bluuebunny/crossref_metadata_2025_split huggingface dataset:
A one health approach for enhancing the integration ofSalmonella entericasurveillance in Colombia
Authors: Bernal Johan F. , Díaz Paula L. , Perez-Sepulveda Blanca M. , Valencia-Guerrero María Fernanda , Weisner Magdalena , Clavijo Viviana , Montaño Lucy Angeline , Arevalo Stefany A. , León Ingrid Maribel , Castellanos Luis Ricardo , Underwood Anthony , Duarte Carolina , Argimón Silvia , Moreno Jaime , Aanensen David , Donado-Godoy Pilar 
Published: March 2023

AbstractFoodborne diseases represent a link between environmental, animal, and human health interfaces from the One Health perspective. Whole genome sequencing (WGS) is becoming the gold standard in foodborne surveillance, worldwide. WGS than provides precision data from pathogens allows laboratories to resolve the genetic relations among all sources from One Health perspective, especially during outbreak investigations, getting insights into their transmission routes and pathogenicity.Salmonellaspp. is the most prevalent foodborne bacteria in Colombia, in 2020, 268 foodborne outbreaks were reported to National health institute (INS) and 3079 invasive and faecal salmonellosis samples from 81% of the Colombian geographical regions. Several studies in different food sources exhibited an increase of contamination withSalmonella, a public health concern due to the steady development of antimicrobial resistance associated to specific serovars. However, integration ofSalmonella spp. data including food-chain supply and clinical interfaces is very scarce in Colombia. This study carried out a national comparison ofSalmonellaisolates collected from food-chain supply and clinical sources. Using an epidemiological and phenotypic approach, we demonstrated the higher resolution of WGS compared with PFGE, routinely used inSalmonellasurveillance in Colombia. For example, the resolution of PFGE allowed the description of two main clusters of foodSalmonellaEnteritidis isolates which were expanded to eight clades by using WGS. Virulence factors and antimicrobial determinant genes observed in the foodborne clades should be considered a public health concern in Colombia. WGS is a technology that provides precise and valid evidence for the establishment of dissemination routes of foodborne high-riskSalmonellaclades, but it requires an integrative and continued collaboration between the stakeholders across the One Health interfaces to promote and support integrated real-time actions in public health.
Interobserver Variability in Target Definition for Stereotactic Arrhythmia Radioablation
Authors: van der Ree Martijn H. , Cuculich Phillip S. , van Herk Marcel , Hugo Geoffrey D. , Balt Jippe C. , Bates Matthew , Ho Gordon , Pruvot Etienne , Herrera-Siklody Claudia , Hoeksema Wiert F. , Lee Justin , Lloyd Michael S. , Kemme Michiel , Sacher Frederic , Tixier Romain , Balgobind Brian V. , Robinson Clifford G. , Rasch Coen R.N. , Postema Pieter G. 
Published: March 2023

ABSTRACTBackgroundStereotactic arrhythmia radioablation (STAR) is emerging as a potential new therapy for patients with refractory ventricular tachycardia (VT). The arrhythmogenic substrate (target) is synthesized from clinical and electro-anatomical information. This study was designed to evaluate the baseline interobserver variability in target delineation for STAR.MethodsDelineation software designed for research purposes was used. The study was split into three phases. Firstly, electrophysiologists (observers) delineated a well-defined structure in three patients (spinal canal). Secondly, observers delineated the arrhythmogenic cardiac VT target in three patients previously treated with STAR based on case descriptions. To evaluate baseline performance, a basic workflow approach was used, no advanced techniques were allowed (e.g. image integration). Thirdly, observers delineated three predefined segments from the cardiac 17-segment model. Interobserver variability was evaluated by assessing volumes, variation in distance to the median volume as expressed by the root-mean-square of the observer standard deviation (RMS SD) over the target volume, and the Dice coefficient.ResultsTen electrophysiologists completed the study. For the first phase (spinal canal delineation), interobserver variability was low as indicated by low variation in distance to the median volume (RMS SD range: 0.02-0.02cm) and high Dice coefficients (mean: 0.97±0.01). In the second phase (VT-target delineation), distance to the median volume was large (RMS SD range: 0.52-1.02cm) and the Dice coefficients low (mean: 0.40±0.15). In the third phase (segment delineation), similar results were observed (RMS SD range: 0.51-1.55cm, Dice coefficient mean: 0.31±0.21)ConclusionsInterobserver variability is high for manual delineation of the VT-target and ventricular segments. Difficulties in cardiac anatomical orientation on traditional radiation oncology CT scans appear to be an important driver of variability. This evaluation of the baseline observer variation shows that there is a need for methods and tools to improve variability and allows for future comparison of interventions aiming to reduce observer variation.
A Supervised Text Classification System Detects Fontan Patients in Electronic Records with Higher Accuracy than ICD Codes
Authors: Guo Y , Al-Garadi MA , Book WM , Ivey LC , Rodriguez FH , Raskind-Hood CL , Robichaux C , Sarker A 
Published: March 2023

AbstractBackgroundThe Fontan operation palliates single ventricle heart defects and is associated with significant morbidity and premature mortality. Native anatomy varies; thus, Fontan cases cannot always be identified byInternational Classification of Diseases, Ninth and Tenth Revision, Clinical Modification (ICD-9-CM and ICD-10-CM)codes, making it challenging to create large Fontan patient cohorts. We sought to develop natural language processing (NLP) based machine learning (ML) models, which utilize free text notes of patients, to automatically detect Fontan cases, and compare their performances with ICD code based classification.Methods and ResultsWe included free text notes of 10,935 manually validated patients, of whom 778 (7.1%) were Fontan and 10,157 (92.9%) non-Fontan patients, from two large, diverse healthcare systems. Using 5-fold cross validation, we trained and evaluated multiple ML models, namely support vector machines (SVM) and a transformer based model for language understanding named RoBERTa (2 versions), for automatically identifying Fontan cases based on free text notes. To optimize classifier performances, we experimented with different text representation techniques, including a sliding window strategy to overcome the length limit imposed by RoBERTa. We compared the performances of the ML models to ICD code based classification using the F1score metric. The ICD classification model, SVM, and RoBERTa achieved F1scores of 0.81 (95% CI: 0.79-0.83), 0.95 (95% CI: 0.92-0.97), and 0.89 (95% CI: 0.88-0.85) for the positive (Fontan) class, respectively. SVM obtained the best performance (p<0.05), and both NLP models outperformed ICD code based classification (p<0.05). The novel sliding window strategy improved performance over the base RoBERTa model (p<0.05) but did not outperform SVM. ICD code based classification tended to have more false positives compared to both NLP models.ConclusionsOur proposed NLP models can automatically detect Fontan patients based on clinical notes with higher accuracy than ICD codes. Since the sensitivity of ICD codes is high but the positive predictive value is low, it may be beneficial to apply ICD codes as a filter prior to applying NLP/ML to achieve optimal performance.
Approach to Machine Learning for Extraction of Real-World Data Variables from Electronic Health Records
Authors: Adamson Blythe , Waskom Michael , Blarre Auriane , Kelly Jonathan , Krismer Konstantin , Nemeth Sheila , Gippetti James , Ritten John , Harrison Katherine , Ho George , Linzmayer Robin , Bansal Tarun , Wilkinson Samuel , Amster Guy , Estola Evan , Benedum Corey M. , Fidyk Erin , Estevez Melissa , Shapiro Will , Cohen Aaron B. 
Published: March 2023

ABSTRACTBackgroundAs artificial intelligence (AI) continues to advance with breakthroughs in natural language processing (NLP) and machine learning (ML), such as the development of models like OpenAI’s ChatGPT, new opportunities are emerging for efficient curation of electronic health records (EHR) into real-world data (RWD) for evidence generation in oncology. Our objective is to describe the research and development of industry methods to promote transparency and explainability.MethodsWe applied NLP with ML techniques to train, validate, and test the extraction of information from unstructured documents (eg, clinician notes, radiology reports, lab reports, etc.) to output a set of structured variables required for RWD analysis. This research used a nationwide electronic health record (EHR)-derived database. Models were selected based on performance. Variables curated with an approach using ML extraction are those where the value is determined solely based on an ML model (ie, not confirmed by abstraction), which identifies key information from visit notes and documents. These models do not predict future events or infer missing information.ResultsWe developed an approach using NLP and ML for extraction of clinically meaningful information from unstructured EHR documents and found high performance of output variables compared with variables curated by manually abstracted data. These extraction methods resulted in research-ready variables including initial cancer diagnosis with date, advanced/metastatic diagnosis with date, disease stage, histology, smoking status, surgery status with date, biomarker test results with dates, and oral treatments with dates.ConclusionsNLP and ML enable the extraction of retrospective clinical data in EHR with speed and scalability to help researchers learn from the experience of every person with cancer.
Severe haemolysis during primaquine radical cure ofPlasmodium vivaxmalaria: two systematic reviews and individual patient data descriptive analyses
Authors: Yilma Daniel , Groves Emily S , Brito-Sousa Jose Diego , Monteiro Wuelton M , Chu Cindy , Thriemer Kamala , Commons Robert J , Lacerda Marcus V G , Price Ric N , Douglas Nicholas M 
Published: March 2023

AbstractBackgroundPrimaquine (PQ) killsPlasmodium vivaxhypnozoites but can cause haemolysis in patients with glucose-6-phosphate dehydrogenase (G6PD) deficiency.MethodsWe did two systematic reviews: the first used data from clinical trials to determine the spectrum of definitions and frequency of haematological serious adverse events (SAE) related to PQ treatment of vivax malaria. The second used data from prospective studies and case reports to describe the clinical presentation, management and outcome of ‘severe’ PQ-associated haemolysis necessitating hospitalisation.FindingsIn the first review, SAEs were reported in 70 of 249 clinical trials. There were 34 haematological SAEs amongst 9,824 patients with vivax malaria treated with PQ, 9 of which necessitated hospitalisation or blood transfusion. Criteria used to define SAEs were diverse. In the second review, 21 of 8,487 articles screened reported 163 patients hospitalised following PQ radical cure; 79.9% (123/154) of whom were prescribed PQ at ≥0.5mg/kg/day. Overall, 101 patients were categorised as having probable or possible ‘severe’ PQ-associated haemolysis, 96.8% of whom were G6PD deficient (<30% activity). The first symptoms of haemolysis were mostly reported on day 2 or 3 (45.5%) and all patients were hospitalised within 7 days of PQ commencement. 57.9% (77/133) of patients had blood transfusion. Seven (6.9%) patients with probable or possible haemolysis died.InterpretationEven when G6PD testing is available, enhanced monitoring for haemolysis is warranted following PQ treatment. Clinical review within the first 5 days of treatment may facilitate early detection and management of haemolysis. More robust definitions of severe PQ-associated haemolysis are required.FundingWHO-TDR, Australian National Health and Medical Research (NHMRC), The Bill & Melinda Gates Foundation.
Clonal spread ofPlasmodium falciparumcandidate artemisinin partial resistanceKelch13622I mutation and co-occurrence withpfhrp2/3deletions in Ethiopia
Authors: Fola Abebe A. , Feleke Sindew M. , Mohammed Hussein , Brhane Bokretsion G. , Hennelly Christopher M. , Assefa Ashenafi , Crudal Rebecca M. , Reichert Emily , Juliano Jonathan J. , Cunningham Jane , Mamo Hassen , Solomon Hiwot , Tasew Geremew , Petros Beyene , Parr Jonathan B , Bailey Jeffrey A. 
Published: March 2023

AbstractThe emergence and spread of drug- and diagnostic-resistantPlasmodium falciparumare major impediments to malaria control and elimination. We deep sequenced known drug resistance mutations and other informative loci across the genome of 609 samples collected during a study across three regions of Ethiopia. We found that 8.0% (95% CI 7.0-9.0) of malaria cases were caused byP. falciparumcarrying the candidate artemisinin partial-resistanceK13622I mutation, which occurred less commonly in diagnostic-resistantpfhrp2/3-deleted than normal non-deleted parasites (p=0.03). Identity-by-descent analysis showed that 622I parasites were significantly more related than wild-type (p<0.001), consistent with recent expansion and spread.Pfhrp2/3-deleted parasites were also highly related, with evidence of clonal transmissions at the district level. Parasites carrying bothpfhrp2/3deletion and 622I mutation were observed in some sites. These findings raise concern for future spread of combined drug- and diagnostic-resistant parasites and warrant close monitoring.
Visit-to-visit blood pressure variability and progression of white matter hyperintensities over 14 years
Authors: Janssen Esther , van Dalen Jan-Willem , Cai Mengfei , Jacob Mina A. , Marques José , Duering Marco , Richard Edo , Tuladhar Anil M. , de Leeuw Frank-Erik , Hilkens Nina 
Published: March 2023

AbstractThere is evidence that blood pressure variability (BPV) is associated with cerebral small vessel disease (SVD) and may therefore increase the risk of stroke and dementia. It remains unclear if BPV is associated with SVD progression over years. We examined whether visit-to-visit BPV is associated with White Matter Hyperintensity (WMH) progression over 14 years and MRI markers after 14 years.We included participants with SVD from the Radboud University Nijmegen Diffusion tensor Magnetic resonance imaging Cohort (RUNDMC) who underwent baseline assessment in 2006 and follow-up in 2011, 2015 and 2020. BPV was calculated as coefficient of variation of BP at all visits. Association between WMH progression rates over 14 years and BPV was examined using linear-mixed effects model. Regression models were used to examine association between BPV and MRI markers at final visit in participants.A total of 199 participants (60.5 SD 6.6 years) who underwent four MRI scans and blood pressure measurements were included, with mean follow-up of 13.7 (SD 0.5) years. Systolic BPV was associated with higher progression of WMH (β = 0.013, 95% CI 0.005 – 0.022) and higher risk of incident lacunes (OR: 1.10, 95% CI 1.01-1.21). There was no association between systolic BPV and grey and white matter volumes, Peak Skeleton of Mean Diffusivity (PSMD) or microbleed count after 13.7 years.Visit-to-visit systolic BPV is associated with increased progression of WMH volumes and higher risk of incident lacunes over 14 years in participants with SVD. Future studies are needed to examine causality of this association.
A meta-analysis of genome-wide association studies of childhood wheezing phenotypes identifiesANXA1as a susceptibility locus for persistent wheezing
Authors: Granell R , Curtin JA , Haider S , Kitaba N , Mathie S , Gregory L , Yates LL , Tutino M , Hankinson J , Perretti M , Vonk JM , Arshad SH , Cullinan P , Fontanella S , Roberts G , Koppelman GH , Simpson A , Turner S , Murray CS , Lloyd CM , Holloway JW , Custovic A 
Published: March 2023

ABSTRACTBackgroundMany genes associated with asthma explain only a fraction of its heritability. Most genome-wide association studies (GWASs) used a broad definition of “doctor-diagnosed asthma”, thereby diluting genetic signals by not considering asthma heterogeneity. The objective of our study was to identify genetic associates of childhood wheezing phenotypes.MethodsWe conducted a novel multivariate GWAS meta-analysis of wheezing phenotypes jointly derived using unbiased analysis of data collected from birth to 18 years in 9,568 individuals from five UK birth-cohorts.Results44 independent SNPs were associated with early-onset persistent, 25 with preschool remitting, 33 with mid-childhood remitting and 32 with late onset wheeze. We identified a novel locus on chr9q21.13 (close to annexin 1 (ANXA1), p<6.7×10−9), associated exclusively with early-onset persistent wheeze. We identified rs75260654 as the most likely causative single nucleotide polymorphism (SNP) using Promoter Capture Hi-C loops, and then showed that the risk allele (T) confers a reduction inANXA1expression. Finally, in a murine model of house dust mite (HDM)-induced allergic airway disease, we demonstrated that anxa1 protein expression increased and anxa1 mRNA was significantly induced in lung tissue following HDM exposure. Using anxa1−/−deficient mice, we showed that loss of anxa1 results in heightened airway hyperreactivity and Th2 inflammation upon allergen challenge.ConclusionsWe discovered a novel locus uniquely associated with early-onset persistent wheeze, identified the most likely causative variant, and showed thatANXA1may play a role in regulating the pulmonary immune response to allergens. Targeting this pathway in persistent disease may represent an exciting therapeutic prospect.
Trends in Antibody Titers after SARS-CoV-2 Vaccination - Insights from a Self-Paid Tests at a General Internal Medicine Clinic
Authors: Kusunoki Hiroshi , Ekawa Kazumi , Ekawa Masakazu , Kato Nozomi , Yamasaki Keita , Motone Masaharu , Shimizu Hideo 
Published: March 2023

AbstractBackgroundThe rise in antibody titers against the novel coronavirus (SARS-CoV-2), and its duration is considered an important indicator for confirming the efficacy of the COVID-19 vaccine, and self-paid tests of antibody titer are conducted at many facilities nationwide.MethodsThe relationship between the number of days after the second and third dose of vaccines, age, and antibody titer was determined from the medical records of general internal medicine clinics that conducted self-paid testing of SARS-CoV-2 antibody titer using Elecsys Anti-SARS-CoV-2 S (Roche Diagnostics), as well as the relationship between the number of days after two or more dose of vaccines and antibody titer. We also examined antibody titers in cases of spontaneous infection with SARS-CoV-2 after two or more doses of the vaccine.ResultsAge and antibody titer were negatively correlated in 86 subjects whose antibody titer was measured within 1 month after the second vaccination with the COVID-19 vaccine. In 31 subjects whose antibody titer was measured within one month after the third dose of vaccine, age and antibody titer showed a negative correlation (p<0.01). The mean antibody titer after the third vaccination was 20704.9±16820.7 U/mL, more than 10 times the mean antibody titer after the second dose of vaccine of 1601.9±1297.9 U/mL. There were also cases of infection after the third or fourth dose of vaccine, with antibody titers in the tens of thousands after infection, but they still received further booster vaccinations after infection.DiscussionSARS-CoV-2 antibody titers measured within 1 month of the second or third dose of vaccine showed a negative correlation with age, and antibody titers also showed a negative correlation trend with the number of days after the second dose of vaccine. It is considered that many people in Japan received further booster vaccinations after spontaneous infection, even though they already had antibody titers in the tens of thousands U/mL by “hybrid immunity” after spontaneous infection following two or more dose of vaccine.ConclusionAfter measuring SARS-CoV-2 antibody titers, booster vaccination of those with low antibody titers should be done on a priority basis.
Timing of selective serotonin reuptake inhibitor use and risk for preterm birth and related adverse events
Authors: Hwang Yeon Mi , Roper Ryan T. , Piekos Samantha N. , Enquobahrie Daniel A. , Hebert Mary F. , Paquette Alison G. , Baloni Priyanka , Price Nathan D. , Hood Leroy , Hadlock Jennifer J. 
Published: March 2023

AbstractPurposeThere is uncertainty around the safety of SSRIs for treating depression during pregnancy. We aimed 1) to address confounding by indication, as well as socioeconomic and environmental factors associated with depression and 2) evaluate associations of timing of SSRI exposure in pregnancy with the risk of preterm birth and related outcomes (small for gestational age and low birthweight) among women with depression before pregnancy.MethodsWe conducted propensity score-adjusted regression to calculate odds ratios (OR) of preterm birth, small for gestational age, and low birth weight. We accounted for maternal/pregnancy characteristics, pre-pregnancy comorbidity/depression severity, social vulnerability, rural health disparity, and pre-natal depression severity. We additionally conducted a drug-specific analysis and assessed the impact of other classes of antidepressants within our cohort of interest.ResultsAmong women with a history of depression, we identified women with indication of depression ≤ 180 days before pregnancy (n=6,408). Women with no SSRI order during pregnancy (n=3,122) constituted the unexposed group (no SSRI exposure group). The late SSRI exposure group consisted of women with an SSRI order after the first trimester (n=2,596). The early-only SSRI exposure group consisted of women with SSRI orders only in the first trimester (n=691). Late SSRI exposure group had an increased risk of preterm birth of OR=1.7 ([1.3,2.2], p<0.0001), and low birth weight of OR = 1.7 ([1.3,2.4], p<0.001), relative to the no SSRI exposure group.ConclusionsThese findings suggest associations between preterm birth/low birthweight and SSRI exposure is dependent on exposure timing during pregnancy. Small for gestational age is not associated with SSRI exposure.