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LibOCS project promotional video
<p>LibOCS project promotional video. </p> <p>Project entitled: “University libraries strengthening the academia-society connection through citizen science in the Baltics” under the Erasmus+ Programme, Key Action 2: Partnerships for Cooperation.</p> <p>PROJECT NUMBER 2021-1-EE01-KA220-HED-000031125<br> AGREEMENT NUMBER – 2021-KA220-HED-01</p>
YB1 dephosphorylation attenuates atherosclerosis by promoting CCL2 mRNA decay
<p> Y-box binding protein 1 (YB1) is an RNA binding protein (RBP) that has been reported to play important roles in inflammation and atherosclerotic plaque formation. To explore the molecular mechanism of phosphorylated YB1 (pYB1) in atherosclerosis <em>in vitro</em>, we constructed YB1 phosphorylation site (Ser-100) mutant stable smooth muscle cell line (3ds-V5) and performed RNA profile screening through RNA-seq. We found inflammatory pathways and CCL2 was significantly decreased in the 3dS-V5 YB1 mutant compared with the control group (YB1-V5).</p>
Senescent preosteoclast secretome promotes metabolic syndrome-associated osteoarthritis through COX2-PGE2
<p><span>Metabolic syndrome–associated osteoarthritis (MetS-OA)</span><span> is a distinct osteoarthritis phenotype defined by the coexistence of MetS or its individual components. Despite the high prevalence of MetS-OA, its pathogenic mechanisms are unclear. Here, we report that humans and mice with MetS are more likely to develop osteoarthritis-related subchondral bone alterations than those without MetS. </span><span>MetS-OA mice exhibited</span><span> a rapid</span> <span>increase in joint </span><span>subchondral bone plate and trabecular thickness </span><span>before articular cartilage degeneration. Subchondral preosteoclasts undergo senescence </span><span>at the pre- or early</span><span>-osteoarthritis stage</span><span> and </span><span>acquire a unique secretome to</span><span> stimulate osteoblast differentiation and inhibit osteoclast differentiation. Antagonizing preosteoclast senescence markedly mitigates pathological subchondral alterations and osteoarthritis progression in MetS-OA mice. </span><span>At the molecular level,</span> <span>preosteoclast secretome activates </span><span>COX2-PGE2, resulting in stimulated differentiation of osteoblast progenitors for subchondral bone formation. Administration of a selective COX2 inhibitor attenuated subchondral bone alteration and osteoarthritis progression in MetS-OA mice. Longitudinal analyses of the human Osteoarthritis Initiative (OAI) cohort dataset also revealed that </span><span>COX2 inhibitor use, relative to non-selective nonsteroidal anti-inflammatory drug use</span><span>, is associated with less</span><span> progression of </span><span>osteoarthritis and subchondral bone marrow lesion worsening in participants with MetS-OA. Our findings suggest a central role of a senescent preosteoclast secretome-COX2/PGE2 axis in the pathogenesis of MetS-OA.</span></p>
Unique structure and positive selection promote the rapid divergence of Drosophila Y chromosomes
Y chromosomes across diverse species convergently evolve a gene-poor, heterochromatic organization enriched for duplicated genes, LTR retrotransposons, and satellite DNA. Sexual antagonism and a loss of recombination play major roles in the degeneration of young Y chromosomes. However, the processes shaping the evolution of mature, already degenerated Y chromosomes are less well-understood. Because Y chromosomes evolve rapidly, comparisons between closely related species are particularly useful. We generated de novo long read assemblies complemented with cytological validation to reveal Y chromosome organization in three closely related species of the Drosophila simulans complex, which diverged only 250,000 years ago and share >98% sequence identity. We find these Y chromosomes are divergent in their organization and repetitive DNA composition and discover new Y-linked gene families whose evolution is driven by both positive selection and gene conversion. These Y chromosomes are also enriched for large deletions, suggesting that the repair of double-strand breaks on Y chromosomes may be biased toward microhomology-mediated end joining over canonical non-homologous end-joining. We propose that this repair mechanism contributes to the convergent evolution of Y chromosome organization across organisms.
Matrix N, TEs vs promoters, 100kb-wide windows, hg19
<p>Regulatory susceptibility matrix N, with rows as hg19 protein coding genes and columns as TE subfamilies. A TE is counted if it is found within 100kb of a gene promoter, strictly out of any promoter and any exon belonging to that gene.</p>
Wallacean and Melanesian islands promote higher rates of diversification within the global passerine radiation Corvides: Supplementary information
<p class="MsoNormal"><span>The complex island archipelagoes of Wallacea and Melanesia have provided empirical data behind integral theories in evolutionary biology, including allopatric speciation and island biogeography. Yet, questions regarding the relative impact of the layered biogeographic barriers, such as deep-water trenches and isolated island systems, on faunal diversification remain underexplored. One such barrier is Wallace's Line, a significant biogeographic boundary that largely separates Australian and Asian biodiversity. To assess the relative roles of biogeographic barriers—specifically isolated island systems and Wallace's Line—we investigated the tempo and mode of diversification in a diverse avian radiation, Corvides (Crows and Jays, Birds-of-paradise, Vangas, and allies). We combined a genus-level dataset of thousands of ultraconserved elements (UCEs) and a species-level, 12-gene Sanger sequence matrix to produce a well-resolved supermatrix tree that we leveraged to explore the group's historical biogeography and effects of biogeographic barriers on their macroevolutionary dynamics. The tree is well-resolved and differs substantially from what has been used extensively for past comparative analyses within this group. We confirmed that Corvides, and its major constituent clades, arose in Australia and a burst of dispersal west across Wallace's Line occurred after the uplift of Wallacea during the mid-Miocene. We found that dispersal across this biogeographic barrier were generally rare, though westward dispersals were two times more frequent than eastward dispersals. Wallacea's central position between Sundaland and Sahul no doubt acted as a bridge for island-hopping dispersal out of Australia, across Wallace's Line, to colonize the rest of Earth. In addition, we found that the complex island archipelagos east of Wallace's Line harbor the highest rates of net diversification and are a substantial source of colonists to continental systems on both sides of this biogeographic barrier. Our results support emerging evidence that island systems, particularly the geologically complex archipelagoes of the Indo-pacific, are drivers of species diversification.<br></span></p>
Rapid increase in transferrin receptor recycling promotes adhesion during T cell activation
<p>This Dataset contains primary data used for the publication "Rapid increase in transferrin receptor recycling promotes adhesion during T cell activation" accepted for publication in BMC Biology on 15. July 2022</p> <p><strong>Abstract:</strong></p> <p>Background<br> T cell activation leads to increased expression of the receptor for the iron transporter transferrin (TfR) to provide iron required for the cell differentiation and clonal expansion that takes place during the days after encounter with a cognate antigen. However, T cells mobilise TfR to their surface within minutes after activation, although the reason and mechanism driving this process remain unclear.</p> <p>Results<br> Here we show that T cells transiently increase endocytic uptake and recycling of TfR upon activation, thereby boosting their capacity to import iron. We demonstrate that increased TfR recycling is powered by a fast endocytic sorting pathway relying on the membrane proteins flotillins, Rab5 and Rab11a-positive endosomes. Our data further reveal that iron import is required for a non-canonical signalling pathway involving the kinases Zap70 and PAK, which controls adhesion of the integrin LFA-1 and eventually leads to conjugation with antigen-presenting cells.</p> <p>Conclusions<br> Altogether, our data suggest that T cells boost their iron importing capacity immediately upon activation to promote adhesion to antigen-presenting cells.</p> <p> </p> <p>Data are organised in compressed (.zip) folders entitled as the corresponding Figures in the publication.</p> <p>Programs we recommend to view the files are:<br> .fcs files: FlowJo software v10 (Tree Star, Ashland, OR, USA)<br> .lsm and .czi files: ZEN 2012 SP1 and higher (Carl Zeiss, Jena, Germany)<br> .lif files: LAS X v3 (Leica Microsystems, Wetzlar, Germany)<br> .pzfx files: Prism v7 software (GraphPad, San Diego, CA, USA)</p>
RBBP4 regulates the expression of Mre11-Rad50-NBS1(MRN)complex and promotes DNA double-strand breaks repair to mediate glioblastoma Chemoradiotherapy resistance
<p>Article <a>related</a> SUPPLEMENTARY data.</p> <p> </p>
Biochar and nitrogen fertilizer promote rice yield by altering soil enzyme activity and microbial community structure
<p><span>Biochar can significantly change soil properties and improve soil quality.</span> <span>However, the effects of long-term combined application of biochar (B) and nitrogen (N) fertilizer on relationships between soil enzyme activity, microbial community structure and crop yield are still obscure. We characterized these relationships in a long-term (8 years) field experiment with rice, two biochar rates of 0 and 13.5 t ha<sup>-1</sup> year<sup>-1</sup> (B0 and B) and two N fertilizer rates of 0 and 300 kg N ha<sup>-1</sup> year<sup>-1</sup> (N0 and N).</span><span> The repeated, long-term combined applications of biochar and N fertilizer significantly increased microbial biomass carbon and nitrogen (MBC and MBN), but biochar decreased the abundance of total bacteria, fungi, actinomycetes, Gram-positive and Gram-negative bacteria as well as the amount of total phospholipid fatty acids. </span><span>The activity of leucine aminopeptidase (LAP) </span><span>decreased significantly in the biochar-amended and N fertilized treatment, but</span><span> the LAP activity either remained unchanged or increased with biochar amendment at N0. The relative abundance of bacterial phylum <em>Chloroflexi</em> was increased in the combined biochar and N fertilizer treatment. The changes in soil organic matter and the activity of α-1,4-xylosidase were the major properties influencing soil bacterial community composition, whereas the structure of fungal community was governed by MBC, MBN and LAP activity. In addition, long-term biochar and N fertilizer applied together significantly increased rice yield (more than biochar and nitrogen fertilizer applied alone). Yield</span> <span>was significantly positively correlated with LAP activity, but significantly negatively correlated with the relative abundance of Chloroflexi. In conclusion, long-term biochar and nitrogen fertilizer applications increased rice yield, which was associated with altered soil microbial community and enhanced activity of some enzymes.</span></p>
Data from: Ecosystem multifunctionality is promoted by organic farming and hedgerows at the local scale but not at the landscape scale
<p><span>This dataset gathers information used for the paper Couthouis et al. "Ecosystem multifunctionality is promoted by organic farming and hedgerows at the local scale but not at the landscape scale", part of the BIOMHE project (2019-2022) funded by the Fondation de France. It contains data about (i) species richness and abundances used for calculating ecological performance, (ii) crop yield used for calculating agronomic performance, (iii) labour and semi-net margin used for calculating socio-economic performance. Combined, these information allows for the calculation of ecosystem multifunctionaliy indices.</span></p>
Linked selection, differential introgression and recombination rate variation promote heterogeneous divergence in a pair of yellow croakers
<p><span>Understanding the mechanisms underlying heterogeneous genomic divergence is of particular interest in evolutionary biology. Highly differentiated genomic regions, known as genomic islands, often evolve between diverging lineages. These genomic islands may be related to selection promoting adaptation or reproductive isolation. Based on whole genome assembly and genome-wide RAD sequencing in a pair of yellow croakers (genus: <em>Larimichthys</em>), we investigated the evolutionary processes shaping genomic landscapes of divergence. Demographic modelling indicated that the two species diverged following a secondary contact scenario, where differential introgression and linked selection were suggested to be involved in heterogeneous genomic divergence. We identified reduced recombination rate in genomic islands and a relatively good conservation of both genetic diversity and recombination landscapes between species, which highlight the roles of linked selection and recombination rate variation in promoting heterogeneous divergence in the common ancestral lineage of the two species. In addition, we found a positive correlation between differentiation (F<sub>ST</sub>) and absolute sequence divergence (<em>D</em><sub>xy</sub>), and elevated </span><span><span><em>D</em><sub>xy</sub></span> in genomic islands, which were different from the patterns under linked selection. Restricted gene flow in highly differentiated regions has likely remodeled the landscape of heterogeneous genomic divergence. Moreover, genomic islands showed little evidence of overlapping within and between species, implying that high gene flow and divergent selection when colonizing new habitats have reshaped the patterns of intraspecific divergence. This study highlights that highly differentiated genomic regions can also be from linked selection and variation of recombination rate, and thus are not necessarily related to speciation islands or local adaptation. </span></p>
Supplementary Data for "Adoption of Transparency and Openness Promotion (TOP) guidelines across journals"
<p>Supplementary data for: https://zenodo.org/record/7129250</p>
Data set associated to simulations performed within the manuscript "Endosperm turgor pressure both promotes and restricts seed growth and size".
<p>This dataset contains the following files</p> <ul> <li>2F4-Col0-iku2-Fig.3f and Supp. Fig.9 <ul> <li>Slices of seeds from 3 to 9 Days post-anthesis (DPA) stained with calcofluor (channel 1) and whose unesterified pectins are labelled with the 2F4 antibody (channel 2)</li> <li>2 genotypes: Col0 and iku2</li> <li>3 independent experiments</li> </ul> </li> <li>JIM5-Col0-ap2-Fig. 4d and Supp Fig. 12b <ul> <li>Slices of seeds from 3 to 9 Days post-anthesis (DPA) stained with calcofluor (channel 1) and whose demethylesterified pectins are labelled with the JIM5 antibody (channel 2)</li> <li>2 genotypes: Col0 and ap2-6</li> <li>2 independent experiments</li> </ul> </li> <li>JIM5-Col0-iku2-Fig. 3h and Supp Fig. 10 <ul> <li>Slices of seeds from 3 to 9 Days post-anthesis (DPA) stained with calcofluor (channel 1) and whose demethylesterified pectins are labelled with the JIM5 antibody (channel 2)</li> <li>2 genotypes: Col0 and iku2</li> <li>3 independent experiments</li> </ul> </li> <li>LM19-Col0-ap2-Fig. 4b and Supp Fig. 12a <ul> <li>Slices of seeds from 3 to 9 Days post-anthesis (DPA) stained with calcofluor (channel 1) and whose demethylesterified pectins are labelled with the LM19 antibody (channel 2)</li> <li>2 genotypes: Col0 and ap2-6</li> <li>2 independent experiments</li> </ul> </li> <li>LM19-Col0-iku2-Fig. 3d and Supp Fig. 8 <ul> <li>Slices of seeds from 3 to 9 Days post-anthesis (DPA) stained with calcofluor (channel 1) and whose demethylesterified pectins are labelled with the LM19 antibody (channel 2)</li> <li>2 genotypes: Col0 and iku2</li> <li>3 independent experiments</li> </ul> </li> <li>pELA1-VENUS-Col0-iku2-Fig3c <ul> <li>Confocal stack of developing seeds expressing <em>pELA1::3X-VENUS-N7</em></li> <li>2 genotypes: Col0 and iku2</li> <li>1 independent experiments</li> </ul> </li> <li>pELA1-VENUS-Col0-iku2-Supp Fig. 6 <ul> <li>Confocal stack of developing seeds expressing <em>pELA1::3X-VENUS-N7</em></li> <li>2 genotypes: Col0 and iku2</li> <li>1 independent experiments</li> </ul> </li> <li>Seed-size-ap26-iku2-Fig.5e-Supp-Fig. 12c <ul> <li>Pictures of dry seeds</li> <li>4 genotypes: Col0, iku2, ap2-6 and iku2 ap2-6</li> <li>2 independent experiments</li> </ul> </li> <li>Wall-rupture-Col0-iku2-Fig3k <ul> <li>Confocal stack of developing seeds expressing <em>LTi6b-GFP </em>(First channel) and dyed with FM4-64 (second channel) imaged after a 40 µm indentation to break testa wall</li> <li>2 genotypes: Col0 and iku2</li> <li>2 replicates</li> </ul> </li> <li>Wall-rupture-Col0-iku2-Supp Fig. 11 <ul> <li>Confocal stack of developing seeds expressing <em>LTi6b-GFP </em>(First channel) and dyed with FM4-64 (second channel) imaged after a 30 µm or a 50µm indentation to break testa wall</li> <li>2 genotypes: Col0 and iku2</li> <li>2 replicates</li> </ul> </li> <li>181211-Col0-iku2-Timelapse-Seed-Size <ul> <li>Pictures of developing seeds from 0 (ovules) days post-anthesis (DPA) to 10 DPA</li> <li>2 genotypes: Col0 and iku2</li> </ul> </li> <li>190125-Col0-iku2-Timelapse-Seed-Size <ul> <li>Pictures of developing seeds from 0 (ovules) days post-anthesis (DPA) to 10 DPA (no 9DPA)</li> <li>2 genotypes: Col0 and iku2</li> </ul> </li> <li>190523-Col0-ede13-Timelapse-Seed-Size <ul> <li>Pictures of developing seeds from 0 (ovules) days post-anthesis (DPA) to 9DPA</li> <li>2 genotypes: Col0 and <em>ede1-3</em></li> </ul> </li> <li>200724-Col0-iku2-Timelapse-Seed-Size <ul> <li>Pictures of developing seeds from 0 (ovules) days post-anthesis (DPA) to 10DPA</li> <li>2 genotypes: Col0 and <em>iku2</em></li> </ul> </li> <li>200921-Col0-iku2-Timelapse-Seed-Size <ul> <li>Pictures of developing seeds from 0 (ovules) days post-anthesis (DPA) to 10DPA</li> <li>2 genotypes: Col0 and <em>iku2</em></li> </ul> </li> <li>201023-Col0-ede13-Timelapse-Seed-Size <ul> <li>Pictures of developing seeds from 0 (ovules) days post-anthesis (DPA) to 10DPA</li> <li>2 genotypes: Col0 and <em>ede1-3</em></li> </ul> </li> <li>210519-Col0-Timelapse-invitro-Sorbitol <ul> <li>Picture of developing WT seeds (Col-0) at 3, 6, 9 and 12DPA</li> <li>Fruits were grown <em>in planta </em>(uncut) or <em>in vitro</em> from 3DPA onwards</li> <li>Fruits growing <em>in vitro</em> were cultivated in ½ MS + 1% Sucrose + 0.1X PPM (Plant Preservative Medium) + 1X Gamborg Vitamins + 0 to 200mM Sorbitol</li> <li>Note that the file containing the pictures from this experiment was too large for Zenodo, the pictures were thus transformed into 8 bit black/white pictures, a 2x2 binning was applied, before a saving into tiff. The original pictures are available at: <a href="http://flower.ens-lyon.fr/">http://flower.ens-lyon.fr/</a></li> </ul> </li> <li>210709-Col0-Timelapse-invitro-Sorbitol <ul> <li>Picture of developing WT seeds (Col-0) at 3, 6, 9 and 12DPA</li> <li>Fruits were grown <em>in planta </em>(uncut) or <em>in vitro</em> from 3DPA onwards</li> <li>Fruits growing <em>in vitro</em> were cultivated in ½ MS + 1% Sucrose + 0.1X PPM (Plant Preservative Medium) + 1X Gamborg Vitamins + 0 to 200mM Sorbitol</li> <li>Note that the file containing the pictures from this experiment was too large for Zenodo, the pictures were thus transformed into 8 bit black/white pictures, a 2x2 binning was applied, before a saving into tiff. The original pictures are available at: <a href="http://flower.ens-lyon.fr/">http://flower.ens-lyon.fr/</a></li> </ul> </li> <li>data.zip file: <ul> <li>Measurements of seed growth tracking experiments performed on WT plants as well as iku2 and ede1-3 mutants.</li> <li>Measurements of endosperm pressure performed on WT plants and iku2 mutants.</li> <li>Simulation results from a parameter space exploration of the system of ODEs we studied within the scope of the work described in the manuscript.</li> </ul> </li> </ul>
Scrub encroachment promotes biodiversity in temperate European wetlands under eutrophic conditions
<p>Wetlands are important habitats, often threatened by drainage, eutrophication and suppression of grazing. In many countries, considerable resources are spent combatting scrub encroachment. Here, we hypothesize that encroachment may benefit biodiversity – especially under eutrophic conditions where asymmetric competition among plants compromises conservation targets. We studied the effects of scrub cover, nutrient levels and soil moisture on richness of vascular plants, bryophytes, soil fungi and microbes in open and overgrown wetlands. We also tested the effect of encroachment, eutrophication and soil moisture on indicators of conservation value (red-listed species, indicator species and uniqueness). Plant and bryophyte species richness peaked at low soil fertility, whereas soil fertility promoted soil microbes. Soil fungi responded negatively to increasing soil moisture. Lidar-derived variables reflecting degree of scrub cover had predominantly positive effects on species richness measures. Conservation value indicators had a negative relationship to soil fertility and a positive to encroachment. For plant indicator species, the negative effect of high nutrient levels was offset by encroachment, supporting our hypothesis of competitive release under shade. The positive effect of soil moisture on indicator species was strong in open habitats only. Nutrient poor mires and meadows host many rare species and require conservation management by grazing and natural hydrology. On former agricultural lands, where restoration of infertile conditions is unfeasible, we recommend rewilding with opportunities for encroachment towards semi-open willow scrub and swamp forest, with the prospect of high species richness in bryophytes, fungi and soil microbes and competitive release in the herb layer.</p>
Using nudges to promote clinical decision making of healthcare professionals: A scoping review
<p>Nudging has been discussed in the context of policy and public health, but not so much within healthcare and how it can be applied to change the behavior of healthcare professionals (HCPs). This scoping review aimed to assess the empirical evidence on how nudging techniques can be used to affect the behavior of HCPs in clinical settings.</p> <p>A systematic database search was conducted for the period January 2010-December 2020 using the PRISMA extension for Scoping Review checklist. Two reviewers independently screened each article for inclusion. Included articles were reviewed to extract key information about each intervention, including purpose, target behavior, measured outcomes, key findings, nudging strategies used, and their theoretical underpinnings. Two independent dimensions were used to describe nudging strategies according to action and timing where each of the identified nudging strategies and objectives was characterized as active, passive, synchronous, or asynchronous. </p> <p>Of the included 51 articles, 40 reported statistically positive results, six reported no success and two reported mixed results. Thirteen different nudging strategies were identified aimed at modifying four types of HPCs behavior:prescriptions/orders, procedure, hand hygiene, and vaccination. The most common nudging strategy used involved default/pre-order nudges, followed by alerts/reminders and active choice. Both passive and active nudges showed positive results, highlighting the importance of long-term studies that evaluate if the desired outcome is maintained. Careful ethical consideration should however be given to passive strategies where the user might not be aware of the nudge. </p>
INHIBITION OF NITRIC OXIDE SYNTHESIS PROMOTES INCREASED MORTALITY DESPITE REDUCTION OF PARASITEMIA IN Plasmodium berghei-INFECTED MICE
<p><strong>Backgrounds:</strong> Nitric oxide (NO) is an important mediator molecule in inflammatory processes, but its role in the pathophysiology of malaria is still uncertain.</p> <p><strong>Methods:</strong> To investigate the NO synthesis inhibition on the oxidative changes induced by <em>Plasmodium berghei </em>infection in mice, malaria was induced in 150 animals, of which 75 animals were treated with NO inhibitor L-NAME; the remaining are sham controls. All animals underwent euthanasia after 1, 5, 10, 15 or 20 days after the infection for the collection of lungs, brain, and blood. Parasitemia was determined and the survival of the animals evaluated. Tissue samples were assayed for nitrites and nitrates (NN), thiobarbituric acid reactive substances (TBARS), and total Trolox equivalent antioxidant capacity (TEAC). A histopathological study was performed.</p> <p><strong>Results:</strong> Mortality rates in the L-NAME were always higher in relation to the controls. In brains, NN was lower in groups L-NAME. Parasitemia and its progression rate were greater in control groups. From the 5<sup>th</sup> day of infection, mice treated with L-NAME showed cerebral edema and interstitial pneumonia of greater intensity than controls.</p> <p><strong>Conclusions:</strong> Anti-inflammatory and hemodynamic effects of NO surpasses its pro-oxidant role in murine malaria.</p> <p><strong>Backgrounds:</strong> Nitric oxide (NO) is an important mediator molecule in inflammatory processes, but its role in the pathophysiology of malaria is still uncertain.</p> <p><strong>Methods:</strong> To investigate the NO synthesis inhibition on the oxidative changes induced by <em>Plasmodium berghei </em>infection in mice, malaria was induced in 150 animals, of which 75 animals were treated with NO inhibitor L-NAME; the remaining are sham controls. All animals underwent euthanasia after 1, 5, 10, 15 or 20 days after the infection for the collection of lungs, brain, and blood. Parasitemia was determined and the survival of the animals evaluated. Tissue samples were assayed for nitrites and nitrates (NN), thiobarbituric acid reactive substances (TBARS), and total Trolox equivalent antioxidant capacity (TEAC). A histopathological study was performed.</p> <p><strong>Results:</strong> Mortality rates in the L-NAME were always higher in relation to the controls. In brains, NN was lower in groups L-NAME. Parasitemia and its progression rate were greater in control groups. From the 5<sup>th</sup> day of infection, mice treated with L-NAME showed cerebral edema and interstitial pneumonia of greater intensity than controls.</p> <p><strong>Conclusions:</strong> Anti-inflammatory and hemodynamic effects of NO surpasses its pro-oxidant role in murine malaria.</p>
Data from: Who is taking our roe deer's breath away? – Prevalence and promotive factors of lung parasites in roe deer (Capreolus capreolus) in southeast Germany
<p>The existence of bronchopulmonary nematodes in German roe deer (<em>Capreolus capreolus</em>) is well documented, with two types of lung parasites that have been described previously (<em>Dictyocaulus capreolus </em>and<em> Varestrongylus capreoli)</em>. However, little is known about the impact of these parasites on their host animal or which parameters influence outbreak and intensity of infection. The aim of this study was to obtain new information on the relevance of factors such as season, environmental conditions or age, sex, and body mass of the infected roe deer. To obtain our results, the respiratory tracts of 762 roe deer from south-eastern Germany were examined.</p> <p>In the sample, 42.5 % of roe deer were infested with <em>V. capreoli</em> and 14.0 % with <em>D. capreolus</em>, 51.3 % of animals were completely free of lung parasites. Testing for influencing variables, our regression models found both sex and age of the roe deer to statistically influence infestation, with male sex and younger age correlating with both stronger infestation and higher infestation rates. Accordingly, in male animals, the infestation rates with <em>V. capreoli</em> and <em>D. capreolus</em> (45.1 % and 20.1 %) were higher than in females (39.4 % and 8.0 %).</p> <p>The overall infestation rate of juvenile animals was remarkably higher (73 %) than those of sub-adults (38.3 %) or adults (28.4 %).</p> <p>Across all age groups, infested animals showed lower body weights compared to non-infested animals. According to our multiple linear regression model Roe deer infected with <em>D. capreolus</em> on average weighed 0.65 kg less than their healthy counterparts, in case of <em>V. capreoli</em> 0.72 kg less on average. While the burden on the well-being of infested animals can only be assumed, these concrete figures (reduced body weight in infested compared to healthy animals) demonstrate the economic damage lung parasites cause to meat harvesting from bagged roe deer.</p>
Supplementary figures and data for "Complete phylogeny of Micrathena spiders suggests multiple dispersal events among Neotropical rainforests, islands, and landmasses, and indicates Andean orogeny promotes speciation"
<p>Supplementary figures and data for "Complete phylogeny of <em>Micrathena</em> spiders suggests multiple dispersal events among Neotropical rainforests, islands, and landmasses, and indicates Andean orogeny promotes speciation" by Ivan L. F. Magalhaes, Pedro H. Martins, Bárbara T. Faleiro, Teofânia H. D. A. Vidigal, Fabrício R. Santos, Leonardo S. Carvalho, Adalberto J. Santos, submitted to <em>Cladistics</em>. </p> <p>Supplementary Figures S1 – S15</p> <p>Supplementary data S16: Complete specimen data of specimens used as vouchers for morphological scorings in Excel spreadsheet format.<br>Supplementary data S17: Discrete character matrix with morphological scorings in Nexus format.<br>Supplementary data S18: Complete specimen data of specimens used as vouchers for DNA sequencing in Excel spreadsheet format.<br>Supplementary data S19: Alignment of cytochrome oxidase I sequences in Fasta format.<br>Supplementary data S20: Alignment of histone H3 sequences in Fasta format.<br>Supplementary data S21: Alignment of 28S ribosomal sequences in Fasta format.<br>Supplementary data S22: Alignment of internal transcribed spacer sequences in Fasta format.<br>Supplementary data S23: Alignment of 16S ribosomal sequences in Fasta format.<br>Supplementary data S24: Zipped folder containing the inputs for estimating the phylogeny using morphological data in IQ-Tree: matrix in nexus format, partition file, and command file in plain text.<br>Supplementary data S25: Zipped folder containing the inputs for estimating the phylogeny using sequence data aligned with Muscle in IQ-Tree: matrix in nexus format, partition file, and command file in plain text.<br>Supplementary data S26: Zipped folder containing the inputs for estimating the phylogeny using sequence data aligned with MAFFT in IQ-Tree: matrix in nexus format, partition file, and command file in plain text.<br>Supplementary data S27: Zipped folder containing the inputs for estimating the phylogeny using morphological and sequence data aligned with MUSCLE in IQ-Tree: matrix in nexus format, partition file, and command file in plain text.<br>Supplementary data S28: Input Nexus for estimating the phylogeny using morphological data in MrBayes.<br>Supplementary data S29: Input Nexus for estimating the phylogeny using sequence data aligned with Muscle in MrBayes.<br>Supplementary data S30: Input Nexus for estimating the phylogeny using sequence data aligned with MAFFT in MrBayes.<br>Supplementary data S31: Input Nexus for estimating the phylogeny using morphological and sequence data aligned with Muscle in MrBayes.<br>Supplementary data S32: Input XML for estimating the dated phylogeny under Bayesian inference in BEAST.<br>Supplementary data S33: Distribution maps for all Micrathena species included in this study, the database with the original records and their source, and the R script used to generate the maps.<br>Supplementary data S34: Zipped folder containing all the inputs for estimating ancestral ranges and performing biogeographic stochastic mapping in R. This contains (0) the scripts for performing model selection and estimating ancestral states over a distribution of posterior trees, followed by stochastic mapping; (1) the geography and tree files (MMCT, and 100 trees randomly drawn from the posterior distribution); (2) the dispersal matrix and (3) the files for performing the time-stratified analysis to test the influence of the closure of the Isthmus of Panama on Micrathena dispersal.<br>Supplementary data S35: R script for generating the in-situ-speciation-through-time graphs from the results of biogeographic stochastic maps, as seen in Fig. 5.<br>Supplementary data S36: R script for getting and plotting elevations from individual records of Micrathena.<br>Supplementary data S37: R script for performing the GeoHiSSE estimation of net diversification rates among areas.<br>Supplementary data S38: Zipped folder containing the optimal trees found as a result of analysing inputs S24–S32 (IQ-Tree, MrBayes and BEAST).<br>Supplementary data S39: Zipped folder containing the ancestral range estimation results under competing models in BioGeoBEARS.<br>Supplementary data S40: Excel spreadsheet with parameter values of competing biogeographic models in BioGeoBEARS.<br>Supplementary data S41: Excel spreadsheet with results of biogeographic stochastic mapping over 100 different trees from the posterior distribution; includes all Micrathena species.<br>Supplementary data S42: Excel spreadsheet with results of biogeographic stochastic mapping over 100 different trees from the posterior distribution; includes only Micrathena species which had their DNA sequenced.<br>Supplementary data S43: Excel spreadsheet with the geography matrix, indicating which Micrathena species may be found in each area, and indicating the proportion of species from each area that are missing from the incomplete dataset (i.e., excluding species with unavailable DNA sequences).<br>Supplementary data S44: Excel spreadsheet with parameter values of competing biogeographic models estimated in GeoHiSSE.</p>
Sexual selection and species recognition promote complex male courtship displays in ungulates
<p>Identifying the evolutionary drivers of sexual signal complexity is a key challenge in the study of animal communication. Among mammals, male bovids and cervids often perform elaborate gestural displays during courtship, consisting of ritualized movements of various parts of the body but the causes underlying interspecific variation in complexity of such displays remain poorly understood. Here we apply the comparative method to investigate which factors may have either promoted or constrained gestural repertoire size. </p> <p>We found that sexual selection was a strong predictor of gestural display complexity in male bovids and cervids. Repertoire size was positively correlated with breeding group size, an indicator of the intensity of sexual selection on males. Moreover, repertoires were larger in species adopting non-territorial and lek breeding mating systems than in species adopting resource-defence territoriality, a finding that can be explained by more emphasis on direct benefits than indirect benefits in resource-defence systems, where male mating success may also be less skewed due to difficulty in monopolising mates.</p> <p>The results also indicate that gestural repertoire size was positively correlated with the number of closely-related species occurring in sympatry. This is consistent with display complexity being selected to facilitate species recognition during courtship and thereby avoid interspecific hybridization. At the same time, repertoire size was negatively associated with male body mass, possibly due to the energetic and mechanical constraints imposed on movements in very large species. By contrast, we found no evidence that the habitat drives selection for complex gestural courtship displays.</p>
Arsenic-poor fluids promote strong As partitioning into pyrite
<p>The data presented here includes all tabulated data contained in the manuscript draft entitled "Extreme As partitioning into pyrite from low-As fluids" by Martin Kutzschbach, Frederik Dunkel, Christof Kusebauch, Ferry Schiperski, Frederik Börner, Henrik Drake, and Manuel Keith and the associated supplementary material (in .pdf "_Data_repository_Kutzschbach_etal_2024")</p> <p>Additionally, it includes:</p> <p>-the location of all investigated transects across the pyrite rims (.png_files; name is the # of the experiment)</p> <p>- the location of all segments assigned to the core phase assemblage (.png files; name is the # of the experiment + _core)</p> <p>-The elemental distribution across the transects (.xlxs file "transet locations")</p> <p>-The input code for the PhreeqC calculation of As-speciation presented in Figure 5 (.pqi file)</p> <p>-All literature data used to construct Figure 8 (in .pdf "_Data_repository_Kutzschbach_etal_2024")</p> <p>-The detailed results of the modelling of As sequestration from fluids by formation of pyrite as a function of fluid volume and DAs (py/fluid) values presented in Figure 9 (in .pdf "_Data_repository_Kutzschbach_etal_2024")</p> <p>-This is the abstract of the manuscript draft:</p> <p>Pyrite is a ubiquitous sulfide mineral found in diverse geological settings and holds great significance in the formation of Au deposits as well as the safe utilization of groundwater due to its remarkable ability to incorporate substantial amounts of As. However, despite its importance, there remains a dearth of fundamental data on the partitioning of As between pyrite and fluid, which is key for accurately modeling the As distribution in these environments.</p> <p>Here, we present new insights into the partitioning behavior of As between pyrite and fluid at conditions that mimic natural fluid systems. Pyrite was synthesized by replacement of natural siderite in hydrothermal experiments at 200°C and pH 5 applying a wide range of fluid As concentrations, spanning from 0.001 to 100 µg/g. The As distribution and concentration in synthetic pyrite was analyzed by quantitative LA-ICP-MS mapping providing a high spatial resolution and sensitivity at 2-3 µm image pixel size at a detection limit of ~1 µg/g at the single pixel scale. Pyrite-fluid partition coefficients (D<sub>As</sub><sup>(py/fluid)</sup>) between synthetic pyrite and experimental fluid agree with previously published data for high fluid As concentrations of 1 µg/g to 100 µg/g (D<sub>As</sub> < 2000). However, at low As concentrations in the experimental fluid (<1 µg/g), a steep increase in the D<sub>As</sub><sup>(py/fluid)</sup> values of up to ~30,000 was detected, demonstrating even stronger As partitioning into pyrite. This previously unknown relation holds significant implications for natural fluid systems which frequently exhibit similar As concentrations. Our findings contribute to a better understanding of As mobility and scavenging, which in turn is important for understanding the formation and fingerprinting of mineral deposits as well as for secure utilization of groundwater resources.</p>
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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.