept being so broad and inclusive that it becomes meaningless, or at least meaning-light.</p>
Global patents related to the biotechnological production of biofuels and high-value bioproducts
<p>The table includes the most relevant patents related to the biotechnological production of biofuels and high-added-value products obtained from lignocellulosic raw material.</p>
Data from: Relational values of nature in empirical research: A systematic review
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Understanding relational values in cultural landscapes in Romania and Germany
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Data from: Value-related learning in the olfactory bulb occurs through pathway-dependent peri-somatic inhibition of mitral cells
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Pairwise distance demarcation of species in the family Coronaviridae. a, Diagonal matrix of PPDs of 2,505 viruses clustered according to 49 coronavirus species, 39 established and 10 pending or tentative, and ordered from the most to least populous species, from left to right; green and white, PPDs smaller and larger than the inter-species threshold, respectively. Areas of the green squares along the diagonal are proportional to the virus sampling of the respective species, and virus prototypes of the five most sampled species are specified to the left; asterisks indicate species that include viruses whose intra-species PPDs crossed the inter-species threshold (threshold 'violators'). b, Maximal intra-species PPDs (x axis, linear scale) plotted against virus sampling (y axis, log scale) for 49 species (green dots) of the Coronaviridae. Indicated are the acronyms of virus prototypes of the seven most sampled species. Green and blue plot sections represent intra-species and intra-subgenera PPD ranges. The vertical black line indicates the inter-species threshold. c, Shown are the PDs of non-identical residues (y axis) for four viruses representing three major phylogenetic lineages (clades) of the species Severe acute respiratorysyndrome-related coronavirus (panel b) and all pairs of the 256 viruses of this species ('all pairs'). The PD values were derived from pairwise distances in the MSA that were calculated using an identity matrix. Panels a and b were adopted from the DEmARC v.1.4 output. in The species Severe acute respiratory syndromerelated coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2
Pairwise distance demarcation of species in the family Coronaviridae. a, Diagonal matrix of PPDs of 2,505 viruses clustered according to 49 coronavirus species, 39 established and 10 pending or tentative, and ordered from the most to least populous species, from left to right; green and white, PPDs smaller and larger than the inter-species threshold, respectively. Areas of the green squares along the diagonal are proportional to the virus sampling of the respective species, and virus prototypes of the five most sampled species are specified to the left; asterisks indicate species that include viruses whose intra-species PPDs crossed the inter-species threshold (threshold 'violators'). b, Maximal intra-species PPDs (x axis, linear scale) plotted against virus sampling (y axis, log scale) for 49 species (green dots) of the Coronaviridae. Indicated are the acronyms of virus prototypes of the seven most sampled species. Green and blue plot sections represent intra-species and intra-subgenera PPD ranges. The vertical black line indicates the inter-species threshold. c, Shown are the PDs of non-identical residues (y axis) for four viruses representing three major phylogenetic lineages (clades) of the species Severe acute respiratorysyndrome-related coronavirus (panel b) and all pairs of the 256 viruses of this species ('all pairs'). The PD values were derived from pairwise distances in the MSA that were calculated using an identity matrix. Panels a and b were adopted from the DEmARC v.1.4 output.
Data from: Study of regional differences in GC content values in chromosomes of the guppy and related fish species
<p><span><span><span><span><span><span><span><span><span><span><span>Genetic and physical mapping of the guppy (<i>P. reticulata</i>) have shown that recombination patterns differ greatly between males and females. Crossover events occur evenly across the chromosomes in females, but in male meiosis they are restricted to the tip furthest from the centromere of each chromosome, creating very high recombination rates per megabase, similar to the high rates in of pseudo-autosomal regions (PARs) of mammalian sex chromosomes. We here used the intronic GC content to indirectly infer the recombination patterns on guppy chromosomes. This is based on evidence that recombination is associated with GC-biased gene conversion, so that genome regions with high recombination rates should be detectable by high GC content. We used intron sequences and 3<sup>rd</sup> positions of codons, in order to make comparisons between sequences that are matched, as far as possible, with respect to selective constraints. Both these types of sites are likely to be under weak selection. Almost all guppy chromosomes, including the sex chromosome (LG12), prove to have very high GC values near their assembly ends, suggesting high recombination rates due to strong crossover localisation in male meiosis. Our test does not suggest that the guppy XY pair has stronger crossover localisation than the autosomes, or than the homologous chromosome in a closely related fish, the platyfish (<i>Xiphophorus maculatus</i>). We therefore conclude that the guppy XY pair has not recently undergone an evolutionary change to a different recombination pattern, or reduced its crossover rate, but that the guppy evolved Y-linkage due to acquiring a male-determining factor that also conferred the male crossover pattern. The results also identify the centromere ends of guppy chromosomes, which were not determined in the guppy genome assembly. </span></span></span></span></span></span></span></span></span></span></span></p>
FIGURE 2 in A new species of Typhlocharis Dieck, 1869 (Coleoptera: Carabidae: Anillini) from South Spain, with notes on the phylogenetic value of sexually related characters and the presence of stridulatory organ (pars stridens) in the genus
FIGURE 2. Abdomen (ventral view) of female and male, showing the median tubercle, the foveae, the chaetotaxy of the last segment and the "belt" of scaly microsculpture (shaded in grey).
FIGURE 4 in A new species of Typhlocharis Dieck, 1869 (Coleoptera: Carabidae: Anillini) from South Spain, with notes on the phylogenetic value of sexually related characters and the presence of stridulatory organ (pars stridens) in the genus
FIGURE 4. Pattern of microreticulation in the vertex region of T. monastica (a) and T. farinosae (b) showing the differences between species with and without pars stridens. (Modified from Zaballos & Wrase 1998, Zaballos & Ruíz-Tapiador 1997).
FIGURE 3 in A new species of Typhlocharis Dieck, 1869 (Coleoptera: Carabidae: Anillini) from South Spain, with notes on the phylogenetic value of sexually related characters and the presence of stridulatory organ (pars stridens) in the genus
FIGURE 3. Aedeagus in lateral and dorsal view, parameres in lateral view (a). Female genitalia in ventral view (b).
FIGURE Phylogenetic relationships of the Coelastrella genus inferred from the 18S-ITS1-5.8S-ITS2 region. The Neighbor-Joining (NJ), Maximum Likelihood (ML) bootstrap values and Bayesian posterior probabilities (PP) are presented at the nodes (NJ/ML/PP). Only values above 75 are shown. Strains provided in this study are indicated in bold font. Authentic strains marked with asterisks. The scale bar represents the number of substitutions per site. The GenBank accession numbers of Coelastrella can be found in the Table 3. in Morphological and phylogenetic relations of members of the genus Coelastrella (Scenedesmaceae, Chlorophyta) from the Ural and Khentii Mountains (Russia, Mongolia)
FIGURE Phylogenetic relationships of the Coelastrella genus inferred from the 18S-ITS1-5.8S-ITS2 region. The Neighbor-Joining (NJ), Maximum Likelihood (ML) bootstrap values and Bayesian posterior probabilities (PP) are presented at the nodes (NJ/ML/PP). Only values above 75 are shown. Strains provided in this study are indicated in bold font. Authentic strains marked with asterisks. The scale bar represents the number of substitutions per site. The GenBank accession numbers of Coelastrella can be found in the Table 3.
FIGURE. Phylogenetic tree of specimens on Poaceae and related host plants constructed by MP method based on ITS+28S regions of rDNA. Bootstrap values of MP and ML are followed by the Bayesian posterior probabilities (Bpp) on the nodes in the topology. Asterisk (*) represents bootstrap values or Bpp less than 50% in the topology. Sample data are shown with voucher specimen number or GenBank accession number, and host plant. Sequence data determined in this study are shown in color. Teliospore shapes are shown in each clade detected, and new species are shown by asterisk (*) on clades. 0, I: Spermogonial and aecial host genus. Asterisk (*) on host plants: Spermogonial and aecial host plants. in Phylogenetic approach for identification and life cycles of Puccinia (Pucciniaceae) species on Poaceae from northeastern China
FIGURE. Phylogenetic tree of specimens on Poaceae and related host plants constructed by MP method based on ITS+28S regions of rDNA. Bootstrap values of MP and ML are followed by the Bayesian posterior probabilities (Bpp) on the nodes in the topology. Asterisk (*) represents bootstrap values or Bpp less than 50% in the topology. Sample data are shown with voucher specimen number or GenBank accession number, and host plant. Sequence data determined in this study are shown in color. Teliospore shapes are shown in each clade detected, and new species are shown by asterisk (*) on clades. 0, I: Spermogonial and aecial host genus. Asterisk (*) on host plants: Spermogonial and aecial host plants.
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