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Proteolytic Profiling of Streptococcal Pyrogenic Exotoxin B (SpeB) by Complementary HPLC-MS Approaches.
<p>Streptococcal pyrogenic exotoxin B (SpeB) is a cysteine protease expressed during group A streptococcal infection that represents a major virulence factor. Although subject to several studies, its role during infection is still under debate, and its proteolytic properties remain insufficiently characterized. Here, we revisited this protease through a set of complementary approaches relying on state of-the-art HPLC-MS methods. After conceiving an efficient protocol to recombinantly express SpeB, the zymogen of the protease and its activation were characterized. Employing proteome-derived peptide libraries, a strong preference for hydrophobic and aromatic residues at P2 alongside negatively charged amino acids at P3′ to P6′ was revealed. To identify relevant in vivo substrates, native proteins were obtained from monocytic secretome and plasma to assess their cleavage under physiological conditions. Besides corroborating our findings concerning specificity, more than 200 cleaved proteins were identified, including proteins of the extracellular matrix, proteins of the immune system, and proteins involved in inflammation. Finally, the cleavage of IgG subclasses was studied in detail. This study precisely depicts the proteolytic properties of SpeB and provides a library of potential host substrates, including their exact cleavage positions, as a valuable source for further research to unravel the role of SpeB during streptococcal infection.</p>
Individual EEG profiling of attention deficits in left spatial neglect: A pilot study
<p>Electrophysiological group studies in brain-damaged patients can be run to capture the EEG correlates of specific cognitive impairments. Nonetheless, this procedure is not adequate to characterize the inter-individual variability present in major neuropsychological syndromes. We tested the possibility of getting a reliable individual EEG characterization of deficits of endogenous orienting of spatial attention in right-brain damaged (RBD) patients with left spatial neglect (N+). We used a single-trial topographical analysis (STTA; [39] of individual scalp EEG topographies recorded during leftward and rightward orienting of attention with central cues in RBD patients with and without (N−) neglect and in healthy controls (HC). We found that the STTA successfully decoded EEG signals related to leftward and rightward orienting in five out of the six N+, five out of the six N− patients and in all the six HC. In agreement with findings from conventional average-group studies, successful classifications of EEG signals in N+ were observed during the 400–800 ms period post-cue-onset, which reflects preserved voluntary engagement of attention resources (ADAN component). </p>
Appendix: Association between hemostatic profile and migraine: a Mendelian randomization analysis
<p><b>Objective: </b><span>To assess support for a causal relationship between </span>hemostatic measures and migraine susceptibility using genetic instrumental analysis.</p> <p><b>Methods: </b>Two-sample Mendelian randomization (MR) instrumental leveraging available genome-wide association study (GWAS) summary statistics was applied to hemostatic measures as potential causal for migraine and its subtypes, migraine with aura (MA) and migraine without aura (MO). Twelve blood-based measures of hemostasis were examined, including plasma level or activity of eight hemostatic factors and two <span>fibrinopeptides together with </span>two hemostasis clinical tests<span>.</span></p> <p><b>Results: </b>There were significant instrumental effects between increased coagulation factor VIII activity (FVIII, odds ratio[95% confidence interval]=1.05[1.03, 1.08]/standard deviation (SD), <i>P</i>=6.08×10<sup>-05</sup>), von Willebrand factor level (VWF, 1.05[1.03, 1.08]/SD, <i>P</i>=2.25×10<sup>-06</sup>), and phosphorylated <span>fibrinopeptide A level</span> (1.13[1.07, 1.19]/SD, <i>P</i>=5.44×10<sup>-06</sup>) with migraine susceptibility. When extended to migraine subtypes, FVIII, VWF, and phosphorylated <span>fibrinopeptide A</span> showed slightly stronger effects with MA than overall migraine. Fibrinogen level was inversely linked with MA (0.76[0.64, 0.91]/SD, <i>P</i>=2.32×10<sup>-03</sup>) but not overall migraine. None of the hemostatic factors was linked with MO. In sensitivity analysis, effects for fibrinogen and phosphorylated <span>fibrinopeptide A</span> were robust, while independent effects of FVIII and VWF could not be distinguished, and FVIIII associations were potentially affected by pleiotropy at the <i>ABO</i> locus. Causal effects from migraine to the hemostatic measures were not supported in reverse MR. However, MA was not included due to lack of instruments.</p> <p><b>Conclusions:</b> The current study supports potential causality of increased FVIII, VWF, and phosphorylated <span>fibrinopeptide A,</span> and decreased fibrinogen in migraine susceptibility, especially for MA, and may provide insights into the etiology underlying the relationship between <span>hemostasis</span> and migraine.</p>
Validating x-ray line-profile defect analysis using atomistic models of deformed material
<p>Data and analysis (scripts and Jupyter notebooks) associated with publications:</p> <p>Validating x-ray line-profile defect analysis using atomistic models of deformed material (submitted to Physical Review Materials)</p> <p>Validation of x-ray line-profile analysis of extended defects in deformed crystals (submitted to Physical Review Letters)</p> <p>Preprints of these papers are included here</p>
Metabolite profiling of the social spider Stegodyphus dumicola along a climate gradient
<p>Animals experience climatic variation in their natural habitats, which may lead to variation in phenotypic responses among populations through local adaptation or phenotypic plasticity. In ectotherm arthropods, the expression of thermoprotective metabolites such as free amino acids, sugars, and polyols, in response to temperature stress, may facilitate temperature tolerance by regulating cellular homeostasis. If populations experience differences in temperatures, individuals may exhibit population-specific metabolite profiles through differential accumulation of metabolites that facilitate thermal tolerance. Such thermoprotective metabolites may originate from the animals themselves or from their associated microbiome, and hence microbial symbionts may contribute to shape the thermal niche of their host.</p> <p>The social spider Stegodyphus dumicola has extremely low genetic diversity, yet it occupies a relatively broad temperature range occurring across multiple climate zones in Southern Africa. We investigated whether the metabolome, including thermoprotective metabolites, differs between populations, and whether population genetic structure or the spider microbiome may explain potential differences. To address these questions, we assessed metabolite profiles, phylogenetic relationships, and microbiomes in three natural populations along a temperature gradient.</p> <p>The spider microbiomes in three genetically distinct populations of S. dumicola showed no significant population-specific pattern, and none of its dominating genera (Borrelia, Diplorickettsia, and Mycoplasma) are known to facilitate thermal tolerance in hosts. These results do not support a role of the microbiome in shaping the thermal niche of S. dumicola. Metabolite profiles of the three spider populations were significantly different. The variation was driven by multiple metabolites that can be linked to temperature stress (e.g. lactate, succinate or xanthine) and thermal tolerance (e.g. polyols, trehalose, or glycerol): these metabolites had higher relative abundance in spiders from the hottest geographic region. These distinct metabolite profiles are consistent with a potential role of the metabolome in temperature response.</p>
Pyroconvection Classification based on Atmospheric Vertical Profiling Correlation with Extreme Fire Spread Observations
<p>1. Isochrones for Martorell, Santa Coloma Queralt, Torroella, Pobla Massaluca and Sierra Bermeja fires, in shapefile format. Each file has associated an attribute table identifying the hour (in UTC), the affected area, the rate of spread, and direction. Source: Catalan Fire and Rescue Service (Bombers de la Generalitat de Catalunya)</p> <p>2. ERA5 reanalysis data obtained for each fire, hourly and at different pressure levels (37) from the Copernicus Climate Change Service (C3S) Climate Data Store (CDS). The files are in netCDF format, and the variables requested were temperature, relative humidity, U-component of wind, V-component of wind. Source: Hersbach, H., Bell, B., Berrisford, P., Biavati, G., Horányi, A., Muñoz Sabater, J., Nicolas, J., Peubey, C., Radu, R., Rozum, I., Schepers, D., Simmons, A., Soci, C., Dee, D., Thépaut, J-N. (2018): ERA5 hourly data on pressure levels from 1979 to present. Copernicus Climate Change Service (C3S) Climate Data Store (CDS). 10.24381/cds.bd0915c6</p> <p>3. Data from sondes launched in fires during the 2021 Spain wildfire campaign. The files are in CSV format, and there are two per fire: the sounding data corrected and the raw flight history. The information provided is Hour (UTC), Wind speed (m/s), Wind direction (true deg), Dew point (C), Latitude, Longitude, Altitude (in m MSL and m AGL), Pressure (Pascal), Speed (m/s), Heading (degrees), Temperature (C), Relative humidity (%), Internal temperature (C), Latitude, Longitude, Rise speed (m/s). Source: Catalan Fire and Rescue Service (Bombers de la Generalitat de Catalunya)</p> <p>4. Data from the closest weather station to each fire. The file is an Excel file. The table fields are: fire name, weather station name, day, hour, average temperature (°C), maximum temperature(°C), minimum temperature (°C), average relative humidity (%), precipitation (mm), wind speed (10 m, km/h), wind direction (10 m, degrees), wind gusts (10 m, km/h), pressure (hPa), radiation (W/m). Source: Meteo.cat, Servei Meteorològic de Catalunya</p> <p>5. Fire behavior resume for Martorell, Santa Coloma Queralt, Torroella, Pobla Massaluca, Llançà, Alfarràs and Sierra Bermeja fires (Spain). The differences in the data shown respond to the possibility of launching sondes, recreating isochrones, and observing the plume column during each fire. In those cases where the information was obtained through these three ways, the variables available are: column type, ABL and LCL height (m), sonde ID, rate of spread (km/h), ROS observed / ROS expected ratio, fireline intensity expected and observed (kW/m), and affected area (ha).</p> <p>6. Photographic registry of the fire plume evolution and a brief description of the pyroconvective moments in the Alfarràs, Martorell, Llançà, Torroella, Santa Coloma de Queralt, Pobla Massaluca, and Sierra Bermeja fires (Spain). Pictures sources: Catalan Fire and Rescue Service (Bombers de la Generalitat de Catalunya)</p>
Carson Valley Fault Profiles
<p>These are topographic profiles across fault scarps extracted from lidar data in Carson Valley. </p>
Single Cell Profiling of Human Dura and Meningioma Reveals Cellular Meningeal Landscape and Insights into Meningioma Immune Response
<p>This repository contains the single-cell RNA-seq data described in the publication “Single Cell Profiling of Human Dura and Meningioma Reveals Cellular Meningeal Landscape and Insights into Meningioma Immune Response.” Data is provided as count matrices and Seurat objects.</p>
HLA class I and class II allelic profile of healthy Lebanese population
<p class="MsoNormal"><strong><span>Background</span></strong><span>. This study examined the origin of present-day Lebanese using high-resolution HLA class I and class II allele and haplotype distributions. The study subjects comprised 152 unrelated individuals, and their HLA class I and class II alleles and two-locus and five-locus haplotypes were compared with those of neighboring and distant communities </span><span>using genetic distances, neighbor-joining dendrograms, correspondence, and<strong> </strong>haplotype analyses</span><span>. </span><span>HLA class I (<em>A</em>, <em>B</em>, <em>C</em>) and class II (<em>DRB1</em>, <em>DQB1</em>) were genotyped at a high-resolution level by PCR-SSP. </span></p> <p class="MsoNormal"><strong><span>Results</span></strong><span>. In total, 76 alleles across the five HLA loci were detected: <em>A*03:01</em> (17.1%), <em>A*24:02</em> (16.5%), <em>B*</em></span><em><span>35:01</span></em><span> (25.7%), <em>C*</em></span><em><span>04:01</span></em><span> (25.3%), and </span><em><span>C*</span></em><em><span>07:01</span></em><span> (20.7%) were t</span><span>he most frequent class I alleles, while <em>DRB1*</em></span><em><span>11:01</span></em><span> (34.2%) and <em>DQB1*03:01</em> (43.8%) were the most frequent class II alleles. All pairs of HLA loci were in significant linkage disequilibrium. The most frequent two-locus haplotypes recorded were <em>DRB1*11:01</em></span><span>~</span><em><span>DQB1*03:01</span></em><span> (30.9%), <em>B*35:01</em>-<em>C*04:01</em> (20.7%), <em>B*35:01</em></span><span>~</span><em><span>DRB1*11:01</span></em><span> (13.8%), and <em>A*24:02</em></span><span>~</span><em><span>B*35:01</span></em><span> (10.3%). Lebanese appear to be closely related to East Mediterranean communities such as Levantines (Palestinians, Syrians, and Jordanians), Turks, Macedonians, and Albanians. However, Lebanese appear to be distinct from North African, Iberian, and Sub-Saharan communities. </span></p> <p class="MsoNormal"><strong><span>Conclusions</span></strong><span>. Collectively, this indicates a limited genetic contribution of Arabic-speaking populations </span><span>(from North Africa or the Arabian Peninsula</span><span>) and Sub-Saharan communities to the present-day Lebanese gene pool.</span><strong><span> </span></strong><span>This confirms the notion that Lebanese population are of mixed East Mediterranean and Asian origin, with a marked European component.</span></p>
Peripheral blood DNA methylation profiles predict future development of B-cell Non-Hodgkin Lymphoma
<p>Lack of accurate methods for early lymphoma detection limits the ability to cure patients. Patients with Non-Hodgkin lymphomas (NHL) who present with advanced disease have worse outcomes.</p> <p>We developed a DNA methylation-based prediction tool for NHL, based on blood samples collected prospectively from 278 apparently healthy patients who were followed for up to 16 years to monitor for NHL development. A predictive score was developed using machine learning methods in a robust training/validation framework.</p> <p>Our predictive score incorporates CpG DNA methylation at 135 genomic positions, with higher scores predicting higher risk. It was 85% and 78% accurate for identifying patients at risk of developing future NHL, in patients with high or low epigenetic mitotic clock respectively, in a validation cohort. It was also sensitive at detecting active NHL (96.3% accuracy) and healthy status (95.6% accuracy) in additional independent cohorts. Scores optimized for specific NHL subtypes showed significant but lower accuracy for predicting other subtypes. Our score incorporates hyper-methylation of Polycomb and <em>HOX</em> genes, which have roles in NHL development, as well as <em>PAX5</em> - a master transcriptional regulator of B-cell fate. Subjects with higher risk scores showed higher regulatory T-cells, memory B-cells, but lower naïve T helper lymphocytes fractions in the blood.</p> <p>A score based on DNA methylation in blood is accurate at predicting NHL development with lead time of up to 16 years. Future prospective studies will be required to confirm the utility of our signature for managing patients who are at high risk for developing future NHL.</p>
Distribution. Known only from type locality on S coast of Seram I, Indonesia. Descriptive notes. Head-body 123 mm, tail 128 mm, ear 14-6 mm, hindfoot 26-2 mm; weight 65 g (all mensural data are from holotype). Pavel's Seram Mosaic-tailed Rat is very small-bodied, with dorsal pelage soft and brightly colored rufescent reddish brown, hairs with graybases, and venter contrastingly pure white; tail is slightly longer than head-body length, all black in color, tail scales raised, one hair per scale, scale hairs very short. Upper surfaces of feet are dark gray; hindfeet broad, with first digit long. Cranium is relatively narrow, with nasal profile flat; teeth very small. Single known specimen (the holotype), a pregnant female, has four mammae. in Muridae
Distribution. Known only from type locality on S coast of Seram I, Indonesia. Descriptive notes. Head-body 123 mm, tail 128 mm, ear 14-6 mm, hindfoot 26-2 mm; weight 65 g (all mensural data are from holotype). Pavel's Seram Mosaic-tailed Rat is very small-bodied, with dorsal pelage soft and brightly colored rufescent reddish brown, hairs with graybases, and venter contrastingly pure white; tail is slightly longer than head-body length, all black in color, tail scales raised, one hair per scale, scale hairs very short. Upper surfaces of feet are dark gray; hindfeet broad, with first digit long. Cranium is relatively narrow, with nasal profile flat; teeth very small. Single known specimen (the holotype), a pregnant female, has four mammae.
First Lidar Profiling of Meteoric Ca+ Ion Transport from ~80 to 300 km in the Midlatitude Nighttime Ionosphere
<p>The attached data is used for the paper.</p>
Replication package: Evidence Profiles for Validity Threats in Program Comprehension Experiments
<p>Replication package for:</p> <p><em>M. Muñoz Barón, M. Wyrich, D. Graziotin, S. Wagner. ‘Evidence Profiles for Validity Threats in Program Comprehension Experiments’. In: 2023 IEEE/ACM 45th International Conference on Software Engineering (ICSE). IEEE</em></p>
Supporting information: VISA Metabolomics Profiling Metadata
<p> Metadata for metabolomics profiling of vancomycin-intermediate S. aureus (VISA) strains: Mu50Ω (VSSA), Mu50Ω-<em>vraS</em>m (VISA) and Mu50Ω-<em>vraS</em>m-<em>graR</em>m (VISA)</p>
CALIOP SR profiles
<p>Scattering ratio vertical profiles derived from CALIOP data for the period Mach-May 2008 at night time, after data processing.</p>
ATB CALIOP profiles
<p>Total attenuated backscatter CALIOP vertical profiles, for the period March-May 2008, at night time, after data processing.</p>
Proteomic Profiling for Identification of Animal Skin Species in Ancient Egyptian Archaeological Leather using Liquid Chromatography Coupled with Tandem Mass Spectrometry (Nano LC-MS/MS)
<p><strong>Proteomic Profiling for Identification of Animal Skin Species in Ancient Egyptian Archaeological Leather using Liquid Chromatography Coupled with Tandem Mass Spectrometry (Nano LC-MS/MS)</strong></p>
Evaluating deep learning for predicting epigenomic profiles
<p>Datasets and static codebase to replicate figures and results from the project.</p>
Timing of blood sample processing affects the transcriptomic and epigenomic profiles in CD4+ T-cells of atopic subjects
<p><span>Optimal</span><span> pre-analytical conditions for blood sample processing and isolation of selected cell populations for subsequent transcriptomic and epigenomic studies are required to obtain robust and reproducible results. This pilot study was conducted to investigate the potential effects of timing of CD4<sup>+</sup> T-cell processing from peripheral blood of atopic and non-atopic adults on their transcriptomic and epigenetic profiles. Two heparinized blood samples were drawn from each of three atopic and three healthy individuals. For each individual, </span><span>CD4<sup>+</sup></span><span> T-cells were isolated from the first blood sample within 2 hours (immediate) or from the second blood sample after 24 hours storage (delayed). RNA sequencing (RNA-Seq) and histone H3K27 acetylation chromatin immunoprecipitation sequencing (ChIP-Seq) analyses were performed. A multiplicity of genes was shown to be differentially expressed in immediately processed </span><span>CD4<sup>+</sup></span><span> T-cells from atopic versus healthy subjects. These differences disappeared when comparing delayed processed cells due to a drastic change in expression levels of atopy-related genes in delayed processed </span><span>CD4<sup>+</sup></span><span> T-cells from atopic donors. This finding was further validated on the epigenomic level by examining H3K27 acetylation profiles. In contrast, transcriptomic and epigenomic profiles of blood </span><span>CD4<sup>+</sup></span><span> T-cells of healthy donors remained rather unaffected. Taken together, for successful transcriptomics and epigenomics studies, detailed standard operating procedures developed on the basis of samples from both healthy and disease conditions are implicitly recommended.</span></p>
Fig. 1 in Cuticular Hydrocarbon Profile Analyses Help Clarify the Species Identity of Dry-Mounted Cuckoo Wasps (Hymenoptera: Chrysididae), Including Type Material, and Reveal Evidence for a Cryptic Species
Fig. 1. Adult female paratype of the cuckoo wasp Chrysis parabrevitarsis n. sp. (Germany, Rhineland-Palatinate, Bellheim, 10 June 2012; voucher ID: ZFMK-TIS-36479), Photograph: O. Niehuis.
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.