Genetic Risk Factors for Early-Onset Merkel Cell Carcinoma

Importance

Merkel cell carcinoma (MCC) is a rare, aggressive neuroendocrine skin cancer. Of the patients who develop MCC annually, only 4% are younger than 50 years.

Objective

To identify genetic risk factors for early-onset MCC via genomic sequencing.

Design, Setting, and Participants

The study represents a multicenter collaboration between the National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), the National Institute of Allergy and Infectious Diseases (NIAID), and the University of Washington. Participants with early-onset and later-onset MCC were prospectively enrolled in an institutional review board-approved study at the University of Washington between January 2003 and May 2019. Unrelated controls were enrolled in the NIAID Centralized Sequencing Program (CSP) between September 2017 and September 2021. Analysis was performed from September 2021 and March 2023. Early-onset MCC was defined as disease occurrence in individuals younger than 50 years. Later-onset MCC was defined as disease occurrence at age 50 years or older. Unrelated controls were evaluated by the NIAID CSP for reasons other than familial cancer syndromes, including immunological, neurological, and psychiatric disorders.

Results

This case-control analysis included 1012 participants: 37 with early-onset MCC, 45 with later-onset MCC, and 930 unrelated controls. Among 37 patients with early-onset MCC, 7 (19%) had well-described variants in genes associated with cancer predisposition. Six patients had variants associated with hereditary cancer syndromes (ATM = 2, BRCA1 = 2, BRCA2 = 1, and TP53 = 1) and 1 patient had a variant associated with immunodeficiency and lymphoma (MAGT1). Compared with 930 unrelated controls, the early-onset MCC cohort was significantly enriched for cancer-predisposing pathogenic or likely pathogenic variants in these 5 genes (odds ratio, 30.35; 95% CI, 8.89-106.30; P < .001). No germline disease variants in these genes were identified in 45 patients with later-onset MCC. Additional variants in DNA repair genes were also identified among patients with MCC.

Conclusions and Relevance

Because variants in certain DNA repair and cancer predisposition genes are associated with early-onset MCC, genetic counseling and testing should be considered for patients presenting at younger than 50 years.

Rab12 is a regulator of LRRK2 and its activation by damaged lysosomes

Leucine-rich repeat kinase 2 (LRRK2) variants associated with Parkinson's disease (PD) and Crohn's disease lead to increased phosphorylation of its Rab substrates. While it has been recently shown that perturbations in cellular homeostasis including lysosomal damage can increase LRRK2 activity and localization to lysosomes, the molecular mechanisms by which LRRK2 activity is regulated have remained poorly defined. We performed a targeted siRNA screen to identify regulators of LRRK2 activity and identified Rab12 as a novel modulator of LRRK2-dependent phosphorylation of one of its substrates, Rab10. Using a combination of imaging and immunopurification methods to isolate lysosomes, we demonstrated that Rab12 is actively recruited to damaged lysosomes and leads to a local and LRRK2-dependent increase in Rab10 phosphorylation. PD-linked variants, including LRRK2 R1441G and VPS35 D620N, lead to increased recruitment of LRRK2 to the lysosome and a local elevation in lysosomal levels of pT73 Rab10. Together, these data suggest a conserved mechanism by which Rab12, in response to damage or expression of PD-associated variants, facilitates the recruitment of LRRK2 and phosphorylation of its Rab substrate(s) at the lysosome.

Early Inflammatory Response of Dental Pulp in Response to Biodentin and Mineral Trioxide Aggregate as Pulp-capping Agents

This study was carried out to observe immediate inflammatory response of Human Dental Pulp capped with Biodentin and Mineral Trioxide Aggregate (MTA). This prospective clinical study was carried out in the Department of Conservative Dentistry and Endodontics together with the Department of Orthodontia, Bangabandhu Sheikh Mujib Medical University (BSMMU), Bangladesh from 2016 to 2018. A total number of eighty (80) permanent premolars teeth planned to be extracted for orthodontic alignment of occlusion were used as study sample. Those teeth were divided into two groups; Group A and Group B, having 40 teeth in each (n=40). An occlusal exposure of approximately 1.5mm in diameter was made. Then in -group A, exposed pulp were capped with 2-mm-thick layer of sterile Biodentin (Septodont) and in-group B with ProRoot White MTA (Dentsply). After pulp capping with the experimental material in respective group, cavities in all teeth were restored with glass ionomer cement. After 24 hours the teeth were extracted, fixed in 10% buffered formalin solution, then decalcified by 10.0% nitric acid and embedded in paraffin. Now 2 to 3-micron-thick serial sections were made in the linguo-buccal plane and finally stained with hematoxylin-eosin. Now pulpal inflammation in respect of type, intensity and extension, were determined by using a predetermined evaluation criterion under an optical microscope at 40× magnifications. Statistical differences among the experimental groups were analyzed by Descriptive analysis (Cross Tabulation) (p<0.05). Histologically both the tested materials produced immediate pulpal tissue reaction. 'Biodentin' found to be most immediate pulpal tissue reactive (reactive in 100% cases), Whereas, MTA produced immediate tissue reaction only in 50.0% cases. Immediate pulpal inflammatory reaction in response to tested material found to be statistically significant different between 'Biodentin' and 'MTA' (p=0.001). According to present study Biodentin is found to be more immediate pulpal tissue reactive than MTA when used as a pulp capping material.

Higher-level gait disorder as a presenting manifestation of progressive supranuclear palsy: a video case report

INTRODUCTION

Frontal gait disorder/gait apraxia is a higher-order motor deficit with various causes, characterized by difficulties with gait initiation, such as freezing or ignition failure. We aimed to report a patient who presented with progressive higher-level gait disorder and fall episodes as the initial manifestations of progressive supranuclear palsy (PSP). Patient data were obtained from medical records from the Department of General Medicine, Burdwan Medical College and Hospital (Burdwan, West Bengal, India).

CASE REPORT

A 58-year-old previously healthy woman presented with a gait disorder and fall episodes. Detailed neurological examination highlighted characteristic facial appearance (wide-eyed staring, furrowing of the forehead with a frowning expression, and fixed expression of the lower face). She was hypokinetic-rigid with symmetrical signs and predominant axial rigidity with retrocolic trunk and neck posture. Gait examination revealed a higher-level gait pattern characterized by an exhibition of profound start hesitation requiring assistance from nearby objects/persons. Once walking was underway, steps became relatively better, but ineffective gait re-emerged when she attempted turning. She had short strides, freezing, broad stance base, disequilibrium, slow leg movement, shuffling, and loss of normal fluidity of trunk and limbs. Postural reflexes were impaired. Brain magnetic resonance imaging revealed atrophy of the midbrain, dilated aqueduct of Sylvius and third ventricle, atrophy of frontal lobes and typical hummingbird sign. Diagnosis of probable PSP was finally made.

CONCLUSIONS

Several etiologies, including PSP, should be considered in appropriate clinical contexts if gait examination demonstrates a higher-order gait disorder.

Vulnerable newborn types: analysis of subnational, population-based birth cohorts for 541 285 live births in 23 countries, 2000-2021

OBJECTIVE

To examine prevalence of novel newborn types among 541 285 live births in 23 countries from 2000 to 2021.

DESIGN

Descriptive multi-country secondary data analysis.

SETTING

Subnational, population-based birth cohort studies (n = 45) in 23 low- and middle-income countries (LMICs) spanning 2000-2021.

POPULATION

Liveborn infants.

METHODS

Subnational, population-based studies with high-quality birth outcome data from LMICs were invited to join the Vulnerable Newborn Measurement Collaboration. We defined distinct newborn types using gestational age (preterm [PT], term [T]), birthweight for gestational age using INTERGROWTH-21st standards (small for gestational age [SGA], appropriate for gestational age [AGA] or large for gestational age [LGA]), and birthweight (low birthweight, LBW [<2500 g], nonLBW) as ten types (using all three outcomes), six types (by excluding the birthweight categorisation), and four types (by collapsing the AGA and LGA categories). We defined small types as those with at least one classification of LBW, PT or SGA. We presented study characteristics, participant characteristics, data missingness, and prevalence of newborn types by region and study.

RESULTS

Among 541 285 live births, 476 939 (88.1%) had non-missing and plausible values for gestational age, birthweight and sex required to construct the newborn types. The median prevalences of ten types across studies were T+AGA+nonLBW (58.0%), T+LGA+nonLBW (3.3%), T+AGA+LBW (0.5%), T+SGA+nonLBW (14.2%), T+SGA+LBW (7.1%), PT+LGA+nonLBW (1.6%), PT+LGA+LBW (0.2%), PT+AGA+nonLBW (3.7%), PT+AGA+LBW (3.6%) and PT+SGA+LBW (1.0%). The median prevalence of small types (six types, 37.6%) varied across studies and within regions and was higher in Southern Asia (52.4%) than in Sub-Saharan Africa (34.9%).

CONCLUSIONS

Further investigation is needed to describe the mortality risks associated with newborn types and understand the implications of this framework for local targeting of interventions to prevent adverse pregnancy outcomes in LMICs.

Chromosomal microarray analysis supplements exome sequencing to diagnose children with suspected inborn errors of immunity

Purpose

Though copy number variants (CNVs) have been suggested to play a significant role in inborn errors of immunity (IEI), the precise nature of this role remains largely unexplored. We sought to determine the diagnostic contribution of CNVs using genome-wide chromosomal microarray analysis (CMA) in children with IEI.

Methods

We performed exome sequencing (ES) and CMA for 332 unrelated pediatric probands referred for evaluation of IEI. The analysis included primary, secondary, and incidental findings.

Results

Of the 332 probands, 134 (40.4%) received molecular diagnoses. Of these, 116/134 (86.6%) were diagnosed by ES alone. An additional 15/134 (11.2%) were diagnosed by CMA alone, including two likely de novo changes. Three (2.2%) participants had diagnostic molecular findings from both ES and CMA, including two compound heterozygotes and one participant with two distinct diagnoses. Half of the participants with CMA contribution to diagnosis had CNVs in at least one non-immune gene, highlighting the clinical complexity of these cases. Overall, CMA contributed to 18/134 diagnoses (13.4%), increasing the overall diagnostic yield by 15.5% beyond ES alone.

Conclusion

Pairing ES and CMA can provide a comprehensive evaluation to clarify the complex factors that contribute to both immune and non-immune phenotypes. Such a combined approach to genetic testing helps untangle complex phenotypes, not only by clarifying the differential diagnosis, but in some cases by identifying multiple diagnoses contributing to the overall clinical presentation.

Health-related quality of life and perceived stress of informal caregivers of children and adolescents with intellectual disabilities and ADHD

Introduction

Informal caregivers of children and adolescents with intellectual disabilities and attention deficit/hyperactivity disorder (ADHD) face numerous challenges. However, no study has yet compared the HRQoL of the caregivers of children and adolescents with these two conditions. We aimed to compare the HRQoL and perceived stress of caregivers of children and adolescents with intellectual disabilities and ADHD.

Methods

The HRQoL and perceived stress of informal caregivers of children and adolescents with intellectual disabilities and ADHD (40 in each group) were compared using the perceived stress scale and the Quality of Life Enjoyment and Satisfaction Questionnaire - Short Form, respectively.

Results

HRQoL was significantly worse in most dimensions in caregivers of children and adolescents with severe ADHD than in caregivers of children and adolescents with severe intellectual disabilities. However, perceived stress was similar.

Conclusion

Differences in the impact of intellectual disability and ADHD on family members' HRQoL should be considered while developing educational programs for patients and their families.

Associated Injuries Related to Patients With Facial Fractures

Study Design: Retrospective Study. Objective: To find out the incidence, type, and severity of injuries in other parts of the body in patients diagnosed with facial fractures. The study also analyzed any correlation between these injuries and facial fractures. Methods: A retrospective study of 991 patients with facial fractures during the period of 2006-2016. Results: 111 patients reported associated injuries (11.1%). The most common type of injury was limb injury (33.33%), followed by head injury (22.5%), clavicle fracture (14.7%), rib fracture (10.9%), cervical spine injury (5.4%), and other injuries constituted (13.2%). Multiple associated injuries were observed in 14% of patients. Conclusion: The findings show that facial fracture management is a multidisciplinary approach. Prompt diagnosis and proper management are important to reduce the mortality rate and improve the prognosis of the patient.

Manganese substitution induced magnetic transformation and magnetoelectricity in SrFe12O19

In this study, manganese substituted strontium hexaferrite (SrFe_12-xMn_xO₁₉; x = 0, 3, 5, and 7) prepared by the sol-gel auto-combustion method are studied. We observed that the substituted Mn preferentially goes to the 2a and 12k sites of Fe. Raman modes related to the 12k site suggest the stiffening of the lattice. The transformation of the grain's shape from hexagonal (x = 0 and 3) to rhombohedral (x = 7) was observed, as shown in the micrographs obtained from FESEM. The thermomagnetic curves show the shift of T_C to lower temperatures with the increase in the Mn content. From x = 5 onwards, the growth of another magnetic phase (FiM2) of lower coercivity apart from the parent phase (FiM1) of higher coercivity is seen. The FiM2 phase was found to increase with the Mn content in the sample (16.4(3)% for x = 5 but 66.2(5)% for x = 7). Although the magnetization for both FiM1 and FiM2 decreases with the increase in temperature, both magnetic phases behave in contrast to each other for x = 5 and x = 7. The study suggests a transformation of the compound from high magnetic anisotropy (x = 0) to low magnetic anisotropy (x = 7). The x = 5 composition sample displays the highest value of the first-order ME coefficient (0.83(2) mV × cm^-1 × Oe^-1). The observed value for x = 5 composition is ∼2.5 times higher than that of the parent x = 0 composition sample (0.33(2) mV × cm^-1 × Oe^-1). The studies thus suggest that the x = 5 composition is one of the viable candidates for magnetoelectric applications.

Challenges to manage primary chylopericardium in children

Primary chylopericardium (PC) is a rare entity in the pediatric population with very few reported cases. Most cases of chylopericardium manifest after trauma or following cardiac surgery. The other etiologies which may lead to chylopericardium are malignancy, tuberculosis, or congenital lymphangiomatosis. We report two cases of PC in the pediatric population with contrasting outcomes. Both failed conservative management with dietary modification and octreotide. Surgery with pleuropericardial and pleuroperitoneal windows was performed in both. The first case had a thoracic duct ligation. The first patient died, and the second survived.

FOXI3 haploinsufficiency contributes to low T-cell receptor excision circles and T-cell lymphopenia

BACKGROUND

Newborn screening can identify neonatal T-cell lymphopenia through detection of a low number of copies of T-cell receptor excision circles in dried blood spots collected at birth. After a positive screening result, further diagnostic testing is required to determine whether the subject has severe combined immunodeficiency or other causes of T-cell lymphopenia. Even after thorough evaluation, approximately 15% of children with a positive result of newborn screening for T-cell receptor excision circles remain genetically undiagnosed. Identifying the underlying genetic etiology is necessary to guide subsequent clinical management and family planning.

OBJECTIVE

We sought to elucidate the genetic basis of patients with T-cell lymphopenia without an apparent genetic diagnosis.

METHODS

We used clinical genomic testing as well as functional and immunologic assays to identify and elucidate the genetic and mechanistic basis of T-cell lymphopenia.

RESULTS

We report 2 unrelated individuals with nonsevere T-cell lymphopenia and abnormal T-cell receptor excision circles who harbor heterozygous loss-of-function variants in forkhead box I3 transcription factor (FOXI3).

CONCLUSION

Our findings support the notion that haploinsufficiency of FOXI3 results in T-cell lymphopenia with variable expressivity and that FOXI3 may be a key modulator of thymus development.

Clinical Exome Sequencing of 1000 Families with Complex Immune Phenotypes: Towards comprehensive genomic evaluations

BACKGROUND

Prospective genetic evaluation of patients at our referral research hospital presents clinical research challenges.

OBJECTIVE

This study sought not only a single-gene explanation for participants' immune-related presentations, but viewed each participant holistically, with the potential to have multiple genetic contributions to their immune-phenotype and other heritable comorbidities relevant to their presentation and health.

METHODS

We developed a program integrating exome sequencing, chromosomal microarray, phenotyping, results return with genetic counseling, and reanalysis in 1505 individuals from 1000 families with suspected or known inborn errors of immunity.

RESULTS

Probands were 50.8% female, 71.5% >18 years, and had diverse immune presentations. Overall, 327/1000 probands (32.7%) received 361 molecular diagnoses. These included 17 probands with diagnostic copy number variants, 32 probands with secondary findings, and 31 probands with multiple molecular diagnoses. Reanalysis added 22 molecular diagnoses, predominantly due to new disease-gene associations (9/22, 40.9%). One-quarter of the molecular diagnoses (92/361) did not involve immune-associated genes. Molecular diagnosis was correlated with younger age, male sex, and a higher number of organ systems involved. This program also facilitated the discovery of new gene-disease associations such as SASH3-related immunodeficiency. A review of treatment options and ClinGen actionability curations suggest that at least 251/361 (69.5%) of these molecular diagnoses could translate into >1 management option.

CONCLUSION

This program contributes to our understanding of the diagnostic and clinical utility whole exome analysis on a large scale.

CLINICAL

Implication: Comprehensive analysis of exome data has diagnostic and clinical utility for patients with suspected inborn errors of immunity.

Preclinical and clinical evaluation of the LRRK2 inhibitor DNL201 for Parkinson's disease

Mutations in leucine-rich repeat kinase 2 (LRRK2) are the most common genetic risk factors for Parkinson's disease (PD). Increased LRRK2 kinase activity is thought to impair lysosomal function and may contribute to the pathogenesis of PD. Thus, inhibition of LRRK2 is a potential disease-modifying therapeutic strategy for PD. DNL201 is an investigational, first-in-class, CNS-penetrant, selective, ATP-competitive, small-molecule LRRK2 kinase inhibitor. In preclinical models, DNL201 inhibited LRRK2 kinase activity as evidenced by reduced phosphorylation of both LRRK2 at serine-935 (pS935) and Rab10 at threonine-73 (pT73), a direct substrate of LRRK2. Inhibition of LRRK2 by DNL201 demonstrated improved lysosomal function in cellular models of disease, including primary mouse astrocytes and fibroblasts from patients with Gaucher disease. Chronic administration of DNL201 to cynomolgus macaques at pharmacologically relevant doses was not associated with adverse findings. In phase 1 and phase 1b clinical trials in 122 healthy volunteers and in 28 patients with PD, respectively, DNL201 at single and multiple doses inhibited LRRK2 and was well tolerated at doses demonstrating LRRK2 pathway engagement and alteration of downstream lysosomal biomarkers. Robust cerebrospinal fluid penetration of DNL201 was observed in both healthy volunteers and patients with PD. These data support the hypothesis that LRRK2 inhibition has the potential to correct lysosomal dysfunction in patients with PD at doses that are generally safe and well tolerated, warranting further clinical development of LRRK2 inhibitors as a therapeutic modality for PD.

PhenoRerank: A re-ranking model for phenotypic concept recognition pre-trained on human phenotype ontology

The study aims at developing a neural network model to improve the performance of Human Phenotype Ontology (HPO) concept recognition tools. We used the terms, definitions, and comments about the phenotypic concepts in the HPO database to train our model. The document to be analyzed is first split into sentences and annotated with a base method to generate candidate concepts. The sentences, along with the candidate concepts, are then fed into the pre-trained model for re-ranking. Our model comprises the pre-trained BlueBERT and a feature selection module, followed by a contrastive loss. We re-ranked the results generated by three robust HPO annotation tools and compared the performance against most of the existing approaches. The experimental results show that our model can improve the performance of the existing methods. Significantly, it boosted 3.0% and 5.6% in F1 score on the two evaluated datasets compared with the base methods. It removed more than 80% of the false positives predicted by the base methods, resulting in up to 18% improvement in precision. Our model utilizes the descriptive data in the ontology and the contextual information in the sentences for re-ranking. The results indicate that the additional information and the re-ranking model can significantly enhance the precision of HPO concept recognition compared with the base method.

Comparison of phenolic content and antioxidant activity of two common fruits of Bangladesh in solvents of varying polarities

Phenolic content and antioxidant activity of two common fruits of Bangladesh, namely Phyllunthus emblica and Elaeocarpus floribundus, were measured in water, methanol, ethanol, acetone and hexane extracts. Several in vitro models including phosphomolybdenum assay, DPPH free radical scavenging assay, FRAP assay and reducing power assay were used to assess the antioxidant activity of these extracts in comparison with reference antioxidants. Between the two fruits, P. emblica showed higher phenolic content and antioxidant activity in all the solvents used. In the DPPH scavenging assay, the activity of P. emblica extracts was close to reference antioxidants, ascorbic acid and BHT. Besides, considering the solvents used, extracts of both fruits had the highest phenolic and antioxidant activity in polar solvents. The correlation coefficient between total phenolics and antioxidant activities was found statistically significant. These findings suggest that P. emblica could be an excellent antioxidant resource for industries like food, pharmaceutical, and cosmetics.

NP-MRD: the Natural Products Magnetic Resonance Database

The Natural Products Magnetic Resonance Database (NP-MRD) is a comprehensive, freely available electronic resource for the deposition, distribution, searching and retrieval of nuclear magnetic resonance (NMR) data on natural products, metabolites and other biologically derived chemicals. NMR spectroscopy has long been viewed as the ‘gold standard’ for the structure determination of novel natural products and novel metabolites. NMR is also widely used in natural product dereplication and the characterization of biofluid mixtures (metabolomics). All of these NMR applications require large collections of high quality, well-annotated, referential NMR spectra of pure compounds. Unfortunately, referential NMR spectral collections for natural products are quite limited. It is because of the critical need for dedicated, open access natural product NMR resources that the NP-MRD was funded by the National Institute of Health (NIH). Since its launch in 2020, the NP-MRD has grown quickly to become the world's largest repository for NMR data on natural products and other biological substances. It currently contains both structural and NMR data for nearly 41,000 natural product compounds from >7400 different living species. All structural, spectroscopic and descriptive data in the NP-MRD is interactively viewable, searchable and fully downloadable in multiple formats. Extensive hyperlinks to other databases of relevance are also provided. The NP-MRD also supports community deposition of NMR assignments and NMR spectra (1D and 2D) of natural products and related meta-data. The deposition system performs extensive data enrichment, automated data format conversion and spectral/assignment evaluation. Details of these database features, how they are implemented and plans for future upgrades are also provided. The NP-MRD is available at https://np-mrd.org.

Bioefficacy, residue dynamics and dietary risk assessment of gibberellic acid in improving the potential yield of tomato (Solanum lycopersicum L.)

The increasing use of gibberellic acid (GA₃) to promote fruit growth and yield has necessitated research into its trace level determination and estimation in harvested product. The phytohormone has increased the tomato yield (tonne ha^-1) up to 24.7% with uniform fruit shape, size colour and lustre. A fast, simple, high-throughput analytical method was standardised based on electrospray ionisation - liquid chromatography-tandem mass spectrometry (LC-MS/MS). The samples were extracted using acidified (1% formic acid) methanol. The method was validated as per the SANTE/12682/2019 guidelines. The limits of detection (LOD) and quantification (LOQ) were 0.01 and 0.05 mg kg^-1. The average recoveries at LOQ and higher levels were in the range of 86-108% with relative standard deviation (RSD) < 20%. The validated method was successfully applied under field condition by following first-order kinetics with half-lives (T_1/2) 1.76 days (recommended dose) and 1.99 days (double dose). The estimated pre-harvest intervals (PHIs) were 6 days (recommended dose) and 8 days (double dose). Studies on dietary risk assessment concluded that even after spray of GA₃ at recommended dose, the harvested produce (tomato) could be consumed safely.

Recent Developments Toward Integrated Metabolomics Technologies (UHPLC-MS-SPE-NMR and MicroED) for Higher-Throughput Confident Metabolite Identifications

Metabolomics has emerged as a powerful discipline to study complex biological systems from a small molecule perspective. The success of metabolomics hinges upon reliable annotations of spectral features obtained from MS and/or NMR. In spite of tremendous progress with regards to analytical instrumentation and computational tools, < 20% of spectral features are confidently identified in most untargeted metabolomics experiments. This article explores the integration of multiple analytical instruments such as UHPLC-MS/MS-SPE-NMR and the cryo-EM method MicroED to achieve large-scale and confident metabolite identifications in a higher-throughput manner. UHPLC-MS/MS-SPE allows for the simultaneous automated purification of metabolites followed by offline structure elucidation and structure validation by NMR and MicroED. Large-scale study of complex metabolomes such as that of the model plant legume Medicago truncatula can be achieved using an integrated UHPLC-MS/MS-SPE-NMR metabolomics platform. Additionally, recent developments in MicroED to study structures of small organic molecules have enabled faster, easier and precise structure determinations of metabolites. A MicroED small molecule structure elucidation workflow (e.g., crystal screening, sample preparation, data collection and data processing/structure determination) has been described. Ongoing MicroED methods development and its future scope related to structure elucidation of specialized metabolites and metabolomics are highlighted. The incorporation of MicroED with a UHPLC-MS/MS-SPE-NMR instrumental ensemble offers the potential to accelerate and achieve higher rates of metabolite identification.

PhenoTagger: a hybrid method for phenotype concept recognition using human phenotype ontology

MOTIVATION

Automatic phenotype concept recognition from unstructured text remains a challenging task in biomedical text mining research. Previous works that address the task typically use dictionary-based matching methods, which can achieve high precision but suffer from lower recall. Recently, machine learning-based methods have been proposed to identify biomedical concepts, which can recognize more unseen concept synonyms by automatic feature learning. However, most methods require large corpora of manually annotated data for model training, which is difficult to obtain due to the high cost of human annotation.

RESULTS

In this article, we propose PhenoTagger, a hybrid method that combines both dictionary and machine learning-based methods to recognize Human Phenotype Ontology (HPO) concepts in unstructured biomedical text. We first use all concepts and synonyms in HPO to construct a dictionary, which is then used to automatically build a distantly supervised training dataset for machine learning. Next, a cutting-edge deep learning model is trained to classify each candidate phrase (n-gram from input sentence) into a corresponding concept label. Finally, the dictionary and machine learning-based prediction results are combined for improved performance. Our method is validated with two HPO corpora, and the results show that PhenoTagger compares favorably to previous methods. In addition, to demonstrate the generalizability of our method, we retrained PhenoTagger using the disease ontology MEDIC for disease concept recognition to investigate the effect of training on different ontologies. Experimental results on the NCBI disease corpus show that PhenoTagger without requiring manually annotated training data achieves competitive performance as compared with state-of-the-art supervised methods.

AVAILABILITYAND IMPLEMENTATION

The source code, API information and data for PhenoTagger are freely available at https://github.com/ncbi-nlp/PhenoTagger.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.