bluuebunny/crossref_metadata_2025_split huggingface dataset:
Estimating epidemic dynamics with genomic and time series data
Authors: Zarebski Alexander E. , Zwaans Antoine , Gutierrez Bernardo , du Plessis Louis , Pybus Oliver G. 
Published: August 2023

AbstractAccurately estimating the prevalence and transmissibility of an infectious disease is an important task in genetic infectious disease epidemiology. However, generating accurate estimates of these quantities, that are informed by both epidemic time series and pathogen genome sequence data, is a challenging problem. While birth-death processes and coalescent-based models are popular methods for modelling the transmission of infectious diseases, they both struggle (for different reasons) with estimating the prevalence of infection.Here we extended our approximate likelihood, which combines phylogenetic information from sampled pathogen genomes and epidemiological information from a time series of case counts, to estimate historical prevalence (in addition to the effective reproduction number). We implement this new method in a BEAST2 package called Timtam. In a simulation study our approximation is well-calibrated and can recover the parameters of simulated data.To demonstrate how Timtam can be applied to real data sets we carried out empirical analyses of data from two infectious disease outbreaks: the outbreak of SARS-CoV-2 onboard the Diamond Princess cruise ship in early 2020 and poliomyelitis in Tajikistan in 2010. In both cases we recover estimates consistent with previous analyses.
Predictors of Affective and Cognitive Alterations in Minor Stroke Patients: clinical, omics, neuropsychological and radiological signatures
Authors: Pereira Cristina , Mauri Gerard , Vázquez-Justes Daniel , Mitjana Raquel , Piñol Gerard , Arqué Gloria , Purroy Francisco 
Published: August 2023

ABSTRACTBackground. Despite the mild severity of initial symptoms, minor stroke (MS) is a common clinical condition that can be associated with significant affective and cognitive alterations. Methods. The PSICOICTUS project aimed to investigate the predictors of these alterations in a cohort of 118 consecutive MS patient. This observational, longitudinal, and prospective study included comprehensive evaluation at baseline (within the first five days of symptom onset) and follow-ups at 15 days, 6 months, and 12 months. A screening battery consisting of the Montreal Cognitive Assessment (MoCA), Montgomery-Åsberg Depression Rating Scale (MADRS), and Apathy Evaluation Scale-Clinician version (AES-c) was used to identify patients with affective and/or cognitive alterations. Results. Cognitive alterations were further assessed using a comprehensive neuropsychological battery. Screening tests revelated that 17.0% of patients had affective alterations, 9.3% had cognitive alterations, and 14.4% presented with both affective and cognitive alterations. Among patients with cognitive alterations, executive functions, attention and processing speed were found to be the most affected domains. The study also concluded a biomarker discovery analysis involving MRI-based neuroimaging and untargeted metabolomics/lipidomics analysis. Several predictors of affective and cognitive alterations were identified. A history of previous depressions, lower levels of Isoleucyl-Isoleucine, and PC (38:4) were associated with affective alterations. On the other hand, age above 70, the presence of a middle cerebral artery ischemic lesion, higher creatinine levels, lower triglyceride levels, and higher concentrations of 2-hydroxyhexadecanoylcarnitine were predictive of cognitive alterations. Female sex, previous history of depressive syndrome, and a higher number of chronic strokes were identified as predictors for both affective and cognitive alterations. Conclusions. These findings highlight the importance of considering affective and cognitive alterations in the management of patients with MS. The identification of specific predictors would improve the development of a differential management approach tailored to the needs of MS patients.
Chronic Pain and Eye Movements: A NeuroIS Approach to Designing Smart Clinical Decision Support Systems
Authors: Alrefaei Doaa , Djamasbi Soussan , Strong Diane 
Published: August 2023

AbstractThe pressing need for objective measures in the evaluation of chronic pain both in research and practice highlights the role that neuro information systems (NeuorIS) research plays in designing smart clinical decision support systems. A first step in such a research agenda is identifying practical stimuli-task paradigms that can reliably detect chronic pain from physiological measures such as eye movements. In this study, we propose and test a new stimuli-task paradigm. Our results show that our proposed stimuli-task paradigm can detect differences in information processing behavior of people with and without chronic pain. The results also show that our proposed stimuli-task paradigm can reliably predict a person’s reported subjective pain experience from his/her eye movements. These findings provide support for our proposed stimuli-task paradigm. They also show that the eye-tracking variables that we selected to test our proposed paradigm are effective in capturing the impact of chronic pain on visual attention and suggest that eye movements have the potential to serve as reliable biomarkers of chronic pain. In other words, our results provide support for the potential of eye movements to facilitate the development of smart information systems that can detect the presence and/or the severity of chronic pain from an individual’s ocular behavior.
Diagnostic efficacy of leukocyte esterase dipstick in diagnosing spontaneous bacterial peritonitis among cirrhotic patients in tertiary hospitals, Dodoma, Tanzania
Authors: Mwinyi Salum Ali , Sindato Emmanuel 
Published: August 2023

AbstractBackgroundSpontaneous bacterial peritonitis (SBP) is complications of end stage liver disease, it associated with morbidity and mortality, the gold standard for diagnosing SBP is an ascitic fluid Polymorphonuclear neutrophil count (PMN) of ≥ 250 cells/mm3, this examination is time consuming and costly. Urine reagent dipstick detecting leukocyte esterase activity has been suggested as quick and affordable substitute. The purpose of this study was to evaluate the CYBOW™ 10 strip’s ability to diagnose SBP.MethodsA Crossectional analytical study was conducted from November 2022 to June 2023. 224 patients with confirmed cirrhotic ascites, aged ≥ 18 years and met inclusion criteria were recruited in the study. By following sterile procedure ascitic fluid was collected, bedside ascitic fluid examination by CYBOW™ 10 reagent strips, and the samples for cytological examination were taken. Ascitic fluid with PMN ≥ 250cells/mm3was considered positive for SBP, and +1 to +3 of CYBOW™ 10 reagent strip, was used as cut off levels for a positive SBP. By using SPSS version 25, 2 by 2 table was applied to determine the sensitivity (Sn), Specificity (Sp), Positive Predictive value (PPV), and Negative Predictive Value (NPV), and Receiver Operating Characteristic (ROC) was applied to determine the area under the curve of the leukocyte esterase dipstick.ResultsOn the basis of the ascitic fluid PMN count, 42 (18.75%) individuals had SBP. At cut-off point of +2 CYBOW™ 10 urine reagent strip had Sensitivity of 82.14%, Specificity of 99.39%, PPV of 95.83% and NPV of 96.79%, with AUC of 0.9074.ConclusionCYBOW™ 10 reagent strip test might be a helpful tool for doctors, when a rapid cell count for SBP diagnosis is not available. These strips are readily available and inexpensive, can be very helpful in areas with low resources and to patients who are unable to pay for cytology.
Long COVID in a highly vaccinated population infected during a SARS-CoV-2 Omicron wave – Australia, 2022
Authors: Woldegiorgis Mulu , Cadby Gemma , Ngeh Sera , Korda Rosemary , Armstrong Paul , Maticevic Jelena , Knight Paul , Jardine Andrew , Bloomfield Lauren , Effler Paul 
Published: August 2023

AbstractObjectiveTo characterise Long COVID in a highly vaccinated population infected by Omicron.DesignFollow-up survey of persons testing positive for SARS-CoV-2 in Western Australia, 16 July-3 August 2022.SettingCommunityParticipants22,744 persons with COVID-19 who had agreed to participate in research at the time of diagnosis were texted a survey link 90 days later; non-responders were telephoned. Post stratification weights were applied to responses from 11,697 (51.4%) participants, 94.0% of whom had received >= 3 vaccine doses.Main outcome measuresPrevalence of ‘Long COVID’ - defined as reporting new or ongoing COVID-19 illness-related symptoms or health issues 90 days post diagnosis; associated health care utilisation, reductions in work/study and risk factors were assessed using log-binomial regression.Results18.2% (n=2,130) of respondents met case definition for Long COVID. Female sex, being 50-69 years of age, pre-existing health issues, residing in a rural or remote area, and receiving fewer vaccine doses were significant independent predictors of Long COVID (p < 0.05). Persons with Long COVID reported a median of 6 symptoms, most commonly fatigue (70.6%) and difficulty concentrating (59.6%); 38.2% consulted a GP and 1.6% reported hospitalisation in the month prior to the survey due to ongoing symptoms. Of 1,778 respondents with Long COVID who were working/studying before their COVID-19 diagnosis, 17.9% reported reducing/discontinuing work/study.Conclusion90 days post Omicron infection, almost 1 in 5 respondents reported Long COVID symptoms; 1 in 15 of all persons with COVID-19 sought healthcare for associated health concerns >=2 months after the acute illness.Significance of the studyThe knownThe prevalence of Long COVID varies widely across studies conducted in diverse settings globally (range: 9%-81%).The newIn a highly vaccinated population (94% with >=3 vaccine doses), almost 20% of persons infected with the SARS-CoV-2 Omicron variant reported symptoms consistent with Long COVID 90 days post diagnosis. Long COVID was associated with sustained negative impacts on work/study and a substantial utilisation of GP services 2-3 months after the acute illness; however, ED presentations and hospitalisations for Long COVID were rare.The implicationsGP clinics play a significant role in managing the burden of Long COVID in Australia.
In severe first episode major depressive disorder, psychosomatic, chronic fatigue syndrome, and fibromyalgia symptoms are driven by immune activation and increased immune-associated neurotoxicity
Authors: Maes Michael , Almulla Abbas F , Zhou Bo , Abo Algon Ali Abbas , Sodsai Pimpayao 
Published: August 2023

AbstractBackgroundMajor depressive disorder (MDD) is accompanied by activated neuro-immune pathways, increased physiosomatic and chronic fatigue-fibromyalgia (FF) symptoms. The most severe MDD phenotype, namely major dysmood disorder (MDMD), is associated with adverse childhood experiences (ACEs) and negative life events (NLEs) which induce cytokines/chemokines/growth factors.AimsTo delineate the impact of ACE+NLEs on physiosomatic and FF symptoms in first episode (FE)-MDMD, and examine whether these effects are mediated by immune profiles.MethodsACEs, NLEs, physiosomatic and FF symptoms, and 48 cytokines/chemokines/growth factors were measured in 64 FE-MDMD patients and 32 normal controls.ResultsPhysiosomatic, FF and gastro-intestinal symptoms belong to the same factor as depression, anxiety, melancholia, and insomnia. The first factor extracted from these seven domains is labeled the physio-affective phenome of depression. A part (59.0%) of the variance in physiosomatic symptoms is explained by the independent effects of interleukin (IL)-16 and IL-8 (positively), CCL3 and IL-1 receptor antagonist (inversely correlated). A part (46.5%) of the variance in physiosomatic (59.0%) symptoms is explained by the independent effects of interleukin (IL)-16, tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) (positively) and combined activities of negative immunoregulatory cytokines (inversely associated). Partial Least Squares analysis shows that ACE+NLEs exert a substantial influence on the physio-affective phenome which are partly mediated by an immune network composed of IL-16, CCL27, TRAIL, macrophage-colony stimulating factor, and stem cell growth factor.ConclusionsThe physiosomatic and FF symptoms of FE-MDMD are partly caused by immune-associated neurotoxicity due to T helper (Th)-1 polarization, Th-1, and M1 macrophage activation and relative lowered compensatory immunoregulatory protection.
Predicting Clinical Outcomes of SARS-CoV-2 Infection During the Omicron Wave Using Machine Learning
Authors: Cogill Steven , Nallamshetty Shriram , Fullenkamp Natalie , Heberer Kent , Lynch Julie , Lee Kyung Min , Aslan Mihaela , Shih Mei-Chiung , Lee Jennifer S 
Published: August 2023

AbstractThe Omicron SARS-CoV-2 variant continues to strain healthcare systems. Developing tools that facilitate the identification of patients at highest risk of adverse outcomes is a priority. The study objectives are to develop population-scale predictive models that: 1) identify predictors of adverse outcomes with Omicron surge SARS-CoV-2 infections, and 2) predict the impact of prioritized vaccination of high-risk groups for said outcome. We prepared a retrospective longitudinal observational study of a national cohort of 192,984 patients in the U.S. Veteran Health Administration who tested positive for SARS-CoV-2 from January 15 to August 15, 2022. We utilized sociodemographic characteristics, comorbidities, vaccination status, and prior COVID-19 infections, at time of testing positive for SARS-CoV-2 to predict hospitalization, escalation of care (high-flow oxygen, mechanical ventilation, vasopressor use, dialysis, or extracorporeal membrane oxygenation), and death within 30 days. Machine learning models demonstrated that advanced age, high comorbidity burden, lower body mass index, unvaccinated status, prior SARS-CoV-2 infection, and oral anticoagulant use were the important predictors of hospitalization and escalation of care. Similar factors predicted death. However, prior SARS-CoV-2 infection was associated with lower 30-day mortality, and anticoagulant use did not predict mortality risk. The all-cause death model showed the highest discrimination (Area Under the Curve (AUC) = 0.895, 95% Confidence Interval (CI): 0.885, 0.906) followed by hospitalization (AUC = 0.829, CI: 0.825, 0.834), then escalation of care (AUC=0.805, CI: 0.795, 0.814). Assuming a vaccine efficacy range of 70.8 to 78.7%, our simulations projected that targeted prevention in the highest risk group may have reduced 30-day hospitalization, care escalation, and death in more than 2 of 5 unvaccinated patients.
New-onset infective endocarditis in diabetic patients receiving SGLT2I, DPP4I and GLP1a: A population-based cohort study
Authors: Chou Oscar Hou-In , Gao Tianyu , Chung Cheuk To , Jing Fengshi , Chan Jeffrey Shi Kai , Satti Danish Iltaf , Pang Ronald TK , Lee Sharen , Wong Wing Tak , Liu Tong , Lip Gregory Y H , Cheung Bernard Man Yung , Tse Gary , Zhou Jiandong 
Published: August 2023

AbstractBackgroundSodium-glucose cotransporter-2 inhibitors (SGLT2I) have been suggested to have beneficial effects against infection. However, the comparative risks of new onset infective endocarditis between SGLT2Is, dipeptidyl peptidase-4 inhibitors (DPP4Is) and glucagon-like peptide-1 receptor agonist (GLP1a) remain unknown.ObjectiveThis real-world study aims to compare the risks of infective endocarditis upon exposure to SGLT2I and dipeptidyl peptidase-4 inhibitors (DPP4I).MethodsThis was a retrospective population-based cohort study of patients with type-2 diabetes mellitus (T2DM) on either SGLT2I or DPP4I between 1st January 2015 and 31st December 2020 using a territory-wide registry in Hong Kong. The primary outcome was new-onset infective endocarditis. The secondary outcome was cardiovascular-related mortality. Propensity score matching (1:1 ratio) using the nearest neighbour search was performed. Multivariable Cox regression was applied to identify significant associations. A three-arm sensitivity analysis including the GLP1a cohort was conducted.ResultsThis cohort included 75638 T2DM patients (median age: 62.3 years old [SD: 12.8]; 55.79 % males). The SGLT2I and DPP4I groups consisted of 28774 patients and 46864 patients, respectively. After matching, 104 and 161 infective endocarditis in the SGLT2I and DPP4I groups occurred over a follow-up of 5.6 years. SGLT2I use was associated with lower risks of infective endocarditis (Hazard ratio [HR]: 0.58; 95% Confidence Interval [CI]: 0.41-0.81) and cardiovascular mortality (HR: 0.49; 95% CI: 0.33-0.72) compared to DPP4I use after adjustments for demographics, comorbidities, medications, renal function, and HbA1c levels. Similar associations were observed in subgroup analyses regardless of gender, hypertension, prior valvular disease, renal disease, or immunodeficiency. In the sensitivity analysis, SGLT2I was not associated with lower risks of infective endocarditis compared to GLP1a. The results remained consistent in the competing risk and the other sensitivity analyses.ConclusionsSGLT2I use was associated with lower risks of new-onset infective endocarditis compared to DPP4I after adjustments.Illustrated abstract
Assessing the performance of GPT-4 in the filed of osteoarthritis and orthopaedic case consultation
Authors: Li Juntan , Gao Xiang , Dou Tianxu , Gao Yuyang , Zhu Wannan 
Published: August 2023

AbstractBackgroundLarge Language Models (LLMs) like GPT-4 demonstrate potential applications in diverse areas, including healthcare and patient education. This study evaluates GPT-4’s competency against osteoarthritis (OA) treatment guidelines from the United States and China and assesses its ability in diagnosing and treating orthopedic diseases.MethodsData sources included OA management guidelines and orthopedic examination case questions. Queries were directed to GPT-4 based on these resources, and its responses were compared with the established guidelines and cases. The accuracy and completeness of GPT-4’s responses were evaluated using Likert scales, while case inquiries were stratified into four tiers of correctness and completeness.ResultsGPT-4 exhibited strong performance in providing accurate and complete responses to OA management recommendations from both the American and Chinese guidelines, with high Likert scale scores for accuracy and completeness. It demonstrated proficiency in handling clinical cases, making accurate diagnoses, suggesting appropriate tests, and proposing treatment plans. Few errors were noted in specific complex cases.ConclusionsGPT-4 exhibits potential as an auxiliary tool in orthopedic clinical practice and patient education, demonstrating high accuracy and completeness in interpreting OA treatment guidelines and analyzing clinical cases. Further validation of its capabilities in real-world clinical scenarios is needed.
Longitudinal enlargement of choroid plexus is associated with inflammation and neurodegeneration in RRMS patients
Authors: Klistorner Samuel , Klistorner Alexander 
Published: August 2023

AbstractBackgroundThe Choroid Plexus (CP) plays a potential role in the initiation and propagation of neuroinflammatory processes in MS. However, the progressive change of the CP and its associations with biomarkers of acute and chronic inflammation, along with MS-related brain structure atrophy, have not been investigated.ObjectiveThis study aims to explore the longitudinal dynamics of the CP in RRMS patients and assess its relationship with inflammation and with atrophy in various brain compartments.Methods57 RRMS patients were examined annually for a minimum of 60 months using following MRI protocols: pre- and post-contrast (gadolinium) Sagittal 3D T1, FLAIR CUBE, diffusion weighted MRI. CP was manually segmented at baseline and last follow-up and normalised by head size. Annually lesion segmentation was performed by iQ-MSTM software suite and brain was segmented using AssemblyNet.ResultsOver the study period, the volume of CP increased by an average of 1.4% annually. The magnitude of CP enlargement significantly correlated with central brain atrophy, and to a lesser extent, total brain atrophy, white matter, and deep grey matter atrophy. Furthermore, progressive CP enlargement was significantly associated with the volume and severity of chronic lesion expansion (r=0.66, p<0.001), but not with the number or volume of new lesions.ConclusionOur findings indicate that ongoing inflammatory activity in the CP is linked to low-grade demyelination at the rim of chronic lesions and associated neurodegeneration of periventricular white and grey matter.
Sexual exposures associated with mpox infection: California, November 2022 to June 2023
Authors: Snyder Robert E. , Saadeh Kayla , Tang Eric C. , Johnson Kelly A. , Holland Samuel N. , Quint Joshua , Burghardt Nicole O. , Chai Shua J. , Fernando Roshani , Gonzalez Barrera Kimberly , Hernandez Cindy , McManus Korie , Lorenz Kieran , Maycott Jarett , McGinley John , Lewnard Joseph A. 
Published: August 2023

ABSTRACTBackgroundExposures associated with mpox infection remain imperfectly understood.MethodsWe conducted a case-control study enrolling participants who received molecular tests for mpox/orthopoxvirus in California from November 2022 through June 2023. We collected data on behaviors during a 21-day risk period before symptom onset or testing among mpox cases and test-negative controls.ResultsThirteen of 54 (24.1%) cases and 5/117 (4.3%) controls reported sexual exposure to individuals they identified as potential mpox cases (“index contacts”; odds ratio [OR]=7.7 [95% confidence interval: 2.5-19.3]). Among these participants, 10/13 (76.9%) cases and 2/5 (40.0%) controls reported their index contacts were not experiencing symptoms visible to participants during sex (OR=14.9 [3.6-101.8]). Only 3/54 cases (5.6%) recalled exposure to symptomatic index contacts. Cases reported greater numbers of anal/vaginal sex partners than controls (adjusted OR=2.2 [1.0-4.8] for 2-3 partners and 3.8 [1.7-8.8] for ≥4 partners). Male cases with penile lesions more commonly reported insertive anal/vaginal sex than those without penile lesions (adjusted OR=9.3 [1.6-54.8]). Cases with anorectal lesions more commonly reported receptive anal sex than cases without anorectal lesions (adjusted OR=14.4 [1.0-207.3]).ConclusionsSexual exposure to contacts known or suspected to have experienced mpox was associated with increased risk of infection, often when index contacts lacked apparent symptoms. Exposure to greater numbers of sex partners, including those whom participants did not identify as index contacts, was associated with increased risk of infection in a site-specific manner. While participants’ assessment of symptoms in partners may be imperfect, these findings suggest individuals without visibly prominent mpox symptoms transmit infection.