Trace compounds in Early Medieval Egyptian blue carry information on provenance, manufacture, application, and ageing.
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ABSTRACT:
SUBMITTER: Dariz P
PROVIDER: S-EPMC8163881 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:The Celtic linguistic community dominated large spans of Central and Western Europe between 800 BC and 500 AD, but knowledge of their traditional medicine is very limited. Multiple progressive plant gains in Neolithic settlements along the Danube and up the Rhine valleys suggested that taxon diversity of gathered plants peaked at the Balkans and was subsequently reduced as crop and gathered plants packages were adopted and dispersed throughout Neolithic Europe. This process coincided with the Bronze Age migration of the R1b proto-Celtic tribes, and their herbal traditions were occasionally recorded in the classic Greco-Roman texts on herbal medicines. The provenance of Celtic (Gallic) healing methods and magical formulas as recorded by Pliny, Scribonius Largus, and Marcellus Empiricus can still be found in the first part of the medieval Welsh (Cymry) herbal manuscript Meddygon Myddfai (recipes 1-188). Although the majority of Myddfai I recipes were based on the Mediterranean herbal tradition of Dioscorides and Macer Floridus, they preserved the unique herbal preparation signatures distinct from continental and Anglo-Saxon counterparts in increased use of whey and ashes as vehicles for formulation of herbal remedies. Six plants could be hypothetically attributed to the Celtic (Welsh) herbal tradition including foxglove (Digitalis purpurea L.), corn bellflower (Legousia speculum-veneris L.), self-heal (Prunella vulgaris L.), sharp dock (Rumex conglomeratus Murray), water pimpernel (Samolus valerandi L.), and river startip (Scapania undulata L.) This review provides initial evidence for traces of Celtic framework in the Welsh herbal tradition and warrants further investigations of bioactivity and clinical applications of the described plant leads.
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Project description:Even within the early sensory areas, the majority of the input to any given cortical neuron comes from other cortical neurons. To extend our knowledge of the contextual information that is transmitted by such lateral and feedback connections, we investigated how visually nonstimulated regions in primary visual cortex (V1) and visual area V2 are influenced by the surrounding context. We used functional magnetic resonance imaging (fMRI) and pattern-classification methods to show that the cortical representation of a nonstimulated quarter-field carries information that can discriminate the surrounding visual context. We show further that the activity patterns in these regions are significantly related to those observed with feed-forward stimulation and that these effects are driven primarily by V1. These results thus demonstrate that visual context strongly influences early visual areas even in the absence of differential feed-forward thalamic stimulation.
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Project description:The hippocampus is critical for human episodic memory, but its role remains controversial. One fundamental question concerns whether the hippocampus represents specific objects or assigns context-dependent representations to objects. Here, we used multivoxel pattern similarity analysis of fMRI data during retrieval of learned object sequences to systematically investigate hippocampal coding of object and temporal context information. Hippocampal activity patterns carried information about the temporal positions of objects in learned sequences, but not about objects or temporal positions in random sequences. Hippocampal activity patterns differentiated between overlapping object sequences and between temporally adjacent objects that belonged to distinct sequence contexts. Parahippocampal and perirhinal cortex showed different pattern information profiles consistent with coding of temporal position and object information, respectively. These findings are consistent with models proposing that the hippocampus represents objects within specific temporal contexts, a capability that might explain its critical role in episodic memory.
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Project description:Unraveling the network of interactions in ecological communities is a daunting task. Common methods to infer interspecific interactions from cross-sectional data are based on co-occurrence measures. For instance, interactions in the human microbiome are often inferred from correlations between the abundances of bacterial phylogenetic groups across subjects. We tested whether such correlation-based methods are indeed reliable for inferring interaction networks. For this purpose, we simulated bacterial communities by means of the generalized Lotka-Volterra model, with variation in model parameters representing variability among hosts. Our results show that correlations can be indicative for presence of bacterial interactions, but only when measurement noise is low relative to the variation in interaction strengths between hosts. Indication of interaction was affected by type of interaction network, process noise and sampling under non-equilibrium conditions. The sign of a correlation mostly coincided with the nature of the strongest pairwise interaction, but this is not necessarily the case. For instance, under rare conditions of identical interaction strength, we found that competitive and exploitative interactions can result in positive as well as negative correlations. Thus, cross-sectional abundance data carry limited information on specific interaction types. Correlations in abundance may hint at interactions but require independent validation.
| S-EPMC9518925 | biostudies-literature
Project description:From eukaryotes to prokaryotes, all cells secrete extracellular vesicles (EVs) as part of their regular homeostasis, intercellular communication, and cargo disposal. Accumulating evidence suggests that small EVs carry functional small RNAs, potentially serving as extracellular messengers and liquid-biopsy markers. Yet, the complete transcriptomic landscape of EV-associated small RNAs during disease progression is poorly delineated due to critical limitations including the protocols used for sequencing, suboptimal alignment of short reads (20-50 nt), and uncharacterized genome annotations-often denoted as the 'dark matter' of the genome. In this study, we investigate the EV-associated small unannotated RNAs that arise from endogenous genes and are part of the genomic 'dark matter', which may play a key emerging role in regulating gene expression and translational mechanisms. To address this, we created a distinct small RNAseq dataset from human prostate cancer & benign tissues, and EVs derived from blood (pre- & post-prostatectomy), urine, and human prostate carcinoma epithelial cell line. We then developed an unsupervised data-based bioinformatic pipeline that recognizes biologically relevant transcriptional signals irrespective of their genomic annotation. Using this approach, we discovered distinct EV-RNA expression patterns emerging from the un-annotated genomic regions (UGRs) of the transcriptomes associated with tissue-specific phenotypes. We have named these novel EV-associated small RNAs as 'EV-UGRs' or "EV-dark matter". Here, we demonstrate that EV-UGR gene expressions are downregulated by ∼100 fold (FDR < 0.05) in the circulating serum EVs from aggressive prostate cancer subjects. Remarkably, these EV-UGRs expression signatures were regained (upregulated) after radical prostatectomy in the same follow-up patients. Finally, we developed a stem-loop RT-qPCR assay that validated prostate cancer-specific EV-UGRs for selective fluid-based diagnostics. Overall, using an unsupervised data driven approach, we investigate the 'dark matter' of EV-transcriptome and demonstrate that EV-UGRs carry tissue-specific Information that significantly alters pre- and post-prostatectomy in the prostate cancer patients. Although further validation in randomized clinical trials is required, this new class of EV-RNAs hold promise in liquid-biopsy by avoiding highly invasive biopsy procedures in prostate cancer.
| S-EPMC11327273 | biostudies-literature
Project description:BackgroundBiomedical knowledge graphs have become important tools to computationally analyse the comprehensive body of biomedical knowledge. They represent knowledge as subject-predicate-object triples, in which the predicate indicates the relationship between subject and object. A triple can also contain provenance information, which consists of references to the sources of the triple (e.g. scientific publications or database entries). Knowledge graphs have been used to classify drug-disease pairs for drug efficacy screening, but existing computational methods have often ignored predicate and provenance information. Using this information, we aimed to develop a supervised machine learning classifier and determine the added value of predicate and provenance information for drug efficacy screening. To ensure the biological plausibility of our method we performed our research on the protein level, where drugs are represented by their drug target proteins, and diseases by their disease proteins.ResultsUsing random forests with repeated 10-fold cross-validation, our method achieved an area under the ROC curve (AUC) of 78.1% and 74.3% for two reference sets. We benchmarked against a state-of-the-art knowledge-graph technique that does not use predicate and provenance information, obtaining AUCs of 65.6% and 64.6%, respectively. Classifiers that only used predicate information performed superior to classifiers that only used provenance information, but using both performed best.ConclusionWe conclude that both predicate and provenance information provide added value for drug efficacy screening.
| S-EPMC6127943 | biostudies-literature
Project description:Sensory processing involves information flow between neocortical areas, assumed to rely on direct intracortical projections. However, cortical areas may also communicate indirectly via higher-order nuclei in the thalamus, such as the pulvinar or lateral posterior nucleus (LP) in the visual system of rodents. The fine-scale organization and function of these cortico-thalamo-cortical pathways remains unclear. We find that responses of mouse LP neurons projecting to higher visual areas likely derive from feedforward input from primary visual cortex (V1) combined with information from many cortical and subcortical areas, including superior colliculus. Signals from LP projections to different higher visual areas are tuned to specific features of visual stimuli and their locomotor context, distinct from the signals carried by direct intracortical projections from V1. Thus, visual transthalamic pathways are functionally specific to their cortical target, different from feedforward cortical pathways, and combine information from multiple brain regions, linking sensory signals with behavioral context.
| S-EPMC8221812 | biostudies-literature
Project description:OBJECTIVES:A multi-isotope study was conducted on individuals buried at Skriðuklaustur monastery (AD 1493-1554) to investigate their geographic origins and dietary composition. Comparative material from individuals excavated from Skeljastaðir, an inland farm site was also analyzed. MATERIALS AND METHODS:Bone collagen was extracted from 50 humans (Skriðuklaustur and Skeljastaðir) and 25 animals (Skriðuklaustur) and analyzed for ?13 C, ?15 N, and ?34 S. Dental enamel samples from 31 individuals (Skriðuklaustur) were also analyzed for 87 Sr/86 Sr, ?18 O, ?13 C, and trace elements (Pb, Sr, Zn, Ba). RESULTS:The mean value determined from individuals from Skriðuklaustur (n = 36) was ?13 C = -18.7?±?0.8‰, ?15 N = 12.8?±?1.1‰, and ?34 S = 9.0?±?1.6‰, whereas at Skeljastaðir (n = 14), it was ?13 C = -20.5?±?0.8‰, ?15 N = 7.8?±?0.9‰, and ?34 S = 9.4?±?1.6‰. At Skriðuklaustur, human dental enamel samples (n = 31) provided a 87 Sr/86 Sr range of 0.7060-0.7088, ?18 Ophosphate from 13.9 to 16.1‰ and ?13 Ccarbonate from -16.6 to -12.9‰. Inferred drinking water (?18 Odw ) values range from -12.3 to -8.9‰. Sr concentrations range from 25.8 to 156.7 ppm, Ba from 0.11 to 0.81?ppm, Zn from 43.8 to 145.8 ppm, and Pb from 0.13 to 9.40?ppm. DISCUSSION:A combination of results indicates that the people from Skriðuklaustur were born in Iceland, but some lived inland during childhood while others lived closer to the coast. Since Skriðuklaustur was a hospital, these individuals may have sought medical treatment at the monastery. The ?13 C and ?15 N values determined from bone collagen indicate that the people residing at Skriðuklaustur consumed a diet high in marine protein, while those residing at Skeljastaðir exhibit values more consistent with terrestrial resources.
| S-EPMC6973133 | biostudies-literature
Project description:Gamma rhythms in many brain regions, including the primary visual cortex (V1), are thought to play a role in information processing. Here, we report a surprising finding of 3 narrowband gamma rhythms in V1 that processed distinct spatial frequency (SF) signals and had different neural origins. The low gamma (LG; 25 to 40 Hz) rhythm was generated at the V1 superficial layer and preferred a higher SF compared with spike activity, whereas both the medium gamma (MG; 40 to 65 Hz), generated at the cortical level, and the high gamma HG; (65 to 85 Hz), originated precortically, preferred lower SF information. Furthermore, compared with the rates of spike activity, the powers of the 3 gammas had better performance in discriminating the edge and surface of simple objects. These findings suggest that gamma rhythms reflect the neural dynamics of neural circuitries that process different SF information in the visual system, which may be crucial for multiplexing SF information and synchronizing different features of an object.
| S-EPMC8691622 | biostudies-literature
Project description:Abstract The lateral occipital complex (LOC) is a set of areas in the human occipito-temporal cortex responding to objects as opposed to low-level control stimuli. Conventional functional magnetic resonance imaging (fMRI) analysis methods based on regional averages could not detect signals discriminative of different types of objects in this region. Here, we examined fMRI signals using multivariate pattern recognition (support vector classification) to systematically explore the nature of object-related information available in fine-grained activity patterns in the LOC. Distributed fMRI signals from the LOC allowed for above-chance discrimination not only of the category but also of within-category exemplars of everyday man-made objects, and such exemplar-specific information generalized across changes in stimulus size and viewpoint, particularly in posterior subregions. Object identity could also be predicted from responses of the early visual cortex, even significantly across the changes in size and viewpoint used here. However, a dissociation was observed between these two regions of interest in the degree of discrimination for objects relative to size: In the early visual cortex, two different sizes of the same object were even better discriminated than two different objects (in accordance with measures of pixelwise stimulus similarity), whereas the opposite was true in the LOC. These findings provide the first evidence that direct evoked fMRI activity patterns in the LOC can be different for individual object exemplars (within a single category). We propose that pattern recognition methods as used here may provide an alternative approach to study mechanisms of neuronal representation based on aspects of the fMRI response independent of those assessed in adaptation paradigms.
| S-EPMC2832116 | biostudies-literature