Endothelial Cells Induced Progenitors Into Brown Fat to Reduce Atherosclerosis.

BACKGROUND: Insulin resistance (IR) can increase atherosclerotic and cardiovascular risk by inducing endothelial dysfunction, decreasing nitric oxide (NO) production, and accelerating arterial inflammation. The aim is to determine the mechanism by which insulin action and NO production in endothelial cells can improve systemic bioenergetics and decrease atherosclerosis via differentiation of perivascular progenitor cells (PPCs) into brown adipocytes (BAT). METHODS: Studies used various endothelial transgenic and deletion mutant ApoE-/- mice of insulin receptors, eNOS (endothelial NO synthase) and ETBR (endothelin receptor type B) receptors for assessments of atherosclerosis. Cells were isolated from perivascular fat and micro-vessels for studies on differentiation and signaling mechanisms in responses to NO, insulin, and lipokines from BAT. RESULTS: Enhancing insulin's actions on endothelial cells and NO production in ECIRS1 transgenic mice reduced body weight and increased systemic energy expenditure and BAT mass and activity by inducing differentiation of PPCs into beige/BAT even with high-fat diet. However, positive changes in bioenergetics, BAT differentiation from PPCs and weight loss were inhibited by N(gamma)-nitro-L-arginine methyl ester (L-NAME), an inhibitor of eNOS, in ECIRS1 mice and eNOSKO mice. The mechanism mediating NO's action on PPC differentiation into BAT was identified as the activation of solubilized guanylate cyclase/PKGIα (cGMP protein-dependent kinase Iα)/GSK3ß (glycogen synthase kinase 3ß) pathways. Plasma lipidomics from ECIRS1 mice with NO-induced increased BAT mass revealed elevated 12,13-diHOME production. Infusion of 12,13-diHOME improved endothelial dysfunction and decreased atherosclerosis, whereas its reduction had opposite effects in ApoE-/-mice. CONCLUSIONS: Activation of eNOS and endothelial cells by insulin enhanced the differentiation of PPC to BAT and its lipokines and improved systemic bioenergetics and atherosclerosis, suggesting that endothelial dysfunction is a major contributor of energy disequilibrium in obesity.

CLINICAL CHARACTERIZATION OF AQUEOUS AND VITREOUS RETINOL-BINDING PROTEIN 3 CONCENTRATIONS IN RELATION TO DIABETIC RETINOPATHY SEVERITY, RETINAL STRUCTURES, AND SYSTEMIC COMPLICATIONS.

PURPOSE: To evaluate Retinol-Binding Protein 3 (RBP3) from photoreceptors in aqueous and its association with vitreous concentrations, diabetic retinopathy (DR) severity, retinal layer thickness, and clinical characteristics in people with diabetes. METHODS: RBP3 concentration was measured by custom-developed enzyme-linked immunosorbent assay in aqueous and correlated with vitreous concentrations in patients from the 50-Year Medalist study and Beetham Eye Institute at Joslin Diabetes Center. RESULTS: Aqueous RBP3 concentration (N = 131) was elevated in eyes with no to mild DR (mean ± SD 0.7 nM ± 0.2) and decreased in eyes with moderate to severe DR (0.65 nM ± 0.3) and proliferative DR (0.5 nM ± 0.2, P < 0.001) compared to eyes without diabetes. Aqueous and vitreous RBP3 concentrations correlated with each other (r = 0.34, P = 0.001) and between fellow eyes (P < 0.0001). History of retinal surgery did not affect aqueous RBP3 concentrations, but cataract surgery affected both vitreous and aqueous levels. Elevated aqueous RBP3 concentration associated with increased thickness of the outer nuclear layer (P = 0.004) and correlated with hemoglobin A1c, whereas vitreous RBP3 concentrations correlated with diabetic systemic complications. CONCLUSION: These findings suggest that aqueous RBP3 concentration may be an important endogenous clinical retinal protective factor, a biomarker for DR severity, and a promising VEGF-independent clinical intervention target in DR.

Remaining Useful Life Prediction of Lithium-Ion Batteries Using Neural Networks with Adaptive Bayesian Learning.

With smart electronic devices delving deeper into our everyday lives, predictive maintenance solutions are gaining more traction in the electronic manufacturing industry. It is imperative for the manufacturers to identify potential failures and predict the system/device's remaining useful life (RUL). Although data-driven models are commonly used for prognostic applications, they are limited by the necessity of large training datasets and also the optimization algorithms used in such methods run into local minima problems. In order to overcome these drawbacks, we train a Neural Network with Bayesian inference. In this work, we use Neural Networks (NN) as the prediction model and an adaptive Bayesian learning approach to estimate the RUL of electronic devices. The proposed prognostic approach functions in two stages-weight regularization using adaptive Bayesian learning and prognosis using NN. A Bayesian framework (particle filter algorithm) is adopted in the first stage to estimate the network parameters (weights and bias) using the NN prediction model as the state transition function. However, using a higher number of hidden neurons in the NN prediction model leads to particle weight decay in the Bayesian framework. To overcome the weight decay issues, we propose particle roughening as a weight regularization method in the Bayesian framework wherein a small Gaussian jitter is added to the decaying particles. Additionally, weight regularization was also performed by adopting conventional resampling strategies to evaluate the efficiency and robustness of the proposed approach and to reduce optimization problems commonly encountered in NN models. In the second stage, the estimated distributions of network parameters were fed into the NN prediction model to predict the RUL of the device. The lithium-ion battery capacity degradation data (CALCE/NASA) were used to test the proposed method, and RMSE values and execution time were used as metrics to evaluate the performance.

Scaffolding protein Gab2 is involved in postnatal development and lipopolysaccharide-induced activation of microglia in the mouse brain.

Grb2-associated-binding protein-2 (Gab2) is a member of the Gab/DOS family and functions as an adapter protein downstream of several growth factor signaling pathways. Gab2 is considered an Alzheimer's disease susceptibility gene. However, the role of Gab2 in the brain is still largely unknown. Herein, we report that Gab2 is involved in the postnatal development of microglia in mice. The Gab2 expression in the brain was detected at postnatal day 1 (P1) and increased until P14 but decreased thereafter. The tyrosine phosphorylation of Gab2 (pGab2) was also detected at P1 and increased until P14. Next, we focused on microglial development in Gab2 knockout and heterozygous mice. Although differences were not detected in the cytoplasmic area of Iba1-labeled microglia between Gab2(±) and Gab2(-/-) mice, the analysis of CD68 and cathepsin D (indicators of microglial lysosomal activation) immunolabeling within Iba1+ cells revealed significant underdevelopment of microglial lysosomes in Gab2(-/-) mice at P60. In addition to the developmental abnormality of microglia in Gab2(-/-) mice, lipopolysaccharide-induced lysosomal activation was selectively suppressed in Gab2(-/-) mice compared to that in Gab2(±) mice. Our findings suggest that Gab2 is involved not only in postnatal development but also in lysosomal activation of microglia, therefore Gab2 dysfunction in microglia might potentially contribute to the development of neurodegenerative diseases.

Thrombolysis in Large Diffusion-Weighted Imaging Lesions: Lower Chance but Still a Chance.

BACKGROUND: We sought to investigate whether early thrombolytic treatment can result in favorable functional outcome even in patients with large diffusion-weighted imaging (DWI) lesions. MATERIALS AND METHODS: We analyzed 566 patients who received intravenous alteplase within 4.5 hours from onset, initially underwent DWI and magnetic resonance angiography, and had acute infarction confined to anterior circulation. DWI lesion volumes were measured semiautomatically. The association between DWI lesion volume and 3-month outcome in patients who achieved early recanalization was assessed. The DWI lesion volume cutoff, which predicts unfavorable outcome despite recanalization, was determined. In patients with large DWI lesions, the distributions of modified Rankin Scale (mRS) score were compared according to the recanalization status. RESULTS: Four hundred thirty-six patients achieved early recanalization. Among these patients, 283 (65%) patients had a favorable functional outcome (mRS score 0-2). DWI lesion volume (odds ratio [OR], 1.38 per 10 mL; 95% confidence interval [CI], 1.22-1.56) was an independent variable associated with poor outcome, along with hypertension (OR, 1.87; 95% CI, 1.12-3.10), National Institutes of Health Stroke Scale (NIHSS) score (OR, 1.13; 95% CI, 1.08-1.19), and onset-to-needle time (OR, 1.08 per 10 minutes; 95% CI, 1.03-1.13). The DWI lesion of 60 mL or higher highly predicted an unfavorable outcome with a positive predictive value of 95.3%. In patients with a DWI lesion of 60 mL or higher, recanalization had no benefit for an mRS score of 0-2 but was significantly associated with an mRS score of 0-3 (OR, 4.64; 95% CI, 1.08-19.97). CONCLUSIONS: Despite early recanalization, the probability of favorable outcome is low in patients with a DWI lesion of 60 mL or higher. Nevertheless, the benefit of recanalization still persists in large DWI lesions.

High residual platelet reactivity (HRPR) for adenosine diphosphate (ADP) stimuli is a determinant factor for long-term outcomes in acute ischemic stroke with anti-platelet agents: The meaning of HRPR after ADP might be more prominent in large atherosclerotic infarction than other subtypes of AIS.

High residual platelet activation (HRPA) after ADP stimuli has associated with recurrent vascular events in acute atherothrombosis with the use of antiplatelet agents (APAs). However, there has been little evidence supporting this association in acute ischemic stroke (AIS). In this study, we evaluated the influences of HRPR after ADP stimuli on the 1-year incidence of recurrent cardiovascular events and mortality in AIS with APAs. We conducted an observational, referral center cohort study on 968 AIS patients with APAs from January 2010 to December 2013 who were evaluated using optical platelet aggregometry (OPA). All patients received the dual APA combination of aspirin and clopidogrel or aspirin alone. We evaluated their platelet function 5 days after hospital admission using OPA. HRPR after ADP stimuli was defined as platelet aggregation of 70 % or greater according to OPA after 10 µM ADP stimuli. The primary endpoint was a composite of all causes of death, myocardial infarction, and stroke at the 1-year follow-up. The secondary endpoints were each component of the primary endpoint. The event rate of primary endpoint was 11.3 % (109/968). Its rate was significantly higher in the patients with HRPR (16.7 %) than in those without (9.7 %). HPRP was independently associated with the primary endpoint (OR = 1.97, CI 1.22-3.18, p < 0.01). According to the AIS subtype, the presence of HRPR was independently significant for the occurrence of the primary endpoint in the large artery atherosclerosis (LAA) subtype only (OR = 2.26, CI 1.15-4.45, p = 0.02). In this study, the presence of HRPR after ADP stimuli is associated with a poor long-term outcome after acute ischemic stroke. In particular, the influence of this factor might be more prominent in LAA compared with other types of AIS.

Impact of Prehospital Intervention on Delay Time to Thrombolytic Therapy in a Stroke Center with a Systemized Stroke Code Program.

BACKGROUND: The use of emergency medical services (EMS) and notification to hospitals by paramedics for patients with suspected stroke are crucial determinants in reducing delay time to acute stroke treatment. The aim of this study is to investigate whether EMS use and prehospital notification (PN) can shorten the time to thrombolytic therapy in a stroke center with a systemized stroke code program. METHODS: Beginning in January 2012, stroke experts in our stroke center received direct calls via mobile phone from paramedics prenotifying the transport of patients with suspected stroke. We compared baseline characteristics and prehospital/in-hospital delay time in stroke patients treated with intravenous recombinant tissue plasminogen activator for 44 months with and without EMS use and/or PN. RESULTS: Intravenous thrombolytic therapy was performed on 274 patients. Of those patients, 215 (78.5%) were transported to the hospital via EMS and 59 (21.5%) were admitted via private modes of transportation. The patients who used EMS had shorter median onset-to-arrival times (62 minutes versus 116 minutes, P < .001). There was no difference in in-hospital delay time between the 2 groups. In 28 cases (13%) of EMS transport, EMS personnel called the clinical staff to notify the incoming patient. Prenotification by EMS was associated with shorter median door-to-imaging time (9 minutes versus 12 minutes, P = .045) and door-to-needle time (20 minutes versus 29 minutes, P = .011). CONCLUSIONS: We found that EMS use reduces prehospital delay time. However, EMS use without prenotification does not shorten in-hospital processing time in a stroke center with a systemized stroke code program.

A systemized stroke code significantly reduced time intervals for using intravenous tissue plasminogen activator under magnetic resonance imaging screening.

BACKGROUND: A stroke code can shorten time intervals until intravenous tissue plasminogen activator (IV t-PA) treatment in acute ischemic stroke (AIS). Recently, several reports demonstrated that magnetic resonance imaging (MRI)-based thrombolysis had reduced complications and improved outcomes in AIS despite longer processing compared with computed tomography (CT)-based thrombolysis. METHODS: In January 2009, we implemented CODE RED, a computerized stroke code, at our hospital with the aim of achieving rapid stroke assessment and treatment. We included patients with thrombolysis from January 2007 to December 2008 (prestroke code period) and from January 2009 to May 2013 (poststroke code period). The IV t-PA time intervals and 90-day modified Rankin Scale (mRS) scores were collected. RESULTS: During the observation period, 252 patients used IV t-PA under the CODE RED (MRI based: 208; CT based: 44). The remaining 71 patients (MRI based: 53; CT based: 18) received it before the implementation of our stroke code. After implementation of CODE RED, door-to-image time, door-to-needle time, and the onset-to-needle time were significantly reduced by 11, 18, and 22 minutes in MRI-based thrombolysis. Particularly, the proportion of favorable outcome (mRS score 0-2) was significantly increased (from 41.5% to 60.1%, P = .02) in poststroke than in prestroke code period in MRI-based thrombolysis. However, in ordinal regression, the presence of stroke code showed just a trend for favorable outcome (odds ratio, .99-2.87; P = .059) at 90 days of using IV t-PA after correction of age, sex, and National Institutes of Health Stroke Scale. CONCLUSIONS: In this study, we demonstrated that a systemized stroke code shortened time intervals for using IV t-PA under MRI screening. Also, our results showed a possibility that a systemized stroke code might enhance the efficacy of MRI-based thrombolysis. In the future, we need to carry out a more detailed prospective study about this notion.

Outcomes after tissue plasminogen activator administration under the drip and ship paradigm may differ according to the regional stroke care system.

The drip and ship paradigm for stroke patients enhances the rate of using intravenous tissue plasminogen activator (IVT) in community hospitals. The safety and outcomes of patients treated with IVT for acute ischemic stroke (AIS) under the drip and ship paradigm were compared with patients directly treated at a comprehensive stroke center in the Busan metropolitan area of Korea. This was a retrospective study of patients with AIS treated with IVT between January 2009 and January 2012. Information on patients' baseline characteristics, neuroimaging, symptomatic intracerebral hemorrhage (sICH), and outcome 90 days after using IVT was obtained from our stroke registry. We surveyed stroke neurologists regarding their pattern of post-thrombolysis care. During the observation periods, we selected 317 patients using IVT. Among these, 239 patients received IVT at our stroke center, and 78 were treated at 21 community hospitals under the drip and ship paradigm. Initial neurologic deficits and the size of ischemic lesions on magnetic resonance imaging were much more severe in patients treated with IVT under the drip and ship paradigm compared with patients treated at our comprehensive stroke center. The prevalence of a poor outcome (modified Rankin Scale score 3-6) 90 days after IVT was much higher in patients treated with the drip and ship paradigm than in those treated at our comprehensive stroke center. Regarding the occurrence of sICH, there was no significant difference between the 2 groups. The clinical characteristics and outcomes after using IVT under the drip and ship paradigm may differ greatly among stroke care systems.

FX: an RNA-Seq analysis tool on the cloud.

UNLABELLED: FX is an RNA-Seq analysis tool, which runs in parallel on cloud computing infrastructure, for the estimation of gene expression levels and genomic variant calling. In the mapping of short RNA-Seq reads, FX uses a transcriptome-based reference primarily, generated from ~160 000 mRNA sequences from RefSeq, UCSC and Ensembl databases. This approach reduces the misalignment of reads originating from splicing junctions. Unmapped reads not aligned on known transcripts are then mapped on the human genome reference. FX allows analysis of RNA-Seq data on cloud computing infrastructures, supporting access through a user-friendly web interface. AVAILABILITY: FX is freely available on the web at (http://fx.gmi.ac.kr), and can be installed on local Hadoop clusters. Guidance for the installation and operation of FX can be found under the 'Documentation' menu on the website. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Dissemination and Symptoms of Monkeypox Virus Infection.

The monkeypox virus is endemic in Africa. However, the virus has spread worldwide since May 2022, and it has now been confirmed in 109 countries (as of September 22, 2022). Thus, an urgent investigation of the outbreak patterns of confirmed cases and evidence of viral infection is needed. This study investigated the spread of monkeypox in 109 countries, including 15 Asian-Pacific countries, by examining the number of cases, symptoms of infection, and the period between diagnosis and death.

A Python-based educational software tool for visualizing bioinformatics alignment algorithms.

Bioinformatics education can be defined as the teaching and learning of how to use software tools, along with mathematical and statistical analysis, to solve biological problems. Although many resources are available, most students still struggle to understand even the simplest sequence alignment algorithms. Applying visualizations to these topics benefits both lecturers and students. Unfortunately, educational software for visualizing step-bystep processes in the user experience of sequence alignment algorithms is rare. In this article, an educational visualization tool for biological sequence alignment is presented, and the source code is released in order to encourage the collaborative power of open-source software, with the expectation of further contributions from the community in the future. Two different modules are integrated to enable a student to investigate the characteristics of alignment algorithms.

Feasibility of Prompt Lumbar Drainage in Patients with Aneurysmal Subarachnoid Hemorrhage.

BACKGROUND: Numerous studies have shown that continuous lumbar drainage (LD) reduces spontaneous subarachnoid hemorrhage (SAH)-related complications, decreasing the incidence of cerebral vasospasm, delayed cerebral ischemia , and hydrocephalus in patients treated with coiling or clipping, but performing LD before securing the aneurysm is still controversial. Our hospital has been implementing prompt LD for several years, and we present the results in this paper. METHODS: Between January 2014 and December 2020, a total of 438 patients with SAH were included in this retrospective study. The indication for prompt LD was aneurysmal SAH of modified Fisher grade III or higher without dense intraventricular hemorrhage with obstructive hydrocephalus requiring extraventricular drainage or large intracranial hemorrhage requiring immediate decompression. Prompt LD was performed for 229 patients with SAH, and the control group included 209 patients. We compared in-hospital mortality and vasospasm or hydrocephalus occurrence and procedure-related complications between the two groups. RESULTS: The in-hospital mortality rate was 7.4% for patients with prompt LD and 14.4% for patients without LD, and the difference was significant (P = 0.019). Vasospasm occurred in 10% of patients with prompt LD and 16.7% of controls (P = 0.039). Hydrocephalus requiring extraventricular drainage occurred in 10.9% of the LD group and 28.7% of the control group (P < 0.001). Rebleeding occurrence was 3.1% in the prompt LD group and 5.7% in the non-LD group (P = 0.168). Cerebrospinal fluid infection occurred in 0.4% of the prompt LD group and 1.4% of controls(P = 0.272). CONCLUSIONS: Prompt LD is a feasible option for treating patients with selective aneurysmal SAH.

TcellInflamedDetector: an R package to distinguish T cell inflamed tumor types from non-T cell inflamed tumor types.

A major issue in the use of immune checkpoint inhibitors is their lack of efficacy in many patients. Previous studies have reported that the T cell inflamed signature can help predict the response to immunotherapy. Thus, many studies have investigated mechanisms of immunotherapy resistance by defining the tumor microenvironment based on T cell inflamed and non-T cell inflamed subsets. Although methods of calculating T cell inflamed subsets have been developed, valid screening tools for distinguishing T cell inflamed from non-T cell inflamed subsets using gene expression data are still needed, since general researchers who are unfamiliar with the details of the equations can experience difficulties using extant scoring formulas to conduct analyses. Thus, we introduce TcellInflamedDetector, an R package for distinguishing T cell inflamed from non-T cell inflamed samples using cancer gene expression data via bulk RNA sequencing.

Analysis of the Rate of Confirmed COVID-19 Cases in Seoul and Factors Affecting It Using Big Data Analysis.

Coronavirus disease (COVID-19) is caused by infection with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and presents with mild to severe symptoms. Vaccines have been developed, but COVID-19 persists. Therefore, it is necessary to analyze big data at an early stage to establish an effective infection prevention strategy. To reduce SARS-CoV-2 infection, this study aimed to analyze the infection factors by region within Seoul, Korea and identify the major factors affecting the infection rate. For ease of data aggregation, the study was conducted after a data refinement operation that organized data in the same group into categories, and classified them in detail by specific keywords. Based on the results of this study, if preventive measures are established after identifying the representative infectious factors, periods, and routes of COVID-19 infection, the infection rate could be effectively reduced in the future.

Elevated Retinol Binding Protein 3 Concentrations Are Associated With Decreased Vitreous Inflammatory Cytokines, VEGF, and Progression of Diabetic Retinopathy.

OBJECTIVE: To correlate inflammatory cytokines and vascular endothelial growth factor (VEGF) in vitreous and plasma with vitreous retinol binding protein 3 (RBP3), diabetic retinopathy (DR) severity, and DR worsening in a population with type 1 and type 2 diabetes. RESEARCH DESIGN AND METHODS: RBP3, VEGF, and inflammatory cytokines were measured in plasma and vitreous samples (n = 205) from subjects of the Joslin Medalist Study and Beetham Eye Institute. RESULTS: Higher vitreous RBP3 concentrations were associated with less severe DR (P < 0.0001) and a reduced risk of developing proliferative DR (PDR) (P < 0.0001). Higher RBP3 correlated with increased photoreceptor segment thickness and lower vitreous interleukin-12 (IL-12), tumor necrosis factor-α (TNF-α), and TNF-ß (P < 0.05). PDR was associated with lower vitreous interferon-γ and IL-10 and higher VEGF, IL-6, and IL-15 (P < 0.05), but was not associated with their plasma concentrations. CONCLUSIONS: Higher vitreous RBP3 concentrations are associated with less severe DR and slower rates of progression to PDR, supporting its potential as a biomarker and therapeutic agent for preventing DR worsening, possibly by lowering retinal VEGF and inflammatory cytokines.

Estimation of the journal distance of Genomics & Informatics from other bioinformatics-driven journals, 2003-2018.

This study explored the trends of Genomics & Informatics during the period of 2003-2018 in comparison with 11 other scholarly journals: BMC Bioinformatics, Algorithms for Molecular Biology: AMB, BMC Systems Biology, Journal of Computational Biology, Briefings in Bioinformatics, BMC Genomics, Nucleic Acids Research, American Journal of Human Genetics, Oncogenesis, Disease Markers, and Microarrays. In total, 22,423 research articles were reviewed. Content analysis was the main method employed in the current research. The results were interpreted using descriptive analysis, a clustering analysis, word embedding, and deep learning techniques. Trends are discussed for the 12 journals, both individually and collectively. This is an extension of our previous study (PMCID: PMC6808643).

Investigation on the Microscopic/Macroscopic Mechanical Properties of a Thermally Annealed Nafion® Membrane.

The Nafion® electrolyte membrane, which provides a proton pathway, is an essential element in fuel cell systems. Thermal treatment without additional additives is widely used to modify the mechanical properties of the membrane, to construct reliable and durable electrolyte membranes in the fuel cell. We measured the microscopic mechanical properties of thermally annealed membranes using atomic force microscopy with the two-point method. Furthermore, the macroscopic property was investigated through tensile tests. The microscopic modulus exceeded the macroscopic modulus over all annealing temperature ranges. Additionally, the measured microscopic modulus increased rapidly near 150 °C and was saturated over that temperature, whereas the macroscopic modulus continuously increased until 250 °C. This mismatched micro/macroscopic reinforcement trend indicates that the internal reinforcement of the clusters is induced first until 150 °C. In contrast, the reinforcement among the clusters, which requires more thermal energy, probably progresses even at a temperature of 250 °C. The results showed that the annealing process is effective for the surface smoothing and leveling of the Nafion® membrane until 200 °C.

Using the PubAnnotation ecosystem to perform agile text mining on Genomics & Informatics: a tutorial review.

The prototype version of the full-text corpus of Genomics & Informatics has recently been archived in a GitHub repository. The full-text publications of volumes 10 through 17 are also directly downloadable from PubMed Central (PMC) as XML files. During the Biomedical Linked Annotation Hackathon 6 (BLAH6), we experimented with converting, annotating, and updating 301 PMC full-text articles of Genomics & Informatics using PubAnnotation, a system that provides a convenient way to add PMC publications based on PMCID. Thus, this review aims to provide a tutorial overview of practicing the iterative task of named entity recognition with the PubAnnotation/PubDictionaries/TextAE ecosystem. We also describe developing a conversion tool between the Genia tagger output and the JSON format of PubAnnotation during the hackathon.

Organizing an in-class hackathon to correct PDF-to-text conversion errors of Genomics & Informatics 1.0.

This paper describes a community effort to improve earlier versions of the full-text corpus of Genomics & Informatics by semi-automatically detecting and correcting PDF-to-text conversion errors and optical character recognition errors during the first hackathon of Genomics & Informatics Annotation Hackathon (GIAH) event. Extracting text from multi-column biomedical documents such as Genomics & Informatics is known to be notoriously difficult. The hackathon was piloted as part of a coding competition of the ELTEC College of Engineering at Ewha Womans University in order to enable researchers and students to create or annotate their own versions of the Genomics & Informatics corpus, to gain and create knowledge about corpus linguistics, and simultaneously to acquire tangible and transferable skills. The proposed projects during the hackathon harness an internal database containing different versions of the corpus and annotations.