Biolink Model: A universal schema for knowledge graphs in clinical, biomedical, and translational science

Within clinical, biomedical, and translational science, an increasing number of projects are adopting graphs for knowledge representation. Graph‐based data models elucidate the interconnectedness among core biomedical concepts, enable data structures to be easily updated, and support intuitive queries, visualizations, and inference algorithms. However, knowledge discovery across these “knowledge graphs” (KGs) has remained difficult. Data set heterogeneity and complexity; the proliferation of ad hoc data formats; poor compliance with guidelines on findability, accessibility, interoperability, and reusability; and, in particular, the lack of a universally accepted, open‐access model for standardization across biomedical KGs has left the task of reconciling data sources to downstream consumers. Biolink Model is an open‐source data model that can be used to formalize the relationships between data structures in translational science. It incorporates object‐oriented classification and graph‐oriented features. The core of the model is a set of hierarchical, interconnected classes (or categories) and relationships between them (or predicates) representing biomedical entities such as gene, disease, chemical, anatomic structure, and phenotype. The model provides class and edge attributes and associations that guide how entities should relate to one another. Here, we highlight the need for a standardized data model for KGs, describe Biolink Model, and compare it with other models. We demonstrate the utility of Biolink Model in various initiatives, including the Biomedical Data Translator Consortium and the Monarch Initiative, and show how it has supported easier integration and interoperability of biomedical KGs, bringing together knowledge from multiple sources and helping to realize the goals of translational science.

Monazite, rhabdophane, xenotime & churchite: Vibrational spectroscopy of gadolinium phosphate polymorphs

Rare-earth phosphates with the general formula REEPO₄·nH₂O belong to four distinct structural types: monazite, rhabdophane, churchite, and xenotime. We report herein the first direct comparison between vibrational spectra of these compounds for the same metal cation i.e. gadolinium. The four GdPO₄·nH₂O samples were prepared through wet chemistry methods and first characterized by X-ray diffraction. Three distinct spectral domains, associated to the deformation and stretching modes of phosphate tetrahedra (PO₄) and to water molecules vibrations were then analyzed from FTIR and Raman data, and discussed regarding the structural characteristics of each sample. The most obvious differences between the spectra were associated to δ(H₂O) and δ_s(PO₄) modes and led to propose a simple method to rapidly and unambiguously discriminate the four polymorphs.

A randomised clinical trial comparing the flexible fibrescope and the Pentax Airway Scope (AWS)(®) for awake oral tracheal intubation

We compared awake fibreoptic intubation with awake intubation using the Pentax Airway Scope(®) in 40 adult patients. Sedation was achieved using a target-controlled remifentanil infusion of 1-5 ng.ml(-1) and midazolam. The airway was anaesthetised with lidocaine spray and gargle. The total procedure time - a composite of sedation time, topical anaesthesia time and intubation time - was recorded. The operator's impression of the ease of the procedure and the patients' reported comfort were recorded on a 0-100 mm visual analogue scale. The median (IQR [range]) for total procedure time was 900 (739-1059 [616-1215]) s with the fibrescope and 651 (601-720 [498-900]) s with the Pentax Airway Scope (p = 0.0001). The median (IQR [range]) intubation time was 420 (283-480 [120-608]) s with the fibrescope and 183 (144-220 [107-420]) s with the Pentax Airway Scope (p = 0.0002). The median (IQR [range]) visual analogue scores for the operator's ease of intubation for the fibrescope and Pentax Airway Scope were 83.6 (72.0-98.0 [49.0-100.0]) and 86.8 (84.0-91.0 [61.0-100.0]), respectively (p = 0.3507). The median (IQR [range]) visual analogue score for patient comfort was 85.5 (81.0-97.0 [69.0-100.0]) and 79.4 (74.0-85.0 [59.0-100.0]) for the fibrescope and Pentax Airway Scope, respectively (p = 0.06). Total procedure time was significantly shorter with the Pentax Airway Scope compared with the fibrescope, with no difference in procedure difficulty or patient discomfort.

Vibrational spectroscopy of synthetic analogues of ankoleite, chernikovite and intermediate solid solution

Ankoleite (K(UO2)PO4·nH2O), chernikovite (H3O(UO2)PO4·nH2O) and intermediate solid solutions are frequently encountered in the uranium ores that result from the alteration of uranium primary minerals. This paper reports a thorough FTIR and Raman study related to synthetic analogues for these minerals. First, the vibration bands associated to the UO2(2 +) uranyl ion were used to calculate the U = O bond length which appeared in good agreement with the data coming from PXRD. Then, the examination of the phosphate vibration modes in both sets of spectra confirmed the general formulation of the samples and ruled out the presence of hydrogenphosphate groups. Finally, the presence of H2O as well as protonated H3O(+) and/or H5O2(+) species was also pointed out, and could be used to clearly differentiate the various phases prepared. Vibrational spectroscopy then appeared as an efficient method for the investigation of such analogues of natural samples. It should be particularly relevant when identifying these phases in mineral ores or assemblies.

Characterization of selenium in UO2 spent nuclear fuel by micro X-ray absorption spectroscopy and its thermodynamic stability

Direct disposal of spent nuclear fuel (SNF) in deep geological formations is the preferred option for the final storage of nuclear waste in many countries. In order to assess to which extent radionuclides could be released to the environment, it is of great importance to understand how they are chemically bound in the waste matrix. This is particularly important for long-lived radionuclides such as (79)Se, (129)I, (14)C or (36)Cl, which form poorly sorbing anionic species in water and therefore migrate without significant retardation through argillaceous repository materials and host rocks. We present here X-ray absorption spectroscopic data providing evidence that in the investigated SNF samples selenium is directly bound to U atoms as Se(-II) (selenide) ion, probably replacing oxygen in the cubic UO2 lattice. This result is corroborated by a simple thermodynamic analysis, showing that selenide is the stable form of Se under reactor operation conditions. Because selenide is almost insoluble in water, our data indirectly explain the unexpectedly low release of Se in short-term aqueous leaching experiments, compared to iodine or cesium. These results have a direct impact on safety analyses for potential nuclear waste repository sites, as they justify assuming a small fractional release of selenium in performance assessment calculations.

From thorite to coffinite: a spectroscopic study of Th(1-x)U(x)SiO4 solid solutions

Coffinite (USiO4), along with Th(1-x)U(x)SiO4 uranothorite solid solutions, are frequently present in reduced economically exploitable uranium ores. They could also control the concentration of uranium in the environment in the case of accidental release from underground radwaste repository. This paper reports for the first time a thorough FTIR and Raman study relative to the Th(1-x)U(x)SiO4 system, including synthetic analogues of thorite and coffinite end-members. Both sets of spectra confirmed the formulation of the samples and allowed to rule out the presence of structural water molecules and/or hydroxyl groups in the coffinite. Also, no characteristic signal of UO2(2+) uranyl ion was recorded, ensuring that uranium was fully incorporated under its tetravalent oxidation state. The variation of the positions corresponding to SiO4 internal vibration modes was then followed versus the chemical composition of the samples. If the FTIR spectra did not revealed any significant shift in the bands position, several Raman modes followed a linear trend as a function of the uranium incorporation rate. On this basis, Raman spectroscopy could be considered as a promising tool for the semi-quantitative determination of chemical composition of uranothorite samples, particularly for those coming from mineral ores. Finally, the data collected for the coffinite end-member, as the first to be obtained on pure synthetic samples, allowed a review of the results previously reported in the literature for this compound.

Preparation and characterisation of uranium oxides with spherical shapes and hierarchical structures

One of the first reports on shape-controlled uranium oxides with hierarchical structures and their mechanism of formation.

Determination of the relationship between Basal cell carcinoma and human papilloma virus, based on immunohistochemistry staining method

Background:

Basal cell carcinoma (BCC) is the most common skin cancer among Caucasians, and in most cases, occurs in the sun-exposed areas. In recent years, in addition to many other etiologies such as exposure to UV radiation, and occasionally xeroderma pigmentosa, burns, tattoos, and pox scars, human papillomavirus (HPV) is also considered to have an etiologic role. Different studies were conducted with varied results in this regard.

Aims:

We evaluate this plausible relationship between HPV and BCC by means of immunohistochemistry (IHC) staining method.

Methods:

This is an analytic cross-sectional study in which 160 samples were selected randomly consisting of 80 BCC lesions and 80 safe margins. Sampling was done among paraffin-embedded blocks in pathology ward of Kashani and Alzahra hospitals, Isfahan-Iran, from 2004-2007. A section of each block was IHC stained for HPV immunoreactivity (DAKO, Denmark). This was followed by microscopic evaluation in terms of being positive or negative.

Results:

Fifty seven point five percent of the samples belonged to men and the others to women. In 10%, HPV marker was positive, both in lesion and margin. In 83.8% neither the lesions nor the margins were immunoreactive for HPV. Only in 5 cases (6.3%) the lesion was positive and the margin was negative for this marker. There was no case of immunoreactivity for HPV marker in margins, while it was negative in lesions. Our study results followed by McNemar analysis did not show a significant relationship between BCC incidence and HPV existence. This was consistent in both genders (P > 0.05, power > 90%).

Conclusion:

In this study we did not find a significant relationship between BCC and HPV, but based on review of articles it appears that large multicentric studies are to be conducted in this regard.

Thorough analysis of silicon substitution in biphasic calcium phosphate bioceramics: a multi-technique study

Four samples of composition Ca(10)(PO(4))(6-x)(SiO(4))(x)(OH)(2-x), with x=0.0, 0.1, 0.2 and 0.5, were prepared and characterized using powder X-ray and neutron powder diffraction, and (1)H, (31)P and (29)Si nuclear magnetic resonance (NMR) spectroscopy. The composition of the Si-substituted HAp phases was determined by joint Rietveld refinements from powder X-ray and powder neutron diffraction data. Taking into account electroneutrality, a chemical formula for the Si-substituted HAp phases with indication of the incorporated silicate amount is proposed. Solid-state (29)Si NMR confirms the presence of only Q(0) species, in good agreement with the presence of substituted HAp and beta-TCP phases only. Thanks to NMR spectroscopy, two types of protons in the Si-substituted HAp phase were identified, the new site corresponding to species engaged in hydrogen bonding with silicate anions. This allowed further refinement of the formulae for these phases with very good quantitative agreement for populations derived from the refinement and integration of NMR data.

Prevention of fungal colonization and digestion of cellulose by the addition of methylcellulose

When the attachment of cellulolytic rumen fungi to cellulose is blocked by the addition of methylcellulose, cellulose digestion is entirely inhibited. Even after these fungi have colonized and penetrated the cellulosic fibers of filter paper, the addition of methylcellulose effectively halts cellulose digestion. This effect of methylcellulose is accompanied by the complete inhibition of fungal attachment to cellulose fibers; the addition of methylcellulose does not affect the growth of these organisms on soluble substrates. We conclude that fungal cellulose digestion, like bacterial cellulose digestion, requires the spatial juxtaposition of the cellulolytic organism and its insoluble substrate. The simultaneous inhibition of both attachment and digestion by the same inhibitor suggests that these two processes are functionally linked in the fungi.