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Distribution. Known only in NW Zimbabwe (Lutope-Ngolangola Gorge S of Zambezi Escarpment) and NE South Africa (Limpopo Province). Specific status ofsimilarly looking populations throughout the rest of southern Africa (Zambia, Malawi, Mozambique, Zimbabwe, and Botswana) has not been assessed, and additional sampling is needed. in Rhinolophidae
Distribution. Known only in NW Zimbabwe (Lutope-Ngolangola Gorge S of Zambezi Escarpment) and NE South Africa (Limpopo Province). Specific status ofsimilarly looking populations throughout the rest of southern Africa (Zambia, Malawi, Mozambique, Zimbabwe, and Botswana) has not been assessed, and additional sampling is needed.
orientation of emu femur shows dense CB, distinct ELB, and a thin layer of MB. (I) Ostrich MB appears more laminar than in (C) or (F) because of the longitudinal orientation of tubelike medullary spicules. in Gender-Specific Reproductive Tissue in Ratites and Tyrannosaurus rex
orientation of emu femur shows dense CB, distinct ELB, and a thin layer of MB. (I) Ostrich MB appears more laminar than in (C) or (F) because of the longitudinal orientation of tubelike medullary spicules.
Figure 4 in Chemistry supports the identification of gender-specific reproductive tissue in Tyrannosaurus rex
Figure 4. High iron diamine (HID) staining of demineralized CB and MB. (A) Low, and (B) high magnification of chicken femur showing deposition of darkly staining MB on pre-existing CB. (C) low, and (D) high magnification of ostrich femoral MB. Similar to the pattern seen using Alcian blue (Fig. 3), the distribution of MB is less distinct but can be chemically differentiated from pre-existing CB in a more mixed fashion. CB from T. rex femur in low (E) and high (F) magnification shows slight staining, as seen in modern samples, but staining is much more pronounced in T. rex MB in low (G) and higher (H) magnifications. Scale bars as indicated.
Figure 1 in Chemistry supports the identification of gender-specific reproductive tissue in Tyrannosaurus rex
Figure 1. Morphological differentiation between MB and CB. (A) Mid shaft section from reproductively active laying hen femur shows textural differences between CB and MB. (B) more proximal region of hen femur shows that trabecular bone (T) can be differentiated from MB in hand sample, and that MB is deposited between trabeculae, infilling trabecular spaces. (C) MB in hand sample of ostrich femur appears to grade from CB, but can be differentiated by color and spiculation, as well as the presence of large erosion rooms (ER, arrows) at the boundary between layers. Infilling of erosion rooms with crystalline MB is also seen (*). (D) Ground section of ostrich at higher magnification shows clear separation of MB and CB. Bone fragment of MOR 1125 femur in (E) cross section and (F) medial, or medullary face orientation shows both textural and color differences between CB and MB, as well as the distinct separation between bone types. (G) Transverse section of MOR 1125 whole femur, showing almost complete infilling of the medullary cavity with MB. No gross deformation (corresponding to fracture callus) or bony expansion (corresponding to osteopetrosis) can be seen. Red line marks boundary between dense cortical bone and endosteal lamellar bone penetrated by multiple erosion rooms. Erosion rooms can be seen extending deep into the cortex in one region of the bone (*). (H) Petrographic ground section of deep CB layer and adjacent, internal MB of MOR 1125, showing change in texture and vascularity. Black arrows show distinct separation between innermost endosteal bone with erosion rooms, and region of MB deposition. Trabeculae (T) of laminar bone can be seen surrounded by MB. Scale bars as indicated.
Fig. 1 in Gender-Specific Reproductive Tissue in Ratites and Tyrannosaurus rex
Fig. 1. Extant avian MB and homologous dinosaurian bone tissues. (A) Domestic laying hen, midshaft femur cross section showing the extension of spongy MB deep into the mar row cavity and surrounding preexisting trabeculae (T). (B) Laying emu, midshaft cross section, with a thin layer of MB on the endosteal bone surface, separated from overlying CB by ELB. (C) Ostrich MB arising from CB. Convoluted bony projections surround large cavities and form by continued deposition on hairlike spicules of calcified bone (S). (D) MB on endosteal surface of MOR 1125 femur fragment delineated from overlying CB by large vascular sinuses and change in color, texture, and density. (E) Emu and (F) ostrich bone taken at same aspect as (D), showing mor phological distinction between bone types. (G) Higher magnification of dinosaur femur fragment in oblique view shows dense CB lined with newly described bone tissue, also seen in oblique view of emu (H) and ostrich (I) tibia. Ostrich MB is apparently unique in forming longitudinal tubules.
Fig. 4 in Gender-Specific Reproductive Tissue in Ratites and Tyrannosaurus rex
Fig. 4. Scanning elec tron microscope images of demineralized MB [(A) to (D)] and CB [(E) to (K)]. Demineralized, aldehyde-fixed (14) MB tissues from (A) MOR 1125, (B) extant laying hen, (C) emu, and (D) ostrich show random, crumbly texture. Organized collagen fiber bundles are not distinct in any sample because of rapid deposition and woven character. Scale bars for (A) and (B), 40 um; for (C) and (D), 20 um. Demineralized fragments of cortical bone from (E) MOR 1125, (F) chicken, (G) emu, and (H) ostrich are shown. A fibrous character dominates all samples. Scale bars for (E), (F), and (H), 30 mm; for (G), 10 mm. Higher magnification of demineralized CB from (I) MOR 1125, (J) emu, and (K) ostrich CB demonstrates the structural similarity between samples, although the MOR 1125 matrix is highly degraded. Scale bars for (I) and (K), 6 um; for (J), 5 um.
Data from the manuscript: Machine learning reveals structural characteristics of stereochemistry-specific interdigitation of synthetic monomycoloyl glycerol analogs
<h2>Four membrane configurations:</h2> <p>1. single = single bilayer (512 MMG molecules and 25600 water molecule) <br>2. db_large = large double bilayer (1024 MMG molecules and 51200 water molecules)<br>3. id_small = interdigitated double bilayer (256 MMG molecules and 12800 water molecules)<br>4. db_small = small double bilayer (256 MMG molecules and 12800 water molecules)</p> <p>Each membrane configuration has 2 different MMG analogs:</p> <p><br>1. MMG1 = MMG-1, 1:1 racemic mixture of stereoisomers with (2R,3S)/(2S,3R) configurations<br>2. MMG6 = MMG-6, 1:1 racemic mixture of stereoisomers with (2R,3R)/(2S,3S) configurations</p> <h2>File names:</h2> <p><br>Each trajectory folder contains starting structures, input structure files, trajectory, energy file and system topology file.<br>Additionally, the .mdp files and topologies are located in their own folders.</p> <p>- start.gro = starting structure before energy minimization**<br>- eq.gro = input structure file for production<br>- eq.cpt = equilibration checkpoint file<br>- run.gro = final frame structure file<br>- run.cpt = production checkpoint file<br>- run.tpr = production tpr file <br>- run.xtc = production trajectory file, final 500 ns<br>- run.edr = production energy file, final 500 ns</p> <p>the <em>db_large</em> system is built with equilibrated <em>db_small</em> system, hence the starting structure is before the equilibration.</p> <h2>MDP-files:</h2> <p><br>Molecular dynamics parameter files can be found in their own folder (05_mdps/). Files for energy minimization,<br>equilibration and production run are provided.</p> <p>- em1_charmm36.mdp = 1st energy minimization (for all systems)<br>- em_charmm36.mdp = 2nd energy minimization (for all systems)<br>- eq1_noposres_charmm36.mdp = equilibration without position restraints (for single)<br>- eq1_posresin_charmm36.mdp = equilibration with O1 atoms constrained in Z-direction (for db_large, id_small, db_small)<br>- production_charmm36.mdp = production run (for all systems)</p> <h2>Topologies and position restraint files:</h2> <p><br>System topologies for each MMG analog can be found in their own folders (06_top/MMG1/, 06_top/MMG6/). <br>Molecular topologies, forcefield parameters and position restraint files can be found from their respective folders (06_top/MMG1/topol/, 06_top/MMG6/topol/).</p> <h3>MMG-1:</h3> <p><br>- db_large-MMG1.top = MMG-1 large double-bilayer system<br>- db_small-MMG1.top = MMG-1 small systems: interdigitated and non-interdigitated double bilayers <br>- single-MMG1.top = MMG-1 single bilayer system<br>- forcefield.itp = force field parameters<br>- TIP3_CHARMM36.itp = water model<br>- MMG1_2R3S_outer.itp = outer leaflet 2R3S MMG-1 <br>- MMG1_2S3R_outer.itp = outer leaflet 2S3R MMG-1 <br>- MMG1_2R3S_inner.itp = inner leaflet 2R3S MMG-1<br>- MMG1_2S3R_inner.itp = inner leaflet 2S3R MMG-1<br>- posres_MMG1_tail_z.itp = position restraints on MMG tails in z-direction<br>- posres_MMG1_O1_z.itp = position restraints on MMG headgroup O1 atom in z-direction</p> <h3>MMG-6:</h3> <p><br>- db_large-MMG6.top = MMG-6 large double-bilayer system<br>- db_small-MMG6.top = MMG-6 small systems: interdigitated and non-interdigitated double bilayers<br>- single-MMG6.top = MMG-6 single bilayer system<br>- forcefield.itp = force field parameters<br>- TIP3_CHARMM36.itp = water model<br>- MMG6_2S3S_outer.itp = outer leaflet 2S3S MMG-6 <br>- MMG6_2R3R_outer.itp = outer leaflet 2R3R MMG-6<br>- MMG6_2S3S_inner.itp = inner leaflet 2S3S MMG-6<br>- MMG6_2R3R_inner.itp = inner leaflet 2R3R MMG-6 <br>- posres_MMG6_tail_z_2R3R.itp = position restraints on tails in z-direction <br>- posres_MMG6_tail_z_2S3S.itp = position restraints on tails in z-direction<br>- posres_MMG6_O1_z.itp = position restraints on MMG headgroup O1 atom in z-direction</p>
Fig. 3. Flavonoids with and without 6 in Polar auxin transport May Be responsive to specific features of flavonoid structure
Fig. 3. Flavonoids with and without 6-hydroxyl groups have different effects on root length. The effects of scutellarin, scutellarein, rutin and naringenin on A. thaliana root length were examined. Seeds were germinated and mock-treated or grown in 50 μM scutellarin, 50 μM scutellarein, 50 μM rutin or 50 μM naringenin for 7 days.
Fig. 2 in Polar auxin transport May Be responsive to specific features of flavonoid structure
Fig. 2. Scutellarin promotes root length. (a) Physiological effects of scutellarin on A. thaliana root length. Photographs of root length after scutellarin treatment for 7 days. S, scutellarin. (b) Measurements of A. thaliana root length after scutellarin treatment for 7 days. The values are the means ± SDs (n = 25). * indicates that the value is different from that of the control (P <0.05). (c) Effects of scutellarin (100 μM for 7 d) on the elongation zone in A. thaliana root tips. Confocal images of root tips stained with propidium iodide.
Phenotype-specific gene expression signature in unmutated sALS patients' peripheral blood
<p>The database includes the raw data of the article "Phenotype-specific gene expression signature in unmutated sALS patients' peripheral blood". Aim of this work was to define the transcriptomic signature of distinct ALS phenotypes, and to use this information for biomarkers development. We characterized n=48 sALS patients by clinical and paraclinical parameteres, and subdivided them in "Classic" (n=12), "Bulbar" (n=10), "Flail Arm" (n=7), "Flail Leg" (n=10) and "Pyramidal" (n=9) phenotypes. RNAs extracted from PBMCs isolated from patients and n=19 controls were sequenced. Our analysis allowed the visualization of gene expression clusters between patients and controls, except for "Flail Arm" group. Only one gene (Y-RNA, a misc_RNA component of the Ro60 ribonucleoprotein involved in cellular response to interferon-alpha) was upregulated at different levels across all phenotypes, whereas the other genes appeared to be more phenotype-specific. Taken together, our results indicate both the specificity of gene expression for each phenotype, and the presence of a shared altered transcript able to distinguish the analyzed phenotypes. Future goal is to determine a 'Y-RNA signature' in plasma and a multi-parametric prognostic score that could represent a simple and fast element for early diagnosis and discrimination among sALS phenotypes.</p>
Larval-adult diet interactions affect fitness in a life phase-specific manner in an outbred population.
<p>A set of data files containing lifespan and fecundity data for a study Drosophila melanogaster, tentatively titled "<span><span>Larval-adult diet interactions affect fitness in a life phase-specific manner in an outbred population</span></span>". Fruit flies were reared on four diet combinations (made up of 2 diets, a protein restricted, and a control diet) as larvae and adult. Over lifespan, we counted the number of eggs and kept death event records. The aim is to characterize the effect of larval-adult diet interactions in matched and mismatched combinations. </p>
Unravelling cell type-specific responses to Parkinson's Disease at single cell resolution
<p>Data set including raw and pre-processed files of spatial transcriptomics associated with the study mentioned above.</p>
raw data related to project "Circulating biomarkers as predictors of gender-specific response to Immune Checkpoint Inhibitors in melanoma and non-small-cell lung cancer patients"
<p><strong>Sex-related differences in serum biomarker levels predict the activity and efficacy of Immune Checkpoint Inhibitors in advanced melanoma and Non-Small Cell Lung Cancer patients.</strong></p> <p><strong>Abstract </strong></p> <p><strong>Background:</strong> Immune Checkpoint Inhibitors (ICIs) lead to durable response and a significant increase in long-term survival in patients with advanced malignant melanoma (MM) and Non-Small Cell Lung Cancer (NSCLC). The identification of serum cytokines that can predict their activity and efficacy, and their sex interaction, could improve treatment personalization. </p> <p><strong>Methods: </strong>In this prospective study, we enrolled immunotherapy-naïve patients affected by advanced MM and NSCLC treated with ICIs. The primary endpoint was to dissect the potential sex correlations between serum cytokines (IL-1β, IL-2, IL-4, IL-5, IL-6, IL-8, IL-10, GM-CSF, MCP-1, TNF-ɑ, IP-10, VEGF, sPD-L1) and the overall response rate (ORR). Secondly, we analyzed biomarker changes during treatment related to ORR, disease control rate (DCR), progression free survival (PFS) and overall survival (OS). Blood samples, collected at baseline and during treatment until disease progression (PD) or up to 2 years, were analyzed using Luminex xMAP or ELLA based technology. </p> <p>Three Luminex xMAP assays and two ELLA microfluidic cartridges were used to screen 28 immune-related biomarkers in 38 paired serum and citrate-theophylline-adenosine-dipyridamole (CTAD) plasma samples collected from 10 advanced melanoma or non-small cell lung cancer (NSCLC) patients at different time points during immunotherapy.</p> <p><strong>Results</strong>: Serum samples from 161 patients (98 males/63 females; 92 MM/69 NSCLC) were analyzed for treatment response. At baseline, IL-6 was significantly lower in females (F) <em>versus</em> males (M); lower levels of IL-4 in F and of IL-6 in both sexes significantly correlated with a better ORR, while higher IL-4 and TNF-ɑ values were predictive of a lower probability of ORR in F <em>versus</em> M. One hundred and sixty-five patients were evaluable for survival analysis: at multiple Cox regression, an increased risk of PD was observed in F with higher baseline values of IL-4, sPD-L1 and IL-10, while higher IL-6 was a negative predictor in males. In males, higher levels of GM-CSF predict a longer survival, whereas higher IL-1β predicts a shorter survival. Regardless of sex, high baseline IL-8 values were associated with an increased risk of both PD and death, and high IL-6 levels only with shorter OS. </p> <p>Twenty-three of 28 biomarkers were detected both in serum and plasma by at least one of the assays, including IL-1β, IL-2, IL-4, IL-5, IL-6, IL-8, IL-10, IL-12p70, GM-CSF, IFN-γ, TNF-α, VEGF, IP-10, MCP-1, eotaxin, fractalkine, G-CSF, IFN-α, IL-1RA, IL-13, IL-17A, MIP-1β and sPD-L1. Conversely, FGF-2 and IL-1α were not detected in both matrices; GRO-α factor and EGF were detected only in serum and MIP-1α only in plasma. sPD-L1, MCP-1, IFN-γ, IL-8, MIP-1β and VEGF were, respectively, 1.15-, 1.44-, 1.83-, 2.43-, 2.82-, 6.72-fold higher in serum, whereas IL-10, IL-4, IL-2 and IL-5 were 1.05-, 1.19-, 1.92- and 2.17-fold higher, respectively, in plasma. IP-10 levels were higher in plasma but, as well as for VEGF, the bias serum versus plasma varied depending on the assay used (IP-10: −5.7% to −145%; VEGF: 115% to 165%). No significant differences were found for the remaining nine analyzed cytokines.</p> <p><strong>Conclusions</strong></p> <p>Serum IL-1β, IL-4, IL-6, IL-10, GM-CSF, TNFɑ, and sPDL1 had a significant independent sex-related predictive impact on ORR, PFS and OS in melanoma and NSCLC patients treated with ICIs. These results will potentially pave the way for new ICI combinations, designed according to baseline and early changes of these cytokines and stratified by sex. </p> <p>The cytokine and sPD-L1 levels may differ between serum and plasma samples collected from cancer patients treated with immunotherapy, and the results obtained can be influenced by the different characteristics of the tested assays.</p>
High-throughput Pore-C reveals the single-allele topology and cell type-specificity of 3D genome folding
<p>The processed data from the HiPore-C study.</p>
Mitigating the non-specific rolling circle amplification: a comprehensive assessment of the role of ligation and digestion methods
<ul> <li>List of Experiments</li> <li>rt-PCR instrument measurements of RCA</li> <li>Gel files</li> <li>Origin plots</li> </ul>
Distribution. Turkey (Anatolia), Armenia, SE Georgia, Azerbaijan, NW & W Iran, and Lebanon; individuals of still unresolved specific status have been recently found in NE Iran (Kopet Dag Mts). in Dipodidae
Distribution. Turkey (Anatolia), Armenia, SE Georgia, Azerbaijan, NW & W Iran, and Lebanon; individuals of still unresolved specific status have been recently found in NE Iran (Kopet Dag Mts).
FIGURE. Cumulative number of currently accepted specific and infraspecific cycad taxa described over time (taxonomic framework sensu Calonje et al. 2022). in Etymological compendium of cycad names
FIGURE. Cumulative number of currently accepted specific and infraspecific cycad taxa described over time (taxonomic framework sensu Calonje et al. 2022).
FIGURES –. Relatively rare Achnanthales (SEM, New Caledonia, Melanesia). Cocconeis margaritata Riaux-Gobin & Al-Handal, oblong SV areolae bordered by siliceous small beads (37–38), Cocconeis paucistriata Riaux-Gobin, Romero, Compère & Al-Handal (39, 40), SV striae composed of a unique areola on each side of the SV sternum (40, arrow), two (to three) marginal areolae (39, 40), simple process apertures on SV mantle (40, twin arrowheads). Cocconeis sigillata Riaux-Gobin & Al-Handal (41), low marginal crista marginalis and biseriate striae (41, arrowhead) split in two parts by an axial raised area. Achnanthidium glyphos Riaux-Gobin, Compère & Witkowski (42), naviculoïd SV shape, one row of marginal oblong SV areolae (42, arrowhead). See the RV of these taxa on their original description (refs cited above). Scale bars = 3 µm (37), 2 µm (42), 500 nm (40), 400 nm (38). in Marine Achnanthales (Bacillariophyceae) from New Caledonia (Melanesia): assemblage specificities, ultramafic environment
FIGURES –. Relatively rare Achnanthales (SEM, New Caledonia, Melanesia). Cocconeis margaritata Riaux-Gobin & Al-Handal, oblong SV areolae bordered by siliceous small beads (37–38), Cocconeis paucistriata Riaux-Gobin, Romero, Compère & Al-Handal (39, 40), SV striae composed of a unique areola on each side of the SV sternum (40, arrow), two (to three) marginal areolae (39, 40), simple process apertures on SV mantle (40, twin arrowheads). Cocconeis sigillata Riaux-Gobin & Al-Handal (41), low marginal crista marginalis and biseriate striae (41, arrowhead) split in two parts by an axial raised area. Achnanthidium glyphos Riaux-Gobin, Compère & Witkowski (42), naviculoïd SV shape, one row of marginal oblong SV areolae (42, arrowhead). See the RV of these taxa on their original description (refs cited above). Scale bars = 3 µm (37), 2 µm (42), 500 nm (40), 400 nm (38).
K5 Gene-specific TAIL-seq
<p>Gene-specific TAIL-seq experiment </p>
Within Uromys, U. porculus in included in subgenus Cyromys along with the other two Guadalcanal species, namely U. imperator and U. rex. Monotypic. Distribution. Guadalcanal I, Solomon Is. Descriptive notes. Head-body 220 mm, tail 130 mm, ear 19 mm, hindfoot 43 mm. No specific data are available for body weight. The Guadalcanal Giant Rat is the second smallest species in the distinctive genus Uromys. Pelage is short and soft, with longer bristly guard hairs. Dorsal pelage is reddish brown, being browner near head, redder near rump, and grayer as it fades to ventral pelage on the side; ventral pelage is grayish white with grayunderfur. Feet are very broad and of a dull white coloration. Ears are very small and rounded; vibrissae are long. Tail is very short (59% of head-body length), naked, has fine scaling, and is monocolored black. Skull is longer and narrower than that of the King Giant Rat (U. rex), and with narrower molars than in the Emperor Giant Rat (U. imperator). in Muridae
Within Uromys, U. porculus in included in subgenus Cyromys along with the other two Guadalcanal species, namely U. imperator and U. rex. Monotypic. Distribution. Guadalcanal I, Solomon Is. Descriptive notes. Head-body 220 mm, tail 130 mm, ear 19 mm, hindfoot 43 mm. No specific data are available for body weight. The Guadalcanal Giant Rat is the second smallest species in the distinctive genus Uromys. Pelage is short and soft, with longer bristly guard hairs. Dorsal pelage is reddish brown, being browner near head, redder near rump, and grayer as it fades to ventral pelage on the side; ventral pelage is grayish white with grayunderfur. Feet are very broad and of a dull white coloration. Ears are very small and rounded; vibrissae are long. Tail is very short (59% of head-body length), naked, has fine scaling, and is monocolored black. Skull is longer and narrower than that of the King Giant Rat (U. rex), and with narrower molars than in the Emperor Giant Rat (U. imperator).
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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.