Improving the interoperability of drugs terminologies: Infusing local standardization with an international perspective.

OBJECTIVES: The objective of this study is to describe how OCRx (Canadian Drug Ontology) has been built to address the dual need for local drug information integration in Canada and alignment with international standards requirements. METHODS: This paper delves into (i) the implementation efforts to meet the Identification of Medicinal Product (IDMP) requirements in OCRx, alongside the ontology update strategy, (ii) the structure of the ontology itself, (iii) the alignment approach with several reference Knowledge Organization Systems, including SNOMED CT, RxNorm, and the list of "Code Identifiant de Spécialité" (CIS-Code), and (iv) the look-up services developed to facilitate its access and utilization. RESULTS: Each OCRx release contains two distinct versions: the full and the up-to-date version. The full version encompasses all drugs with a DIN code sanctioned by Health Canada, while the up-to-date version is limited to drugs currently marketed in Canada. In the last release of OCRx, the full version comprises 162,400 classes; meanwhile, the up-to-date version consists of 36,909 classes. In terms of mappings with OCRx, substances in RxNorm and SNOMED CT fall below 40%, registering at 37% and 22% respectively. Meanwhile, mappings for CIS-Code achieve coverage of 61%. The strength mappings are notably low for RxNorm at 40% and for CIS-code at 28%. This affects the mapping of clinical drugs, which are predominantly alignable through post-coordinated expressions: 56% for RxNorm, 80% for SNOMED CT, and 35% for CIS-Code. The main support service of OCRx is a look-up service known as PaperRx that displays OCRx's entities based on description logic queries (DL-queries) performed through the classified structure of OCRx. The look-up services also contain a SPARQL endpoint, an OCRx OWL file downloader, and a RESTful API. DISCUSSION: The OCRx ontology demonstrates a significant effort towards integrating Canadian drug information with international standards. However, there are areas for improvement. In the future, our focus will be on refining the structure of OCRx for better classification capability and improvement of dosage conversion. Additionally, we aim to harness OCRx in constructing an ontology-based annotator, setting our sights on its deployment in real-world data integration scenarios.

Tripartite Feature Enhanced Pyramid Network for Dense Prediction.

Learning pyramidal feature representations is important for many dense prediction tasks (e.g., object detection, semantic segmentation) that demand multi-scale visual understanding. Feature Pyramid Network (FPN) is a well-known architecture for multi-scale feature learning, however, intrinsic weaknesses in feature extraction and fusion impede the production of informative features. This work addresses the weaknesses of FPN through a novel tripartite feature enhanced pyramid network (TFPN), with three distinct and effective designs. First, we develop a feature reference module with lateral connections to adaptively extract bottom-up features with richer details for feature pyramid construction. Second, we design a feature calibration module between adjacent layers that calibrates the upsampled features to be spatially aligned, allowing for feature fusion with accurate correspondences. Third, we introduce a feature feedback module in FPN, which creates a communication channel from the feature pyramid back to the bottom-up backbone and doubles the encoding capacity, enabling the entire architecture to generate incrementally more powerful representations. The TFPN is extensively evaluated over four popular dense prediction tasks, i.e., object detection, instance segmentation, panoptic segmentation, and semantic segmentation. The results demonstrate that TFPN consistently and significantly outperforms the vanilla FPN. Our code is available at https://github.com/jamesliang819.

Manganese Tricarbonyl Diimine Bromide Complexes as Electrocatalysts for Proton Reduction.

Manganese tricarbonyl diimine complexes bearing pyridine and imidazole ligands have been prepared as electrocatalysts for proton reduction using acetic acid as the proton source. The electron-donor ability of the diimine ligand is found to play an important role in determining the efficiency of the electrocatalysts with [MnBr(pybz)(CO)3] (pybz = 2-(2-pyridyl)benzimidazole) exhibiting the lowest overpotential (0.28 V) toward proton reduction. The [Mn(pybz)(CO)3(MeCN)]+ cationic complex prepared via debromination of [MnBr(pybz)(CO)3] by a silver salt has also been shown to catalyze proton reduction upon its electrochemical reduction. A neutral complex [Mn(pyridine-benzimidazolate)(CO)3(MeCN)], which can be synthesized by reacting [MnBr(pybz)(CO)3] with a strong base, has been detected using IR-SEC (infrared spectroelectrochemistry) as an intermediate species in the catalytic process. Using [MnBr(pybz)(CO)3] as the model electrocatalyst, we have carried out density functional calculations to propose a proton reduction mechanism consistent with our experimental observations.

A short interspersed nuclear element-based quantitative PCR assay for simultaneous human and dog DNA detection and quantification.

This study aimed to develop a quantitative PCR assay to simultaneously quantify human and dog DNA in a multispecies mixture to inform downstream analyses in routine forensic casework and scientific research. The human target is the Alu Yb8 element, which has approximately 2000 copies per cell, and the canine target is the SINEC_Cf element, which has approximately 200,000 copies per cell. The internal positive control is a universal exogenous assay consisting of forward and reverse primers, a NED-labeled probe with an MGBNFQ quencher and a 65-bp synthetic template. Results suggest a potentially robust assay with a fast run time and a high degree of sensitivity, precision and species specificity, with direct application to domestic pet samples in veterinary genetics and forensics.

Platelets in myeloproliferative neoplasms have a distinct transcript signature in the presence of marrow fibrosis.

Marrow fibrosis is a significant complication of myeloproliferative neoplasms (MPN) that affects up to 20% of patients and is associated with a poor prognosis. The pathological processes that lead to fibrotic progression are not well understood, but megakaryocytes have been implicated in the process. The aim of this study was to determine whether platelets, derived from megakaryocytes, have transcriptomic alterations associated with fibrosis. Platelets from MPN patients with and without fibrosis and non-malignant control individuals were assessed using next generation sequencing. Results from the initial training cohort showed discrete changes in platelet transcripts in the presence of marrow fibrosis. We identified more than 1000 differentially expressed transcripts from which a putative 3-gene fibrotic platelet signature (CCND1, H2AX [previously termed H2AFX] and CEP55) could be identified. This fibrosis-associated signature was assessed blinded on platelets from an independent test MPN patient cohort. The 3-gene signature was able to discriminate between patients with and without marrow fibrosis with a positive predictive value of 71% (93% specificity, 71% sensitivity). This demonstrates that assessment of dysregulated transcripts in platelets may be a useful monitoring tool in MPN to identify progression to marrow fibrosis. Further, sequential monitoring could have clinical applications for early prediction of progression to fibrosis.

Bis(cyclopentadienyl)nickel(II) µ-Thiolato Complexes as Proton Reduction Electrocatalysts.

Thiolato-bridged cyclopentadienylnickel dimeric complexes have been prepared and found to be efficient and robust proton reduction electrocatalysts using acetic acid as the proton source. From cyclic voltammetry studies, moderate overpotentials of around 0.6 V and ic/ip values from 7.8 to 12.2 have been determined for 20 equiv of acetic acid at a scan rate of 100 mV/s. A turnover number of around 7 has been determined for each of the nickel complexes. The thiolato substituent of the complex does not appear to influence the catalysis significantly. Each of the nickel complexes acts as a robust homogeneous catalyst that could sustain continuous proton reduction for hours. On the basis of the experimental data, an electrochemical-chemical-electrochemical-chemical mechanism describing the catalytic process has been proposed as well.

Automated enumeration of lymphoid and plasma cells in bone marrow to establish normal reference ranges.

AIMS: The number of precursor and mature lymphoid cells and plasma cells in normal bone marrow trephine (BMT) biopsies throughout the human lifespan is unknown. Reference ranges have been established from aspirated marrow, but due to haemodilution errors, these do not accurately reflect the native marrow milieu. We aimed to define age-specific, normal reference ranges for lymphoid and plasma cells in BMT biopsy specimens using a combined immunophenotyping and digital enumeration approach. METHODS: Morphologically normal BMT biopsy specimens (n=483) were obtained from patients aged 1 month to 90 years of age. Immunohistochemistry was performed to identify lymphoid progenitors , T-lymphocytes (CD3), B-lymphocytes (CD20) and plasma cells (CD138 and MUM1). Positive cells were counted using digital enumeration software, and the percent positivity for each antigen was determined per case. Mean values were generated for specific age groups, and age-defined reference ranges were determined for each antigen using normalised data. RESULTS: A mean of 16 609 cells (range: 7210-34 097) were counted per biopsy. Infant marrows showed a predominance of immature lymphoid progenitors and B cells. With increasing age, an increase in mean T cell and plasma cell numbers were observed. The results showed the same trends to flow cytometry references for aspirate material although the absolute values differed. CONCLUSIONS: Combined immunohistochemistry and automated enumeration gives an accurate, reproducible number of antigen-positive cells and has generated normal reference ranges for these cell types in BMT biopsies. The method and ranges we have established have the potential to be applied in routine clinical practice.

Imaging flow cytometry to assess chromosomal abnormalities in chronic lymphocytic leukaemia.

Chronic Lymphocytic Leukaemia (CLL), the most common leukaemia in the Western world, has a characteristic phenotype and prognosis largely defined by the presence of cytogenetic aberrations. The gold standard for detecting these cytogenetic abnormalities is interphase fluorescence in situ hybridisation (FISH) performed on cell smears or tissue sections on glass slides. Fluorescently labelled DNA probes bind to specific chromosomal regions and the signal detected by fluorescent microscopy. Generally only 200 cells are assessed and the limit of sensitivity is 3% positive cells. Here we report the development and use of imaging flow cytometry to assess chromosomes by FISH in phenotyped CLL cells in suspension. Thousands of CLL cells, identified by their phenotype, are assessed for specific FISH probe signals using an automated, high throughput imaging flow cytometer. The "extended depth of field" capability of the imaging flow cytometer enables FISH probe signals ("spots") to be resolved and localised within the (stained) nucleus of the immunophenotyped cells. We report the development of the automated "immuno-flowFISH" on normal blood using the Amnis ImageStreamX mark II platform and illustrate the clinical application of the method for the assessment of chromosome 12 in CLL. It is a powerful new method which has potential to be applied at diagnosis for disease stratification, and following treatment to assess residual disease. These applications will assist clinicians in optimising therapeutic decision making and thereby improve patient outcome.

Megakaryocytes in Myeloproliferative Neoplasms Have Unique Somatic Mutations.

Myeloproliferative neoplasms (MPNs) are a group of related clonal hemopoietic stem cell disorders associated with hyperproliferation of myeloid cells. They are driven by mutations in the hemopoietic stem cell, most notably JAK2V617F, CALR, and MPL. Clinically, they have the propensity to progress to myelofibrosis and transform to acute myeloid leukemia. Megakaryocytic hyperplasia with abnormal features are characteristic, and it is thought that these cells stimulate and drive fibrotic progression. The biological defects underpinning this remain to be explained. In this study we examined the megakaryocyte genome in 12 patients with MPNs to determine whether there are somatic variants and whether there is any association with marrow fibrosis. We performed targeted next-generation sequencing for 120 genes associated with myeloid neoplasms on megakaryocytes isolated from aspirated bone marrow. Ten of the 12 patients had genomic defects in megakaryocytes that were not present in nonmegakaryocytic hemopoietic marrow cells from the same patient. The greatest allelic burden was in patients with increased reticulin deposition. The megakaryocyte-unique mutations were predominantly in genes that regulate chromatin remodeling, chromosome alignment, and stability. These findings show that genomic abnormalities are present in megakaryocytes in MPNs and that these appear to be associated with progression to bone marrow fibrosis.

Ultrasound-guided suprascapular nerve block: a correlation with fluoroscopic and cadaveric findings.

PURPOSE: Previous work on the ultrasound-guided injection technique and the sonoanatomy of the suprascapular region relevant to the suprascapular nerve (SSN) block suggested that the ultrasound scan showed the presence of the suprascapular notch and transverse ligament. The intended target of the ultrasound-guided injection was the notch. The objective of this case report and the subsequent cadaver dissection findings is to reassess the interpretation of the ultrasound images when locating structures for SSN block. CLINICAL FEATURES: A 45-yr-old man with chronic shoulder pain received an ultrasound-guided SSN block using the suprascapular notch as the intended target. The position of the needle was verified by fluoroscopy, which showed the tip of the needle well outside the suprascapular notch. Similar ultrasound-guided SSN blocks were performed in two cadavers. Dissections were performed which showed that the needle tips were not at the suprascapular notch but, more accurately, were close to the SSN but at the floor of the suprascapular fossa between the suprascapular and spinoglenoid notch. CONCLUSION: Our fluoroscopic and cadaver dissection findings both suggest that the ultrasound image of the SSN block shown by the well-described technique is actually targeting the nerve on the floor of the suprascapular spine between the suprascapular and spinoglenoid notches rather than the suprascapular notch itself. The structure previously identified as the transverse ligament is actually the fascia layer of the supraspinatus muscle.