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sex reversal transcriptomic analysis in Chinese tongue sole
<p>sex reseveral transcriptome data</p>
Brownian Motion or Mean Reversion? A Parameter Based Approach to Stochastic Process Selection
<p>Data set and supporting files for article "Brownian Motion or Mean Reversion? A Parameter Based Approach to Stochastic Process Selection"</p> <ul> <li>ADF Tests log commodities SA (Excel and PDF files) – EViews outputs (18) of Augmented Dickey-Fuller tests run on all 9 Seasonally Adjusted time series (S A) with trend and intercept, and with only intercept.</li> <li>Commodities data historical x Inflation (Excel file) – Time series used in the paper in 3 versions: <ul> <li>In historical monthly averages prices US$,</li> <li>In December 2018 US$ prices (with US inflation adjustment in appropriate tab),</li> <li>In December 2018 US$ prices Seasonally Adjusted (S A) from EViews output.</li> </ul> </li> <li>commodities log SA data Ev1 (Excel file) – for the log of 9 commodities time series in Dec 2018 values, after STL decomposition in EViews: original series, seasonally adjusted, seasonal factor and trend</li> <li>commodities log SA Regressions (Excel and PDF files) - EViews outputs of OLS regression on log of seasonally adjusted times series: Dx = α + β x.</li> <li>GBMVaratAVG, GBMVaratPaths, MRMVaratAVG, MRMVaratPaths (Matlab codes) – Matlab codes for Variance ratio tests for GBM and MRM, sample paths (200) and averages of 2,500 paths.</li> <li>Series Seasonal data decomposition (PDF file) – graphical display of seasonal decomposition of log of 9 price series into: original series, trend, seasonal factor, remainder, and seasonally adjusted.</li> <li>Variance Ratio Comm SA (Excel file) - EViews outputs of variance ratio tests run of seasonal adjusted log of 9 price series in Dec 2018 values. </li> <li>ADF Tests log commodities SA (Excel and PDF files) – EViews outputs (18) of Augmented Dickey-Fuller tests run on all 9 Seasonally Adjusted time series (S A) with trend and intercept, and with only intercept.</li> <li>Commodities data historical x Inflation (Excel file) – Time series used in the paper in 3 versions: <ul> <li>In historical monthly averages prices US$,</li> <li>In December 2018 US$ prices (with US inflation adjustment in appropriate tab),</li> <li>In December 2018 US$ prices Seasonally Adjusted (S A) from EViews output.</li> </ul> </li> <li>commodities log SA data Ev1 (Excel file) – for the log of 9 commodities time series in Dec 2018 values, after STL decomposition in EViews: original series, seasonally adjusted, seasonal factor and trend</li> <li>commodities log SA Regressions (Excel and PDF files) - EViews outputs of OLS regression on log of seasonally adjusted times series: Dx = α + β x.</li> <li>GBMVaratAVG, GBMVaratPaths, MRMVaratAVG, MRMVaratPaths (Matlab codes) – Matlab codes for Variance ratio tests for GBM and MRM, sample paths (200) and averages of 2,500 paths.</li> <li>Series Seasonal data decomposition (PDF file) – graphical display of seasonal decomposition of log of 9 price series into: original series, trend, seasonal factor, remainder, and seasonally adjusted.</li> <li>Variance Ratio Comm SA (Excel file) - EViews outputs of variance ratio tests run of seasonal adjusted log of 9 price series in Dec 2018 values. </li> </ul>
Text-fig. 9. Alternating field demagnetization - sample No. 230, Section No. 2 (reversed polarity). Top left - DRM vector directions during demagnetization process, white circles - projection of vector directions to the upper hemisphere; top right - Zijderveld diagram, black circles - projection of vector directions into xy plane, white circles - projection of vector directions into xz plane; bottom left - normalised magnetization intensity values during the alternation field demagnetization. in New Updated Results Of Paleomagnetic Dating Of Cave Deposits Exposed In Za Hájovnou Cave, Javoříčko Karst
Text-fig. 9. Alternating field demagnetization - sample No. 230, Section No. 2 (reversed polarity). Top left - DRM vector directions during demagnetization process, white circles - projection of vector directions to the upper hemisphere; top right - Zijderveld diagram, black circles - projection of vector directions into xy plane, white circles - projection of vector directions into xz plane; bottom left - normalised magnetization intensity values during the alternation field demagnetization.
Nitrate trend reversal in Dutch dual-permeability chalk springs, evaluated by tritium-based groundwater travel time distributions [Data set]
<p>Data set covering measured nitrate and sulfate data of 90 springs, the tritium and nitrate input data for the convolution models and the age distributions metrics for the base case model and the stringent denitrification model, which were described in the publication in Science of the Total Environment (2024); doi: <em>10.1016/j.scitotenv.2024.175250</em></p>
Spontaneous reversal of spin chirality and competing phases in the topological magnet EuAl4 - Data set
Open the record for dataset details and reuse information.
Data from: Sex ratio and density affect sexual selection in a sex-role reversed fish
Understanding how demographic processes influence mating systems is important to decode ecological influences on sexual selection in nature. We manipulated sex ratio and density in experimental populations of the sex-role reversed pipefish Syngnathus typhle. We quantified sexual selection using the Bateman gradient (ß′ss), the opportunity for selection (I), and sexual selection (Is), and the maximum standardized sexual selection differential (s′max). We also measured selection on body length using standardized selection differentials (s′) and mating differentials (m′), and tested whether the observed I and Is differ from values obtained by simulating random mating. We found that I, Is, and s′max, but not ß′ss, were higher for females under female- than male-bias and the opposite for males, but density did not affect these measures. However, higher density decreased sexual selection (m′ but not s′) on female length, but selection on body length was not affected by sex ratio. Finally, Is but not I was higher than expected from random mating, and only for females under female bias. This study demonstrates that both sex ratio and density affect sexual selection and that disentangling interrelated demographic processes is essential to a more complete understanding of mating behavior and the evolution of mating systems.
Data from: The behavioural consequences of sex reversal in dragons
Sex differences in morphology, physiology, and behaviour are caused by sex-linked genes, as well as by circulating sex-steroid levels. Thus, a shift from genotypic to environmental sex determination may create an organism that exhibits a mixture of male-like and female-like traits. We studied a lizard species (Central Bearded Dragon, Pogona vitticeps), in which the high-temperature incubation of eggs transforms genetically male individuals into functional females. Although they are reproductively female, sex-reversed dragons (individuals with ZZ genotype reversed to female phenotype) resemble genetic males rather than females in morphology (relative tail length), general behaviour (boldness and activity level), and thermoregulatory tactics. Indeed, sex-reversed 'females' are more male-like in some behavioural traits than are genetic males. This novel phenotype may impose strong selection on the frequency of sex reversal within natural populations, facilitating rapid shifts in sex-determining systems. A single period of high incubation temperatures (generating thermally induced sex reversal) can produce functionally female individuals with male-like (or novel) traits that enhance individual fitness, allowing the new temperature-dependent sex-determining system to rapidly replace the previous genetically based one.
Data from: Increased root herbivory under elevated atmospheric carbon dioxide concentrations is reversed by silicon-based plant defences
Predicted increases in atmospheric concentrations of CO2 may alter the susceptibility of many plants to insect herbivores due to changes in plant nutrition and defences. Silicon plays a critical role in plant defence against herbivores, so increasing such silicon-based defences in plants may help remediate situations where plants become more susceptible to herbivores. Sugarcane (Saccharum spp. hybrid) were subjected to fully factorial treatment combinations of ambient (aCO2) or elevated (eCO2) atmospheric CO2 concentrations; ambient silicon or silicon supplementation; insect-free or subject to root herbivory by greyback canegrub (Dermolepida albohirtum). A glasshouse study was used to determine how these factors affected rates of photosynthesis, growth, chemistry (concentrations of silicon, carbon, nitrogen and non-structural carbohydrates). Changes in canegrub mass were determined in the glasshouse pot study, together with more detailed assessment of how eCO2 and silicon supplementation affected performance and feeding behaviour (relative growth rate and relative consumption) in a 24-hour feeding efficiency assay. eCO2 and silicon supplementation increased rates of photosynthesis (+32% and 14%, respectively) sugarcane biomass (+45% and 69%, respectively). Silicon supplementation increased silicon concentrations in both leaves and roots by 54% and 75%, respectively. eCO2 caused root C:N to increase by 12%. Canegrub performance and consumption increased under eCO2; relative growth rate (RGR) increased by 116% and consumed 57% more root material (suggestive of compensatory feeding). Silicon application reversed these effects, with large decreases in mass change, RGR and root consumption (65% less root mass consumed). Synthesis and applications. Our results suggest future atmospheric carbon dioxide concentrations could lead to increased crop damage by a below-ground herbivore. Increasing bioavailable silicon in soil stimulated silicon-based defences which dramatically decreased herbivory and herbivore performance. Our findings suggest future pest management strategies could benefit from characterising deficiencies in bioavailable silicon in agricultural soils and targeted application of silicon fertilisers. Moreover, future breeding programmes should exploit variation in silicon uptake between cultivars to enhance silicon uptake in new crop varieties. Silicon-based plant defence proved to be highly beneficial for remediating the negative effects of atmospheric change on sugarcane susceptibility to herbivory and could be applicable in other crops.
Data from: Sexual selection on female ornaments in the sex-role-reversed Gulf pipefish (Syngnathus scovelli)
Understanding how selection acts on traits individually and in combination is an important step in deciphering the mechanisms driving evolutionary change, but for most species, and especially those in which sexual selection acts more strongly on females than on males, we have no estimates of selection coefficients pertaining to the multivariate sexually selected phenotype. Here, we use a laboratory-based mesocosm experiment to quantify pre- and post-mating selection on female secondary sexual traits in the Gulf pipefish (Syngnathus scovelli), a sexually dimorphic, sex-role-reversed species in which ornamented females compete for access to choosy males. We calculate selection differentials and gradients on female traits, including ornament area, ornament number and body size for three episodes of selection related to female reproductive success (number of mates, number of eggs transferred and number of surviving embryos). Selection is strong on both ornament area and ornament size, and the majority of selection occurs during the premating episode of selection. Interestingly, selection on female body size, which has been detected in previous studies of Gulf pipefish, appears to be indirect, as evidenced by a multivariate analysis of selection gradients. Our results show that sexual selection favours either many bands or larger bands in female Gulf pipefish.
Data from: Reversion of antibiotic resistance in Mycobacterium tuberculosis by spiroisoxazoline SMARt-420
Antibiotic resistance is one of the biggest threats to human health globally. Alarmingly, multidrug-resistant and extensively drug-resistant Mycobacterium tuberculosis have now spread worldwide. Some key antituberculosis antibiotics are prodrugs, for which resistance mechanisms are mainly driven by mutations in the bacterial enzymatic pathway required for their bioactivation. We have developed drug-like molecules that activate a cryptic alternative bioactivation pathway of ethionamide in M. tuberculosis, circumventing the classic activation pathway in which resistance mutations have now been observed. The first-of-its-kind molecule, named SMARt-420 (Small Molecule Aborting Resistance), not only fully reverses ethionamide-acquired resistance and clears ethionamide-resistant infection in mice, it also increases the basal sensitivity of bacteria to ethionamide.
Supplementary material 1 from: Mantelatto FL, Pileggi LG, Pantaleão JAF, Magalhães C, Villalobos JL, Alvarez F (2021) Multigene phylogeny and taxonomic revision of American shrimps of the genus Cryphiops Dana, 1852 (Decapoda, Palaemonidae) implies a proposal for reversal of precedence with Macrobrachium Spence Bate, 1868. ZooKeys 1047: 155-198. https://doi.org/10.3897/zookeys.1047.66933
Table S1
Figure 1 from: Mantelatto FL, Pileggi LG, Pantaleão JAF, Magalhães C, Villalobos JL, Alvarez F (2021) Multigene phylogeny and taxonomic revision of American shrimps of the genus Cryphiops Dana, 1852 (Decapoda, Palaemonidae) implies a proposal for reversal of precedence with Macrobrachium Spence Bate, 1868. ZooKeys 1047: 155-198. https://doi.org/10.3897/zookeys.1047.66933
Figure 1 Concatenated phylogenetic tree of selected species of Macrobrachium representing wide geographical distribution of the group, based on the method of maximum likelihood of the 16S rDNA, COI mtDNA, 18S nDNA and H3 nDNA genes. Numbers on nodes refer to significance values of 1000 bootstrap replicates; values ≤ 50% are not shown. ARG: Argentina; BR: Brazil; CH: Chile; CR: Costa Rica; JAP: Japan; MX: México; NIG: Nigeria; PN: Panamá; VZ: Venezuela. ALD: Abbreviated larval development. ELD: Extended larval development. Blue: species from Indo-Pacific. Red: species from Africa. Green: former Cryphiops species.
Data from: A transient ischemic environment induces reversible compaction of chromatin
Background: Cells detect and adapt to hypoxic and nutritional stress through immediate transcriptional, translational and metabolic responses. The environmental effects of ischemia on chromatin nanostructure were investigated using single molecule localization microscopy of DNA binding dyes and of acetylated histones, by the sensitivity of chromatin to digestion with DNAseI, and by fluorescence recovery after photobleaching (FRAP) of core and linker histones. Results: Short-term oxygen and nutrient deprivation of the cardiomyocyte cell line HL-1 induces a previously undescribed chromatin architecture, consisting of large, chromatin-sparse voids interspersed between DNA-dense hollow helicoid structures 40–700 nm in dimension. The chromatin compaction is reversible, and upon restitution of normoxia and nutrients, chromatin transiently adopts a more open structure than in untreated cells. The compacted state of chromatin reduces transcription, while the open chromatin structure induced upon recovery provokes a transitory increase in transcription. Digestion of chromatin with DNAseI confirms that oxygen and nutrient deprivation induces compaction of chromatin. Chromatin compaction is associated with depletion of ATP and redistribution of the polyamine pool into the nucleus. FRAP demonstrates that core histones are not displaced from compacted chromatin; however, the mobility of linker histone H1 is considerably reduced, to an extent that far exceeds the difference in histone H1 mobility between heterochromatin and euchromatin. Conclusions: These studies exemplify the dynamic capacity of chromatin architecture to physically respond to environmental conditions, directly link cellular energy status to chromatin compaction and provide insight into the effect ischemia has on the nuclear architecture of cells.
Figure 1 in Prolonged parental behaviour by males of Limnonectes palavanensis (Boulenger 1894), a frog with possible sex-role reversal
Figure 1. Male of Limnonectes palavanensis attending a clutch of eggs.
Figure 5. A in Prolonged parental behaviour by males of Limnonectes palavanensis (Boulenger 1894), a frog with possible sex-role reversal
Figure 5. A male (striped morph) Limnonectes palavanensis transporting tadpoles on his back.
Figure 2 in Nest-site microhabitat association of red-billed leiothrix in subtropical fragmented forest in central China: evidence for a reverse edge effect on nest predation risk?
Figure 2. Nest sites of red-billed leiothrix (a) in the forest and (b) in the scrub-grassland.
Text-fig. 5. Eomys schluneggeri n. sp. from Rigi 2. a) P4 – M3; P4 sin.: Rgi 31, M1/2 sin.: DKRgi1, M1/2 dext. (reversed): DKRgi2, M3 dext. (reversed): DKRgi3. b) P – M sin.; P sin.: DKRgi4, M sin.: DKRgi5, M sin. Rgi 23, M sin.: DKRgi6. All figures at 4 3 4 1 2 3 magnification 35×. in Eomys Helveticus N. Sp. And Eomys Schluneggeri N. Sp., Two New Small Eomyids Of The Chattian (Mp 25/Mp 26) Subalpine Lower Freshwater Molasse Of Switzerland
Text-fig. 5. Eomys schluneggeri n. sp. from Rigi 2. a) P4 – M3; P4 sin.: Rgi 31, M1/2 sin.: DKRgi1, M1/2 dext. (reversed): DKRgi2, M3 dext. (reversed): DKRgi3. b) P – M sin.; P sin.: DKRgi4, M sin.: DKRgi5, M sin. Rgi 23, M sin.: DKRgi6. All figures at 4 3 4 1 2 3 magnification 35×.
Input data and analysis codes for "Reversal of trends in global fine particulate matter air pollution"
<p>This dataset contains Input data and analysis codes used for the following article:</p> <p>Li, C., A. van Donkelaar, M. S. Hammer, E. E. McDuffie, R. T. Burnett, J. V. Spadaro, D. Chatterjee, A. J. Cohen, J. S. Apte, V. A. Southerland, S. C. Anenberg, M. Brauer, & R. V. Martin, Reversal of trends in global fine particulate matter air pollution, submitted, 2023.</p> <p> </p> <p><strong>Input Data</strong></p> <p>Baseline mortality data (204 countries and territories, 17 age groups, 6 diseases, 22 years)</p> <p>Concentration-response functions (GEMM and MRBRT)</p> <p>PM<sub>2.5</sub> exposure for 204 territories and 22 years</p> <p>Age-specific population for 204 territories and 22 years</p> <p> </p> <p><strong>Derived Data</strong></p> <p>Age- and disease-specific PM<sub>2.5</sub>-attributable Mortality estimates for 204 territories and 22 years.</p> <p>Sensitivity of PM<sub>2.5</sub>-attributable Mortality to marginal PM<sub>2.5</sub> reduction for 204 territories and 22 years.</p> <p>Attributable of changes in PM<sub>2.5</sub>-attributable Mortality (and its sensitivity to marginal PM<sub>2.5</sub> reduction) to four driving factors.</p> <p> </p> <p><strong>Code</strong></p> <p>Necessary python scripts to verify and replicate analysis results in the manuscript.</p>
Datasets accompanying "Ultrafast reversible self-assembly of living tangled matter"
<p>Datasets showing the structure and dynamics of tangling worms</p>
Tetrel-Centered Exchange Cascades to Decouple Inhibition and Induction of Thiol-Mediated Uptake: Introducing Cell-Penetrating Thiolactones, Focus on Reversible Michael Acceptor Dimers
<p>Original data</p>
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Allen Brain Atlas
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